diff --git a/rbo-base.owl b/rbo-base.owl index 596f5dd..0067056 100644 --- a/rbo-base.owl +++ b/rbo-base.owl @@ -13,12 +13,12 @@ xmlns:dcterms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. Radiation Biology Ontology - 2024-05-31 + 2024-10-23 @@ -52,6 +52,12 @@ + + + + + + @@ -159,12 +165,6 @@ - - - - - - @@ -224,9 +224,9 @@ - + - + has atomic number @@ -764,9 +764,9 @@ - + The amount of ionizing radiation to which a member of the population on Earth is exposed from natural sources, such as terrestrial radiation from naturally-occurring radionuclides in the soil, cosmic radiation originating in outer space, and naturally-occurring ra - background ionizing radiation + ionizing background radiation @@ -3167,17 +3167,10 @@ - + - - - - 1 - - - A process involving the emission of energy from an atomic nucleus resulting in change in the character of the nucleus radioactive decay @@ -3276,7 +3269,16 @@ - Atomic nuclei, with atomic number 2 or greater and kinetic energy imparted by natural or artificial means + A type of ionizing radiation consisting of charged particles that are relatively massive compared to other types of radiation, such as alpha, beta, and gamma radiation. Heavy ion radiation is composed of atomic nuclei that have been stripped of their electrons, resulting in positively charged particles. + Heavy ion radiation has several notable characteristics and contexts: + +High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. + +Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation. + +Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. + +In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. heavy ion radiation @@ -4340,7 +4342,7 @@ https://orcid.org/0000-0001-9227-0670 ambient radiation background radiation - anthropogenic background radiation + anthropogenic ionizing background radiation @@ -4352,7 +4354,7 @@ Radiation originating in the terrestrial or extra-terrestrial environment. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 - natural background radiation + natural ionizing background radiation @@ -4416,6 +4418,81 @@ + + + + + thermal neutron + A neutron that has (by collision with other particles) reached an energy state equal to that of its surroundings, typically on the order of 0.025 eV. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + https://www.nrc.gov/reading-rm/basic-ref/glossary/neutron-thermal.html + thermal neutron + + + + + + + + + epithermal neutron + a neutron with energy greater than a thermal neutron, but less than a fast neutron. The approximate energy range is 0.025-0.4 eV. + http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670 + https://ns.ph.liv.ac.uk/~ajb/radiometrics/glossary/epithermal_neutron.html + epithermal neutron + + + + + + + + + background radiation + The ambient radiation in a defined environment emanating from natural or anthropogenic sources. + For uses involving experimentation or radiation therapy, use "anthropogenic background radiation" instead. Use this concept to indicate source is a mixture of anthropogenic and naturally occurring (ambient), or unknown or if the discrimination is not sought. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + background radiation + + + + + + + + + non-ionizing background radiation + Background radiation that does not result in ionization of target material + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + non-ionizing background radiation + + + + + + + + + anthropogenic non-ionizing background radiation + Non-ionizing background radiation that is the result of a human planned process. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + anthropogenic non-ionizing background radiation + + + + + + + + + natural non-ionizing background radiation + Non-ionizing background radiation that is not the result of a human planned process. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + natural non-ionizing background radiation + + + + diff --git a/rbo-full.owl b/rbo-full.owl index 3f6b47f..a8f7d09 100644 --- a/rbo-full.owl +++ b/rbo-full.owl @@ -39,11 +39,11 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. Radiation Biology Ontology - 2024-05-31 + 2024-10-23 @@ -198,6 +198,7 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon @@ -265,6 +266,12 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + @@ -337,6 +344,12 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + @@ -681,14 +694,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - @@ -809,14 +814,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - @@ -833,14 +830,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - @@ -1927,6 +1916,12 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + @@ -1935,9 +1930,9 @@ We also have the outstanding issue of how to aim different definitions to differ - + - + @@ -2021,6 +2016,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part + http://www.ebi.ac.uk/efo/has_part BFO:0000051 @@ -2636,6 +2632,15 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + executed by + + + + @@ -2745,7 +2750,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + has measurement unit label + has measurement unit label @@ -2754,84 +2760,16 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - This document is about information artifacts and their representations - + http://purl.obolibrary.org/obo/IAO_0000136 + is about A (currently) primitive relation that relates an information artifact to an entity. - 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. - person:Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy + + is about is about - - - - - - - - m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later - From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] - -This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. --- -From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] - -unit of measure is a quality, e.g. the length of a ruler. - -[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] - -[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] - -a represents b means either a denotes b or a describes - -describe: -a describes b means a is about b and a allows an inference of at least one quality of b - -We have had a long discussion about denotes versus describes. - From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. - -a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. - From the second meeting on IAO: - -An attempt at defining assay using Barry's "reliability" wording - -assay: -process and has_input some material entity -and has_output some information content entity -and which is such that instances of this process type reliably generate -outputs that describes the input. - This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. - Alan Ruttenberg - is quality measurement of - - - - - - - - - inverse of the relation of is quality measurement of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - is quality measured as - - - - @@ -2840,7 +2778,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which is_supported_by_data The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. - The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process + The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop @@ -2852,18 +2790,10 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - - - has_specified_input - has_specified_input + has specified input see is_input_of example_of_usage The inverse property of is_specified_input_of @@ -2872,13 +2802,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot - - http://www.ebi.ac.uk/efo/has_input - OBI:0000293 has specified input - has_input - has_specified_input - has_specified_input @@ -2887,18 +2811,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - is_specified_input_of + is specified input of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - http://www.ebi.ac.uk/efo/is_input_of is specified input of - is_input_of - is_specified_input_of @@ -2906,15 +2826,11 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - + has specified output has_specified_output has_specified_output @@ -2938,15 +2854,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - is_specified_output_of - is_specified_output_of + is specified output of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - is specified output of - is_specified_output_of @@ -2960,7 +2873,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' - This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch @@ -2976,7 +2889,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which objective_achieved_by - This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. + This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by @@ -2992,7 +2905,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which has value specification - A relation between an information content entity and a value specification that specifies its value. + A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification @@ -3124,30 +3037,11 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - @@ -3209,10 +3103,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + has function this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function + RO:0000085 has_function has function @@ -3225,10 +3121,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + has quality this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality + http://www.ebi.ac.uk/efo/has_quality RO:0000086 uberon @@ -3247,10 +3145,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + has role this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role + RO:0000087 chebi_ontology has_role @@ -4404,10 +4304,12 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + has component w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + RO:0002180 external @@ -5924,8 +5826,10 @@ where + has member has member is a mereological relation between a collection and an item. SIO + RO:0002351 uberon @@ -8252,6 +8156,18 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + executes + + + + @@ -8566,22 +8482,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - has atomic number - - - - + Number of protons in an atomic nucleus We are undecided as to whether to ultimately model this as a data property of object property + cardinality, but for now we are using DPs as these are faster for reasoning + has atomic number has atomic number @@ -8597,17 +8506,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - has measurement value - - - - @@ -8616,7 +8514,7 @@ For example, A and B may be gene products and binding of B by A positively regul has specified numeric value - A relation between a value specification and a number that quantifies it. + A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI @@ -8631,7 +8529,7 @@ For example, A and B may be gene products and binding of B by A positively regul has specified value - A relation between a value specification and a literal. + A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI has specified value @@ -8669,82 +8567,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A planned process that has specified output a software product and that involves the creation of source code. - Mathias Brochhausen - William R. Hogan - http://en.wikipedia.org/wiki/Software_development - A planned process resulting in a software product involving the creation of source code. - software development - - - - - - - - - - - - - - - - - - - - - - - - - - creating a data set - A planned process that has a data set as its specified output. - William R. Hogan - data set creation - dataset creation - dataset creating - - - - @@ -8796,11 +8618,9 @@ For example, A and B may be gene products and binding of B by A positively regul continuant Continuant - continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) @@ -9273,7 +9093,6 @@ For example, A and B may be gene products and binding of B by A positively regul quality Quality - quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist @@ -9282,7 +9101,6 @@ For example, A and B may be gene products and binding of B by A positively regul the shape of your nostril A quality is an entity that describes some aspect which is intrinsic to that particular object and is dependent on or more material entities in which it inheres in or is borne by. Example the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee James Malone - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] @@ -9328,7 +9146,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -9344,6 +9162,7 @@ For example, A and B may be gene products and binding of B by A positively regul sdc SpecificallyDependentContinuant + characteristic specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato @@ -9363,8 +9182,7 @@ For example, A and B may be gene products and binding of B by A positively regul Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. James Malone Sirarat Sarntivijai - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] sample characteristic http://www.ebi.ac.uk/efo/EFO_0001443 @@ -9384,7 +9202,7 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 - + @@ -9395,15 +9213,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + We should name the inverse in COB and avoid the confusing inverse(..) construct - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - @@ -9417,12 +9229,6 @@ For example, A and B may be gene products and binding of B by A positively regul per discussion with Barry Smith - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - @@ -9669,9 +9475,7 @@ For example, A and B may be gene products and binding of B by A positively regul BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. James Malone - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) @@ -14506,99 +14310,99 @@ For example, A and B may be gene products and binding of B by A positively regul - PMID:27189145 - Europe PMC + CAS:14378-33-7 + ChemIDplus - PMID:27306032 - Europe PMC + PMID:12447866 + SUBMITTER - - ((66)Zn)zinc - IUPAC - + + PMID:19836537 + Europe PMC - - (66)30Zn - ChEBI + + PMID:20155761 + Europe PMC - - (66)Zn - ChemIDplus + + PMID:21047059 + Europe PMC - - Zn-66 - ChemIDplus + + PMID:24196216 + Europe PMC - - zinc, isotope of mass 66 - ChemIDplus + + PMID:26065372 + Europe PMC - - zinc-66 - ChemIDplus + + PMID:26808401 + Europe PMC - CAS:14378-33-7 - ChemIDplus + PMID:27189145 + Europe PMC - PMID:12447866 - SUBMITTER + PMID:27306032 + Europe PMC - - PMID:19836537 - Europe PMC + + ((66)Zn)zinc + IUPAC + - - PMID:20155761 - Europe PMC + + (66)30Zn + ChEBI - - PMID:21047059 - Europe PMC + + (66)Zn + ChemIDplus - - PMID:24196216 - Europe PMC + + Zn-66 + ChemIDplus - - PMID:26065372 - Europe PMC + + zinc, isotope of mass 66 + ChemIDplus - - PMID:26808401 - Europe PMC + + zinc-66 + ChemIDplus @@ -14633,36 +14437,6 @@ For example, A and B may be gene products and binding of B by A positively regul nickel-60 atom - - - - CAS:13981-80-1 - ChemIDplus - - - - - PMID:15308160 - Europe PMC - - - - - PMID:22583786 - Europe PMC - - - - - PMID:23149182 - Europe PMC - - - - - PMID:25126912 - Europe PMC - @@ -14712,6 +14486,36 @@ For example, A and B may be gene products and binding of B by A positively regul nickel-60 ChemIDplus + + + + CAS:13981-80-1 + ChemIDplus + + + + + PMID:15308160 + Europe PMC + + + + + PMID:22583786 + Europe PMC + + + + + PMID:23149182 + Europe PMC + + + + + PMID:25126912 + Europe PMC + @@ -26838,9 +26642,7 @@ For example, A and B may be gene products and binding of B by A positively regul - atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. - CHEBI:22671 CHEBI:23907 MeSH:D004602 @@ -50468,7 +50270,6 @@ For example, A and B may be gene products and binding of B by A positively regul XAO:0003012 - CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). @@ -67733,6 +67534,16 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + http://purl.obolibrary.org/obo/IAO_0000109 + measurement datum + + + + @@ -67764,6 +67575,31 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + A processed material entity which is designed to perform a function. + + 2023-03-24T16:04:27+00:00 + In this definition we assume devices are made of processed material, not natural artifacts, so we involve artifactual function rather than biological function, but align with a general BFO function sense where functions such as pumping, lifting can occur in both contexts. Thus we can compare a biological arm with a robotic arm device. + +We say "designed" to emphasize a device's primary function rather than all the other possible dispositions a device may have that may also be useful. E.g. one can use a hammer for a paper weight. + +Regarding usage then, we don't say a naturally formed rock is a hammering device - it wasn't designed to bear a hammering function per se. However, a given rock may still happen to have the disposition to bear a hammering function, and so we could say it is a hammering "tool", which does not necessarily convey intentional design. + +Example of use: A whole device like an engine; a component like a bolt is also a device. + device + + + + @@ -80940,12 +80776,12 @@ The building envelope provides resistance to air, water, heat, light, and noise - + An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure. Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure. ice - + @@ -80959,7 +80795,7 @@ The building envelope provides resistance to air, water, heat, light, and noise - + https://github.com/EnvironmentOntology/envo/issues/900 @@ -101014,7 +100850,7 @@ consider revising 'pond' semantics - + @@ -101039,14 +100875,14 @@ consider revising 'pond' semantics GO:0005319 lipid transporter activity - + - + GO_REF:0000090 @@ -101127,7 +100963,7 @@ consider revising 'pond' semantics - + @@ -101148,14 +100984,14 @@ consider revising 'pond' semantics GO:0005326 neurotransmitter transmembrane transporter activity - + - + GO_REF:0000090 @@ -101402,32 +101238,32 @@ consider revising 'pond' semantics - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -101839,9 +101675,7 @@ consider revising 'pond' semantics - - cytoplasm @@ -110086,7 +109920,7 @@ consider revising 'pond' semantics - + Enables the transfer of a protein from one side of a membrane to the other. GO:0015266 GO:0015463 @@ -110115,14 +109949,14 @@ consider revising 'pond' semantics GO:0008320 protein transmembrane transporter activity - + - + GO_REF:0000090 @@ -111831,7 +111665,6 @@ consider revising 'pond' semantics response to abiotic stress biological_process GO:0009628 - @@ -120463,7 +120296,7 @@ consider revising 'pond' semantics - + @@ -120478,14 +120311,14 @@ consider revising 'pond' semantics GO:0015075 monoatomic ion transmembrane transporter activity - + - + GO_REF:0000090 @@ -120776,7 +120609,7 @@ consider revising 'pond' semantics - + @@ -120799,14 +120632,14 @@ consider revising 'pond' semantics GO:0015114 phosphate ion transmembrane transporter activity - + - + GO_REF:0000090 @@ -120840,7 +120673,7 @@ consider revising 'pond' semantics - + @@ -120864,14 +120697,14 @@ consider revising 'pond' semantics GO:0015116 sulfate transmembrane transporter activity - + - + GO_REF:0000090 @@ -120916,7 +120749,7 @@ consider revising 'pond' semantics - + @@ -120928,14 +120761,14 @@ consider revising 'pond' semantics GO:0015123 acetate transmembrane transporter activity - + - + GO_REF:0000090 @@ -121110,7 +120943,7 @@ consider revising 'pond' semantics - + @@ -121125,14 +120958,14 @@ consider revising 'pond' semantics GO:0015144 carbohydrate transmembrane transporter activity - + - + GO_REF:0000090 @@ -121204,7 +121037,7 @@ consider revising 'pond' semantics - + @@ -121218,14 +121051,14 @@ consider revising 'pond' semantics GO:0015149 hexose transmembrane transporter activity - + - + GO_REF:0000090 @@ -121310,7 +121143,7 @@ consider revising 'pond' semantics - + @@ -121374,14 +121207,14 @@ consider revising 'pond' semantics GO:0015171 amino acid transmembrane transporter activity - + - + GO_REF:0000090 @@ -165573,14 +165406,12 @@ consider revising 'pond' semantics physiological response to stimulus biological_process GO:0050896 - - Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus @@ -170880,7 +170711,6 @@ consider revising 'pond' semantics Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. biological_process GO:0051716 - Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stimulus @@ -207056,7 +206886,7 @@ consider revising 'pond' semantics - + @@ -207071,14 +206901,14 @@ consider revising 'pond' semantics GO:1901505 carbohydrate derivative transmembrane transporter activity - + - + GO_REF:0000090 @@ -256848,17 +256678,8 @@ consider revising 'pond' semantics measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot + measurement unit label @@ -256869,50 +256690,21 @@ of this, different, term. objective specification - In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." - 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - goal specification - OBI Plan and Planned Process/Roles Branch - OBI_0000217 + objective specification objective specification - - - - - Pour the contents of flask 1 into flask 2 - - A directive information entity that describes an action the bearer will take. - Alan Ruttenberg - OBI Plan and Planned Process branch - action specification - - - - datum label - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - + datum label @@ -256923,54 +256715,14 @@ of this, different, term. software - Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. - see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI + software - - - - - - - - - - - - - - - - - - - - - - information carrier - In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. - - A quality of an information bearer that imparts the information content - 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. - 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. - PERSON: Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - information carrier - - - - @@ -256995,6 +256747,7 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data + data item @@ -257009,7 +256762,7 @@ JAR: A data item is an approximately justified approximately true approximate be - + @@ -257023,17 +256776,10 @@ JAR: A data item is an approximately justified approximately true approximate be information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - A generically dependent continuant that is about some thing. An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set. - 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. James Malone - PERSON: Chris Stoeckert - OBI_0000142 + information http://www.ebi.ac.uk/efo/EFO_0001435 @@ -257053,33 +256799,16 @@ Previous. An information content entity is a non-realizable information entity t - + - - - - 1 - - - - - - 1 - - - 10 feet. 3 ml. - + scalar measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form - Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot + scalar measurement datum @@ -257089,20 +256818,9 @@ this case we explicitly refer to the singular form - - - - - - - + directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters + IAO:0000033 directive information entity directive information entity @@ -257115,13 +256833,8 @@ this case we explicitly refer to the singular form dot plot - Dot plot of SSC-H and FSC-H. - A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000123 - group:OBI + dot plot @@ -257130,15 +256843,10 @@ this case we explicitly refer to the singular form - + graph - A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - PERSON: Lawrence Hunter - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000240 - group:OBI + graph @@ -257149,13 +256857,8 @@ this case we explicitly refer to the singular form algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) + algorithm @@ -257187,43 +256890,20 @@ this case we explicitly refer to the singular form PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 + curation status specification - - - - - source code module - The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. - - A source code module is a directive information entity that specifies, using a programming language, some algorithm. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000039 - group:OBI - source code module - - - - data format specification - A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes -information. Example: The ISO document specifying what encompasses an -XML document; The instructions in a XSD file" - PERSON: Alan Ruttenberg - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000187 + data format specification @@ -257234,15 +256914,8 @@ XML document; The instructions in a XSD file" data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI + data set @@ -257253,13 +256926,8 @@ XML document; The instructions in a XSD file" image - An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - person:Alan Ruttenberg - person:Allyson - person:Chris Stoeckert - OBI_0000030 - group:OBI + image @@ -257287,31 +256955,11 @@ XML document; The instructions in a XSD file" - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2014-03-31: A plan specification can have other parts, such as conditional specifications. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - OBI Plan and Planned Process branch - OBI_0000344 + IAO:0000104 - 2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them plan specification plan specification @@ -257322,12 +256970,6 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. @@ -257342,61 +256984,14 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - material information bearer - A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. - a brain - a hard drive - - A material entity in which a concretization of an information content entity inheres. - GROUP: IAO - material information bearer - - - - histogram - A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI + histogram @@ -257407,14 +257002,10 @@ distribution in terms of occurrence frequencies of different event classes. heatmap - A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI + heatmap @@ -257425,16 +257016,10 @@ two-dimensional map. dendrogram - Dendrograms are often used in computational biology to -illustrate the clustering of genes. - A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Dendrogram + dendrogram @@ -257445,14 +257030,8 @@ clustering algorithm. scatter plot - Comparison of gene expression values in two samples can be displayed in a scatter plot - A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - scattergraph - WEB: http://en.wikipedia.org/wiki/Scatterplot + scatter plot @@ -257501,38 +257080,20 @@ clustering algorithm. figure - Any picture, diagram or table - An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - PERSON: Lawrence Hunter + figure - - - - - diagram - A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. - - A figure that expresses one or more propositions - PERSON: Lawrence Hunter - diagram - - - - document - A journal article, patent application, laboratory notebook, or a book - A collection of information content entities intended to be understood together as a whole - PERSON: Lawrence Hunter + document @@ -257542,21 +257103,9 @@ clustering algorithm. - - - - - - - - - - - - - + length measurement datum A scalar measurement datum that is the result of measurement of length quality - Alan Ruttenberg + length measurement datum @@ -257701,8 +257250,6 @@ clustering algorithm. GC_ID:1 - PMID:30365038 - PMID:32761142 ncbi_taxonomy all NCBITaxon:1 @@ -257723,37 +257270,6 @@ clustering algorithm. - - - - - - GC_ID:1 - hamsters - ncbi_taxonomy - Cricetinae - - - - - hamsters - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Mesocricetus - - - - @@ -257977,60 +257493,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Obtectomera - - - - - - - - - - NCBITaxon:1537974 - GC_ID:1 - ncbi_taxonomy - Allolobophorinae - Lumbricinae - - - - - Allolobophorinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Lumbricus terrestris complex - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Lumbricus rubellus complex - - - - @@ -258091,75 +257553,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Sarsostraca - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Phyllopoda - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Anomopoda - - - - - - - - - NCBITaxon:6795 - GC_ID:1 - ncbi_taxonomy - Eubrachyura - - - - - - - - - NCBITaxon:29963 - NCBITaxon:6773 - NCBITaxon:6803 - GC_ID:1 - ncbi_taxonomy - Brachyrhyncha - Heterotremata - - - - - Brachyrhyncha - - - - - @@ -258629,32 +258022,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:25249442 - ncbi_taxonomy - Mesangiospermae - - - - - - - - - - GC_ID:1 - PMID:26350789 - ncbi_taxonomy - Petrosaviidae - - - - @@ -258668,18 +258035,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Pinales - - - - @@ -258801,32 +258156,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Carangimorpha - Carangimorphariae - Carangaria - - - - - Carangimorpha - - - - - - Carangimorphariae - - - - - @@ -258860,59 +258189,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Galloanseri - ducks, geese, chickens, fowl, quail, currasows and allies - Galloanserae - - - - - Galloanseri - - - - - - ducks, geese, chickens, fowl, quail, currasows and allies - - - - - - - - - - - NCBITaxon:29008 - GC_ID:1 - ncbi_taxonomy - Eisenia fetida andrei - Eiseniella andrei - Eisenia andrei - - - - - Eisenia fetida andrei - - - - - - Eiseniella andrei - - - - - @@ -259045,18 +258321,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Enchytraeida - - - - @@ -259356,30 +258620,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Multicrustacea - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Hirudinida - - - - @@ -259470,18 +258710,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Ochrophyta - - - - @@ -259671,121 +258899,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Bovinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Crassiclitellata - - - - - - - - - - GC_ID:1 - PMID:19761858 - ncbi_taxonomy - Conifers I - - - - - - - - - - GC_ID:1 - brown algae - ncbi_taxonomy - Chromophycota - Fucophyceae - Phaeophyta - algae - brown algae - Phaeophyceae - - - - - brown algae - - - - - - Chromophycota - - - - - - Fucophyceae - - - - - - Phaeophyta - - - - - - algae - - - - - - brown algae - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Oryzomys - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cancroidea - - - - @@ -259799,51 +258912,6 @@ clustering algorithm. - - - - - - GC_ID:1 - Ranoidea - ncbi_taxonomy - Ranoidea Rafinesque, 1814 - Ranoidea <superfamily> - - - - - Ranoidea - - - - - - Ranoidea Rafinesque, 1814 - - - - - - - - - - - GC_ID:1 - Anthophila - ncbi_taxonomy - Anthophila <bees> - - - - - Anthophila - - - - - @@ -259864,26 +258932,6 @@ clustering algorithm. - - - - - - NCBITaxon:30946 - GC_ID:1 - ncbi_taxonomy - Soleoidei - Pleuronectoidei - - - - - Soleoidei - - - - - @@ -260012,21 +259060,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:11214318 - PMID:11214319 - PMID:12878460 - ncbi_taxonomy - Laurasiatheria - - - - @@ -260090,18 +259123,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Cercopithecoidea - - - - @@ -260183,47 +259204,6 @@ clustering algorithm. - - - - - - NCBITaxon:3194 - GC_ID:1 - mosses - ncbi_taxonomy - Musci - bryophytes - mosses - Bryophyta - - - - - mosses - - - - - - Musci - - - - - - bryophytes - - - - - - mosses - - - - - @@ -260551,26 +259531,6 @@ clustering algorithm. - - - - - - NCBITaxon:1445965 - GC_ID:1 - ncbi_taxonomy - Coniferales - Pinidae - - - - - Coniferales - - - - - @@ -260614,25 +259574,6 @@ clustering algorithm. - - - - - - GC_ID:1 - pine family - ncbi_taxonomy - Pinaceae - - - - - pine family - - - - - @@ -260762,32 +259703,6 @@ clustering algorithm. - - - - - - GC_ID:1 - carnivores - ncbi_taxonomy - carnivores - Carnivora - - - - - carnivores - - - - - - carnivores - - - - - @@ -260808,46 +259723,6 @@ clustering algorithm. - - - - - - GC_ID:1 - heterokonts - ncbi_taxonomy - Chromophyta - Heterokonta - Straminipila - Stramenopiles - - - - - heterokonts - - - - - - Chromophyta - - - - - - Heterokonta - - - - - - Straminipila - - - - - @@ -260895,19 +259770,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:15371245 - ncbi_taxonomy - Cricetidae - - - - @@ -260936,18 +259798,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Felinae - - - - @@ -261010,39 +259860,6 @@ clustering algorithm. - - - - - - GC_ID:1 - bee - bees - ncbi_taxonomy - bees - Apoidea - - - - - bee - - - - - - bees - - - - - - bees - - - - - @@ -261056,75 +259873,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Suiformes - Suina - - - - - Suiformes - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Pecora - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ditrysia - - - - - - - - - - GC_ID:1 - butterflies - ncbi_taxonomy - butterflies - Papilionoidea - - - - - butterflies - - - - - - butterflies - - - - - @@ -261138,42 +259886,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Feliformia - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Caniformia - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Artemiidae - - - - @@ -261216,21 +259928,6 @@ clustering algorithm. - - - - - - NCBITaxon:4478 - NCBITaxon:4727 - GC_ID:1 - PMID:26350789 - ncbi_taxonomy - Poales - - - - @@ -261245,20 +259942,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:15019624 - PMID:15371245 - ncbi_taxonomy - Sigmodontinae - - - - @@ -261290,43 +259973,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Glossata - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Neolepidoptera - - - - - - - - - - NCBITaxon:37583 - GC_ID:1 - ncbi_taxonomy - Heteroneura - - - - @@ -261465,30 +260111,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Protacanthopterygii - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Clitellata - - - - @@ -261626,81 +260248,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:25249442 - monocots - monocotyledons - ncbi_taxonomy - Monocotyledoneae - monocots - Liliopsida - - - - - monocots - - - - - - monocotyledons - - - - - - Monocotyledoneae - - - - - - monocots - - - - - - - - - - - NCBITaxon:1661618 - GC_ID:1 - grass family - ncbi_taxonomy - Bambusaceae - Gramineae - Poaceae - - - - - grass family - - - - - - Bambusaceae - - - - - - Gramineae - - - - - @@ -261746,33 +260293,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:26350789 - ncbi_taxonomy - Commelinidae - Commeliniflorae - commelinids - - - - - Commelinidae - - - - - - Commeliniflorae - - - - - @@ -262098,25 +260618,6 @@ clustering algorithm. - - - - - - GC_ID:1 - trouts, salmons & chars - ncbi_taxonomy - Salmoninae - - - - - trouts, salmons & chars - - - - - @@ -262159,26 +260660,6 @@ clustering algorithm. - - - - - - NCBITaxon:6403 - GC_ID:1 - leeches - ncbi_taxonomy - Hirudinea - - - - - leeches - - - - - @@ -262205,25 +260686,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - algae - PX clade - - - - - algae - - - - - @@ -262245,25 +260707,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Coniferopsida - Pinopsida - - - - - Coniferopsida - - - - - @@ -262627,257 +261070,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:34811021 - Oligochaeta - ncbi_taxonomy - Oligochaeta <segmented worms> - - - - - Oligochaeta - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Enchytraeidae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Enchytraeus - - - - - - - - - - GC_ID:1 - earthworms - ncbi_taxonomy - Lumbricina - - - - - earthworms - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Lumbricidae - - - - - - - - - - GC_ID:1 - Eisenia - ncbi_taxonomy - Eisenia <segmented worms> - - - - - Eisenia - - - - - - - - - - - GC_ID:1 - brandling worm - common brandling worm - common dung-worm - red wiggler worm - redworm - tiger worm - ncbi_taxonomy - Eisenia foetida - Eiseniella fetida - Eisenia fetida - - - - - brandling worm - - - - - - common brandling worm - - - - - - common dung-worm - - - - - - red wiggler worm - - - - - - redworm - - - - - - tiger worm - - - - - - Eisenia foetida - - - - - - Eiseniella fetida - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Lumbricus - - - - - - - - - - NCBITaxon:2175058 - GC_ID:1 - common earthworm - ncbi_taxonomy - Lumbricus terrestris - - - - - common earthworm - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Hirudiniformes - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Hirudinidae - - - - - - - - - - GC_ID:1 - molluscs - mollusks - ncbi_taxonomy - molluscs - Mollusca - - - - - molluscs - - - - - - mollusks - - - - - - molluscs - - - - - @@ -262905,235 +261097,6 @@ clustering algorithm. - - - - - - GC_ID:1 - crustaceans - ncbi_taxonomy - crustaceans - Crustacea - - - - - crustaceans - - - - - - crustaceans - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Branchiopoda - - - - - - - - - - GC_ID:1 - fairy shrimps - ncbi_taxonomy - Anostraca - - - - - fairy shrimps - - - - - - - - - - - GC_ID:1 - brine shrimps - sea monkeys - ncbi_taxonomy - Artemia - - - - - brine shrimps - - - - - - sea monkeys - - - - - - - - - - - GC_ID:1 - water flea - water fleas - ncbi_taxonomy - Cladocera - - - - - water flea - - - - - - water fleas - - - - - - - - - - - NCBITaxon:77736 - GC_ID:1 - common water fleas - ncbi_taxonomy - Daphniopsis - Daphnia - - - - - common water fleas - - - - - - Daphniopsis - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Malacostraca - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Eucarida - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Decapoda - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Pleocyemata - - - - - - - - - - GC_ID:1 - short-tailed crabs - true crabs - ncbi_taxonomy - Brachyura - - - - - short-tailed crabs - - - - - - true crabs - - - - - - - - - - - GC_ID:1 - rock crabs - ncbi_taxonomy - Cancridae - - - - - rock crabs - - - - - @@ -263182,39 +261145,6 @@ clustering algorithm. - - - - - - GC_ID:1 - butterflies and moths - moths - ncbi_taxonomy - moths - Lepidoptera - - - - - butterflies and moths - - - - - - moths - - - - - - moths - - - - - @@ -263268,18 +261198,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Eumalacostraca - - - - @@ -263363,99 +261281,6 @@ clustering algorithm. - - - - - - NCBITaxon:27522 - NCBITaxon:27527 - NCBITaxon:27531 - GC_ID:1 - hymenopterans - ncbi_taxonomy - hymenopterans - Hymenoptera - - - - - hymenopterans - - - - - - hymenopterans - - - - - - - - - - - GC_ID:1 - wasps, ants & bees - ncbi_taxonomy - wasps, ants & bees - Apocrita - - - - - wasps, ants & bees - - - - - - wasps, ants & bees - - - - - - - - - - - GC_ID:1 - Aculeata - ncbi_taxonomy - Aculeata <wasps, ants & bees> - - - - - Aculeata - - - - - - - - - - - GC_ID:1 - bumble bees and honey bees - ncbi_taxonomy - Apidae - - - - - bumble bees and honey bees - - - - - @@ -263630,19 +261455,6 @@ clustering algorithm. - - - - - - NCBITaxon:77729 - GC_ID:1 - ncbi_taxonomy - Daphniidae - - - - @@ -264083,130 +261895,6 @@ clustering algorithm. - - - - - - GC_ID:1 - salmons and trouts - ncbi_taxonomy - Salmoniformes - - - - - salmons and trouts - - - - - - - - - - - GC_ID:1 - PMID:15062801 - salmonids - ncbi_taxonomy - Salmonidae - - - - - salmonids - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Parasalmo - Oncorhynchus - - - - - Parasalmo - - - - - - - - - - - NCBITaxon:62064 - NCBITaxon:82302 - GC_ID:1 - ncbi_taxonomy - Acantholingua - Salmothymus - Salmo - - - - - Acantholingua - - - - - - Salmothymus - - - - - - - - - - - GC_ID:1 - flatfishes - ncbi_taxonomy - Pleuronectiformes - - - - - flatfishes - - - - - - - - - - - GC_ID:1 - righteye flounders - ncbi_taxonomy - Pleuronectidae - - - - - righteye flounders - - - - - @@ -264413,57 +262101,6 @@ clustering algorithm. - - - - - - NCBITaxon:685149 - GC_ID:1 - riparian frogs - true frogs - ncbi_taxonomy - Ranidae - - - - - riparian frogs - - - - - - true frogs - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Neobatrachia - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Diplostraca - - - - @@ -264510,30 +262147,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Artemia salina - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Amphiesmenoptera - - - - @@ -264695,44 +262308,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ducks, geese and swans - ncbi_taxonomy - Anseriformes - - - - - ducks, geese and swans - - - - - - - - - - - GC_ID:1 - waterfowl - ncbi_taxonomy - Anatidae - - - - - waterfowl - - - - - @@ -264806,168 +262381,6 @@ clustering algorithm. - - - - - - GC_ID:1 - landfowls - ncbi_taxonomy - Galliformes - - - - - landfowls - - - - - - - - - - - NCBITaxon:9099 - GC_ID:1 - turkeys - ncbi_taxonomy - Phasianidae - - - - - turkeys - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Gallus - - - - - - - - - - GC_ID:1 - Gallus domesticus - bantam - chicken - chickens - ncbi_taxonomy - Gallus gallus domesticus - Phasianus gallus - Gallus gallus - - - - - Gallus domesticus - - - - - - bantam - - - - - - chicken - - - - - - chickens - - - - - - Gallus gallus domesticus - - - - - - Phasianus gallus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Phasianinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Enchytraeus crypticus - - - - - - - - - - GC_ID:1 - whales, hippos, ruminants, pigs, camels etc. - ncbi_taxonomy - Cetartiodactyla - even-toed ungulates - Artiodactyla - - - - - whales, hippos, ruminants, pigs, camels etc. - - - - - - Cetartiodactyla - - - - - - even-toed ungulates - - - - - @@ -265110,39 +262523,6 @@ clustering algorithm. - - - - - - GC_ID:1 - New World monkeys - monkey - monkeys - ncbi_taxonomy - Platyrrhini - - - - - New World monkeys - - - - - - monkey - - - - - - monkeys - - - - - @@ -265156,125 +262536,6 @@ clustering algorithm. - - - - - - GC_ID:1 - Old World monkeys - monkey - monkeys - ncbi_taxonomy - Cercopithecidae - - - - - Old World monkeys - - - - - - monkey - - - - - - monkeys - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cercopithecinae - - - - - - - - - - GC_ID:1 - macaque - macaques - ncbi_taxonomy - Macaca - - - - - macaque - - - - - - macaques - - - - - - - - - - - NCBITaxon:36502 - GC_ID:1 - Rhesus monkey - rhesus macaque - rhesus macaques - rhesus monkeys - ncbi_taxonomy - Cercopithecus mulatta - Macaca mulatta - - - - - Rhesus monkey - - - - - - rhesus macaque - - - - - - rhesus macaques - - - - - - rhesus monkeys - - - - - - Cercopithecus mulatta - - - - - @@ -265346,446 +262607,6 @@ clustering algorithm. - - - - - - GC_ID:1 - dog, coyote, wolf, fox - ncbi_taxonomy - Canidae - - - - - dog, coyote, wolf, fox - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Canis - - - - - - - - - - NCBITaxon:68731 - NCBITaxon:9609 - GC_ID:1 - ncbi_taxonomy - Fennecus - Vulpes - - - - - Fennecus - - - - - - - - - - - GC_ID:1 - cat family - ncbi_taxonomy - Felidae - - - - - cat family - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Felis - - - - - - - - - - NCBITaxon:36475 - GC_ID:1 - PMID:17600185 - PMID:8581300 - PMID:8603894 - cat - cats - domestic cat - ncbi_taxonomy - Felis domesticus - Felis silvestris catus - Felis catus - - - - - cat - - - - - - cats - - - - - - domestic cat - - - - - - Felis domesticus - - - - - - Felis silvestris catus - - - - - - - - - - - NCBITaxon:39423 - GC_ID:1 - boars - pigs - ncbi_taxonomy - Suidae - - - - - boars - - - - - - pigs - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Sus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ruminantia - - - - - - - - - - GC_ID:1 - deer - ncbi_taxonomy - Cervidae - - - - - deer - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Rangifer - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Odocoileinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Bovidae - - - - - - - - - - GC_ID:1 - oxen, cattle - ncbi_taxonomy - Bos - - - - - oxen, cattle - - - - - - - - - - - NCBITaxon:272461 - GC_ID:1 - bovine - cattle - cow - dairy cow - domestic cattle - domestic cow - ox - ncbi_taxonomy - Bos bovis - Bos primigenius taurus - Bos taurus - - - - - bovine - - - - - - cattle - - - - - - cow - - - - - - dairy cow - - - - - - domestic cattle - - - - - - domestic cow - - - - - - ox - - - - - - Bos bovis - - - - - - Bos primigenius taurus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ovis - - - - - - - - - - NCBITaxon:9936 - GC_ID:1 - domestic sheep - lambs - sheep - wild sheep - ncbi_taxonomy - Ovis ammon aries - Ovis orientalis aries - Ovis ovis - Ovis aries - - - - - domestic sheep - - - - - - lambs - - - - - - sheep - - - - - - wild sheep - - - - - - Ovis ammon aries - - - - - - Ovis orientalis aries - - - - - - Ovis ovis - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Caprinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - rabbits & hares - Lagomorpha - - - - - rabbits & hares - - - - - @@ -265824,35 +262645,23 @@ clustering algorithm. - + - + - - - - - - - - - - - - planned process - planned process + completely executed planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. @@ -265863,7 +262672,6 @@ objectives is a planned process. branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - CHMO:0001840 OBI:0000011 completely executed planned process @@ -265971,12 +262779,14 @@ objectives is a planned process. - processed material + processed material entity Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + A material entity processed by human activity with an intent to produce Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material + processed material entity @@ -266153,6 +262963,7 @@ for now. PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI + Should revisit if we can place outside of material entity - a collection of roles. organization @@ -266179,6 +262990,13 @@ for now. + plan + The plan of researcher X to perform an experiment according to a protocol. + + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. + AR, BP, JM, MC, PRS + branch derived plan @@ -266410,7 +263228,7 @@ for now. manufacturer role With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. - Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. + Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI manufacturer role @@ -266483,7 +263301,7 @@ for now. specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation - A planned process with the objective of collecting a specimen. + A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. @@ -266534,7 +263352,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. - A objective specification to obtain a material entity for potential use as an input during an investigation. + A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective @@ -266554,7 +263372,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ support vector machine - A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. + A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. James Malone Ryan Brinkman SVM @@ -266570,7 +263388,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ decision tree induction objective - A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. + A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. James Malone decision tree induction objective @@ -266609,7 +263427,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ GenePattern software - a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. + a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ @@ -266624,7 +263442,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ peak matching - Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold + Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold James Malone Ryan Brinkman PERSON: Ryan Brinkman @@ -266636,7 +263454,6 @@ http://sourceforge.net/p/obi/obi-terms/716/ - @@ -266698,7 +263515,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ statistical model validation Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia - A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. + A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation @@ -266734,7 +263551,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ manufacturer - A person or organization that has a manufacturer role. + A person or organization that has a manufacturer role. manufacturer @@ -266767,7 +263584,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. - is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person + is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role @@ -266791,7 +263608,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. - A specimen that has been intentionally physically modified. + A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. @@ -266807,7 +263624,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells.categorical label The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. - A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. + A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label @@ -266821,34 +263638,23 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - - - - - - - device + + obsolete_device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. PERSON: Helen Parkinson instrument - OBI development call 2012-12-17. + OBI development call 2012-12-17 + + CHMO:0000998 OBI:0000968 device + obsolete_device + true @@ -266862,11 +263668,11 @@ In the examples above, a reagent is an operational component of a device, but th - + dose An organism has been injected 1ml of vaccine - A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. + A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. dose @@ -266895,7 +263701,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -266903,7 +263709,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -266913,7 +263719,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) - A device which has a function to emit light. + A device which has a function to emit light. Person:Helen Parkinson OBI light emission device @@ -266924,6 +263730,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S + @@ -266934,6 +263741,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S X-ray source A device that is used to generate X-rays. + A device that is used to generate X-rays. PERSON: Erik Segerdell x-ray generator http://en.wikipedia.org/wiki/X-ray_generator @@ -266971,7 +263779,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". - An information content entity that is inferred from data. + An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group @@ -266986,7 +263794,7 @@ The following are NOT conclusions based on data: data themselves; results from p categorical value specification - A value specification that is specifies one category out of a fixed number of nominal categories + A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification @@ -267011,7 +263819,7 @@ The following are NOT conclusions based on data: data themselves; results from p scalar value specification - A value specification that consists of two parts: a numeral and a unit label + A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification @@ -267025,7 +263833,7 @@ The following are NOT conclusions based on data: data themselves; results from p value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. - An information content entity that specifies a value within a classification scheme or on a quantitative scale. + An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification @@ -267069,7 +263877,7 @@ The following are NOT conclusions based on data: data themselves; results from p G1:Well differentiated G4: Undifferentiated - A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -267084,7 +263892,7 @@ The following are NOT conclusions based on data: data themselves; results from p histologic grade according to the Fuhrman Nuclear Grading System - A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. Chris Stoeckert, Helena Ellis Histologic Grade (Fuhrman Nuclear Grading System) NCI BBRB, OBI @@ -267100,7 +263908,7 @@ The following are NOT conclusions based on data: data themselves; results from p histologic grade for ovarian tumor - A categorical value specification that is a histologic grade assigned to a ovarian tumor. + A categorical value specification that is a histologic grade assigned to a ovarian tumor. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -267115,7 +263923,7 @@ The following are NOT conclusions based on data: data themselves; results from p histologic grade for ovarian tumor according to a two-tier grading system - A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. + A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -267130,7 +263938,7 @@ The following are NOT conclusions based on data: data themselves; results from p histologic grade for ovarian tumor according to the World Health Organization - A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). + A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -267145,7 +263953,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic primary tumor stage for colon and rectum according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) NCI BBRB, OBI @@ -267161,7 +263969,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic primary tumor stage for lung according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread lung primary tumor (AJCC 7th Edition) NCI BBRB, OBI @@ -267177,7 +263985,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic primary tumor stage for kidney according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) NCI BBRB, OBI @@ -267193,7 +264001,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic primary tumor stage for ovary according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) NCI BBRB, OBI @@ -267209,7 +264017,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic lymph node stage for colon and rectum according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI @@ -267225,7 +264033,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic lymph node stage for lung according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI @@ -267241,7 +264049,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic lymph node stage for kidney according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) NCI BBRB, OBI @@ -267257,7 +264065,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic lymph node stage for ovary according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) NCI BBRB, OBI @@ -267273,7 +264081,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic distant metastases stage for colon according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: colon distant metastases (AJCC 7th Edition) NCI BBRB, OBI @@ -267289,7 +264097,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic distant metastases stage for lung according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: lung distant metastases (AJCC 7th Edition) NCI BBRB, OBI @@ -267305,7 +264113,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic distant metastases stage for kidney according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: kidney distant Metastases (AJCC 7th Edition) NCI BBRB, OBI @@ -267321,7 +264129,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic distant metastases stage for ovary according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: ovarian distant metastases (AJCC 7th Edition) NCI BBRB, OBI @@ -267337,7 +264145,7 @@ The following are NOT conclusions based on data: data themselves; results from p clinical tumor stage group according to AJCC 7th edition - A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. + A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. Chris Stoeckert, Helena Ellis Clinical tumor stage group (AJCC 7th Edition) NCI BBRB, OBI @@ -267353,7 +264161,7 @@ The following are NOT conclusions based on data: data themselves; results from p International Federation of Gynecology and Obstetrics cervical cancer stage value specification - A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. + A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. Chris Stoeckert, Helena Ellis Clinical FIGO stage NCI BBRB, OBI @@ -267369,7 +264177,7 @@ The following are NOT conclusions based on data: data themselves; results from p International Federation of Gynecology and Obstetrics ovarian cancer stage value specification - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. Chris Stoeckert, Helena Ellis Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) NCI BBRB, OBI @@ -267385,7 +264193,7 @@ The following are NOT conclusions based on data: data themselves; results from p performance status value specification - A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). + A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Chris Stoeckert, Helena Ellis Performance Status Scale https://en.wikipedia.org/wiki/Performance_status @@ -267401,7 +264209,7 @@ The following are NOT conclusions based on data: data themselves; results from p Eastern Cooperative Oncology Group score value specification - A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. + A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. Chris Stoeckert, Helena Ellis ECOG score NCI BBRB, OBI @@ -267417,7 +264225,7 @@ The following are NOT conclusions based on data: data themselves; results from p Karnofsky score vaue specification - A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. + A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Chris Stoeckert, Helena Ellis Karnofsky Score NCI BBRB, OBI @@ -267433,7 +264241,7 @@ The following are NOT conclusions based on data: data themselves; results from p altitude measurement datum - A length measurement datum between a point at sea or ground level and some point above it. + A length measurement datum between a point at sea or ground level and some point above it. Chris Stoeckert Adapted from https://www.merriam-webster.com/dictionary/altitude altitude measurement datum @@ -267469,7 +264277,7 @@ The following are NOT conclusions based on data: data themselves; results from p material supplier - A person or organization that provides material supplies to other people or organizations. + A person or organization that provides material supplies to other people or organizations. Rebecca Jackson https://github.com/obi-ontology/obi/issues/1289 material supplier @@ -267570,10 +264378,10 @@ This issue is outside the scope of OBI. - + - + @@ -267616,7 +264424,6 @@ This issue is outside the scope of OBI. data analysis data processing Branch editors - data transformation @@ -267629,7 +264436,7 @@ This issue is outside the scope of OBI. leave one out cross validation method The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 - is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data + is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 Person:Helen Parkinson leave one out cross validation method @@ -267640,7 +264447,6 @@ This issue is outside the scope of OBI. - @@ -267672,7 +264478,6 @@ This issue is outside the scope of OBI. - @@ -267701,7 +264506,6 @@ This issue is outside the scope of OBI. - @@ -267985,7 +264789,7 @@ class labels for these objects. The resulting predictor can be used to attach cl clustered data visualization - A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. + A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. James Malone clustered data visualization @@ -268026,7 +264830,7 @@ class labels for these objects. The resulting predictor can be used to attach cl light source - A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. + A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. Elizabeth M. Goralczyk John Quinn Olga Tchuvatkina @@ -268071,7 +264875,9 @@ class labels for these objects. The resulting predictor can be used to attach cl + composition A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. + PATO:0002015 composed of compositionality @@ -268210,18 +265016,6 @@ class labels for these objects. The resulting predictor can be used to attach cl - - - - - length - A 1-D extent quality which is equal to the distance between two points. - - length - - - - @@ -268269,7 +265063,9 @@ class labels for these objects. The resulting predictor can be used to attach cl + structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. + PATO:0001452 conformation relational structural quality @@ -272420,7 +269216,7 @@ Classes for population already exist in IDO ('organism population', I - + An anatomical entity that is or was part of a plant. rwalls 2010-11-15T11:41:38Z @@ -272432,14 +269228,14 @@ Classes for population already exist in IDO ('organism population', I Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. plant anatomical entity - + - + cjm @@ -277171,9 +273967,9 @@ Classes for population already exist in IDO ('organism population', I - + The amount of ionizing radiation to which a member of the population on Earth is exposed from natural sources, such as terrestrial radiation from naturally-occurring radionuclides in the soil, cosmic radiation originating in outer space, and naturally-occurring ra - background ionizing radiation + ionizing background radiation @@ -279572,21 +276368,13 @@ Classes for population already exist in IDO ('organism population', I - - + - - - - 1 - - - A process involving the emission of energy from an atomic nucleus resulting in change in the character of the nucleus radioactive decay @@ -279685,7 +276473,16 @@ Classes for population already exist in IDO ('organism population', I - Atomic nuclei, with atomic number 2 or greater and kinetic energy imparted by natural or artificial means + A type of ionizing radiation consisting of charged particles that are relatively massive compared to other types of radiation, such as alpha, beta, and gamma radiation. Heavy ion radiation is composed of atomic nuclei that have been stripped of their electrons, resulting in positively charged particles. + Heavy ion radiation has several notable characteristics and contexts: + +High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. + +Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation. + +Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. + +In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. heavy ion radiation @@ -280761,7 +277558,7 @@ Classes for population already exist in IDO ('organism population', I https://orcid.org/0000-0001-9227-0670 ambient radiation background radiation - anthropogenic background radiation + anthropogenic ionizing background radiation @@ -280773,7 +277570,7 @@ Classes for population already exist in IDO ('organism population', I Radiation originating in the terrestrial or extra-terrestrial environment. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 - natural background radiation + natural ionizing background radiation @@ -280837,6 +277634,81 @@ Classes for population already exist in IDO ('organism population', I + + + + + thermal neutron + A neutron that has (by collision with other particles) reached an energy state equal to that of its surroundings, typically on the order of 0.025 eV. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + https://www.nrc.gov/reading-rm/basic-ref/glossary/neutron-thermal.html + thermal neutron + + + + + + + + + epithermal neutron + a neutron with energy greater than a thermal neutron, but less than a fast neutron. The approximate energy range is 0.025-0.4 eV. + http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670 + https://ns.ph.liv.ac.uk/~ajb/radiometrics/glossary/epithermal_neutron.html + epithermal neutron + + + + + + + + + background radiation + The ambient radiation in a defined environment emanating from natural or anthropogenic sources. + For uses involving experimentation or radiation therapy, use "anthropogenic background radiation" instead. Use this concept to indicate source is a mixture of anthropogenic and naturally occurring (ambient), or unknown or if the discrimination is not sought. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + background radiation + + + + + + + + + non-ionizing background radiation + Background radiation that does not result in ionization of target material + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + non-ionizing background radiation + + + + + + + + + anthropogenic non-ionizing background radiation + Non-ionizing background radiation that is the result of a human planned process. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + anthropogenic non-ionizing background radiation + + + + + + + + + natural non-ionizing background radiation + Non-ionizing background radiation that is not the result of a human planned process. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + natural non-ionizing background radiation + + + + @@ -281223,9 +278095,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -281269,34 +278141,34 @@ Classes for population already exist in IDO ('organism population', I islet of Langerhans http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png - + - + - + - + PMID:16417468 - + PMID:16417468 - + PMID:16417468 @@ -281604,7 +278476,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -281650,7 +278522,7 @@ Classes for population already exist in IDO ('organism population', I sympathetic nervous system http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png - + @@ -281663,7 +278535,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA MA ZFA-modified-from-isa @@ -281863,7 +278735,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -281876,9 +278748,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -281926,19 +278798,19 @@ Classes for population already exist in IDO ('organism population', I endocrine pancreas - + - + - + - + @@ -281951,7 +278823,7 @@ Classes for population already exist in IDO ('organism population', I - + AAO FMA XAO @@ -281959,19 +278831,19 @@ Classes for population already exist in IDO ('organism population', I - + GO - + GO - + GO @@ -282182,7 +279054,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -282210,14 +279082,14 @@ Classes for population already exist in IDO ('organism population', I compound eye https://github.com/obophenotype/uberon/issues/457 - + - + PMID:21062451 @@ -282299,7 +279171,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -282340,14 +279212,14 @@ Classes for population already exist in IDO ('organism population', I camera-type eye - + - + definitional @@ -282785,7 +279657,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a respiratory airway. EMAPA:35877 FMA:265157 @@ -282808,14 +279680,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0000031 lamina propria of trachea - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -283120,8 +279992,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -283172,11 +280044,11 @@ Classes for population already exist in IDO ('organism population', I tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -283189,13 +280061,13 @@ Classes for population already exist in IDO ('organism population', I - + OG - + AEO @@ -283265,8 +280137,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A biological tissue mass, most commonly a mass of nerve cell bodies. TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. @@ -283318,11 +280190,11 @@ Classes for population already exist in IDO ('organism population', I ganglion - + - + @@ -283335,13 +280207,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + Bgee:AN @@ -283980,7 +280852,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -284001,14 +280873,14 @@ Classes for population already exist in IDO ('organism population', I respiratory tract - + - + NCBIBook:NBK10107 @@ -284665,7 +281537,7 @@ Classes for population already exist in IDO ('organism population', I - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) @@ -284691,7 +281563,7 @@ Classes for population already exist in IDO ('organism population', I external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -284704,7 +281576,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -284817,7 +281689,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -284860,14 +281732,14 @@ Classes for population already exist in IDO ('organism population', I morula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png - + - + EHDAA2 @@ -285020,8 +281892,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A mass of cells that develop into the body of the embryo and some extraembryonic tissues. A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG] A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG] @@ -285049,24 +281921,24 @@ Classes for population already exist in IDO ('organism population', I inner cell mass https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg - + - + - + Wikipedia - + Wikipedia @@ -285134,7 +282006,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -285167,14 +282039,14 @@ Classes for population already exist in IDO ('organism population', I trophoblast https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg - + - + MP-def PMID:19829370 @@ -285241,7 +282113,7 @@ Classes for population already exist in IDO ('organism population', I - + A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc. embryonic disc embryonic shield @@ -285261,14 +282133,14 @@ Classes for population already exist in IDO ('organism population', I bilaminar disc http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png - + - + Wikipedia @@ -285369,7 +282241,7 @@ Classes for population already exist in IDO ('organism population', I - + Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]. 2009-07-30T05:19:13Z @@ -285380,14 +282252,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0000094 membrane organ - + - + FMA-def @@ -285410,7 +282282,7 @@ Classes for population already exist in IDO ('organism population', I - + Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]. A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]. ZFA treats this as a subtype of NC. @@ -285427,14 +282299,14 @@ Classes for population already exist in IDO ('organism population', I cardiac neural crest - + - + Wikipedia @@ -285901,7 +282773,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -285937,14 +282809,14 @@ Classes for population already exist in IDO ('organism population', I gastrula stage - + - + BILS @@ -286358,7 +283230,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -286386,7 +283258,7 @@ Classes for population already exist in IDO ('organism population', I lung bud http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png - + @@ -286399,7 +283271,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -286511,7 +283383,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -286537,14 +283409,14 @@ Classes for population already exist in IDO ('organism population', I neural nucleus - + - + we limit this structure by definition to chordate and vertebrate nervous systems @@ -286755,7 +283627,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -286794,14 +283666,14 @@ Classes for population already exist in IDO ('organism population', I anal canal https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png - + - + Wikipathways:WP2062 @@ -286984,8 +283856,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -287018,24 +283890,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -287118,8 +283990,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -287138,24 +284010,24 @@ Classes for population already exist in IDO ('organism population', I embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -287663,7 +284535,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -287709,14 +284581,14 @@ Classes for population already exist in IDO ('organism population', I pair of lungs - + - + FMA-abduced @@ -287892,15 +284764,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. @@ -287944,34 +284816,34 @@ Classes for population already exist in IDO ('organism population', I blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -288087,7 +284959,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -288122,7 +284994,7 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png https://upload.wikimedia.org/wikipedia/commons/5/5b/Frontal_bone.png - + @@ -288135,7 +285007,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -288243,7 +285115,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -288276,14 +285148,14 @@ Classes for population already exist in IDO ('organism population', I atlanto-occipital joint http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png - + - + FMA-abduced-lr @@ -288647,7 +285519,7 @@ Classes for population already exist in IDO ('organism population', I - + The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. BTO:0000503 EMAPA:27181 @@ -288658,7 +285530,7 @@ Classes for population already exist in IDO ('organism population', I gastric gland - + @@ -288671,7 +285543,7 @@ Classes for population already exist in IDO ('organism population', I - + ISBN:0073040584 @@ -289624,7 +286496,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -289651,7 +286523,7 @@ Classes for population already exist in IDO ('organism population', I syncytiotrophoblast http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png - + @@ -289664,7 +286536,7 @@ Classes for population already exist in IDO ('organism population', I - + EMAPA @@ -290784,7 +287656,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -290826,14 +287698,14 @@ Classes for population already exist in IDO ('organism population', I organism substance - + - + this relationship may be too strong and may be weakened in future @@ -291920,7 +288792,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -291964,14 +288836,14 @@ Classes for population already exist in IDO ('organism population', I epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -292572,7 +289444,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -292609,14 +289481,14 @@ Classes for population already exist in IDO ('organism population', I abdomen - + - + MA @@ -292879,7 +289751,7 @@ Classes for population already exist in IDO ('organism population', I - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] @@ -292917,14 +289789,14 @@ Classes for population already exist in IDO ('organism population', I ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -292983,7 +289855,7 @@ Classes for population already exist in IDO ('organism population', I - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal @@ -293020,14 +289892,14 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -293088,7 +289960,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293139,7 +290011,7 @@ Classes for population already exist in IDO ('organism population', I mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + @@ -293152,7 +290024,7 @@ Classes for population already exist in IDO ('organism population', I - + Bgee:AN @@ -293364,7 +290236,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293414,7 +290286,7 @@ Classes for population already exist in IDO ('organism population', I proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -293427,7 +290299,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -293500,7 +290372,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293541,7 +290413,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293621,11 +290493,11 @@ Classes for population already exist in IDO ('organism population', I stomach https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg - + - + @@ -293644,14 +290516,14 @@ Classes for population already exist in IDO ('organism population', I - + absent in lampreys and hagfishes ISBN:0073040584 - + ISBN:0486692132 @@ -293739,7 +290611,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293788,7 +290660,7 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg - + @@ -293801,7 +290673,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -293881,7 +290753,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293990,14 +290862,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -294193,7 +291065,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -294218,7 +291090,7 @@ Classes for population already exist in IDO ('organism population', I - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion @@ -294282,11 +291154,11 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb - + - + @@ -294299,13 +291171,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + Bgee:AN @@ -294558,9 +291430,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -294585,7 +291457,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -294641,44 +291513,44 @@ Classes for population already exist in IDO ('organism population', I cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + - + MA - + MA - + FMA-isa - + definitional @@ -294868,9 +291740,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -294881,7 +291753,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -294938,44 +291810,44 @@ Classes for population already exist in IDO ('organism population', I retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -295049,8 +291921,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -295086,24 +291958,24 @@ Classes for population already exist in IDO ('organism population', I eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -295274,7 +292146,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -295288,7 +292160,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -295355,14 +292227,14 @@ Classes for population already exist in IDO ('organism population', I pleura http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png - + - + https://github.com/obophenotype/uberon/issues/86 @@ -295537,7 +292409,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -295606,14 +292478,14 @@ Classes for population already exist in IDO ('organism population', I pons http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png - + - + neuronames @@ -297415,7 +294287,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -297482,14 +294354,14 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -297593,7 +294465,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -297648,7 +294520,7 @@ Classes for population already exist in IDO ('organism population', I central nervous system - + @@ -297662,7 +294534,7 @@ Classes for population already exist in IDO ('organism population', I - + Bgee:AN @@ -297889,7 +294761,7 @@ Classes for population already exist in IDO ('organism population', I - + A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. AEO:0000201 EHDAA2:0003200 @@ -297904,14 +294776,14 @@ Classes for population already exist in IDO ('organism population', I sensory nerve - + - + AEO @@ -298068,8 +294940,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]. consider splitting class One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG] @@ -298100,11 +294972,11 @@ Classes for population already exist in IDO ('organism population', I yolk sac http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png - + - + @@ -298123,13 +294995,13 @@ Classes for population already exist in IDO ('organism population', I - + ISBN:0073040584 - + ISBN:0073040584 @@ -298289,7 +295161,7 @@ Classes for population already exist in IDO ('organism population', I - + A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] @@ -298331,14 +295203,14 @@ Classes for population already exist in IDO ('organism population', I Consider generalizing to deuterostome pharynx chordate pharynx - + - + EHDAA2 @@ -298641,7 +295513,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -298678,14 +295550,14 @@ Classes for population already exist in IDO ('organism population', I hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -298941,15 +295813,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + @@ -299003,15 +295875,15 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb - + - + - + @@ -299025,19 +295897,19 @@ Classes for population already exist in IDO ('organism population', I - + MA - + EHDAA2 - + ISBN:0073040584 @@ -299145,7 +296017,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -299192,7 +296064,7 @@ Classes for population already exist in IDO ('organism population', I ventral pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png - + @@ -299205,7 +296077,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -299290,7 +296162,7 @@ Classes for population already exist in IDO ('organism population', I - + A zone of skin that is part of a back [Automatically generated definition]. EMAPA:36392 FMA:10462 @@ -299307,7 +296179,7 @@ Classes for population already exist in IDO ('organism population', I EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of back - + @@ -299320,7 +296192,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -299354,9 +296226,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]. not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO @@ -299389,15 +296261,15 @@ Classes for population already exist in IDO ('organism population', I https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722 http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif - + - + - + @@ -299410,19 +296282,19 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + EHDAA2 - + FMA @@ -299733,14 +296605,14 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -299781,11 +296653,11 @@ Classes for population already exist in IDO ('organism population', I pericardial cavity - + - + @@ -299798,13 +296670,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + Wikipedia @@ -299877,7 +296749,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -299909,14 +296781,14 @@ Classes for population already exist in IDO ('organism population', I endocardium of ventricle - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -300054,7 +296926,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -300082,14 +296954,14 @@ Classes for population already exist in IDO ('organism population', I myocardium of ventricle - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -300533,7 +297405,7 @@ Classes for population already exist in IDO ('organism population', I - + The second vertebral bone in the vertebral column. Vertebra that is posteriorly adjacent to vertebra 1.[TAO] @@ -300569,14 +297441,14 @@ Classes for population already exist in IDO ('organism population', I vertebral bone 2 - + - + FMA @@ -300877,7 +297749,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -300888,7 +297760,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -300934,24 +297806,24 @@ Classes for population already exist in IDO ('organism population', I diaphragm - + - + - + PMID:23586979 - + definitional @@ -301251,7 +298123,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -301332,14 +298204,14 @@ Classes for population already exist in IDO ('organism population', I vertebral column - + - + cjm @@ -302025,7 +298897,7 @@ Classes for population already exist in IDO ('organism population', I - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -302050,14 +298922,14 @@ Classes for population already exist in IDO ('organism population', I mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -302172,7 +299044,7 @@ Classes for population already exist in IDO ('organism population', I - + In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002783 @@ -302195,14 +299067,14 @@ Classes for population already exist in IDO ('organism population', I superior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png - + - + Wikipedia:Vitelline_vein @@ -302261,7 +299133,7 @@ Classes for population already exist in IDO ('organism population', I - + Vein that carries blood away from the liver[ZFA]. todo - add developmental relationships for other taxa @@ -302292,14 +299164,14 @@ Classes for population already exist in IDO ('organism population', I hepatic vein http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png - + - + FMA-abduced-lr @@ -302524,7 +299396,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -302560,7 +299432,7 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png - + @@ -302573,7 +299445,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -302621,7 +299493,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -302676,7 +299548,7 @@ Classes for population already exist in IDO ('organism population', I colon - + @@ -302690,7 +299562,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -302756,7 +299628,7 @@ Classes for population already exist in IDO ('organism population', I - + The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. BTO:0000645 @@ -302788,7 +299660,7 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb - + @@ -302801,7 +299673,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia @@ -302907,7 +299779,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -302961,7 +299833,7 @@ Classes for population already exist in IDO ('organism population', I pyloric antrum http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg - + @@ -302974,7 +299846,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia @@ -303479,7 +300351,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -303496,7 +300368,7 @@ Classes for population already exist in IDO ('organism population', I portal lobule - + @@ -303509,7 +300381,7 @@ Classes for population already exist in IDO ('organism population', I - + MA MP @@ -303533,7 +300405,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -303559,14 +300431,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0001172 hepatic acinus - + - + cjm @@ -303802,10 +300674,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + @@ -303834,19 +300706,19 @@ Classes for population already exist in IDO ('organism population', I common hepatic duct http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg - + - + - + - + @@ -303859,25 +300731,25 @@ Classes for population already exist in IDO ('organism population', I - + MA - + Wikipedia - + Wikipedia - + definitional @@ -304141,7 +301013,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -304183,14 +301055,14 @@ Classes for population already exist in IDO ('organism population', I peritoneal cavity - + - + Wikipedia @@ -305832,8 +302704,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]. currently defined as equivalent to any submucosal gland in the duodenum. Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds @@ -305859,11 +302731,11 @@ Classes for population already exist in IDO ('organism population', I duodenal gland - + - + @@ -305876,13 +302748,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA, modified - + unclear for Aves ISBN:9780521617147 @@ -305939,7 +302811,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -305985,7 +302857,7 @@ Classes for population already exist in IDO ('organism population', I intestinal villus http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg - + @@ -305998,7 +302870,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -306111,7 +302983,7 @@ Classes for population already exist in IDO ('organism population', I - + A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002782 @@ -306135,14 +303007,14 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + FMA/obol @@ -306831,7 +303703,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -306863,7 +303735,7 @@ Classes for population already exist in IDO ('organism population', I interlobular bile duct - + @@ -306877,7 +303749,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA MA MP @@ -307019,7 +303891,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -307051,14 +303923,14 @@ Classes for population already exist in IDO ('organism population', I pancreatic acinus - + - + FMA @@ -307108,9 +303980,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]. Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] @@ -307156,34 +304028,34 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pancreas.glb https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png - + - + - + - + PMID:16417468 - + Wikipedia - + Wikipedia @@ -307248,7 +304120,7 @@ Classes for population already exist in IDO ('organism population', I - + A trabecula that is part of a spleen. EMAPA:35808 @@ -307266,14 +304138,14 @@ Classes for population already exist in IDO ('organism population', I trabecula of spleen - + - + FMA @@ -307859,7 +304731,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -307889,14 +304761,14 @@ Classes for population already exist in IDO ('organism population', I liver parenchyma - + - + XAO @@ -307965,7 +304837,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -308015,14 +304887,14 @@ Classes for population already exist in IDO ('organism population', I hepatic sinusoid - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -308087,8 +304959,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -308131,11 +305003,11 @@ Classes for population already exist in IDO ('organism population', I intralobular bile duct - + - + @@ -308148,13 +305020,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + FMA @@ -308215,7 +305087,7 @@ Classes for population already exist in IDO ('organism population', I - + Muscle (organ) which is a part of the pelvis. Examples: levator ani,. @@ -308233,7 +305105,7 @@ Classes for population already exist in IDO ('organism population', I muscle of pelvis - + @@ -308245,7 +305117,7 @@ Classes for population already exist in IDO ('organism population', I - + FMAdef @@ -308298,7 +305170,7 @@ Classes for population already exist in IDO ('organism population', I - + The anus and surrounding regions. Encompasses both internal and external regions, where present. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EFO:0000847 @@ -308324,14 +305196,14 @@ Classes for population already exist in IDO ('organism population', I https://github.com/obophenotype/uberon/issues/507 http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png - + - + cjm @@ -309190,7 +306062,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -309202,7 +306074,7 @@ Classes for population already exist in IDO ('organism population', I - + Skeletal element that is composed of bone tissue. @@ -309252,14 +306124,14 @@ Classes for population already exist in IDO ('organism population', I bone element - + - + VSAO-modified @@ -309458,7 +306330,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -309502,14 +306374,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + EHDAA2 @@ -309564,7 +306436,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. UBERON:0003271 @@ -309586,14 +306458,14 @@ Classes for population already exist in IDO ('organism population', I muscle of pelvic girdle - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -309663,7 +306535,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -309711,14 +306583,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + left arch 4 in human embryology.ch @@ -309782,7 +306654,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -309818,7 +306690,7 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + @@ -309831,7 +306703,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia @@ -309970,7 +306842,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -310019,14 +306891,14 @@ Classes for population already exist in IDO ('organism population', I abdominal aorta http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png - + - + FMA @@ -310196,7 +307068,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -310234,7 +307106,7 @@ Classes for population already exist in IDO ('organism population', I common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg - + @@ -310247,7 +307119,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia @@ -310319,8 +307191,8 @@ Classes for population already exist in IDO ('organism population', I - - + + One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta. Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO) @@ -310358,24 +307230,24 @@ Classes for population already exist in IDO ('organism population', I subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg - + - + - + EHDAA2 - + EHDAA2 @@ -310559,7 +307431,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -310614,14 +307486,14 @@ Classes for population already exist in IDO ('organism population', I digestive tract - + - + NCBIBook:NBK10107 @@ -311035,7 +307907,7 @@ Classes for population already exist in IDO ('organism population', I - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -311058,7 +307930,7 @@ Classes for population already exist in IDO ('organism population', I ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -311077,7 +307949,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -311195,10 +308067,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + A sphincter muscle that is part of the iris. In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted] WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure @@ -311233,19 +308105,19 @@ Classes for population already exist in IDO ('organism population', I sphincter pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png - + - + - + - + @@ -311258,27 +308130,27 @@ Classes for population already exist in IDO ('organism population', I - + ISBN:0781772214 - + encircles iris dbpedia - + encircles iris dbpedia - + dbpedia @@ -311385,10 +308257,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted]. It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina @@ -311425,19 +308297,19 @@ Classes for population already exist in IDO ('organism population', I dilatator pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png - + - + - + - + @@ -311450,27 +308322,27 @@ Classes for population already exist in IDO ('organism population', I - + ISBN:0781772214 - + outer margins of iris dbpedia - + inner margins of iris dbpedia - + dbpedia @@ -312152,10 +309024,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + The first major branch of the abdominal aorta. EHDAA2:0004519 @@ -312187,44 +309059,44 @@ Classes for population already exist in IDO ('organism population', I celiac artery http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png - + - + - + - + - + ISBN:0073040584 - + ISBN:0073040584 - + ISBN:0073040584 - + ISBN:0073040584 @@ -312345,7 +309217,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -312407,14 +309279,14 @@ Classes for population already exist in IDO ('organism population', I trigeminal nerve https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png - + - + Wikipedia @@ -312681,7 +309553,7 @@ Classes for population already exist in IDO ('organism population', I - + The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] @@ -312705,14 +309577,14 @@ Classes for population already exist in IDO ('organism population', I facial vein http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png - + - + FMA @@ -312788,7 +309660,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -312849,7 +309721,7 @@ Classes for population already exist in IDO ('organism population', I trigeminal ganglion http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png - + @@ -312862,7 +309734,7 @@ Classes for population already exist in IDO ('organism population', I - + Bgee:AN @@ -312986,11 +309858,11 @@ Classes for population already exist in IDO ('organism population', I - - - - - + + + + + @@ -313021,23 +309893,23 @@ Classes for population already exist in IDO ('organism population', I occipital bone http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png - + - + - + - + - + @@ -313050,32 +309922,32 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + basi paired exo and supra occipital bones MA-modified - + interparietal (postparietal) - + WP - + PMID:11523816 @@ -313137,10 +310009,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended. part of viscerocranium (facial skeleton) in FMA @@ -313169,19 +310041,19 @@ Classes for population already exist in IDO ('organism population', I sphenoid bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg - + - + - + - + @@ -313194,25 +310066,25 @@ Classes for population already exist in IDO ('organism population', I - + orbito pre and basi sphenoid - + pterygoid process - + alisphenoid - + cjm @@ -313281,7 +310153,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -313317,7 +310189,7 @@ Classes for population already exist in IDO ('organism population', I ethmoid bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg - + @@ -313330,7 +310202,7 @@ Classes for population already exist in IDO ('organism population', I - + definitional @@ -313413,7 +310285,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -313446,14 +310318,14 @@ Classes for population already exist in IDO ('organism population', I orbit of skull - + - + FMA-abduced-lr @@ -313631,7 +310503,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -313697,14 +310569,14 @@ Classes for population already exist in IDO ('organism population', I jaw skeleton - + - + cjm @@ -313914,7 +310786,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -313949,14 +310821,14 @@ Classes for population already exist in IDO ('organism population', I lower jaw region http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png - + - + Wikipedia:Mandibular_prominence @@ -314139,7 +311011,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -314164,14 +311036,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0001731 cavity of pharynx - + - + XAO @@ -314450,7 +311322,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -314493,14 +311365,14 @@ Classes for population already exist in IDO ('organism population', I iris - + - + XAO @@ -314573,7 +311445,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -314625,14 +311497,14 @@ Classes for population already exist in IDO ('organism population', I corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -314729,15 +311601,15 @@ Classes for population already exist in IDO ('organism population', I - - + + - + @@ -314779,34 +311651,34 @@ Classes for population already exist in IDO ('organism population', I sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + FMA - + ZFA - + ISBN:0781772214 @@ -314857,7 +311729,7 @@ Classes for population already exist in IDO ('organism population', I - + A skeletal muscle organ that is part of the trunk region. Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'. Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here. @@ -314882,14 +311754,14 @@ Classes for population already exist in IDO ('organism population', I skeletal muscle of trunk - + - + prolog @@ -314960,7 +311832,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -314999,14 +311871,14 @@ Classes for population already exist in IDO ('organism population', I ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -315054,14 +311926,14 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -315124,24 +311996,24 @@ Classes for population already exist in IDO ('organism population', I optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -315242,7 +312114,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -315291,14 +312163,14 @@ Classes for population already exist in IDO ('organism population', I substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + cjm ISBN:0781772214 Wikipedia @@ -315366,15 +312238,15 @@ Classes for population already exist in IDO ('organism population', I - + - - - + + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -315394,15 +312266,15 @@ Classes for population already exist in IDO ('organism population', I ciliary epithelium - + - + - + @@ -315415,19 +312287,19 @@ Classes for population already exist in IDO ('organism population', I - + MA - + MP - + Wikipedia @@ -315857,7 +312729,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -315893,14 +312765,14 @@ Classes for population already exist in IDO ('organism population', I aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + FMA def states A and P located_in in EHDAA2 VHOG @@ -316024,8 +312896,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -316058,24 +312930,24 @@ Classes for population already exist in IDO ('organism population', I anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - + - + FMA - + cjm @@ -316127,8 +312999,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -316158,24 +313030,24 @@ Classes for population already exist in IDO ('organism population', I posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + FMA - + cjm @@ -316357,7 +313229,7 @@ Classes for population already exist in IDO ('organism population', I - + The elastic, clear, membrane-like structure, that is outer most layer of the lens. The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] @@ -316383,14 +313255,14 @@ Classes for population already exist in IDO ('organism population', I capsule of lens http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + EHDAA2 @@ -316560,7 +313432,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -316599,14 +313471,14 @@ Classes for population already exist in IDO ('organism population', I sympathetic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png - + - + DOI:10.1101/gr.157586.113 ISBN:0073040584 @@ -316670,7 +313542,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -316681,7 +313553,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -316724,11 +313596,11 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg - + - + @@ -316741,7 +313613,7 @@ Classes for population already exist in IDO ('organism population', I - + BTO FMA-implicit VHOG @@ -316750,7 +313622,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -317070,14 +313942,14 @@ Classes for population already exist in IDO ('organism population', I - + - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised @@ -317130,24 +314002,24 @@ Classes for population already exist in IDO ('organism population', I midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - + - + - + definitional - + Bgee:AN @@ -317362,7 +314234,7 @@ Classes for population already exist in IDO ('organism population', I - + Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]. @@ -317398,14 +314270,14 @@ Classes for population already exist in IDO ('organism population', I metencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + definitional @@ -317667,7 +314539,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that is part of a small intestine [Automatically generated definition]. Intestinal epithelium which lines the lumen of the mid intestine.[TAO] BTO:0001258 @@ -317692,14 +314564,14 @@ Classes for population already exist in IDO ('organism population', I epithelium of small intestine - + - + FMA @@ -318097,7 +314969,7 @@ Classes for population already exist in IDO ('organism population', I - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] @@ -318138,14 +315010,14 @@ Classes for population already exist in IDO ('organism population', I midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -318384,7 +315256,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -318443,14 +315315,14 @@ Classes for population already exist in IDO ('organism population', I bile - + - + 0.3% in humans @@ -318661,7 +315533,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a esophagus [Automatically generated definition]. EMAPA:26987 FMA:63050 @@ -318690,14 +315562,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0001974 lamina propria of esophagus - + - + FMA @@ -318929,7 +315801,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -318970,14 +315842,14 @@ Classes for population already exist in IDO ('organism population', I epithelium of esophagus - + - + FMA @@ -319291,8 +316163,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -319305,7 +316177,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -319364,34 +316236,34 @@ Classes for population already exist in IDO ('organism population', I blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -319924,9 +316796,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. @@ -319968,35 +316840,35 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png - + - + - + - + Wikipedia - + EHDAA2 XAO - + EHDAA2 @@ -320391,7 +317263,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -320404,7 +317276,7 @@ Classes for population already exist in IDO ('organism population', I - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. @@ -320455,25 +317327,25 @@ Classes for population already exist in IDO ('organism population', I hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + - + modified-source-relation ABA - + Bgee:AN @@ -320838,7 +317710,7 @@ Classes for population already exist in IDO ('organism population', I - + The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. @@ -320869,14 +317741,14 @@ Classes for population already exist in IDO ('organism population', I pontine raphe nucleus - + - + Wikipedia @@ -320960,7 +317832,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -321063,14 +317935,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb - + - + some species only have a single lung @@ -321383,9 +318255,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. assume spelling error for ncit EHDAA2:0004143 @@ -321403,15 +318275,15 @@ Classes for population already exist in IDO ('organism population', I truncus arteriosus - + - + - + @@ -321430,19 +318302,19 @@ Classes for population already exist in IDO ('organism population', I - + MA - + EHDAA2 - + EHDAA2 @@ -321473,7 +318345,7 @@ Classes for population already exist in IDO ('organism population', I - + The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO] relationship loss: develops_from endocardial ring (TAO:0005072)[TAO] @@ -321505,14 +318377,14 @@ Classes for population already exist in IDO ('organism population', I endocardial cushion http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png - + - + ZFA @@ -321595,8 +318467,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart. Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO] Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO] @@ -321631,24 +318503,24 @@ Classes for population already exist in IDO ('organism population', I sinus venosus http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png - + - + - + VHOG - + Bgee:AN @@ -321751,7 +318623,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -321782,7 +318654,7 @@ Classes for population already exist in IDO ('organism population', I - + The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. Consider adding a layer-of-skin grouping class for all skin layers @@ -321822,24 +318694,24 @@ Classes for population already exist in IDO ('organism population', I dermis http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg - + - + - + FMA - + definitional @@ -321897,7 +318769,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -321916,7 +318788,7 @@ Classes for population already exist in IDO ('organism population', I - + Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] @@ -321952,24 +318824,24 @@ Classes for population already exist in IDO ('organism population', I hypodermis http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg - + - + - + ZFA - + FMA-modified @@ -322401,8 +319273,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A cardiac ventricle that is in the right side of the heart. The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] @@ -322435,24 +319307,24 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + - + PMID:17276708 - + cjm @@ -322631,7 +319503,7 @@ Classes for population already exist in IDO ('organism population', I - + Cardiac chamber through which blood leaves the heart. A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] One of four heart chambers.[TAO] @@ -322670,14 +319542,14 @@ Classes for population already exist in IDO ('organism population', I cardiac ventricle - + - + Bgee:AN @@ -322752,7 +319624,7 @@ Classes for population already exist in IDO ('organism population', I - + A cardiac ventricle that is in the left side of the heart. Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] @@ -322786,14 +319658,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + GO @@ -323439,7 +320311,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -323485,14 +320357,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb - + - + Wikipathways:WP2062 @@ -323842,7 +320714,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -323894,14 +320766,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spleen.glb https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg - + - + multiple sources - true spleen appear in jawed vertebrates @@ -323959,22 +320831,22 @@ Classes for population already exist in IDO ('organism population', I - + - + - - + + @@ -324054,19 +320926,19 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg - + - + - + - + @@ -324081,25 +320953,25 @@ Classes for population already exist in IDO ('organism population', I - + ZFA - + ZFA-weakened - + EHDAA2 - + http://www.stembook.org/node/512 @@ -324331,7 +321203,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -324402,7 +321274,7 @@ Classes for population already exist in IDO ('organism population', I https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg https://upload.wikimedia.org/wikipedia/commons/f/f4/Abdomal_organs.svg - + @@ -324415,7 +321287,7 @@ Classes for population already exist in IDO ('organism population', I - + definitional @@ -325046,7 +321918,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -325085,14 +321957,14 @@ Classes for population already exist in IDO ('organism population', I superior olivary complex http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png - + - + NIFSTD @@ -325191,7 +322063,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -325249,14 +322121,14 @@ Classes for population already exist in IDO ('organism population', I locus ceruleus http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png - + - + check ZFA NIFSTD @@ -325384,7 +322256,7 @@ Classes for population already exist in IDO ('organism population', I - + Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). @@ -325420,14 +322292,14 @@ Classes for population already exist in IDO ('organism population', I superior salivatory nucleus http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png - + - + definitional @@ -325556,7 +322428,7 @@ Classes for population already exist in IDO ('organism population', I - + The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. Layer that lines the lumen of the heart.[TAO] Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] @@ -325598,14 +322470,14 @@ Classes for population already exist in IDO ('organism population', I endocardium http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png - + - + Bgee:AN @@ -326087,7 +322959,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -326147,7 +323019,7 @@ Classes for population already exist in IDO ('organism population', I integument - + @@ -326160,7 +323032,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -326428,7 +323300,7 @@ Classes for population already exist in IDO ('organism population', I - + Vasculature that is part of the eye region. not part of the eye in ZFA. Note this changed to a blood vessel in ZFA @@ -326451,14 +323323,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + ISBN:0781772214 @@ -326518,7 +323390,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -326559,14 +323431,14 @@ Classes for population already exist in IDO ('organism population', I musculoskeletal system - + - + check ctenophore @@ -326851,15 +323723,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). TODO - add superclass to unify with VNC? @@ -326918,34 +323790,34 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb - + - + - + - + ZFA - + definitional - + definitional @@ -327137,7 +324009,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -327188,14 +324060,14 @@ Classes for population already exist in IDO ('organism population', I ventral horn of spinal cord - + - + FMA-abduced-lr @@ -327495,7 +324367,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -327525,14 +324397,14 @@ Classes for population already exist in IDO ('organism population', I dorsal mesentery http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png - + - + EHDAA2 @@ -328000,7 +324872,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -328041,14 +324913,14 @@ Classes for population already exist in IDO ('organism population', I EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct coelemic cavity lumen - + - + definitional @@ -328154,7 +325026,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a back [Automatically generated definition]. EMAPA:35161 @@ -328168,14 +325040,14 @@ Classes for population already exist in IDO ('organism population', I muscle of back - + - + prolog @@ -328224,9 +325096,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -328283,15 +325155,15 @@ Classes for population already exist in IDO ('organism population', I notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -328310,19 +325182,19 @@ Classes for population already exist in IDO ('organism population', I - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -328408,7 +325280,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -328419,7 +325291,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -328471,11 +325343,11 @@ Classes for population already exist in IDO ('organism population', I somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -328488,13 +325360,13 @@ Classes for population already exist in IDO ('organism population', I - + GOTAX:0000352 - + ZFA @@ -328764,12 +325636,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). @@ -328809,66 +325681,66 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells ISBN:0073040584 - + BTO - + PMID:11523831 - + pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - + PMID:11523831 @@ -329241,15 +326113,15 @@ Classes for population already exist in IDO ('organism population', I - - + + - + A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart. External layer of the heart.[TAO] @@ -329279,34 +326151,34 @@ Classes for population already exist in IDO ('organism population', I EDITOR_NOTE TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer. epicardium - + - + - + - + multiple - + FMA-inferred - + FMA @@ -329493,11 +326365,11 @@ Classes for population already exist in IDO ('organism population', I - - - - - + + + + + @@ -329534,23 +326406,23 @@ Classes for population already exist in IDO ('organism population', I conducting system of heart - + - + - + - + - + @@ -329563,31 +326435,31 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + FMA - + FMA - + FMA - + FMA @@ -329654,7 +326526,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -329718,7 +326590,7 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg - + @@ -329731,7 +326603,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -330008,8 +326880,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -330039,11 +326911,11 @@ Classes for population already exist in IDO ('organism population', I cardiac Purkinje fiber http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png - + - + @@ -330056,7 +326928,7 @@ Classes for population already exist in IDO ('organism population', I - + https://github.com/obophenotype/uberon/issues/1785 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9791-0064 @@ -330064,7 +326936,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -330206,7 +327078,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -330219,7 +327091,7 @@ Classes for population already exist in IDO ('organism population', I - + Serous membrane which is divided into parietal and visceral serous pericardium. EMAPA:19030 FMA:9582 @@ -330233,24 +327105,24 @@ Classes for population already exist in IDO ('organism population', I serous pericardium - + - + - + FMA - + FMA @@ -330291,7 +327163,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -330329,14 +327201,14 @@ Classes for population already exist in IDO ('organism population', I peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png - + - + MP @@ -330390,14 +327262,14 @@ Classes for population already exist in IDO ('organism population', I - + - + Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]. most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium] EMAPA:19029 @@ -330413,11 +327285,11 @@ Classes for population already exist in IDO ('organism population', I fibrous pericardium - + - + @@ -330430,13 +327302,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + WP @@ -330648,7 +327520,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -330706,14 +327578,14 @@ Classes for population already exist in IDO ('organism population', I bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -330785,8 +327657,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -330825,24 +327697,24 @@ Classes for population already exist in IDO ('organism population', I defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984) cranial muscle - + - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships - + EHDAA2-abduced @@ -330917,7 +327789,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle that is part of the cervical (neck) region. EMAPA:36050 @@ -330939,14 +327811,14 @@ Classes for population already exist in IDO ('organism population', I muscle of neck - + - + prolog @@ -331004,7 +327876,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -331036,14 +327908,14 @@ Classes for population already exist in IDO ('organism population', I muscle of abdomen - + - + prolog @@ -331301,14 +328173,14 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -331357,24 +328229,24 @@ Classes for population already exist in IDO ('organism population', I hematopoietic system - + - + - + FMA - + definitional @@ -331430,15 +328302,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + @@ -331485,25 +328357,25 @@ Classes for population already exist in IDO ('organism population', I bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png - + - + - + EMAPA MA - + XAO @@ -331815,7 +328687,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -331860,14 +328732,14 @@ Classes for population already exist in IDO ('organism population', I visceral pleura - + - + FMA @@ -331942,7 +328814,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -331988,14 +328860,14 @@ Classes for population already exist in IDO ('organism population', I pleural cavity http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png - + - + Wikipedia @@ -332166,7 +329038,7 @@ Classes for population already exist in IDO ('organism population', I - + A double-walled sac containing the heart and the roots of the great vessels. FMA:9868 RETIRED_EHDAA2:0001443 @@ -332180,14 +329052,14 @@ Classes for population already exist in IDO ('organism population', I pericardial sac http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png - + - + FMA @@ -332206,7 +329078,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -332265,14 +329137,14 @@ Classes for population already exist in IDO ('organism population', I pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png - + - + MA @@ -332465,7 +329337,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -332521,7 +329393,7 @@ Classes for population already exist in IDO ('organism population', I autonomic nervous system http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png - + @@ -332534,7 +329406,7 @@ Classes for population already exist in IDO ('organism population', I - + EMAPA MA NIFSTD @@ -333502,7 +330374,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues. consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar) The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. @@ -333529,14 +330401,14 @@ Classes for population already exist in IDO ('organism population', I oral epithelium - + - + AAO-modified @@ -333599,8 +330471,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -333628,24 +330500,24 @@ Classes for population already exist in IDO ('organism population', I visceral serous pericardium - + - + - + cjm - + FMA @@ -334250,14 +331122,14 @@ Classes for population already exist in IDO ('organism population', I - + - - + + @@ -334283,11 +331155,11 @@ Classes for population already exist in IDO ('organism population', I iris epithelium - + - + @@ -334300,13 +331172,13 @@ Classes for population already exist in IDO ('organism population', I - + MA - + MP @@ -334373,7 +331245,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -334401,14 +331273,14 @@ Classes for population already exist in IDO ('organism population', I trabecula carnea - + - + WP @@ -334493,7 +331365,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -334527,7 +331399,7 @@ Classes for population already exist in IDO ('organism population', I https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg - + @@ -334540,7 +331412,7 @@ Classes for population already exist in IDO ('organism population', I - + VSAO @@ -334812,8 +331684,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -334839,11 +331711,11 @@ Classes for population already exist in IDO ('organism population', I tunica media https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg - + - + @@ -334856,13 +331728,13 @@ Classes for population already exist in IDO ('organism population', I - + cjm - + cjm @@ -334900,8 +331772,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts @@ -334926,11 +331798,11 @@ Classes for population already exist in IDO ('organism population', I tunica intima https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg - + - + @@ -334943,13 +331815,13 @@ Classes for population already exist in IDO ('organism population', I - + check for exceptions, e.g. capillaries - + ISBN:0073040584 @@ -335341,9 +332213,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] @@ -335379,15 +332251,15 @@ Classes for population already exist in IDO ('organism population', I pharyngeal arch http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png - + - + - + @@ -335400,19 +332272,19 @@ Classes for population already exist in IDO ('organism population', I - + PMID:16313389 - + http://tolweb.org/Chordata/2499 - + PMID:16313389 @@ -335481,7 +332353,7 @@ Classes for population already exist in IDO ('organism population', I - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons @@ -335501,7 +332373,7 @@ Classes for population already exist in IDO ('organism population', I cranial placode - + @@ -335514,7 +332386,7 @@ Classes for population already exist in IDO ('organism population', I - + PMID:11523831 PMID:22512454 @@ -336509,7 +333381,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -336522,7 +333394,7 @@ Classes for population already exist in IDO ('organism population', I - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] @@ -336552,11 +333424,11 @@ Classes for population already exist in IDO ('organism population', I midbrain-hindbrain boundary - + - + @@ -336570,13 +333442,13 @@ Classes for population already exist in IDO ('organism population', I - + ZFA - + ZFA @@ -336622,8 +333494,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] @@ -336652,11 +333524,11 @@ Classes for population already exist in IDO ('organism population', I periderm - + - + @@ -336669,13 +333541,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + ZFA @@ -336841,7 +333713,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -336858,7 +333730,7 @@ Classes for population already exist in IDO ('organism population', I - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] @@ -336883,14 +333755,14 @@ Classes for population already exist in IDO ('organism population', I presomitic mesoderm - + - + Bgee:AN @@ -337055,8 +333927,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue. TODO - check; developmental relationship to anterior hypoblast in ZFA? Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] @@ -337081,24 +333953,24 @@ Classes for population already exist in IDO ('organism population', I prechordal plate - + - + - + ZFA - + PMID:16313393 @@ -337156,9 +334028,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -337200,34 +334072,34 @@ Classes for population already exist in IDO ('organism population', I intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -337540,7 +334412,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -337578,7 +334450,7 @@ Classes for population already exist in IDO ('organism population', I eye primordium - + @@ -337591,7 +334463,7 @@ Classes for population already exist in IDO ('organism population', I - + PMID:16496288 XAO @@ -337647,8 +334519,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -337677,24 +334549,24 @@ Classes for population already exist in IDO ('organism population', I optic cup - + - + - + ZFA - + ZFA @@ -337760,7 +334632,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -337801,7 +334673,7 @@ Classes for population already exist in IDO ('organism population', I lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -337814,7 +334686,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -337878,9 +334750,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] @@ -337912,34 +334784,34 @@ Classes for population already exist in IDO ('organism population', I neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -338059,7 +334931,7 @@ Classes for population already exist in IDO ('organism population', I - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] @@ -338088,7 +334960,7 @@ Classes for population already exist in IDO ('organism population', I paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -338101,7 +334973,7 @@ Classes for population already exist in IDO ('organism population', I - + Bgee:AN @@ -338170,8 +335042,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -338197,11 +335069,11 @@ Classes for population already exist in IDO ('organism population', I epibranchial placode - + - + @@ -338215,13 +335087,13 @@ Classes for population already exist in IDO ('organism population', I - + ZFA - + EHDAA2-abduced @@ -338325,7 +335197,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -338369,7 +335241,7 @@ Classes for population already exist in IDO ('organism population', I lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -338382,7 +335254,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 VHOG @@ -338467,7 +335339,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -338510,7 +335382,7 @@ Classes for population already exist in IDO ('organism population', I myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -338523,7 +335395,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2-abduced @@ -338586,7 +335458,7 @@ Classes for population already exist in IDO ('organism population', I - + Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] @@ -338606,14 +335478,14 @@ Classes for population already exist in IDO ('organism population', I trunk neural crest - + - + ZFA @@ -338657,15 +335529,15 @@ Classes for population already exist in IDO ('organism population', I - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] @@ -338685,15 +335557,15 @@ Classes for population already exist in IDO ('organism population', I heart primordium - + - + - + @@ -338706,19 +335578,19 @@ Classes for population already exist in IDO ('organism population', I - + ZFA - + ZFA - + XAO @@ -338850,8 +335722,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] @@ -338879,11 +335751,11 @@ Classes for population already exist in IDO ('organism population', I sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -338902,13 +335774,13 @@ Classes for population already exist in IDO ('organism population', I - + VHOG:0000680 - + ZFA @@ -341112,8 +337984,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -341145,24 +338017,24 @@ Classes for population already exist in IDO ('organism population', I skeleton of lower jaw - + - + - + EHDAA2 - + VHOG-modified @@ -341238,12 +338110,12 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -341270,7 +338142,7 @@ Classes for population already exist in IDO ('organism population', I mesentery of stomach - + @@ -341283,7 +338155,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -341595,13 +338467,13 @@ Classes for population already exist in IDO ('organism population', I - + - + Racemose mucous glands beneath the mucous membrane of the pharynx. BTO:0004849 EHDAA2:0001461 @@ -341614,14 +338486,14 @@ Classes for population already exist in IDO ('organism population', I pharyngeal gland - + - + BTO @@ -341730,7 +338602,7 @@ Classes for population already exist in IDO ('organism population', I - + A blood island that is part of a mesoderm. in EHDAA2, gives rise to blood and dorsal aorta UBERON:0003305 @@ -341743,7 +338615,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003304 mesoderm blood island - + @@ -341756,7 +338628,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -341809,7 +338681,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -341821,14 +338693,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -342022,7 +338894,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a developing upper jaw [Automatically generated definition]. EHDAA2:0002124 EHDAA:8031 @@ -342035,14 +338907,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003323 mesenchyme of upper jaw - + - + EHDAA2 @@ -342094,7 +338966,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. EHDAA2:0001024 EHDAA:8003 @@ -342107,14 +338979,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003324 mesenchyme of lower jaw - + - + EHDAA2 @@ -343506,15 +340378,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + An epithelium that is part of a pharynx [Automatically generated definition]. Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] BSA:0000112 @@ -343534,24 +340406,24 @@ Classes for population already exist in IDO ('organism population', I pharyngeal epithelium - + - + - + ZFA - + ZFA @@ -343603,12 +340475,12 @@ Classes for population already exist in IDO ('organism population', I - + - + An epithelium that is part of a midgut. BTO:0005053 EHDAA2:0001195 @@ -343621,14 +340493,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003352 epithelium of midgut - + - + BTO @@ -343921,7 +340793,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -343934,7 +340806,7 @@ Classes for population already exist in IDO ('organism population', I - + An unilaminar epithelium that surrounds a pelvic appendage bud. UBERON:0005232 EHDAA2:0001034 @@ -343950,24 +340822,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003371 pelvic appendage bud ectoderm - + - + - + EHDAA2 - + EHDAA2 @@ -344035,7 +340907,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -344048,7 +340920,7 @@ Classes for population already exist in IDO ('organism population', I - + An unilaminar epithelium that surrounds a pectoral appendage bud. UBERON:0005231 UBERON:0005663 @@ -344065,24 +340937,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003372 pectoral appendage bud ectoderm - + - + - + EHDAA2 - + EHDAA2 @@ -346522,13 +343394,13 @@ Classes for population already exist in IDO ('organism population', I - + - + A bone that is part of a facial skeleton [Automatically generated definition]. test whether 'facial bone' is an exact synonym EMAPA:19019 @@ -346549,14 +343421,14 @@ Classes for population already exist in IDO ('organism population', I facial bone - + - + MA @@ -346754,7 +343626,7 @@ Classes for population already exist in IDO ('organism population', I - + The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose. EMAPA:37430 @@ -346771,14 +343643,14 @@ Classes for population already exist in IDO ('organism population', I artery of upper lip - + - + FMA @@ -346844,7 +343716,7 @@ Classes for population already exist in IDO ('organism population', I - + The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. EMAPA:37429 @@ -346862,14 +343734,14 @@ Classes for population already exist in IDO ('organism population', I artery of lower lip - + - + FMA @@ -347379,7 +344251,7 @@ Classes for population already exist in IDO ('organism population', I - + An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37575 MA:0001808 @@ -347410,14 +344282,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003489 respiratory system capillary endothelium - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -347649,7 +344521,7 @@ Classes for population already exist in IDO ('organism population', I - + An arteriole that is part of a respiratory system [Automatically generated definition]. EMAPA:37568 MA:0001803 @@ -347657,14 +344529,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003495 respiratory system arteriole - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -347698,7 +344570,7 @@ Classes for population already exist in IDO ('organism population', I - + A blood vessel that is part of a head [Automatically generated definition]. EMAPA:36610 MA:0000575 @@ -347710,14 +344582,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003496 head blood vessel - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -351752,12 +348624,12 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -351784,7 +348656,7 @@ Classes for population already exist in IDO ('organism population', I intrahepatic bile duct - + @@ -351797,7 +348669,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -352783,7 +349655,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a thorax [Automatically generated definition]. MA:0000561 muscle organ of thorax @@ -352793,14 +349665,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003830 thoracic segment muscle - + - + prolog @@ -352912,7 +349784,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a esophagus [Automatically generated definition]. merge muscle and muscle layer? EMAPA:26983 @@ -352929,14 +349801,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003832 esophagus muscle - + - + MA @@ -353795,12 +350667,12 @@ Classes for population already exist in IDO ('organism population', I - + - + A neural plate that develops_from a future spinal cord. Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] @@ -353813,14 +350685,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003854 spinal cord neural plate - + - + ZFA @@ -354023,7 +350895,7 @@ Classes for population already exist in IDO ('organism population', I - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] @@ -354039,14 +350911,14 @@ Classes for population already exist in IDO ('organism population', I intraembryonic coelom - + - + Wikipedia @@ -354142,8 +351014,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -354177,11 +351049,11 @@ Classes for population already exist in IDO ('organism population', I liver primordium - + - + @@ -354200,13 +351072,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + ventral foregut endoderm Zaret 1996 @@ -354329,7 +351201,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -354349,14 +351221,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003898 skeletal muscle tissue of trunk - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -354417,7 +351289,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -354434,7 +351306,7 @@ Classes for population already exist in IDO ('organism population', I - + The part of the retina that contains neurons and photoreceptor cells[GO]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] @@ -354466,14 +351338,14 @@ Classes for population already exist in IDO ('organism population', I retinal neural layer - + - + Bgee:AN @@ -354755,7 +351627,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -354785,14 +351657,14 @@ Classes for population already exist in IDO ('organism population', I pancreas primordium http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png - + - + Wikipedia @@ -354834,16 +351706,16 @@ Classes for population already exist in IDO ('organism population', I - - + + - - + + The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. EFO:0003470 EMAPA:35645 @@ -354864,19 +351736,19 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png - + - + - + - + @@ -354889,26 +351761,26 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + Wikipedia:Pancreas#Embryological_development - + zebrafish Wikipedia:Pancreatic_bud - + EHDAA2-inferred @@ -354950,8 +351822,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Pancreatic bud that gives rise to the accessory pancreatic duct. The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO] In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] @@ -354979,24 +351851,24 @@ Classes for population already exist in IDO ('organism population', I dorsal pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png - + - + - + EHDAA2 - + XAO @@ -355043,8 +351915,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Pancreatic bud that gives rise to the major pancreatic duct. In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP] @@ -355072,24 +351944,24 @@ Classes for population already exist in IDO ('organism population', I ventral pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png - + - + - + EHDAA2 - + PMID:16417468 WP @@ -355920,7 +352792,7 @@ Classes for population already exist in IDO ('organism population', I - + A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. Not to be confused with 'dermatome segment of skin'. AAO:0011028 @@ -355947,7 +352819,7 @@ Classes for population already exist in IDO ('organism population', I dermatome http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png - + @@ -355960,7 +352832,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2-abduced @@ -356086,7 +352958,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -356113,14 +352985,14 @@ Classes for population already exist in IDO ('organism population', I biliary ductule - + - + BTO @@ -356205,7 +353077,7 @@ Classes for population already exist in IDO ('organism population', I - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure The layer of undifferentiated, proliferating cells that line the neural tube lumen @@ -356223,7 +353095,7 @@ Classes for population already exist in IDO ('organism population', I neural tube ventricular layer - + @@ -356236,7 +353108,7 @@ Classes for population already exist in IDO ('organism population', I - + NCBIBook:NBK10047 @@ -356297,7 +353169,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -356321,7 +353193,7 @@ Classes for population already exist in IDO ('organism population', I neural tube mantle layer - + @@ -356334,7 +353206,7 @@ Classes for population already exist in IDO ('organism population', I - + by division NCBIBook:NBK10047 @@ -356372,7 +353244,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -356389,14 +353261,14 @@ Classes for population already exist in IDO ('organism population', I neural tube marginal layer - + - + forms from axons @@ -356438,7 +353310,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -356463,14 +353335,14 @@ Classes for population already exist in IDO ('organism population', I neural tube basal plate - + - + Shh Swenson @@ -356586,14 +353458,14 @@ Classes for population already exist in IDO ('organism population', I - + - + The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it. Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity. EHDAA2:0001076 @@ -356614,24 +353486,24 @@ Classes for population already exist in IDO ('organism population', I medial nasal prominence http://upload.wikimedia.org/wikipedia/commons/8/85/Gray45.png - + - + - + EHDAA2 - + Wikipedia @@ -357422,7 +354294,7 @@ Classes for population already exist in IDO ('organism population', I - + A myocardium trabecular layer that is part of a cardiac ventricle. TODO - check FMA FMA:83511 @@ -357436,14 +354308,14 @@ Classes for population already exist in IDO ('organism population', I trabecular layer of ventricle - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -357478,9 +354350,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -357513,34 +354385,34 @@ Classes for population already exist in IDO ('organism population', I optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -357690,8 +354562,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 @@ -357704,24 +354576,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -357780,7 +354652,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelial tube that will give rise to the mature heart. the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 @@ -357800,14 +354672,14 @@ Classes for population already exist in IDO ('organism population', I heart tube - + - + ZFA-modified @@ -357952,8 +354824,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles. the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles. HPS @@ -357964,11 +354836,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004146 His-Purkinje system - + - + @@ -357981,13 +354853,13 @@ Classes for population already exist in IDO ('organism population', I - + GO - + PMID:12626327 PMID:21234997 github:michaelerice @@ -358162,8 +355034,8 @@ Classes for population already exist in IDO ('organism population', I - - + + An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium. propepicardial Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA] @@ -358175,24 +355047,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004160 proepicardium - + - + - + todo check other taxa - + ZFA @@ -358673,8 +355545,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35469 @@ -358690,24 +355562,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004220 large intestine smooth muscle - + - + - + MA - + consider merging @@ -358788,7 +355660,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -358825,14 +355697,14 @@ Classes for population already exist in IDO ('organism population', I intestine smooth muscle - + - + consider merging @@ -359884,7 +356756,7 @@ Classes for population already exist in IDO ('organism population', I - + A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35783 @@ -359909,14 +356781,14 @@ Classes for population already exist in IDO ('organism population', I small intestine smooth muscle - + - + consider merging @@ -360683,13 +357555,13 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -360705,14 +357577,14 @@ Classes for population already exist in IDO ('organism population', I eye muscle - + - + MA @@ -360802,7 +357674,7 @@ Classes for population already exist in IDO ('organism population', I - + The bilaminar epithelium formed from the myotome and dermatome. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] @@ -360825,7 +357697,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004290 dermomyotome - + @@ -360844,7 +357716,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 ZFA @@ -361128,14 +358000,14 @@ Classes for population already exist in IDO ('organism population', I - + - + Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition. distinction between trophectoderm and trophoblast unclear/inconsistent in many sources The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG] @@ -361153,11 +358025,11 @@ Classes for population already exist in IDO ('organism population', I trophectoderm - + - + @@ -361170,13 +358042,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 @@ -361579,7 +358451,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -361635,14 +358507,14 @@ Classes for population already exist in IDO ('organism population', I pharyngeal arch artery http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png - + - + ZFA @@ -361894,7 +358766,7 @@ Classes for population already exist in IDO ('organism population', I - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] @@ -361926,14 +358798,14 @@ Classes for population already exist in IDO ('organism population', I Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -363334,12 +360206,12 @@ Classes for population already exist in IDO ('organism population', I - + - + A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. Note placement of MA class based on parthood relationship EMAPA:32688 @@ -363350,14 +360222,14 @@ Classes for population already exist in IDO ('organism population', I cardiac muscle tissue of myocardium - + - + MA @@ -363544,21 +360416,21 @@ Classes for population already exist in IDO ('organism population', I - + A portion of trabecula carnea cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. FMA:84429 uberon UBERON:0004525 cardiac muscle tissue of trabecula carnea of right ventricle - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -363587,21 +360459,21 @@ Classes for population already exist in IDO ('organism population', I - + A portion of trabecula carnea cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. FMA:84430 uberon UBERON:0004526 cardiac muscle tissue of trabecula carnea of left ventricle - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -364298,7 +361170,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -364332,7 +361204,7 @@ Classes for population already exist in IDO ('organism population', I liver lobule - + @@ -364345,7 +361217,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA MA @@ -364534,7 +361406,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -364566,14 +361438,14 @@ Classes for population already exist in IDO ('organism population', I interventricular septum membranous part - + - + Wikipedia @@ -364780,8 +361652,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. BAMS:RA EMAPA:35721 @@ -364810,25 +361682,25 @@ Classes for population already exist in IDO ('organism population', I raphe nuclei http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png - + - + - + GO Wikipedia - + Wikipedia @@ -365334,14 +362206,14 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -365372,7 +362244,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -365395,11 +362267,11 @@ Classes for population already exist in IDO ('organism population', I paired limb/fin - + - + @@ -365412,13 +362284,13 @@ Classes for population already exist in IDO ('organism population', I - + VSAO - + definitional @@ -365500,7 +362372,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -365522,14 +362394,14 @@ Classes for population already exist in IDO ('organism population', I pelvic appendage - + - + definitional @@ -365598,7 +362470,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -365622,14 +362494,14 @@ Classes for population already exist in IDO ('organism population', I pectoral appendage - + - + definitional @@ -366162,7 +363034,7 @@ Classes for population already exist in IDO ('organism population', I - + A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 @@ -366176,7 +363048,7 @@ Classes for population already exist in IDO ('organism population', I Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue - + @@ -366189,7 +363061,7 @@ Classes for population already exist in IDO ('organism population', I - + 2012-08-14 VSAO:0000015 VSAO @@ -366368,7 +363240,7 @@ Classes for population already exist in IDO ('organism population', I - + The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) AAO:0000094 @@ -366390,7 +363262,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004761 cartilaginous neurocranium - + @@ -366403,7 +363275,7 @@ Classes for population already exist in IDO ('organism population', I - + PMC1571569 @@ -366500,7 +363372,7 @@ Classes for population already exist in IDO ('organism population', I - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] @@ -366516,14 +363388,14 @@ Classes for population already exist in IDO ('organism population', I skeletal element - + - + VSAO @@ -366652,7 +363524,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -366691,14 +363563,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004770 articular system - + - + FMA @@ -366813,7 +363685,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a respiratory system [Automatically generated definition]. EMAPA:37576 MA:0001821 @@ -366828,14 +363700,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004779 respiratory system lamina propria - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -366911,7 +363783,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a gastrointestinal system. MA:0001899 NCIT:C49299 @@ -366920,14 +363792,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004780 gastrointestinal system lamina propria - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -366962,7 +363834,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a gallbladder [Automatically generated definition]. EMAPA:35371 FMA:278594 @@ -366981,14 +363853,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004781 gallbladder lamina propria - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -367583,10 +364455,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + A mucosa that is part of a gastrointestinal system. BTO:0000546 BTO:0005568 @@ -367602,44 +364474,44 @@ Classes for population already exist in IDO ('organism population', I The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 gastrointestinal system mucosa - + - + - + - + - + PMID:16417468 - + PMID:16417468 - + PMID:16417468 - + BTO-modified @@ -368983,7 +365855,7 @@ Classes for population already exist in IDO ('organism population', I - + An endothelium of artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37566 @@ -369004,14 +365876,14 @@ Classes for population already exist in IDO ('organism population', I respiratory system arterial endothelium - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -369893,7 +366765,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -369916,14 +366788,14 @@ Classes for population already exist in IDO ('organism population', I splanchnopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -369951,7 +366823,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -369974,14 +366846,14 @@ Classes for population already exist in IDO ('organism population', I somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -370529,8 +367401,8 @@ Classes for population already exist in IDO ('organism population', I - - + + EHDAA2:0000171 EMAPA:16561 EMAPA_RETIRED:16565 @@ -370541,11 +367413,11 @@ Classes for population already exist in IDO ('organism population', I biliary bud http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png - + - + @@ -370558,13 +367430,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2-modified @@ -372125,7 +368997,7 @@ Classes for population already exist in IDO ('organism population', I - + A mucosa that is part of a pyloric antrum [Automatically generated definition]. BTO:0004107 FMA:17055 @@ -372158,14 +369030,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004997 mucosa of pyloric antrum - + - + BTO @@ -373809,20 +370681,20 @@ Classes for population already exist in IDO ('organism population', I - + Missing definition for term UBERON:0005064. Please replace it using linked reference. uberon UBERON:0005064 left ventricular trabecular myocardium - + - + GO @@ -373849,20 +370721,20 @@ Classes for population already exist in IDO ('organism population', I - + Missing definition for term UBERON:0005066. Please replace it using linked reference. uberon UBERON:0005066 right ventricular trabecular myocardium - + - + GO @@ -374841,7 +371713,7 @@ Classes for population already exist in IDO ('organism population', I - + An external ectoderm that is part of a optic eminence [Automatically generated definition]. EMAPA:16539 RETIRED_EHDAA2:0001311 @@ -374850,14 +371722,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005216 optic eminence surface ectoderm - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -375306,7 +372178,7 @@ Classes for population already exist in IDO ('organism population', I - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] EFO:0003492 @@ -375328,14 +372200,14 @@ Classes for population already exist in IDO ('organism population', I head mesenchyme - + - + EHDAA2 @@ -375402,7 +372274,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -375418,14 +372290,14 @@ Classes for population already exist in IDO ('organism population', I trunk mesenchyme - + - + EHDAA2 @@ -375447,7 +372319,7 @@ Classes for population already exist in IDO ('organism population', I - + The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] @@ -375472,14 +372344,14 @@ Classes for population already exist in IDO ('organism population', I myelencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + definitional @@ -376457,7 +373329,7 @@ Classes for population already exist in IDO ('organism population', I - + An apical ectodermal ridge that is part of a pectoral appendage bud. An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pectoral fin bud.[TAO] @@ -376484,14 +373356,14 @@ Classes for population already exist in IDO ('organism population', I pectoral appendage apical ectodermal ridge - + - + EHDAA2 @@ -376609,7 +373481,7 @@ Classes for population already exist in IDO ('organism population', I - + An apical ectodermal ridge that is part of a pelvic appendage bud. An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] @@ -376632,14 +373504,14 @@ Classes for population already exist in IDO ('organism population', I pelvic appendage apical ectodermal ridge - + - + EHDAA2 @@ -376965,7 +373837,7 @@ Classes for population already exist in IDO ('organism population', I - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -376973,7 +373845,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005427 corneal primordium - + @@ -376992,7 +373864,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -377092,7 +373964,7 @@ Classes for population already exist in IDO ('organism population', I - + The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates. the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. EHDAA2:0004145 @@ -377107,7 +373979,7 @@ Classes for population already exist in IDO ('organism population', I aortic sac - + @@ -377120,7 +373992,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -377448,7 +374320,7 @@ Classes for population already exist in IDO ('organism population', I - + A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. sulcus limitans BAMS:slim @@ -377459,14 +374331,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005478 sulcus limitans of neural tube - + - + EHDAA2 @@ -377734,7 +374606,7 @@ Classes for population already exist in IDO ('organism population', I - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. BTO:0006179 EHDAA2:0001512 @@ -377753,14 +374625,14 @@ Classes for population already exist in IDO ('organism population', I primitive heart tube - + - + ZFA @@ -377842,7 +374714,7 @@ Classes for population already exist in IDO ('organism population', I - + Cranial neural crest which gives rise to the trigeminal ganglion. todo - compare ZFA and EHDAA2 representation We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] @@ -377859,7 +374731,7 @@ Classes for population already exist in IDO ('organism population', I trigeminal neural crest - + @@ -377878,7 +374750,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -377905,7 +374777,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -377934,7 +374806,7 @@ Classes for population already exist in IDO ('organism population', I gonad primordium - + @@ -377947,7 +374819,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -378005,15 +374877,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + Somite located in the head region, caudal to the otic vesicle. in humans this includes somites 1-4 They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) @@ -378027,24 +374899,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005594 head somite - + - + - + EHDAA2 - + EHDAA2 @@ -378092,7 +374964,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -378112,7 +374984,7 @@ Classes for population already exist in IDO ('organism population', I lung primordium - + @@ -378125,7 +374997,7 @@ Classes for population already exist in IDO ('organism population', I - + XAO @@ -378198,8 +375070,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum. The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG] EHDAA2:0000416 @@ -378215,11 +375087,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005602 dorsal mesogastrium - + - + @@ -378232,13 +375104,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 @@ -378276,8 +375148,8 @@ Classes for population already exist in IDO ('organism population', I - - + + EMAPA:16844 MA:0001636 VHOG:0000215 @@ -378287,24 +375159,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005604 extrahepatic part of hepatic duct - + - + - + MA - + MA @@ -379415,7 +376287,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0000474 EMAPA:31862 EMAPA:31863 @@ -379427,7 +376299,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005728 extraembryonic mesoderm - + @@ -379440,7 +376312,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -379578,7 +376450,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -379594,14 +376466,14 @@ Classes for population already exist in IDO ('organism population', I paired limb/fin field - + - + ISBN:9780878932504 ZFA-inferred @@ -380393,7 +377265,7 @@ Classes for population already exist in IDO ('organism population', I - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -380403,7 +377275,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005856 developing mesenchymal condensation - + @@ -380422,7 +377294,7 @@ Classes for population already exist in IDO ('organism population', I - + AEO-modified-relation @@ -380444,7 +377316,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -380465,7 +377337,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005863 cartilaginous condensation - + @@ -380478,7 +377350,7 @@ Classes for population already exist in IDO ('organism population', I - + AEO @@ -380529,7 +377401,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -380551,14 +377423,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005865 pre-muscle condensation - + - + AEO @@ -380569,7 +377441,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -380589,7 +377461,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005866 pre-cartilage condensation - + @@ -380602,7 +377474,7 @@ Classes for population already exist in IDO ('organism population', I - + AEO @@ -381034,7 +377906,7 @@ Classes for population already exist in IDO ('organism population', I - + trabecula trabecular cartilage EFO:0003677 @@ -381046,7 +377918,7 @@ Classes for population already exist in IDO ('organism population', I neurocranial trabecula - + @@ -381059,7 +377931,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -381161,7 +378033,7 @@ Classes for population already exist in IDO ('organism population', I - + Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk. infundibulum EMAPA:37926 @@ -381184,14 +378056,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005953 outflow part of right ventricle - + - + PMID:17276708 @@ -381673,7 +378545,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -381693,14 +378565,14 @@ Classes for population already exist in IDO ('organism population', I atrium myocardial trabecula - + - + ZFA @@ -381752,7 +378624,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -381776,14 +378648,14 @@ Classes for population already exist in IDO ('organism population', I atrioventricular septum - + - + PMID:15797462 Wikipedia @@ -381830,7 +378702,7 @@ Classes for population already exist in IDO ('organism population', I - + The paired arteries that carry blood to the yolk sac from the dorsal aorta. EHDAA2:0002208 EMAPA:16207 @@ -381842,14 +378714,14 @@ Classes for population already exist in IDO ('organism population', I vitelline artery http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png - + - + ventral branch @@ -382121,7 +378993,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -382152,14 +379024,14 @@ Classes for population already exist in IDO ('organism population', I cervical region of vertebral column - + - + FMA @@ -382237,7 +379109,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -382271,14 +379143,14 @@ Classes for population already exist in IDO ('organism population', I thoracic region of vertebral column - + - + FMA @@ -382459,7 +379331,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -382479,14 +379351,14 @@ Classes for population already exist in IDO ('organism population', I subdivision of vertebral column - + - + FMA @@ -382530,7 +379402,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -382563,14 +379435,14 @@ Classes for population already exist in IDO ('organism population', I aortico-pulmonary spiral septum http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png - + - + PMID:6844926 Wikipedia @@ -382626,7 +379498,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -382670,14 +379542,14 @@ Classes for population already exist in IDO ('organism population', I buccopharyngeal membrane http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png - + - + EHDAA2 @@ -382751,9 +379623,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -382770,34 +379642,34 @@ Classes for population already exist in IDO ('organism population', I ethmoid bone primordium - + - + - + - + FMA - + AAO - + EHDAA2 @@ -383007,8 +379879,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -383027,24 +379899,24 @@ Classes for population already exist in IDO ('organism population', I future central tendon - + - + - + EHDAA2 - + mesenchyme cranial part Wikipedia @@ -383080,7 +379952,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -383104,14 +379976,14 @@ Classes for population already exist in IDO ('organism population', I future spinal cord - + - + EHDAA2 @@ -383157,8 +380029,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -383176,24 +380048,24 @@ Classes for population already exist in IDO ('organism population', I gallbladder primordium - + - + - + EMAPA - + EHDAA2 @@ -383269,7 +380141,7 @@ Classes for population already exist in IDO ('organism population', I - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] @@ -383284,7 +380156,7 @@ Classes for population already exist in IDO ('organism population', I notochordal plate - + @@ -383297,7 +380169,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -383335,7 +380207,7 @@ Classes for population already exist in IDO ('organism population', I - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -383352,14 +380224,14 @@ Classes for population already exist in IDO ('organism population', I The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -383438,7 +380310,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -383471,7 +380343,7 @@ Classes for population already exist in IDO ('organism population', I pleuroperitoneal canal - + @@ -383484,7 +380356,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -383516,8 +380388,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -383548,24 +380420,24 @@ Classes for population already exist in IDO ('organism population', I The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP] future cardiac ventricle - + - + - + ZFA - + EMAPA @@ -383615,8 +380487,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP]. check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme UBERON:0009750 @@ -383633,11 +380505,11 @@ Classes for population already exist in IDO ('organism population', I spleen primordium - + - + @@ -383650,13 +380522,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2-modified - + XAO @@ -383715,7 +380587,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA:924 EMAPA:16663 RETIRED_EHDAA2:0002089 @@ -383727,14 +380599,14 @@ Classes for population already exist in IDO ('organism population', I See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model future trigeminal ganglion - + - + EHDAA2 @@ -385069,14 +381941,14 @@ Classes for population already exist in IDO ('organism population', I - + - + The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers. In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] EMAPA:17702 @@ -385094,24 +381966,24 @@ Classes for population already exist in IDO ('organism population', I central tendon of diaphragm - + - + - + VHOG - + definitional @@ -385592,7 +382464,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -385613,7 +382485,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0006815 areolar connective tissue - + @@ -385626,7 +382498,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -386066,7 +382938,7 @@ Classes for population already exist in IDO ('organism population', I - + A head mesenchyme that develops_from a mesoderm. merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme AAO:0011051 @@ -386094,7 +382966,7 @@ Classes for population already exist in IDO ('organism population', I head mesenchyme from mesoderm - + @@ -386107,7 +382979,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 XAO @@ -386835,7 +383707,7 @@ Classes for population already exist in IDO ('organism population', I - + The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis. CALOHA:TS-1246 @@ -386857,14 +383729,14 @@ Classes for population already exist in IDO ('organism population', I ovary stroma - + - + FMA @@ -387286,7 +384158,7 @@ Classes for population already exist in IDO ('organism population', I - + Cranial neural crest that migrates into the mandibular arch. TAO:0007064 XAO:0000024 @@ -387295,7 +384167,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007098 mandibular neural crest - + @@ -387308,7 +384180,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -387327,7 +384199,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -387338,7 +384210,7 @@ Classes for population already exist in IDO ('organism population', I - + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis SPD:0000130 @@ -387353,14 +384225,14 @@ Classes for population already exist in IDO ('organism population', I Gene notes: Bmp, Nkx, Gata primary circulatory organ - + - + GO uses blood circulation generically to include the haemolymphatic fluid of arthropods @@ -388073,7 +384945,7 @@ Classes for population already exist in IDO ('organism population', I - + relationship to Meckel's cartilage to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000031 @@ -388087,14 +384959,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007237 1st arch mandibular component - + - + EHDAA2 @@ -388132,7 +385004,7 @@ Classes for population already exist in IDO ('organism population', I - + relationship to palatoquadrate to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000038 @@ -388143,14 +385015,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007238 1st arch maxillary component - + - + EHDAA2 @@ -388248,7 +385120,7 @@ Classes for population already exist in IDO ('organism population', I - + A tunica adventitia that is part of a artery. EMAPA:36295 EV:0100030 @@ -388260,14 +385132,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007240 tunica adventitia of artery - + - + FMA @@ -388713,7 +385585,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -388734,14 +385606,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007272 pectoral appendage skeleton - + - + VSAO @@ -388776,7 +385648,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -388794,14 +385666,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007273 pelvic appendage skeleton - + - + VSAO @@ -388834,8 +385706,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -388862,24 +385734,24 @@ Classes for population already exist in IDO ('organism population', I presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -388936,7 +385808,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -388950,14 +385822,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007278 presumptive sinus venosus - + - + ZFA @@ -389043,7 +385915,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -389062,14 +385934,14 @@ Classes for population already exist in IDO ('organism population', I presumptive midbrain hindbrain boundary - + - + ZFA @@ -389108,7 +385980,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -389125,14 +385997,14 @@ Classes for population already exist in IDO ('organism population', I presumptive segmental plate - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 @@ -389231,7 +386103,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -389257,7 +386129,7 @@ Classes for population already exist in IDO ('organism population', I presumptive paraxial mesoderm - + @@ -389273,7 +386145,7 @@ Classes for population already exist in IDO ('organism population', I - + https://github.com/obophenotype/uberon/issues/1277 @@ -389615,7 +386487,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -389661,7 +386533,7 @@ Classes for population already exist in IDO ('organism population', I pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png - + @@ -389674,7 +386546,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -389809,7 +386681,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -389836,14 +386708,14 @@ Classes for population already exist in IDO ('organism population', I outer epithelium - + - + Wikipedia:Epidermis_(zoology) @@ -390445,7 +387317,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -390453,7 +387325,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007524 dense mesenchyme tissue - + @@ -390466,7 +387338,7 @@ Classes for population already exist in IDO ('organism population', I - + AEO @@ -390605,7 +387477,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -390625,14 +387497,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007616 layer of synovial tissue - + - + BTO @@ -390833,7 +387705,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -390859,7 +387731,7 @@ Classes for population already exist in IDO ('organism population', I trigeminal nuclear complex http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png - + @@ -390872,7 +387744,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -391042,7 +387914,7 @@ Classes for population already exist in IDO ('organism population', I - + EFO:0003626 EHDAA2:0001457 EHDAA:962 @@ -391061,14 +387933,14 @@ Classes for population already exist in IDO ('organism population', I early pharyngeal endoderm http://dev.biologists.org/content/128/22/4573.full - + - + cjm @@ -391312,7 +388184,7 @@ Classes for population already exist in IDO ('organism population', I - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -391331,14 +388203,14 @@ Classes for population already exist in IDO ('organism population', I vascular system - + - + MA @@ -391543,7 +388415,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -391595,14 +388467,14 @@ Classes for population already exist in IDO ('organism population', I post-anal tail - + - + possible exception in hemichordates cjm @@ -391767,7 +388639,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesentery that is located in the peritoneum. FMA:20570 TAO:0005129 @@ -391777,14 +388649,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007826 peritoneal mesentery - + - + FMA @@ -392151,7 +389023,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -392194,14 +389066,14 @@ Classes for population already exist in IDO ('organism population', I pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -392366,8 +389238,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -392393,11 +389265,11 @@ Classes for population already exist in IDO ('organism population', I cartilage element - + - + @@ -392410,13 +389282,13 @@ Classes for population already exist in IDO ('organism population', I - + VSAO - + VSAO @@ -392626,12 +389498,12 @@ Classes for population already exist in IDO ('organism population', I - + - + A bone that is part of a craniocervical region. EMAPA:37245 MA:0000569 @@ -392641,7 +389513,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007914 bone of craniocervical region - + @@ -392654,7 +389526,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -393021,12 +389893,12 @@ Classes for population already exist in IDO ('organism population', I - + - + Musculature system of the pharyngeal and head regions. in MA this is restricted to skeletal muscles EMAPA:37259 @@ -393040,7 +389912,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0008229 craniocervical region musculature - + @@ -393053,7 +389925,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -393100,8 +389972,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax. EMAPA:37234 FMA:24217 @@ -393117,25 +389989,25 @@ Classes for population already exist in IDO ('organism population', I UBERON:0008231 dorsal thoracic segment of trunk - + - + - + FMA MA - + FMA @@ -393196,13 +390068,13 @@ Classes for population already exist in IDO ('organism population', I - + - + A muscle of back that is part of a dorsal thoracic segment of trunk. EMAPA:37261 MA:0000508 @@ -393211,7 +390083,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0008243 upper back muscle - + @@ -393224,7 +390096,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -393367,7 +390239,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that is part of a duodenum. CALOHA:TS-2087 @@ -393381,14 +390253,14 @@ Classes for population already exist in IDO ('organism population', I duodenal epithelium - + - + FMA @@ -393489,7 +390361,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -393501,7 +390373,7 @@ Classes for population already exist in IDO ('organism population', I - + An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers. EHDAA2:0000444 EHDAA:42 @@ -393517,14 +390389,14 @@ Classes for population already exist in IDO ('organism population', I The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5. inner cell mass derived epiblast - + - + Wikipedia @@ -393676,7 +390548,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -393691,7 +390563,7 @@ Classes for population already exist in IDO ('organism population', I neural tube derived brain https://github.com/obophenotype/uberon/issues/338 - + @@ -393704,7 +390576,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -393725,8 +390597,8 @@ Classes for population already exist in IDO ('organism population', I - - + + An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10 The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut. @@ -393745,11 +390617,11 @@ Classes for population already exist in IDO ('organism population', I hepatic diverticulum http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png - + - + @@ -393762,14 +390634,14 @@ Classes for population already exist in IDO ('organism population', I - + caudal part EHDAA2 - + EHDAA2 @@ -393808,13 +390680,13 @@ Classes for population already exist in IDO ('organism population', I - + BTO:0001642 uberon UBERON:0008836 liver bud - + @@ -393827,7 +390699,7 @@ Classes for population already exist in IDO ('organism population', I - + http://www.stembook.org/node/512 @@ -393908,7 +390780,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -393935,14 +390807,14 @@ Classes for population already exist in IDO ('organism population', I stomach muscularis externa - + - + MA-abduced @@ -393988,7 +390860,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -394020,7 +390892,7 @@ Classes for population already exist in IDO ('organism population', I pyloric canal https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg - + @@ -394033,7 +390905,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia @@ -394087,7 +390959,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -394112,7 +390984,7 @@ Classes for population already exist in IDO ('organism population', I pyloric gastric gland http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png - + @@ -394125,7 +390997,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia:Tubular_gland @@ -394185,7 +391057,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -394218,14 +391090,14 @@ Classes for population already exist in IDO ('organism population', I hypodermis skeletal muscle layer - + - + MP-def @@ -394326,8 +391198,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Subdivision of endoskeleton derived from pharyngeal arches. @@ -394360,24 +391232,24 @@ Classes for population already exist in IDO ('organism population', I splanchnocranium http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg - + - + - + https://github.com/obophenotype/uberon/issues/83 - + redundant Grays PMID:11237469 @@ -394495,13 +391367,13 @@ Classes for population already exist in IDO ('organism population', I - + - + Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. Intramembranous bone that forms superficially in the organism.[TAO] other AOs are not yet in sync with this classification @@ -394516,7 +391388,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0008907 dermal bone - + @@ -394535,7 +391407,7 @@ Classes for population already exist in IDO ('organism population', I - + VSAO @@ -394647,13 +391519,13 @@ Classes for population already exist in IDO ('organism population', I - + - + A parenchyma that is part of a lung. EMAPA:35522 FMA:27360 @@ -394666,7 +391538,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0008946 lung parenchyma - + @@ -394679,7 +391551,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -395143,13 +392015,13 @@ Classes for population already exist in IDO ('organism population', I - + - + Cranial ganglion which develops from an epibranchial placode. BTO:0006250 TAO:0001555 @@ -395160,7 +392032,7 @@ Classes for population already exist in IDO ('organism population', I Epibranchial ganglia orchestrate the development of the cranial neurogenic crest epibranchial ganglion - + @@ -395173,7 +392045,7 @@ Classes for population already exist in IDO ('organism population', I - + NCBIBook:NBK53175 @@ -395225,8 +392097,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Endocardium that is part of the right atrium. EHDAA2:0000274 FMA:7281 @@ -395240,24 +392112,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009129 right atrium endocardium - + - + - + EHDAA2 - + EHDAA2 @@ -395422,7 +392294,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -395439,14 +392311,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -395462,7 +392334,7 @@ Classes for population already exist in IDO ('organism population', I - + EMAPA:16549 RETIRED_EHDAA2:0001454 pharyngeal region @@ -395470,14 +392342,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009145 pharyngeal region of foregut - + - + EHDAA2 @@ -395508,8 +392380,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -395523,11 +392395,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009191 sphenoid bone pre-cartilage condensation - + - + @@ -395546,13 +392418,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 @@ -395649,12 +392521,12 @@ Classes for population already exist in IDO ('organism population', I - + - + Mesenchyme that is part of a medial nasal prominence. EHDAA2:0001077 EMAPA:16810 @@ -395663,14 +392535,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009204 medial nasal process mesenchyme - + - + EHDAA2 @@ -395905,7 +392777,7 @@ Classes for population already exist in IDO ('organism population', I - + A portion of mesenchymal tissue associated with an individual pharyngeal arch. this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. EMAPA:32755 @@ -395917,7 +392789,7 @@ Classes for population already exist in IDO ('organism population', I pharyngeal arch mesenchymal region - + @@ -395930,7 +392802,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -395977,14 +392849,14 @@ Classes for population already exist in IDO ('organism population', I - + - + An epithelium that is part of a foregut-midgut junction. EHDAA2:0000573 EMAPA:16564 @@ -395993,24 +392865,24 @@ Classes for population already exist in IDO ('organism population', I epithelium of foregut-midgut junction - + - + - + EHDAA2 - + EHDAA2 @@ -396381,7 +393253,7 @@ Classes for population already exist in IDO ('organism population', I - + A submucosa that is part of a intestine. FMA:15696 submucosa of intestine @@ -396389,14 +393261,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009566 intestinal submucosa - + - + FMA @@ -396610,7 +393482,7 @@ Classes for population already exist in IDO ('organism population', I - + A sulcus limitans of neural tube that is part of a future medulla oblongata. EHDAA2:0001100 EMAPA:17561 @@ -396618,14 +393490,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009576 medulla oblongata sulcus limitans - + - + EHDAA2 @@ -396801,12 +393673,12 @@ Classes for population already exist in IDO ('organism population', I - + - + Mesenchyme that is part of a 1st arch mandibular component. UBERON:0010043 EHDAA2:0000034 @@ -396819,14 +393691,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009584 1st arch mandibular mesenchyme - + - + EMAPA @@ -396942,9 +393814,9 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -396958,7 +393830,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009611 midbrain neural plate - + @@ -396967,20 +393839,20 @@ Classes for population already exist in IDO ('organism population', I - + - + ZFA - + ZFA @@ -396995,9 +393867,9 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -397011,7 +393883,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009614 hindbrain neural plate - + @@ -397020,20 +393892,20 @@ Classes for population already exist in IDO ('organism population', I - + - + ZFA - + ZFA @@ -397049,8 +393921,8 @@ Classes for population already exist in IDO ('organism population', I - - + + TODO - developmental relationships for lines TAO:0007044 ZFA:0007044 @@ -397060,24 +393932,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009615 midbrain hindbrain boundary neural plate - + - + - + ZFA - + https://github.com/obophenotype/uberon/issues/438 Bgee:AN @@ -397111,14 +393983,14 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -397143,24 +394015,24 @@ Classes for population already exist in IDO ('organism population', I presumptive midbrain - + - + - + ZFA - + ZFA @@ -397206,7 +394078,7 @@ Classes for population already exist in IDO ('organism population', I - + Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. A major contributor to neurocranium [PMID:16313393] EHDAA2:0000736 @@ -397223,14 +394095,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009617 head paraxial mesoderm - + - + EHDAA2 @@ -397283,7 +394155,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -397291,14 +394163,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -397484,7 +394356,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0004566 EMAPA:32911 MA:0003203 @@ -397495,14 +394367,14 @@ Classes for population already exist in IDO ('organism population', I gut mesentery https://github.com/obophenotype/uberon/issues/509 - + - + EHDAA2 @@ -397590,8 +394462,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -397608,24 +394480,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009670 rectal lumen - + - + - + cjm - + EHDAA2 @@ -397649,9 +394521,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + EHDAA2:0001371 uberon @@ -397661,15 +394533,15 @@ Classes for population already exist in IDO ('organism population', I dorsal pancreas - + - + - + @@ -397682,19 +394554,19 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 - + cjm @@ -397706,9 +394578,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + EHDAA2:0001393 uberon @@ -397718,15 +394590,15 @@ Classes for population already exist in IDO ('organism population', I ventral pancreas - + - + - + @@ -397739,19 +394611,19 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 - + cjm @@ -397778,8 +394650,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Any endocardium that is part of the right ventricle of the heart. Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. EHDAA2:0002188 @@ -397796,24 +394668,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009712 endocardium of right ventricle - + - + - + EHDAA2 - + FMA @@ -397876,7 +394748,7 @@ Classes for population already exist in IDO ('organism population', I - + Any endocardium that is part of the left ventricle of the heart. Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. EHDAA2:0002182 @@ -397892,14 +394764,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009713 endocardium of left ventricle - + - + FMA @@ -397985,7 +394857,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -398000,14 +394872,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009722 entire pharyngeal arch endoderm - + - + EHDAA2 @@ -398164,7 +395036,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -398177,7 +395049,7 @@ Classes for population already exist in IDO ('organism population', I - + A serous sac that has the pleura and the pleural cavity as parts. despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac EHDAA2:0004737 @@ -398188,24 +395060,24 @@ Classes for population already exist in IDO ('organism population', I pleural sac - + - + - + FMA - + FMA-abduced-lr @@ -398320,8 +395192,8 @@ Classes for population already exist in IDO ('organism population', I - - + + An epithelium that is part of a embryonic cloaca. cloacal epithelium EHDAA2:0004585 @@ -398329,24 +395201,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009846 embryonic cloacal epithelium - + - + - + EHDAA2 - + EHDAA2 @@ -398535,7 +395407,7 @@ Classes for population already exist in IDO ('organism population', I - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -398545,14 +395417,14 @@ Classes for population already exist in IDO ('organism population', I anterior lateral plate mesoderm - + - + ZFA @@ -398571,9 +395443,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -398593,34 +395465,34 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009889 secondary heart field - + - + - + - + GO:0003129 - + PMID:17276708 - + PMID:17276708 @@ -398789,14 +395661,14 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -398809,7 +395681,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -399325,8 +396197,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. EHDAA2:0001459 EMAPA:16550 @@ -399338,11 +396210,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010046 entire pharyngeal arch associated mesenchyme - + - + @@ -399355,13 +396227,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + cjm @@ -399543,9 +396415,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -399559,34 +396431,34 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010083 future dermis - + - + - + - + EHDAA2 - + EHDAA2 - + XAO @@ -399613,9 +396485,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -399628,34 +396500,34 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010084 future diaphragm - + - + - + - + EHDAA2 - + PMID:23586979 - + PMID:23586979 @@ -399941,7 +396813,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -399959,14 +396831,14 @@ Classes for population already exist in IDO ('organism population', I post-anal tail tip - + - + MA @@ -400075,7 +396947,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400092,7 +396964,7 @@ Classes for population already exist in IDO ('organism population', I pair of dorsal aortae - + @@ -400105,7 +396977,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -400128,7 +397000,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400140,14 +397012,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010191 aortic system - + - + Wikipedia @@ -400330,7 +397202,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400348,14 +397220,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010227 future cardiac atrium - + - + ZFA @@ -400390,7 +397262,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400415,14 +397287,14 @@ Classes for population already exist in IDO ('organism population', I eyeball of camera-type eye - + - + FMA @@ -400508,7 +397380,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400518,8 +397390,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -400532,11 +397404,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010252 1st arch mandibular mesenchyme from neural crest - + - + @@ -400549,13 +397421,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 @@ -400574,7 +397446,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400584,32 +397456,32 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme. EHDAA2:0000044 uberon UBERON:0010253 1st arch maxillary mesenchyme from neural crest - + - + - + EHDAA2 - + EHDAA2 @@ -400628,7 +397500,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400639,8 +397511,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000098 @@ -400655,24 +397527,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010256 4th arch mesenchyme from neural crest - + - + - + EHDAA2 - + EHDAA2 @@ -400713,7 +397585,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400724,8 +397596,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. EHDAA2:0004077 neural crest derived arch 6 mesenchyme @@ -400735,24 +397607,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010257 6th arch mesenchyme from neural crest - + - + - + EHDAA2 - + EHDAA2 @@ -400779,7 +397651,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400792,14 +397664,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010258 mesenchyme from rhombencephalic neural crest - + - + EHDAA2 @@ -400911,8 +397783,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -400926,11 +397798,11 @@ Classes for population already exist in IDO ('organism population', I midbrain basal plate - + - + @@ -400943,13 +397815,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + ZFA @@ -400978,7 +397850,7 @@ Classes for population already exist in IDO ('organism population', I - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -400987,14 +397859,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010286 midbrain neural tube - + - + ZFA @@ -401011,20 +397883,20 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia:Sclera#Histology uberon UBERON:0010291 layer of sclera - + - + cjm @@ -401296,7 +398168,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401312,14 +398184,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010312 immature eye - + - + definitional @@ -401573,20 +398445,20 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a limb/fin bud. uberon UBERON:0010329 paired limb/fin bud mesenchyme - + - + EHDAA2-abduced @@ -401621,20 +398493,20 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a extraembryonic membrane. uberon UBERON:0010333 extraembryonic membrane mesenchyme - + - + EHDAA2-abduced @@ -401653,7 +398525,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401663,32 +398535,32 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme. EHDAA2:0004601 uberon UBERON:0010334 maxillary process mesenchyme from neural crest - + - + - + EHDAA2 - + EHDAA2 @@ -401707,7 +398579,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401717,32 +398589,32 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme. EHDAA2:0004602 uberon UBERON:0010335 maxillary process mesenchyme from head mesenchyme - + - + - + EHDAA2 - + EHDAA2 @@ -401761,7 +398633,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401771,32 +398643,32 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. EHDAA2:0004603 uberon UBERON:0010336 mandibular process mesenchyme from neural crest - + - + - + EHDAA2 - + EHDAA2 @@ -401815,7 +398687,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401825,32 +398697,32 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. EHDAA2:0004604 uberon UBERON:0010337 mandibular process mesenchyme from head mesenchyme - + - + - + EHDAA2 - + EHDAA2 @@ -401869,7 +398741,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401879,21 +398751,21 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme. EHDAA2:0000043 uberon UBERON:0010338 1st arch maxillary mesenchyme from head mesenchyme - + - + EHDAA2 @@ -401912,7 +398784,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401922,21 +398794,21 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000036 uberon UBERON:0010339 1st arch mandibular mesenchyme from head mesenchyme - + - + EHDAA2 @@ -401955,7 +398827,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401966,7 +398838,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. EMAPA:16130 mesenchyme derived from head mesoderm of mesenchyme of 1st arch @@ -401974,14 +398846,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010341 1st arch mesenchyme from head mesenchyme - + - + EMAPA @@ -402006,7 +398878,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402017,7 +398889,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. EHDAA2:0000097 EMAPA:16771 @@ -402029,14 +398901,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010345 4th arch mesenchyme from head mesenchyme - + - + EHDAA2 @@ -402061,7 +398933,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402072,7 +398944,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. EHDAA2:0004078 head mesenchyme derived arch 6 mesenchyme @@ -402082,14 +398954,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010347 6th arch mesenchyme from head mesenchyme - + - + EHDAA2 @@ -402456,7 +399328,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402471,14 +399343,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010375 pancreas dorsal primordium - + - + EHDAA2 @@ -402507,7 +399379,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402522,14 +399394,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010376 pancreas ventral primordium - + - + EHDAA2 @@ -402563,7 +399435,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402577,7 +399449,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010377 mesenchyme from somatopleure - + @@ -402590,7 +399462,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -402623,7 +399495,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402636,7 +399508,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010378 mesenchyme from splanchnopleure - + @@ -402649,7 +399521,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -402683,7 +399555,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402704,14 +399576,14 @@ Classes for population already exist in IDO ('organism population', I spleen trabecular artery - + - + MP @@ -403124,7 +399996,7 @@ Classes for population already exist in IDO ('organism population', I - + Skeletal element that forms as a replacement or substitution of another element or tissue. VSAO:0000135 XAO:0004016 @@ -403133,7 +400005,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010522 replacement element - + @@ -403146,7 +400018,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -403165,7 +400037,7 @@ Classes for population already exist in IDO ('organism population', I - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -403175,14 +400047,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -403718,7 +400590,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -403741,14 +400613,14 @@ Classes for population already exist in IDO ('organism population', I bone of appendage girdle complex - + - + UBERONREF:0000003 @@ -403923,7 +400795,7 @@ Classes for population already exist in IDO ('organism population', I - + Muscles of the pelvic girdle, hindlimb or pelvic fin. Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] AAO:0000218 @@ -403941,14 +400813,14 @@ Classes for population already exist in IDO ('organism population', I pelvic complex muscle - + - + prolog @@ -404016,7 +400888,7 @@ Classes for population already exist in IDO ('organism population', I - + A muscle of a pectoral girdle, pectoral fin or anterior limb. the MA class belongs here, based on its current child classes Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO] @@ -404033,14 +400905,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010891 pectoral complex muscle - + - + prolog @@ -404092,8 +400964,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 @@ -404106,11 +400978,11 @@ Classes for population already exist in IDO ('organism population', I subdivision of skeleton - + - + @@ -404123,13 +400995,13 @@ Classes for population already exist in IDO ('organism population', I - + UBERONREF:0000003 - + VSAO @@ -404169,7 +401041,7 @@ Classes for population already exist in IDO ('organism population', I - + Skeletal element that forms around the notochord and is part of the vertebral column. we include a distinct subclass for bony vertebra In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG] @@ -404186,7 +401058,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010913 vertebral element - + @@ -404200,7 +401072,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -404264,7 +401136,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of either the head or the neck. NCIT:C32716 UMLS:C0448281 @@ -404274,14 +401146,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010959 craniocervical muscle - + - + prolog @@ -404306,12 +401178,12 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -404330,7 +401202,7 @@ Classes for population already exist in IDO ('organism population', I pharyngeal arch cartilage - + @@ -404343,7 +401215,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -404387,7 +401259,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -404415,7 +401287,7 @@ Classes for population already exist in IDO ('organism population', I palatoquadrate arch - + @@ -404428,7 +401300,7 @@ Classes for population already exist in IDO ('organism population', I - + VHOG @@ -404982,7 +401854,7 @@ Classes for population already exist in IDO ('organism population', I - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system @@ -404993,7 +401865,7 @@ Classes for population already exist in IDO ('organism population', I postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -405006,7 +401878,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -405046,7 +401918,7 @@ Classes for population already exist in IDO ('organism population', I - + Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. BTO:0003751 EMAPA:37970 @@ -405055,14 +401927,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011148 submucosal gland - + - + perforates @@ -405086,7 +401958,7 @@ Classes for population already exist in IDO ('organism population', I - + Subdivision of skull that consists of the facial bones. EHDAA2:0002206 EHDAA:8361 @@ -405105,7 +401977,7 @@ Classes for population already exist in IDO ('organism population', I facial skeleton http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg - + @@ -405118,7 +401990,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -405403,7 +402275,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a large intestine. FMA:15654 @@ -405417,14 +402289,14 @@ Classes for population already exist in IDO ('organism population', I lamina propria of large intestine - + - + FMA @@ -405469,7 +402341,7 @@ Classes for population already exist in IDO ('organism population', I - + A muscle layer that is part of a large intestine. FMA:14971 NCIT:C32927 @@ -405482,14 +402354,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011198 muscle layer of large intestine - + - + FMA @@ -405547,7 +402419,7 @@ Classes for population already exist in IDO ('organism population', I - + A muscle layer that is part of a small intestine. FMA:14932 NCIT:C33569 @@ -405563,14 +402435,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011201 muscle layer of small intestine - + - + FMA @@ -405728,7 +402600,7 @@ Classes for population already exist in IDO ('organism population', I - + Muscles within the eye (bulbus oculi).[AAO] AAO:0010038 EMAPA:18808 @@ -405739,14 +402611,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -405936,7 +402808,7 @@ Classes for population already exist in IDO ('organism population', I - + The part of the trunk that is in the dorsum[cjm]. In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA] EMAPA:35162 @@ -405951,7 +402823,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011270 dorsal trunk - + @@ -405964,7 +402836,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -406000,8 +402872,8 @@ Classes for population already exist in IDO ('organism population', I - - + + compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' EHDAA2:0001845 uberon @@ -406010,11 +402882,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011272 embryonic skin basal layer - + - + @@ -406027,13 +402899,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 @@ -406159,7 +403031,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -406183,14 +403055,14 @@ Classes for population already exist in IDO ('organism population', I lumen of esophagus - + - + FMA @@ -406254,7 +403126,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -406272,14 +403144,14 @@ Classes for population already exist in IDO ('organism population', I paired limb/fin skeleton - + - + ISBN:9780878932504 @@ -406342,19 +403214,19 @@ Classes for population already exist in IDO ('organism population', I - - + + EHDAA2:0002120 upper jaw future lip uberon UBERON:0011592 future upper lip - + - + @@ -406367,13 +403239,13 @@ Classes for population already exist in IDO ('organism population', I - + fusion - + fusion @@ -406401,7 +403273,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -406422,14 +403294,14 @@ Classes for population already exist in IDO ('organism population', I jaw region http://eol.org/collections/11578 - + - + EMAPA FMA-abduced ZFA-abduced @@ -406449,14 +403321,14 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0001020 lower jaw future lip uberon UBERON:0011596 future lower lip - + @@ -406469,7 +403341,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia:Mandibular_prominence @@ -406546,14 +403418,14 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that develops_from a ectoderm and is part of a oral epithelium. EHDAA2:0004137 uberon UBERON:0011642 oral epithelium from ectoderm - + @@ -406566,7 +403438,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -407560,7 +404432,7 @@ Classes for population already exist in IDO ('organism population', I - + A muscle layer that is part of a wall of esophagus. In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle FMA:62998 @@ -407574,14 +404446,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011878 muscle layer of esophagus - + - + upper part Wikipedia:Muscular_layer @@ -407644,7 +404516,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -407686,7 +404558,7 @@ Classes for population already exist in IDO ('organism population', I anterior uvea - + @@ -407699,7 +404571,7 @@ Classes for population already exist in IDO ('organism population', I - + MP @@ -407740,7 +404612,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -407765,7 +404637,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011899 epimysium - + @@ -407778,7 +404650,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -407831,7 +404703,7 @@ Classes for population already exist in IDO ('organism population', I - + Masses of developing blood cells attached to endothelium in the yolk sac. EHDAA2:0000177 EMAPA:16115 @@ -407842,14 +404714,14 @@ Classes for population already exist in IDO ('organism population', I yolk sac blood island - + - + EHDAA2 @@ -408710,7 +405582,7 @@ Classes for population already exist in IDO ('organism population', I - + The deep cervical artery (Profunda cervicalis) is an artery of the neck. FMA:10659 @@ -408722,14 +405594,14 @@ Classes for population already exist in IDO ('organism population', I deep cervical artery - + - + FMA @@ -408873,20 +405745,20 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -408907,7 +405779,7 @@ Classes for population already exist in IDO ('organism population', I - + A muscle layer that is part of an intestine. FMA:15697 intestinal muscularis propria @@ -408917,14 +405789,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0012367 muscle layer of intestine - + - + FMA @@ -409214,7 +406086,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -409236,7 +406108,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0012429 hematopoietic tissue - + @@ -409249,7 +406121,7 @@ Classes for population already exist in IDO ('organism population', I - + defitional @@ -409395,7 +406267,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -409412,14 +406284,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0012463 cloacal lumen - + - + cjm @@ -409609,20 +406481,20 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -409649,7 +406521,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -409669,14 +406541,14 @@ Classes for population already exist in IDO ('organism population', I skeleton of pectoral complex - + - + FMA @@ -409745,7 +406617,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -409765,14 +406637,14 @@ Classes for population already exist in IDO ('organism population', I skeleton of pelvic complex - + - + FMA @@ -409824,8 +406696,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The posterior region of the neck, including the suboccipital region. nuchal nape @@ -409848,11 +406720,11 @@ Classes for population already exist in IDO ('organism population', I dorsal part of neck - + - + @@ -409865,13 +406737,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + FMA @@ -410700,7 +407572,7 @@ Classes for population already exist in IDO ('organism population', I - + A vein that drains a lip. SCTID:367664002 labial vein of face @@ -410711,14 +407583,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0013136 vein of lip - + - + FMA @@ -410897,7 +407769,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -410921,14 +407793,14 @@ Classes for population already exist in IDO ('organism population', I cranial cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg - + - + Wikipedia @@ -411421,7 +408293,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -411438,14 +408310,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0013525 stomach lumen - + - + FMA @@ -411496,7 +408368,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that is part of a intestinal villus. FMA:63587 intestinal villus epithelium @@ -411506,14 +408378,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0013636 epithelium of intestinal villus - + - + FMA @@ -413055,7 +409927,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that is part of a frontonasal prominence. EHDAA2:0004108 EMAPA:32918 @@ -413063,7 +409935,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0014702 frontonasal process epithelium - + @@ -413076,7 +409948,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -413146,7 +410018,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -413161,14 +410033,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0014704 pleuroperitoneal canal lumen - + - + EHDAA2 @@ -413370,8 +410242,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -413400,24 +410272,24 @@ Classes for population already exist in IDO ('organism population', I Classification notes: May be considered an external sphincter[PMID:8224664] crus of diaphragm - + - + - + PMID:23586979 - + PMID:23586979 @@ -413906,20 +410778,20 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). uberon UBERON:0014794 pectoral appendage muscle - + - + prolog @@ -413946,20 +410818,20 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). uberon UBERON:0014795 pelvic appendage muscle - + - + prolog @@ -414120,7 +410992,7 @@ Classes for population already exist in IDO ('organism population', I - + One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites. Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4]. EFO:0003664 @@ -414138,7 +411010,7 @@ Classes for population already exist in IDO ('organism population', I intersomitic vessel - + @@ -414151,7 +411023,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -414378,7 +411250,7 @@ Classes for population already exist in IDO ('organism population', I - + consider merging into myocardial compact layer FMA:83105 perimysial connective tissue of subepicardium @@ -414387,14 +411259,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0015128 subepicardial layer of epicardium - + - + FMA @@ -414494,7 +411366,7 @@ Classes for population already exist in IDO ('organism population', I - + A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104] the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648] @@ -414505,14 +411377,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0015152 gland of ocular region - + - + inferred @@ -414969,7 +411841,7 @@ Classes for population already exist in IDO ('organism population', I - + A basement membrane of epithelium that is part of a respiratory system. EMAPA:37570 MA:0001815 @@ -414977,14 +411849,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0015329 respiratory system basement membrane - + - + MA @@ -415046,7 +411918,7 @@ Classes for population already exist in IDO ('organism population', I - + The hepatic artery proper (also proper hepatic artery), arises from the common hepatic artery and runs alongside the portal vein and the common bile duct to form the portal triad. The hepatic artery proper gives off a small supraduodenal artery to the duodenal bulb. Then the right gastric artery comes off and runs to the left along the lesser curvature of the stomach to meet the left gastric artery, which is a branch of the celiac trunk. It subsequently gives off the cystic artery, which feeds the gallbladder, before bifurcating into the right and left hepatic arteries. Of note, the right and left hepatic arteries may demonstrate variant anatomy. A replaced right hepatic artery may arise from the superior mesenteric artery (SMA) and a replaced left hepatic artery may arise from the left gastric artery. EMAPA:37217 @@ -415061,7 +411933,7 @@ Classes for population already exist in IDO ('organism population', I proper hepatic artery - + @@ -415074,7 +411946,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -415111,13 +411983,13 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -415137,14 +412009,14 @@ Classes for population already exist in IDO ('organism population', I left hepatic artery - + - + FMA @@ -415189,13 +412061,13 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -415215,14 +412087,14 @@ Classes for population already exist in IDO ('organism population', I right hepatic artery - + - + FMA @@ -415586,7 +412458,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a duodenum. EMAPA:27255 @@ -415600,14 +412472,14 @@ Classes for population already exist in IDO ('organism population', I duodenum lamina propria - + - + FMA @@ -416586,7 +413458,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -416609,7 +413481,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0016887 entire extraembryonic component - + @@ -416622,7 +413494,7 @@ Classes for population already exist in IDO ('organism population', I - + AEO @@ -417130,7 +414002,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -417148,14 +414020,14 @@ Classes for population already exist in IDO ('organism population', I skeletal musculature - + - + MA @@ -418526,7 +415398,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -418540,14 +415412,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0034710 spinal cord ventricular layer - + - + EHDAA2 @@ -419793,7 +416665,7 @@ Classes for population already exist in IDO ('organism population', I - + Any of several arteries that arise from the aorta and supply blood to the esophagus. FMA:4149 @@ -419807,7 +416679,7 @@ Classes for population already exist in IDO ('organism population', I esophageal artery - + @@ -419820,7 +416692,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -420298,7 +417170,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -420314,14 +417186,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0035763 cavity of cardiac chamber - + - + FMA @@ -420692,8 +417564,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -420709,24 +417581,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0035831 costal diaphragm - + - + - + PMID:23586979 - + PMID:23586979 @@ -420834,20 +417706,20 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0004070 uberon UBERON:0036072 respiratory primordium epithelium - + - + EHDAA2 @@ -420875,21 +417747,21 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0004071 respiratory primordium associated mesenchyme uberon UBERON:0036073 respiratory primordium mesenchyme - + - + EHDAA2 @@ -421355,12 +418227,12 @@ Classes for population already exist in IDO ('organism population', I - + - + Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall @@ -421368,7 +418240,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0036285 wall of left ventricle - + @@ -421381,7 +418253,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421406,12 +418278,12 @@ Classes for population already exist in IDO ('organism population', I - + - + Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 right ventricular wall @@ -421419,7 +418291,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0036286 wall of right ventricle - + @@ -421432,7 +418304,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421465,7 +418337,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -421477,14 +418349,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0036288 anterior wall of left ventricle - + - + FMA @@ -421719,27 +418591,27 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:14657 gallbladder wall uberon UBERON:0036343 wall of gallbladder - + - + FMA @@ -421758,19 +418630,19 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:15089 brachiocephalic arterial wall uberon UBERON:0036351 wall of brachiocephalic artery - + @@ -421783,7 +418655,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421802,19 +418674,19 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:15090 subclavian arterial wall uberon UBERON:0036352 wall of subclavian artery - + @@ -421827,7 +418699,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421846,7 +418718,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -421856,21 +418728,21 @@ Classes for population already exist in IDO ('organism population', I - + FMA:15704 anal canal wall uberon UBERON:0036362 wall of anal canal - + - + FMA @@ -421889,19 +418761,19 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:18211 pulmonary arterial wall uberon UBERON:0036422 wall of pulmonary artery - + @@ -421914,7 +418786,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421933,19 +418805,19 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:231590 uberon UBERON:0036553 wall of synovial tendon sheath - + @@ -421958,7 +418830,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421971,20 +418843,20 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:58098 eyeball wall uberon UBERON:0036925 wall of eyeball - + @@ -421997,7 +418869,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -422016,21 +418888,21 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:63144 orbit wall uberon UBERON:0037089 wall of orbit - + @@ -422043,7 +418915,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -422062,19 +418934,19 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:66284 common carotid arterial wall uberon UBERON:0037094 wall of common carotid artery - + @@ -422087,7 +418959,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -422106,15 +418978,15 @@ Classes for population already exist in IDO ('organism population', I - + - - - + + + Wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees. FMA:7274 cardiac wall @@ -422122,15 +418994,15 @@ Classes for population already exist in IDO ('organism population', I UBERON:0037144 wall of heart - + - + - + @@ -422143,19 +419015,19 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + FMA - + FMA @@ -422189,7 +419061,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -422205,14 +419077,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + FMA Wikipedia @@ -422253,20 +419125,20 @@ Classes for population already exist in IDO ('organism population', I - + FMA:15395 uberon UBERON:0039228 sigmoid vein - + - + FMA @@ -422328,14 +419200,14 @@ Classes for population already exist in IDO ('organism population', I - + Ovarian vein, each instance of which is a tributary of some inferior vena cava that drains the right pampiniform plexus of some broad ligament. FMA:14342 uberon UBERON:0039856 right ovarian vein - + @@ -422348,7 +419220,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -423284,8 +420156,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A collection of Purkinje fibers that receives signals from the right and left bundle branches and innervates the ventricular cardiac muscle. The Purkinje fiber network creates synchronized contractions of the heart ventricles. Purkinje fibre network @@ -423293,11 +420165,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:8000009 Purkinje fiber network - + - + @@ -423312,7 +420184,7 @@ Classes for population already exist in IDO ('organism population', I - + https://github.com/obophenotype/uberon/issues/1785 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9791-0064 @@ -423320,7 +420192,7 @@ Classes for population already exist in IDO ('organism population', I - + https://github.com/obophenotype/uberon/issues/1785 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9791-0064 @@ -424502,7 +421374,6 @@ Classes for population already exist in IDO ('organism population', I length unit - A unit which is a standard measure of the distance between two points. "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] length unit @@ -424516,7 +421387,6 @@ Classes for population already exist in IDO ('organism population', I mass unit - A unit which is a standard measure of the amount of matter/energy of a physical object. "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia] mass unit @@ -424530,7 +421400,6 @@ Classes for population already exist in IDO ('organism population', I time unit - A unit which is a standard measure of the dimension in which events occur in sequence. time derived unit "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia] @@ -431677,6 +428546,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim + + + + Obsolete Class + + + + @@ -432651,7 +429528,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Affymetrix Affymetrix supplied microarray - An organization which supplies technology, tools and protocols for use in high throughput applications + An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix @@ -432771,7 +429648,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module SVM - GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. + GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. James Malone Ryan Brinkman GenePattern module SVM @@ -432833,7 +429710,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module KMeansClustering - GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. + GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. James Malone PERSON: James Malone GenePattern module KMeansClustering @@ -432861,7 +429738,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module CARTXValidation - GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. + GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. GenePattern module CARTXValidation @@ -432897,7 +429774,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module KNNXValidation - GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. + GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. James Malone PERSON: James Malone GenePattern module KNNXValidation @@ -432924,7 +429801,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module KNN - GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. + GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module KNN @@ -432938,7 +429815,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module HierarchicalClustering - GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. + GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. James Malone PERSON: James Malone GenePattern module HierarchicalClustering @@ -432977,7 +429854,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module PCA - GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. + GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. James Malone PERSON: James Malone GenePattern module PCA @@ -433016,7 +429893,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern HeatMapViewer data visualization - The GenePattern process of generating Heat Maps from clustered data. + The GenePattern process of generating Heat Maps from clustered data. James Malone GenePattern HeatMapViewer data visualization @@ -433029,7 +429906,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern HierarchicalClusteringViewer data visualization - The GenePattern process of generating hierarchical clustering visualization from clustered data. + The GenePattern process of generating hierarchical clustering visualization from clustered data. James Malone GenePattern HierarchicalClusteringViewer data visualization @@ -433043,7 +429920,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module HeatMapViewer - A GenePattern software module which is used to generate a heatmap view of data. + A GenePattern software module which is used to generate a heatmap view of data. James Malone GenePattern module HeatMapViewer @@ -433057,7 +429934,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module HierarchicalClusteringViewer - A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. + A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. James Malone GenePattern module HierarchicalClusteringViewer @@ -433377,7 +430254,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Nimblegen - An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. + An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Person: Jie Zheng Nimblegen @@ -433390,7 +430267,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Pacific Biosciences - An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. + An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. Person: Jie Zheng Pacific Biosciences @@ -433403,7 +430280,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim NanoString Technologies - An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. + An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. NanoString Technologies @@ -433415,7 +430292,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Thermo Fisher Scientific - An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. + An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific Thermo Fisher Scientific @@ -433429,7 +430306,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G1: Well differentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. + A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. Chris Stoeckert, Helena Ellis G1 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet @@ -433445,7 +430322,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G2: Moderately differentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. + A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. Chris Stoeckert, Helena Ellis G2 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet @@ -433461,7 +430338,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G3: Poorly differentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. + A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G3 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet @@ -433477,7 +430354,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G4: Undifferentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. + A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G4 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet @@ -433493,7 +430370,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G1 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. Chris Stoeckert, Helena Ellis Grade 1 NCI BBRB, OBI @@ -433509,7 +430386,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G2 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. Chris Stoeckert, Helena Ellis Grade 2 NCI BBRB, OBI @@ -433525,7 +430402,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G3 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. Chris Stoeckert, Helena Ellis Grade 3 NCI BBRB, OBI @@ -433541,7 +430418,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G4 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. Chris Stoeckert, Helena Ellis Grade 4 NCI BBRB, OBI @@ -433557,7 +430434,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Low grade ovarian tumor - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. Chris Stoeckert, Helena Ellis Low grade NCI BBRB, OBI @@ -433573,7 +430450,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim High grade ovarian tumor - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. Chris Stoeckert, Helena Ellis High grade NCI BBRB, OBI @@ -433589,7 +430466,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G1 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. Chris Stoeckert, Helena Ellis G1 NCI BBRB, OBI @@ -433605,7 +430482,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G2 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. Chris Stoeckert, Helena Ellis G2 NCI BBRB, OBI @@ -433621,7 +430498,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G3 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. Chris Stoeckert, Helena Ellis G3 NCI BBRB, OBI @@ -433637,7 +430514,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G4 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. Chris Stoeckert, Helena Ellis G4 NCI BBRB, OBI @@ -433653,7 +430530,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT0 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433668,7 +430545,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pTis (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433683,7 +430560,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433698,7 +430575,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433713,7 +430590,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433728,7 +430605,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT4a (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433743,7 +430620,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT4b (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433758,7 +430635,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT0 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433773,7 +430650,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pTis (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433788,7 +430665,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433803,7 +430680,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1a (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433818,7 +430695,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1b (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433833,7 +430710,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433848,7 +430725,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2a (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433863,7 +430740,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2b (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433878,7 +430755,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433893,7 +430770,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT4 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433908,7 +430785,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT0 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433923,7 +430800,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433938,7 +430815,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1a (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433953,7 +430830,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1b (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433968,7 +430845,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433983,7 +430860,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2a (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433998,7 +430875,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2b (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434013,7 +430890,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434028,7 +430905,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3a (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434043,7 +430920,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3b (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434058,7 +430935,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3c (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434073,7 +430950,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT4 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434088,7 +430965,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT0 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434103,7 +430980,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434118,7 +430995,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1a (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434133,7 +431010,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1b (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434148,7 +431025,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1c (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434163,7 +431040,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434178,7 +431055,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2a (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434193,7 +431070,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2b (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434208,7 +431085,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2c (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434223,7 +431100,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434238,7 +431115,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3a (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434253,7 +431130,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3b (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434268,7 +431145,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3c (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434283,7 +431160,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN0 (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434298,7 +431175,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1 (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434313,7 +431190,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1a (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434328,7 +431205,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1b (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434343,7 +431220,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1c (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434358,7 +431235,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN2 (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434373,7 +431250,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN2a (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434388,7 +431265,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN2b (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434403,7 +431280,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN0 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. + A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB @@ -434418,7 +431295,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB @@ -434433,7 +431310,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN2 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB @@ -434448,7 +431325,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN3 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB @@ -434463,7 +431340,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN0 (kidney) - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB @@ -434478,7 +431355,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1 (kidney) - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB @@ -434493,7 +431370,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN0 (ovary) - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB @@ -434508,7 +431385,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1 (ovary) - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB @@ -434523,7 +431400,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM0 (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB @@ -434538,7 +431415,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1 (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB @@ -434553,7 +431430,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1a (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB @@ -434568,7 +431445,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1b (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB @@ -434583,7 +431460,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1 (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB @@ -434598,7 +431475,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1a (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB @@ -434613,7 +431490,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1b (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB @@ -434628,7 +431505,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM0 (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434643,7 +431520,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1 (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434658,7 +431535,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1a (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434673,7 +431550,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1b (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434688,7 +431565,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1 (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434703,7 +431580,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1a (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434718,7 +431595,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1b (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434733,7 +431610,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM0 (kidney) - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB @@ -434748,7 +431625,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1 (kidney) - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB @@ -434763,7 +431640,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1 (kidney) - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB @@ -434778,7 +431655,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM0 (ovary) - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB @@ -434793,7 +431670,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1 (ovary) - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB @@ -434808,7 +431685,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1 (ovary) - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB @@ -434823,7 +431700,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Occult Carcinoma (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. + A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. Chris Stoeckert, Helena Ellis Occult Carcinoma http://www.medilexicon.com/dictionary/14371 @@ -434839,7 +431716,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 0 (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. + A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. Chris Stoeckert, Helena Ellis Stage 0 https://en.wikipedia.org/wiki/Cancer_staging @@ -434855,7 +431732,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage I (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. + A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. Chris Stoeckert, Helena Ellis Stage I https://en.wikipedia.org/wiki/Cancer_staging @@ -434871,7 +431748,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIA (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cancer_staging @@ -434887,7 +431764,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIB (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cancer_staging @@ -434903,7 +431780,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIC (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. Chris Stoeckert, Helena Ellis Stage IIC https://en.wikipedia.org/wiki/Cancer_staging @@ -434919,7 +431796,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIIA (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cancer_staging @@ -434935,7 +431812,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIIB (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cancer_staging @@ -434951,7 +431828,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIIC (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. Chris Stoeckert, Helena Ellis Stage IIIC https://en.wikipedia.org/wiki/Cancer_staging @@ -434967,7 +431844,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IVA (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cancer_staging @@ -434983,7 +431860,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IVB (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cancer_staging @@ -434999,7 +431876,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. Chris Stoeckert, Helena Ellis Stage IA https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435015,7 +431892,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IA1 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. Chris Stoeckert, Helena Ellis Stage IA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435031,7 +431908,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IA2 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. Chris Stoeckert, Helena Ellis Stage IA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435047,7 +431924,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA Chris Stoeckert, Helena Ellis Stage IB https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435063,7 +431940,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IB1 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB1 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435079,7 +431956,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IB2 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB2 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435095,7 +431972,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435111,7 +431988,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIA1 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435127,7 +432004,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIA2 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435143,7 +432020,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435159,7 +432036,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIIA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435175,7 +432052,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIIB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435191,7 +432068,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IVA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435207,7 +432084,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IVB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435223,7 +432100,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 1 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435239,7 +432116,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 1A (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435255,7 +432132,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 1B (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435271,7 +432148,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 1C (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435287,7 +432164,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 2 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435303,7 +432180,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 2A (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435319,7 +432196,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 2B (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435335,7 +432212,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 2C (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435351,7 +432228,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 3 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). Chris Stoeckert, Helena Ellis Stage 3 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435367,7 +432244,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 3A (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435383,7 +432260,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 3B (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435399,7 +432276,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 3C (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). Chris Stoeckert, Helena Ellis Stage 3C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435415,7 +432292,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 4 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. Chris Stoeckert, Helena Ellis Stage 4 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435431,7 +432308,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage Unknown (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). Chris Stoeckert, Helena Ellis Stage Unknown https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435447,7 +432324,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 3: symptomatic in bed more than 50% of the day but not bed ridden - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435462,7 +432339,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 2: symptomatic but in bed less than 50% of the day - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435477,7 +432354,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 4: bed ridden - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435492,7 +432369,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 0: asymptomatic - An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. + An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435507,7 +432384,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 1: symptomatic but fully ambulatory - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435522,7 +432399,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 100: asymptomatic - A Karnofsky score vaue specification indicating that a patient is asymptomatic. + A Karnofsky score vaue specification indicating that a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435537,7 +432414,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 80-90: symptomatic but fully ambulatory - A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. + A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435552,7 +432429,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 60-70: symptomatic but in bed less than 50% of the day - A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. + A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435567,7 +432444,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden - A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. + A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435582,7 +432459,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Oxford Nanopore Technologies - An organization that is developing and selling nanopore sequencing products and is based in the UK. + An organization that is developing and selling nanopore sequencing products and is based in the UK. James A. Overton https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies Oxford Nanopore Technologies @@ -435596,7 +432473,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim BioGents - An organization that manufactures mosquito traps and other mosquito control products. + An organization that manufactures mosquito traps and other mosquito control products. John Judkins WEB:https://eu.biogents.com/about-biogents/ BioGents @@ -435610,7 +432487,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Abbott - A manufacturer of rapid point-of-care assay devices. + A manufacturer of rapid point-of-care assay devices. John Judkins ORCID:0000-0001-6595-0902 WEB:https://www.globalpointofcare.abbott/en/about.html https://github.com/obi-ontology/obi/issues/1456 @@ -435625,7 +432502,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim J. Mitra - A manufacturer of in vitro diagnostic assay kits in India. + A manufacturer of in vitro diagnostic assay kits in India. John Judkins ORCID:0000-0001-6595-0902 WEB:https://jmitra.co.in/about-us/ https://github.com/obi-ontology/obi/issues/1456 @@ -435640,7 +432517,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim InBios - A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases. + A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases. John Judkins ORCID:0000-0001-6595-0902 WEB:https://inbios.com/about/ https://github.com/obi-ontology/obi/issues/1456 @@ -435652,6 +432529,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. @@ -435662,6 +432540,20 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim + + + + + The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. + This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). + + https://github.com/information-artifact-ontology/ontology-metadata/issues/136 + https://orcid.org/0000-0002-4142-7153 + domain entity does not exist + + + + @@ -437407,14 +434299,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + - + @@ -437428,14 +434320,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + PMID:16417468 - + @@ -437554,14 +434446,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -437575,14 +434467,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -437776,14 +434668,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA-abduced-lr - + @@ -437797,14 +434689,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + definitional - + @@ -437818,14 +434710,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest - + @@ -437884,14 +434776,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + only in species that have a stomach - + @@ -437935,14 +434827,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + Wikipedia:Vitelline_vein - + @@ -437986,14 +434878,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438022,14 +434914,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + Wikipedia:Vitelline_vein - + @@ -438043,15 +434935,15 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + may be present in other parts in other species FMA - + @@ -438125,15 +435017,15 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + right arch 4 in human embryology.ch - + @@ -438147,14 +435039,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438168,14 +435060,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + Wikipedia:Vitelline_vein - + @@ -438189,14 +435081,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + Wikipedia - + @@ -438210,14 +435102,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + PMID:22179203 - + @@ -438231,14 +435123,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438252,14 +435144,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438273,14 +435165,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438294,14 +435186,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438315,14 +435207,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438336,14 +435228,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438357,14 +435249,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438378,14 +435270,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438399,14 +435291,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438447,14 +435339,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438528,14 +435420,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest - + @@ -438549,14 +435441,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438570,14 +435462,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438591,14 +435483,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438629,14 +435521,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + cjm - + @@ -438682,14 +435574,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + PMID:16417468 - + @@ -438703,14 +435595,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + PMID:16417468 - + @@ -438724,15 +435616,15 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + AAO https://github.com/geneontology/go-ontology/issues/16143 - + @@ -438761,14 +435653,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + teleosts - + @@ -438782,14 +435674,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + Mammals - + @@ -438803,14 +435695,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + conservatively place at deuterostome, excluding acoelomates - + @@ -438899,14 +435791,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + diff --git a/rbo.owl b/rbo.owl index fcf3561..e3f16b4 100644 --- a/rbo.owl +++ b/rbo.owl @@ -39,11 +39,11 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. Radiation Biology Ontology - 2024-05-31 + 2024-10-23 @@ -198,6 +198,7 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon @@ -265,6 +266,12 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + @@ -337,6 +344,12 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + @@ -681,14 +694,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - @@ -809,14 +814,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - @@ -833,14 +830,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - @@ -1927,12 +1916,26 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + + + + + + + + + + + + + executed by + + + + @@ -2737,7 +2750,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + has measurement unit label + has measurement unit label @@ -2746,84 +2760,16 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - This document is about information artifacts and their representations - + http://purl.obolibrary.org/obo/IAO_0000136 + is about A (currently) primitive relation that relates an information artifact to an entity. - 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. - person:Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy + + is about is about - - - - - - - - m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later - From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] - -This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. --- -From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] - -unit of measure is a quality, e.g. the length of a ruler. - -[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] - -[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] - -a represents b means either a denotes b or a describes - -describe: -a describes b means a is about b and a allows an inference of at least one quality of b - -We have had a long discussion about denotes versus describes. - From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. - -a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. - From the second meeting on IAO: - -An attempt at defining assay using Barry's "reliability" wording - -assay: -process and has_input some material entity -and has_output some information content entity -and which is such that instances of this process type reliably generate -outputs that describes the input. - This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. - Alan Ruttenberg - is quality measurement of - - - - - - - - - inverse of the relation of is quality measurement of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - is quality measured as - - - - @@ -2832,7 +2778,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which is_supported_by_data The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. - The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process + The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop @@ -2844,18 +2790,10 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - - - has_specified_input - has_specified_input + has specified input see is_input_of example_of_usage The inverse property of is_specified_input_of @@ -2864,13 +2802,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot - - http://www.ebi.ac.uk/efo/has_input - OBI:0000293 has specified input - has_input - has_specified_input - has_specified_input @@ -2879,18 +2811,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - is_specified_input_of + is specified input of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - http://www.ebi.ac.uk/efo/is_input_of is specified input of - is_input_of - is_specified_input_of @@ -2898,15 +2826,11 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - + has specified output has_specified_output has_specified_output @@ -2930,15 +2854,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - is_specified_output_of - is_specified_output_of + is specified output of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - is specified output of - is_specified_output_of @@ -2952,7 +2873,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' - This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch @@ -2968,7 +2889,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which objective_achieved_by - This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. + This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by @@ -2984,7 +2905,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which has value specification - A relation between an information content entity and a value specification that specifies its value. + A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification @@ -3116,30 +3037,11 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - @@ -3201,10 +3103,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + has function this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function + RO:0000085 has_function has function @@ -3217,10 +3121,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + has quality this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality + http://www.ebi.ac.uk/efo/has_quality RO:0000086 uberon @@ -3239,10 +3145,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + has role this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role + RO:0000087 chebi_ontology has_role @@ -4396,10 +4304,12 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + has component w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + RO:0002180 external @@ -5912,8 +5822,10 @@ where + has member has member is a mereological relation between a collection and an item. SIO + RO:0002351 uberon @@ -8240,6 +8152,18 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + executes + + + + @@ -8554,22 +8478,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - has atomic number - - - - + Number of protons in an atomic nucleus We are undecided as to whether to ultimately model this as a data property of object property + cardinality, but for now we are using DPs as these are faster for reasoning + has atomic number has atomic number @@ -8585,17 +8502,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - has measurement value - - - - @@ -8604,7 +8510,7 @@ For example, A and B may be gene products and binding of B by A positively regul has specified numeric value - A relation between a value specification and a number that quantifies it. + A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI @@ -8619,7 +8525,7 @@ For example, A and B may be gene products and binding of B by A positively regul has specified value - A relation between a value specification and a literal. + A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI has specified value @@ -8657,82 +8563,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A planned process that has specified output a software product and that involves the creation of source code. - Mathias Brochhausen - William R. Hogan - http://en.wikipedia.org/wiki/Software_development - A planned process resulting in a software product involving the creation of source code. - software development - - - - - - - - - - - - - - - - - - - - - - - - - - creating a data set - A planned process that has a data set as its specified output. - William R. Hogan - data set creation - dataset creation - dataset creating - - - - @@ -8784,11 +8614,9 @@ For example, A and B may be gene products and binding of B by A positively regul continuant Continuant - continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) @@ -9261,7 +9089,6 @@ For example, A and B may be gene products and binding of B by A positively regul quality Quality - quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist @@ -9270,7 +9097,6 @@ For example, A and B may be gene products and binding of B by A positively regul the shape of your nostril A quality is an entity that describes some aspect which is intrinsic to that particular object and is dependent on or more material entities in which it inheres in or is borne by. Example the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee James Malone - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] @@ -9316,7 +9142,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -9332,6 +9158,7 @@ For example, A and B may be gene products and binding of B by A positively regul sdc SpecificallyDependentContinuant + characteristic specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato @@ -9351,8 +9178,7 @@ For example, A and B may be gene products and binding of B by A positively regul Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. James Malone Sirarat Sarntivijai - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] sample characteristic http://www.ebi.ac.uk/efo/EFO_0001443 @@ -9372,7 +9198,7 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 - + @@ -9383,15 +9209,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + We should name the inverse in COB and avoid the confusing inverse(..) construct - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - @@ -9405,12 +9225,6 @@ For example, A and B may be gene products and binding of B by A positively regul per discussion with Barry Smith - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - @@ -9657,9 +9471,7 @@ For example, A and B may be gene products and binding of B by A positively regul BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. James Malone - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) @@ -14491,6 +14303,36 @@ For example, A and B may be gene products and binding of B by A positively regul zinc-66 atom + + + + CAS:14378-33-7 + ChemIDplus + + + + + PMID:12447866 + SUBMITTER + + + + + PMID:19836537 + Europe PMC + + + + + PMID:20155761 + Europe PMC + + + + + PMID:21047059 + Europe PMC + @@ -14558,36 +14400,6 @@ For example, A and B may be gene products and binding of B by A positively regul zinc-66 ChemIDplus - - - - CAS:14378-33-7 - ChemIDplus - - - - - PMID:12447866 - SUBMITTER - - - - - PMID:19836537 - Europe PMC - - - - - PMID:20155761 - Europe PMC - - - - - PMID:21047059 - Europe PMC - @@ -14621,6 +14433,43 @@ For example, A and B may be gene products and binding of B by A positively regul nickel-60 atom + + + + PMID:29376683 + Europe PMC + + + + + ((60)Ni)nickel + IUPAC + + + + + + (60)Ni + ChEBI + + + + + Ni-60 + ChEBI + + + + + nickel, isotope of mass 60 + ChemIDplus + + + + + nickel-60 + ChemIDplus + @@ -14663,43 +14512,6 @@ For example, A and B may be gene products and binding of B by A positively regul PMID:26709546 Europe PMC - - - - PMID:29376683 - Europe PMC - - - - - ((60)Ni)nickel - IUPAC - - - - - - (60)Ni - ChEBI - - - - - Ni-60 - ChEBI - - - - - nickel, isotope of mass 60 - ChemIDplus - - - - - nickel-60 - ChemIDplus - @@ -26826,9 +26638,7 @@ For example, A and B may be gene products and binding of B by A positively regul - atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. - CHEBI:22671 CHEBI:23907 MeSH:D004602 @@ -50456,7 +50266,6 @@ For example, A and B may be gene products and binding of B by A positively regul XAO:0003012 - CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). @@ -67721,6 +67530,16 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + http://purl.obolibrary.org/obo/IAO_0000109 + measurement datum + + + + @@ -67752,6 +67571,31 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + A processed material entity which is designed to perform a function. + + 2023-03-24T16:04:27+00:00 + In this definition we assume devices are made of processed material, not natural artifacts, so we involve artifactual function rather than biological function, but align with a general BFO function sense where functions such as pumping, lifting can occur in both contexts. Thus we can compare a biological arm with a robotic arm device. + +We say "designed" to emphasize a device's primary function rather than all the other possible dispositions a device may have that may also be useful. E.g. one can use a hammer for a paper weight. + +Regarding usage then, we don't say a naturally formed rock is a hammering device - it wasn't designed to bear a hammering function per se. However, a given rock may still happen to have the disposition to bear a hammering function, and so we could say it is a hammering "tool", which does not necessarily convey intentional design. + +Example of use: A whole device like an engine; a component like a bolt is also a device. + device + + + + @@ -80928,12 +80772,12 @@ The building envelope provides resistance to air, water, heat, light, and noise - + An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure. Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure. ice - + @@ -80947,7 +80791,7 @@ The building envelope provides resistance to air, water, heat, light, and noise - + https://github.com/EnvironmentOntology/envo/issues/900 @@ -101002,7 +100846,7 @@ consider revising 'pond' semantics - + @@ -101027,14 +100871,14 @@ consider revising 'pond' semantics GO:0005319 lipid transporter activity - + - + GO_REF:0000090 @@ -101115,7 +100959,7 @@ consider revising 'pond' semantics - + @@ -101136,14 +100980,14 @@ consider revising 'pond' semantics GO:0005326 neurotransmitter transmembrane transporter activity - + - + GO_REF:0000090 @@ -101390,32 +101234,32 @@ consider revising 'pond' semantics - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -101827,9 +101671,7 @@ consider revising 'pond' semantics - - cytoplasm @@ -110074,7 +109916,7 @@ consider revising 'pond' semantics - + Enables the transfer of a protein from one side of a membrane to the other. GO:0015266 GO:0015463 @@ -110103,14 +109945,14 @@ consider revising 'pond' semantics GO:0008320 protein transmembrane transporter activity - + - + GO_REF:0000090 @@ -111819,7 +111661,6 @@ consider revising 'pond' semantics response to abiotic stress biological_process GO:0009628 - @@ -120451,7 +120292,7 @@ consider revising 'pond' semantics - + @@ -120466,14 +120307,14 @@ consider revising 'pond' semantics GO:0015075 monoatomic ion transmembrane transporter activity - + - + GO_REF:0000090 @@ -120764,7 +120605,7 @@ consider revising 'pond' semantics - + @@ -120787,14 +120628,14 @@ consider revising 'pond' semantics GO:0015114 phosphate ion transmembrane transporter activity - + - + GO_REF:0000090 @@ -120828,7 +120669,7 @@ consider revising 'pond' semantics - + @@ -120852,14 +120693,14 @@ consider revising 'pond' semantics GO:0015116 sulfate transmembrane transporter activity - + - + GO_REF:0000090 @@ -120904,7 +120745,7 @@ consider revising 'pond' semantics - + @@ -120916,14 +120757,14 @@ consider revising 'pond' semantics GO:0015123 acetate transmembrane transporter activity - + - + GO_REF:0000090 @@ -121098,7 +120939,7 @@ consider revising 'pond' semantics - + @@ -121113,14 +120954,14 @@ consider revising 'pond' semantics GO:0015144 carbohydrate transmembrane transporter activity - + - + GO_REF:0000090 @@ -121192,7 +121033,7 @@ consider revising 'pond' semantics - + @@ -121206,14 +121047,14 @@ consider revising 'pond' semantics GO:0015149 hexose transmembrane transporter activity - + - + GO_REF:0000090 @@ -121298,7 +121139,7 @@ consider revising 'pond' semantics - + @@ -121362,14 +121203,14 @@ consider revising 'pond' semantics GO:0015171 amino acid transmembrane transporter activity - + - + GO_REF:0000090 @@ -165561,14 +165402,12 @@ consider revising 'pond' semantics physiological response to stimulus biological_process GO:0050896 - - Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus @@ -170868,7 +170707,6 @@ consider revising 'pond' semantics Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. biological_process GO:0051716 - Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stimulus @@ -207044,7 +206882,7 @@ consider revising 'pond' semantics - + @@ -207059,14 +206897,14 @@ consider revising 'pond' semantics GO:1901505 carbohydrate derivative transmembrane transporter activity - + - + GO_REF:0000090 @@ -256836,17 +256674,8 @@ consider revising 'pond' semantics measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot + measurement unit label @@ -256857,50 +256686,21 @@ of this, different, term. objective specification - In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." - 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - goal specification - OBI Plan and Planned Process/Roles Branch - OBI_0000217 + objective specification objective specification - - - - - Pour the contents of flask 1 into flask 2 - - A directive information entity that describes an action the bearer will take. - Alan Ruttenberg - OBI Plan and Planned Process branch - action specification - - - - datum label - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - + datum label @@ -256911,54 +256711,14 @@ of this, different, term. software - Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. - see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI + software - - - - - - - - - - - - - - - - - - - - - - information carrier - In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. - - A quality of an information bearer that imparts the information content - 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. - 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. - PERSON: Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - information carrier - - - - @@ -256983,6 +256743,7 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data + data item @@ -256997,7 +256758,7 @@ JAR: A data item is an approximately justified approximately true approximate be - + @@ -257011,17 +256772,10 @@ JAR: A data item is an approximately justified approximately true approximate be information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - A generically dependent continuant that is about some thing. An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set. - 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. James Malone - PERSON: Chris Stoeckert - OBI_0000142 + information http://www.ebi.ac.uk/efo/EFO_0001435 @@ -257041,33 +256795,16 @@ Previous. An information content entity is a non-realizable information entity t - + - - - - 1 - - - - - - 1 - - - 10 feet. 3 ml. - + scalar measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form - Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot + scalar measurement datum @@ -257077,20 +256814,9 @@ this case we explicitly refer to the singular form - - - - - - - + directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters + IAO:0000033 directive information entity directive information entity @@ -257103,13 +256829,8 @@ this case we explicitly refer to the singular form dot plot - Dot plot of SSC-H and FSC-H. - A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000123 - group:OBI + dot plot @@ -257118,15 +256839,10 @@ this case we explicitly refer to the singular form - + graph - A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - PERSON: Lawrence Hunter - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000240 - group:OBI + graph @@ -257137,13 +256853,8 @@ this case we explicitly refer to the singular form algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) + algorithm @@ -257175,43 +256886,20 @@ this case we explicitly refer to the singular form PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 + curation status specification - - - - - source code module - The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. - - A source code module is a directive information entity that specifies, using a programming language, some algorithm. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000039 - group:OBI - source code module - - - - data format specification - A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes -information. Example: The ISO document specifying what encompasses an -XML document; The instructions in a XSD file" - PERSON: Alan Ruttenberg - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000187 + data format specification @@ -257222,15 +256910,8 @@ XML document; The instructions in a XSD file" data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI + data set @@ -257241,13 +256922,8 @@ XML document; The instructions in a XSD file" image - An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - person:Alan Ruttenberg - person:Allyson - person:Chris Stoeckert - OBI_0000030 - group:OBI + image @@ -257275,31 +256951,11 @@ XML document; The instructions in a XSD file" - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2014-03-31: A plan specification can have other parts, such as conditional specifications. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - OBI Plan and Planned Process branch - OBI_0000344 + IAO:0000104 - 2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them plan specification plan specification @@ -257310,12 +256966,6 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. @@ -257330,61 +256980,14 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - material information bearer - A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. - a brain - a hard drive - - A material entity in which a concretization of an information content entity inheres. - GROUP: IAO - material information bearer - - - - histogram - A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI + histogram @@ -257395,14 +256998,10 @@ distribution in terms of occurrence frequencies of different event classes. heatmap - A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI + heatmap @@ -257413,16 +257012,10 @@ two-dimensional map. dendrogram - Dendrograms are often used in computational biology to -illustrate the clustering of genes. - A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Dendrogram + dendrogram @@ -257433,14 +257026,8 @@ clustering algorithm. scatter plot - Comparison of gene expression values in two samples can be displayed in a scatter plot - A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - scattergraph - WEB: http://en.wikipedia.org/wiki/Scatterplot + scatter plot @@ -257489,38 +257076,20 @@ clustering algorithm. figure - Any picture, diagram or table - An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - PERSON: Lawrence Hunter + figure - - - - - diagram - A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. - - A figure that expresses one or more propositions - PERSON: Lawrence Hunter - diagram - - - - document - A journal article, patent application, laboratory notebook, or a book - A collection of information content entities intended to be understood together as a whole - PERSON: Lawrence Hunter + document @@ -257530,21 +257099,9 @@ clustering algorithm. - - - - - - - - - - - - - + length measurement datum A scalar measurement datum that is the result of measurement of length quality - Alan Ruttenberg + length measurement datum @@ -257689,8 +257246,6 @@ clustering algorithm. GC_ID:1 - PMID:30365038 - PMID:32761142 ncbi_taxonomy all NCBITaxon:1 @@ -257711,37 +257266,6 @@ clustering algorithm. - - - - - - GC_ID:1 - hamsters - ncbi_taxonomy - Cricetinae - - - - - hamsters - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Mesocricetus - - - - @@ -257965,60 +257489,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Obtectomera - - - - - - - - - - NCBITaxon:1537974 - GC_ID:1 - ncbi_taxonomy - Allolobophorinae - Lumbricinae - - - - - Allolobophorinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Lumbricus terrestris complex - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Lumbricus rubellus complex - - - - @@ -258079,75 +257549,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Sarsostraca - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Phyllopoda - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Anomopoda - - - - - - - - - NCBITaxon:6795 - GC_ID:1 - ncbi_taxonomy - Eubrachyura - - - - - - - - - NCBITaxon:29963 - NCBITaxon:6773 - NCBITaxon:6803 - GC_ID:1 - ncbi_taxonomy - Brachyrhyncha - Heterotremata - - - - - Brachyrhyncha - - - - - @@ -258617,32 +258018,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:25249442 - ncbi_taxonomy - Mesangiospermae - - - - - - - - - - GC_ID:1 - PMID:26350789 - ncbi_taxonomy - Petrosaviidae - - - - @@ -258656,18 +258031,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Pinales - - - - @@ -258789,32 +258152,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Carangimorpha - Carangimorphariae - Carangaria - - - - - Carangimorpha - - - - - - Carangimorphariae - - - - - @@ -258848,59 +258185,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Galloanseri - ducks, geese, chickens, fowl, quail, currasows and allies - Galloanserae - - - - - Galloanseri - - - - - - ducks, geese, chickens, fowl, quail, currasows and allies - - - - - - - - - - - NCBITaxon:29008 - GC_ID:1 - ncbi_taxonomy - Eisenia fetida andrei - Eiseniella andrei - Eisenia andrei - - - - - Eisenia fetida andrei - - - - - - Eiseniella andrei - - - - - @@ -259033,18 +258317,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Enchytraeida - - - - @@ -259344,30 +258616,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Multicrustacea - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Hirudinida - - - - @@ -259458,18 +258706,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Ochrophyta - - - - @@ -259659,121 +258895,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Bovinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Crassiclitellata - - - - - - - - - - GC_ID:1 - PMID:19761858 - ncbi_taxonomy - Conifers I - - - - - - - - - - GC_ID:1 - brown algae - ncbi_taxonomy - Chromophycota - Fucophyceae - Phaeophyta - algae - brown algae - Phaeophyceae - - - - - brown algae - - - - - - Chromophycota - - - - - - Fucophyceae - - - - - - Phaeophyta - - - - - - algae - - - - - - brown algae - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Oryzomys - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cancroidea - - - - @@ -259787,51 +258908,6 @@ clustering algorithm. - - - - - - GC_ID:1 - Ranoidea - ncbi_taxonomy - Ranoidea Rafinesque, 1814 - Ranoidea <superfamily> - - - - - Ranoidea - - - - - - Ranoidea Rafinesque, 1814 - - - - - - - - - - - GC_ID:1 - Anthophila - ncbi_taxonomy - Anthophila <bees> - - - - - Anthophila - - - - - @@ -259852,26 +258928,6 @@ clustering algorithm. - - - - - - NCBITaxon:30946 - GC_ID:1 - ncbi_taxonomy - Soleoidei - Pleuronectoidei - - - - - Soleoidei - - - - - @@ -260000,21 +259056,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:11214318 - PMID:11214319 - PMID:12878460 - ncbi_taxonomy - Laurasiatheria - - - - @@ -260078,18 +259119,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Cercopithecoidea - - - - @@ -260171,47 +259200,6 @@ clustering algorithm. - - - - - - NCBITaxon:3194 - GC_ID:1 - mosses - ncbi_taxonomy - Musci - bryophytes - mosses - Bryophyta - - - - - mosses - - - - - - Musci - - - - - - bryophytes - - - - - - mosses - - - - - @@ -260539,26 +259527,6 @@ clustering algorithm. - - - - - - NCBITaxon:1445965 - GC_ID:1 - ncbi_taxonomy - Coniferales - Pinidae - - - - - Coniferales - - - - - @@ -260602,25 +259570,6 @@ clustering algorithm. - - - - - - GC_ID:1 - pine family - ncbi_taxonomy - Pinaceae - - - - - pine family - - - - - @@ -260750,32 +259699,6 @@ clustering algorithm. - - - - - - GC_ID:1 - carnivores - ncbi_taxonomy - carnivores - Carnivora - - - - - carnivores - - - - - - carnivores - - - - - @@ -260796,46 +259719,6 @@ clustering algorithm. - - - - - - GC_ID:1 - heterokonts - ncbi_taxonomy - Chromophyta - Heterokonta - Straminipila - Stramenopiles - - - - - heterokonts - - - - - - Chromophyta - - - - - - Heterokonta - - - - - - Straminipila - - - - - @@ -260883,19 +259766,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:15371245 - ncbi_taxonomy - Cricetidae - - - - @@ -260924,18 +259794,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Felinae - - - - @@ -260998,39 +259856,6 @@ clustering algorithm. - - - - - - GC_ID:1 - bee - bees - ncbi_taxonomy - bees - Apoidea - - - - - bee - - - - - - bees - - - - - - bees - - - - - @@ -261044,75 +259869,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Suiformes - Suina - - - - - Suiformes - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Pecora - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ditrysia - - - - - - - - - - GC_ID:1 - butterflies - ncbi_taxonomy - butterflies - Papilionoidea - - - - - butterflies - - - - - - butterflies - - - - - @@ -261126,42 +259882,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Feliformia - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Caniformia - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Artemiidae - - - - @@ -261204,21 +259924,6 @@ clustering algorithm. - - - - - - NCBITaxon:4478 - NCBITaxon:4727 - GC_ID:1 - PMID:26350789 - ncbi_taxonomy - Poales - - - - @@ -261233,20 +259938,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:15019624 - PMID:15371245 - ncbi_taxonomy - Sigmodontinae - - - - @@ -261278,43 +259969,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Glossata - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Neolepidoptera - - - - - - - - - - NCBITaxon:37583 - GC_ID:1 - ncbi_taxonomy - Heteroneura - - - - @@ -261453,30 +260107,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Protacanthopterygii - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Clitellata - - - - @@ -261614,81 +260244,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:25249442 - monocots - monocotyledons - ncbi_taxonomy - Monocotyledoneae - monocots - Liliopsida - - - - - monocots - - - - - - monocotyledons - - - - - - Monocotyledoneae - - - - - - monocots - - - - - - - - - - - NCBITaxon:1661618 - GC_ID:1 - grass family - ncbi_taxonomy - Bambusaceae - Gramineae - Poaceae - - - - - grass family - - - - - - Bambusaceae - - - - - - Gramineae - - - - - @@ -261734,33 +260289,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:26350789 - ncbi_taxonomy - Commelinidae - Commeliniflorae - commelinids - - - - - Commelinidae - - - - - - Commeliniflorae - - - - - @@ -262086,25 +260614,6 @@ clustering algorithm. - - - - - - GC_ID:1 - trouts, salmons & chars - ncbi_taxonomy - Salmoninae - - - - - trouts, salmons & chars - - - - - @@ -262147,26 +260656,6 @@ clustering algorithm. - - - - - - NCBITaxon:6403 - GC_ID:1 - leeches - ncbi_taxonomy - Hirudinea - - - - - leeches - - - - - @@ -262193,25 +260682,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - algae - PX clade - - - - - algae - - - - - @@ -262233,25 +260703,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Coniferopsida - Pinopsida - - - - - Coniferopsida - - - - - @@ -262615,257 +261066,6 @@ clustering algorithm. - - - - - - GC_ID:1 - PMID:34811021 - Oligochaeta - ncbi_taxonomy - Oligochaeta <segmented worms> - - - - - Oligochaeta - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Enchytraeidae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Enchytraeus - - - - - - - - - - GC_ID:1 - earthworms - ncbi_taxonomy - Lumbricina - - - - - earthworms - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Lumbricidae - - - - - - - - - - GC_ID:1 - Eisenia - ncbi_taxonomy - Eisenia <segmented worms> - - - - - Eisenia - - - - - - - - - - - GC_ID:1 - brandling worm - common brandling worm - common dung-worm - red wiggler worm - redworm - tiger worm - ncbi_taxonomy - Eisenia foetida - Eiseniella fetida - Eisenia fetida - - - - - brandling worm - - - - - - common brandling worm - - - - - - common dung-worm - - - - - - red wiggler worm - - - - - - redworm - - - - - - tiger worm - - - - - - Eisenia foetida - - - - - - Eiseniella fetida - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Lumbricus - - - - - - - - - - NCBITaxon:2175058 - GC_ID:1 - common earthworm - ncbi_taxonomy - Lumbricus terrestris - - - - - common earthworm - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Hirudiniformes - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Hirudinidae - - - - - - - - - - GC_ID:1 - molluscs - mollusks - ncbi_taxonomy - molluscs - Mollusca - - - - - molluscs - - - - - - mollusks - - - - - - molluscs - - - - - @@ -262893,235 +261093,6 @@ clustering algorithm. - - - - - - GC_ID:1 - crustaceans - ncbi_taxonomy - crustaceans - Crustacea - - - - - crustaceans - - - - - - crustaceans - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Branchiopoda - - - - - - - - - - GC_ID:1 - fairy shrimps - ncbi_taxonomy - Anostraca - - - - - fairy shrimps - - - - - - - - - - - GC_ID:1 - brine shrimps - sea monkeys - ncbi_taxonomy - Artemia - - - - - brine shrimps - - - - - - sea monkeys - - - - - - - - - - - GC_ID:1 - water flea - water fleas - ncbi_taxonomy - Cladocera - - - - - water flea - - - - - - water fleas - - - - - - - - - - - NCBITaxon:77736 - GC_ID:1 - common water fleas - ncbi_taxonomy - Daphniopsis - Daphnia - - - - - common water fleas - - - - - - Daphniopsis - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Malacostraca - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Eucarida - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Decapoda - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Pleocyemata - - - - - - - - - - GC_ID:1 - short-tailed crabs - true crabs - ncbi_taxonomy - Brachyura - - - - - short-tailed crabs - - - - - - true crabs - - - - - - - - - - - GC_ID:1 - rock crabs - ncbi_taxonomy - Cancridae - - - - - rock crabs - - - - - @@ -263170,39 +261141,6 @@ clustering algorithm. - - - - - - GC_ID:1 - butterflies and moths - moths - ncbi_taxonomy - moths - Lepidoptera - - - - - butterflies and moths - - - - - - moths - - - - - - moths - - - - - @@ -263256,18 +261194,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Eumalacostraca - - - - @@ -263351,99 +261277,6 @@ clustering algorithm. - - - - - - NCBITaxon:27522 - NCBITaxon:27527 - NCBITaxon:27531 - GC_ID:1 - hymenopterans - ncbi_taxonomy - hymenopterans - Hymenoptera - - - - - hymenopterans - - - - - - hymenopterans - - - - - - - - - - - GC_ID:1 - wasps, ants & bees - ncbi_taxonomy - wasps, ants & bees - Apocrita - - - - - wasps, ants & bees - - - - - - wasps, ants & bees - - - - - - - - - - - GC_ID:1 - Aculeata - ncbi_taxonomy - Aculeata <wasps, ants & bees> - - - - - Aculeata - - - - - - - - - - - GC_ID:1 - bumble bees and honey bees - ncbi_taxonomy - Apidae - - - - - bumble bees and honey bees - - - - - @@ -263618,19 +261451,6 @@ clustering algorithm. - - - - - - NCBITaxon:77729 - GC_ID:1 - ncbi_taxonomy - Daphniidae - - - - @@ -264071,130 +261891,6 @@ clustering algorithm. - - - - - - GC_ID:1 - salmons and trouts - ncbi_taxonomy - Salmoniformes - - - - - salmons and trouts - - - - - - - - - - - GC_ID:1 - PMID:15062801 - salmonids - ncbi_taxonomy - Salmonidae - - - - - salmonids - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Parasalmo - Oncorhynchus - - - - - Parasalmo - - - - - - - - - - - NCBITaxon:62064 - NCBITaxon:82302 - GC_ID:1 - ncbi_taxonomy - Acantholingua - Salmothymus - Salmo - - - - - Acantholingua - - - - - - Salmothymus - - - - - - - - - - - GC_ID:1 - flatfishes - ncbi_taxonomy - Pleuronectiformes - - - - - flatfishes - - - - - - - - - - - GC_ID:1 - righteye flounders - ncbi_taxonomy - Pleuronectidae - - - - - righteye flounders - - - - - @@ -264401,57 +262097,6 @@ clustering algorithm. - - - - - - NCBITaxon:685149 - GC_ID:1 - riparian frogs - true frogs - ncbi_taxonomy - Ranidae - - - - - riparian frogs - - - - - - true frogs - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Neobatrachia - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Diplostraca - - - - @@ -264498,30 +262143,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ncbi_taxonomy - Artemia salina - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Amphiesmenoptera - - - - @@ -264683,44 +262304,6 @@ clustering algorithm. - - - - - - GC_ID:1 - ducks, geese and swans - ncbi_taxonomy - Anseriformes - - - - - ducks, geese and swans - - - - - - - - - - - GC_ID:1 - waterfowl - ncbi_taxonomy - Anatidae - - - - - waterfowl - - - - - @@ -264794,168 +262377,6 @@ clustering algorithm. - - - - - - GC_ID:1 - landfowls - ncbi_taxonomy - Galliformes - - - - - landfowls - - - - - - - - - - - NCBITaxon:9099 - GC_ID:1 - turkeys - ncbi_taxonomy - Phasianidae - - - - - turkeys - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Gallus - - - - - - - - - - GC_ID:1 - Gallus domesticus - bantam - chicken - chickens - ncbi_taxonomy - Gallus gallus domesticus - Phasianus gallus - Gallus gallus - - - - - Gallus domesticus - - - - - - bantam - - - - - - chicken - - - - - - chickens - - - - - - Gallus gallus domesticus - - - - - - Phasianus gallus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Phasianinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Enchytraeus crypticus - - - - - - - - - - GC_ID:1 - whales, hippos, ruminants, pigs, camels etc. - ncbi_taxonomy - Cetartiodactyla - even-toed ungulates - Artiodactyla - - - - - whales, hippos, ruminants, pigs, camels etc. - - - - - - Cetartiodactyla - - - - - - even-toed ungulates - - - - - @@ -265098,39 +262519,6 @@ clustering algorithm. - - - - - - GC_ID:1 - New World monkeys - monkey - monkeys - ncbi_taxonomy - Platyrrhini - - - - - New World monkeys - - - - - - monkey - - - - - - monkeys - - - - - @@ -265144,125 +262532,6 @@ clustering algorithm. - - - - - - GC_ID:1 - Old World monkeys - monkey - monkeys - ncbi_taxonomy - Cercopithecidae - - - - - Old World monkeys - - - - - - monkey - - - - - - monkeys - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cercopithecinae - - - - - - - - - - GC_ID:1 - macaque - macaques - ncbi_taxonomy - Macaca - - - - - macaque - - - - - - macaques - - - - - - - - - - - NCBITaxon:36502 - GC_ID:1 - Rhesus monkey - rhesus macaque - rhesus macaques - rhesus monkeys - ncbi_taxonomy - Cercopithecus mulatta - Macaca mulatta - - - - - Rhesus monkey - - - - - - rhesus macaque - - - - - - rhesus macaques - - - - - - rhesus monkeys - - - - - - Cercopithecus mulatta - - - - - @@ -265334,446 +262603,6 @@ clustering algorithm. - - - - - - GC_ID:1 - dog, coyote, wolf, fox - ncbi_taxonomy - Canidae - - - - - dog, coyote, wolf, fox - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Canis - - - - - - - - - - NCBITaxon:68731 - NCBITaxon:9609 - GC_ID:1 - ncbi_taxonomy - Fennecus - Vulpes - - - - - Fennecus - - - - - - - - - - - GC_ID:1 - cat family - ncbi_taxonomy - Felidae - - - - - cat family - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Felis - - - - - - - - - - NCBITaxon:36475 - GC_ID:1 - PMID:17600185 - PMID:8581300 - PMID:8603894 - cat - cats - domestic cat - ncbi_taxonomy - Felis domesticus - Felis silvestris catus - Felis catus - - - - - cat - - - - - - cats - - - - - - domestic cat - - - - - - Felis domesticus - - - - - - Felis silvestris catus - - - - - - - - - - - NCBITaxon:39423 - GC_ID:1 - boars - pigs - ncbi_taxonomy - Suidae - - - - - boars - - - - - - pigs - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Sus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ruminantia - - - - - - - - - - GC_ID:1 - deer - ncbi_taxonomy - Cervidae - - - - - deer - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Rangifer - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Odocoileinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Bovidae - - - - - - - - - - GC_ID:1 - oxen, cattle - ncbi_taxonomy - Bos - - - - - oxen, cattle - - - - - - - - - - - NCBITaxon:272461 - GC_ID:1 - bovine - cattle - cow - dairy cow - domestic cattle - domestic cow - ox - ncbi_taxonomy - Bos bovis - Bos primigenius taurus - Bos taurus - - - - - bovine - - - - - - cattle - - - - - - cow - - - - - - dairy cow - - - - - - domestic cattle - - - - - - domestic cow - - - - - - ox - - - - - - Bos bovis - - - - - - Bos primigenius taurus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ovis - - - - - - - - - - NCBITaxon:9936 - GC_ID:1 - domestic sheep - lambs - sheep - wild sheep - ncbi_taxonomy - Ovis ammon aries - Ovis orientalis aries - Ovis ovis - Ovis aries - - - - - domestic sheep - - - - - - lambs - - - - - - sheep - - - - - - wild sheep - - - - - - Ovis ammon aries - - - - - - Ovis orientalis aries - - - - - - Ovis ovis - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Caprinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - rabbits & hares - Lagomorpha - - - - - rabbits & hares - - - - - @@ -265812,35 +262641,23 @@ clustering algorithm. - + - + - - - - - - - - - - - - planned process - planned process + completely executed planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. @@ -265851,7 +262668,6 @@ objectives is a planned process. branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - CHMO:0001840 OBI:0000011 completely executed planned process @@ -265959,12 +262775,14 @@ objectives is a planned process. - processed material + processed material entity Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + A material entity processed by human activity with an intent to produce Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material + processed material entity @@ -266141,6 +262959,7 @@ for now. PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI + Should revisit if we can place outside of material entity - a collection of roles. organization @@ -266167,6 +262986,13 @@ for now. + plan + The plan of researcher X to perform an experiment according to a protocol. + + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. + AR, BP, JM, MC, PRS + branch derived plan @@ -266398,7 +263224,7 @@ for now. manufacturer role With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. - Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. + Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI manufacturer role @@ -266471,7 +263297,7 @@ for now. specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation - A planned process with the objective of collecting a specimen. + A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. @@ -266522,7 +263348,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. - A objective specification to obtain a material entity for potential use as an input during an investigation. + A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective @@ -266542,7 +263368,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ support vector machine - A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. + A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. James Malone Ryan Brinkman SVM @@ -266558,7 +263384,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ decision tree induction objective - A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. + A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. James Malone decision tree induction objective @@ -266597,7 +263423,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ GenePattern software - a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. + a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ @@ -266612,7 +263438,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ peak matching - Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold + Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold James Malone Ryan Brinkman PERSON: Ryan Brinkman @@ -266624,7 +263450,6 @@ http://sourceforge.net/p/obi/obi-terms/716/ - @@ -266686,7 +263511,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ statistical model validation Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia - A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. + A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation @@ -266722,7 +263547,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ manufacturer - A person or organization that has a manufacturer role. + A person or organization that has a manufacturer role. manufacturer @@ -266755,7 +263580,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. - is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person + is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role @@ -266779,7 +263604,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. - A specimen that has been intentionally physically modified. + A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. @@ -266795,7 +263620,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells.categorical label The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. - A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. + A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label @@ -266809,34 +263634,23 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - - - - - - - device + + obsolete_device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. PERSON: Helen Parkinson instrument - OBI development call 2012-12-17. + OBI development call 2012-12-17 + + CHMO:0000998 OBI:0000968 device + obsolete_device + true @@ -266850,11 +263664,11 @@ In the examples above, a reagent is an operational component of a device, but th - + dose An organism has been injected 1ml of vaccine - A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. + A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. dose @@ -266883,7 +263697,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -266891,7 +263705,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -266901,7 +263715,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) - A device which has a function to emit light. + A device which has a function to emit light. Person:Helen Parkinson OBI light emission device @@ -266912,6 +263726,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S + @@ -266922,6 +263737,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S X-ray source A device that is used to generate X-rays. + A device that is used to generate X-rays. PERSON: Erik Segerdell x-ray generator http://en.wikipedia.org/wiki/X-ray_generator @@ -266959,7 +263775,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". - An information content entity that is inferred from data. + An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group @@ -266974,7 +263790,7 @@ The following are NOT conclusions based on data: data themselves; results from p categorical value specification - A value specification that is specifies one category out of a fixed number of nominal categories + A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification @@ -266999,7 +263815,7 @@ The following are NOT conclusions based on data: data themselves; results from p scalar value specification - A value specification that consists of two parts: a numeral and a unit label + A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification @@ -267013,7 +263829,7 @@ The following are NOT conclusions based on data: data themselves; results from p value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. - An information content entity that specifies a value within a classification scheme or on a quantitative scale. + An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification @@ -267057,7 +263873,7 @@ The following are NOT conclusions based on data: data themselves; results from p G1:Well differentiated G4: Undifferentiated - A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -267072,7 +263888,7 @@ The following are NOT conclusions based on data: data themselves; results from p histologic grade according to the Fuhrman Nuclear Grading System - A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. Chris Stoeckert, Helena Ellis Histologic Grade (Fuhrman Nuclear Grading System) NCI BBRB, OBI @@ -267088,7 +263904,7 @@ The following are NOT conclusions based on data: data themselves; results from p histologic grade for ovarian tumor - A categorical value specification that is a histologic grade assigned to a ovarian tumor. + A categorical value specification that is a histologic grade assigned to a ovarian tumor. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -267103,7 +263919,7 @@ The following are NOT conclusions based on data: data themselves; results from p histologic grade for ovarian tumor according to a two-tier grading system - A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. + A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -267118,7 +263934,7 @@ The following are NOT conclusions based on data: data themselves; results from p histologic grade for ovarian tumor according to the World Health Organization - A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). + A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -267133,7 +263949,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic primary tumor stage for colon and rectum according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) NCI BBRB, OBI @@ -267149,7 +263965,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic primary tumor stage for lung according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread lung primary tumor (AJCC 7th Edition) NCI BBRB, OBI @@ -267165,7 +263981,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic primary tumor stage for kidney according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) NCI BBRB, OBI @@ -267181,7 +263997,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic primary tumor stage for ovary according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) NCI BBRB, OBI @@ -267197,7 +264013,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic lymph node stage for colon and rectum according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI @@ -267213,7 +264029,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic lymph node stage for lung according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI @@ -267229,7 +264045,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic lymph node stage for kidney according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) NCI BBRB, OBI @@ -267245,7 +264061,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic lymph node stage for ovary according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) NCI BBRB, OBI @@ -267261,7 +264077,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic distant metastases stage for colon according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: colon distant metastases (AJCC 7th Edition) NCI BBRB, OBI @@ -267277,7 +264093,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic distant metastases stage for lung according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: lung distant metastases (AJCC 7th Edition) NCI BBRB, OBI @@ -267293,7 +264109,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic distant metastases stage for kidney according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: kidney distant Metastases (AJCC 7th Edition) NCI BBRB, OBI @@ -267309,7 +264125,7 @@ The following are NOT conclusions based on data: data themselves; results from p pathologic distant metastases stage for ovary according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: ovarian distant metastases (AJCC 7th Edition) NCI BBRB, OBI @@ -267325,7 +264141,7 @@ The following are NOT conclusions based on data: data themselves; results from p clinical tumor stage group according to AJCC 7th edition - A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. + A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. Chris Stoeckert, Helena Ellis Clinical tumor stage group (AJCC 7th Edition) NCI BBRB, OBI @@ -267341,7 +264157,7 @@ The following are NOT conclusions based on data: data themselves; results from p International Federation of Gynecology and Obstetrics cervical cancer stage value specification - A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. + A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. Chris Stoeckert, Helena Ellis Clinical FIGO stage NCI BBRB, OBI @@ -267357,7 +264173,7 @@ The following are NOT conclusions based on data: data themselves; results from p International Federation of Gynecology and Obstetrics ovarian cancer stage value specification - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. Chris Stoeckert, Helena Ellis Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) NCI BBRB, OBI @@ -267373,7 +264189,7 @@ The following are NOT conclusions based on data: data themselves; results from p performance status value specification - A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). + A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Chris Stoeckert, Helena Ellis Performance Status Scale https://en.wikipedia.org/wiki/Performance_status @@ -267389,7 +264205,7 @@ The following are NOT conclusions based on data: data themselves; results from p Eastern Cooperative Oncology Group score value specification - A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. + A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. Chris Stoeckert, Helena Ellis ECOG score NCI BBRB, OBI @@ -267405,7 +264221,7 @@ The following are NOT conclusions based on data: data themselves; results from p Karnofsky score vaue specification - A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. + A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Chris Stoeckert, Helena Ellis Karnofsky Score NCI BBRB, OBI @@ -267421,7 +264237,7 @@ The following are NOT conclusions based on data: data themselves; results from p altitude measurement datum - A length measurement datum between a point at sea or ground level and some point above it. + A length measurement datum between a point at sea or ground level and some point above it. Chris Stoeckert Adapted from https://www.merriam-webster.com/dictionary/altitude altitude measurement datum @@ -267457,7 +264273,7 @@ The following are NOT conclusions based on data: data themselves; results from p material supplier - A person or organization that provides material supplies to other people or organizations. + A person or organization that provides material supplies to other people or organizations. Rebecca Jackson https://github.com/obi-ontology/obi/issues/1289 material supplier @@ -267558,10 +264374,10 @@ This issue is outside the scope of OBI. - + - + @@ -267604,7 +264420,6 @@ This issue is outside the scope of OBI. data analysis data processing Branch editors - data transformation @@ -267617,7 +264432,7 @@ This issue is outside the scope of OBI. leave one out cross validation method The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 - is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data + is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 Person:Helen Parkinson leave one out cross validation method @@ -267628,7 +264443,6 @@ This issue is outside the scope of OBI. - @@ -267660,7 +264474,6 @@ This issue is outside the scope of OBI. - @@ -267689,7 +264502,6 @@ This issue is outside the scope of OBI. - @@ -267973,7 +264785,7 @@ class labels for these objects. The resulting predictor can be used to attach cl clustered data visualization - A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. + A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. James Malone clustered data visualization @@ -268014,7 +264826,7 @@ class labels for these objects. The resulting predictor can be used to attach cl light source - A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. + A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. Elizabeth M. Goralczyk John Quinn Olga Tchuvatkina @@ -268059,7 +264871,9 @@ class labels for these objects. The resulting predictor can be used to attach cl + composition A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. + PATO:0002015 composed of compositionality @@ -268198,18 +265012,6 @@ class labels for these objects. The resulting predictor can be used to attach cl - - - - - length - A 1-D extent quality which is equal to the distance between two points. - - length - - - - @@ -268257,7 +265059,9 @@ class labels for these objects. The resulting predictor can be used to attach cl + structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. + PATO:0001452 conformation relational structural quality @@ -272408,7 +269212,7 @@ Classes for population already exist in IDO ('organism population', I - + An anatomical entity that is or was part of a plant. rwalls 2010-11-15T11:41:38Z @@ -272420,14 +269224,14 @@ Classes for population already exist in IDO ('organism population', I Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. plant anatomical entity - + - + cjm @@ -277159,9 +273963,9 @@ Classes for population already exist in IDO ('organism population', I - + The amount of ionizing radiation to which a member of the population on Earth is exposed from natural sources, such as terrestrial radiation from naturally-occurring radionuclides in the soil, cosmic radiation originating in outer space, and naturally-occurring ra - background ionizing radiation + ionizing background radiation @@ -279560,21 +276364,13 @@ Classes for population already exist in IDO ('organism population', I - - + - - - - 1 - - - A process involving the emission of energy from an atomic nucleus resulting in change in the character of the nucleus radioactive decay @@ -279673,7 +276469,16 @@ Classes for population already exist in IDO ('organism population', I - Atomic nuclei, with atomic number 2 or greater and kinetic energy imparted by natural or artificial means + A type of ionizing radiation consisting of charged particles that are relatively massive compared to other types of radiation, such as alpha, beta, and gamma radiation. Heavy ion radiation is composed of atomic nuclei that have been stripped of their electrons, resulting in positively charged particles. + Heavy ion radiation has several notable characteristics and contexts: + +High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. + +Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation. + +Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. + +In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. heavy ion radiation @@ -280749,7 +277554,7 @@ Classes for population already exist in IDO ('organism population', I https://orcid.org/0000-0001-9227-0670 ambient radiation background radiation - anthropogenic background radiation + anthropogenic ionizing background radiation @@ -280761,7 +277566,7 @@ Classes for population already exist in IDO ('organism population', I Radiation originating in the terrestrial or extra-terrestrial environment. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 - natural background radiation + natural ionizing background radiation @@ -280825,6 +277630,81 @@ Classes for population already exist in IDO ('organism population', I + + + + + thermal neutron + A neutron that has (by collision with other particles) reached an energy state equal to that of its surroundings, typically on the order of 0.025 eV. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + https://www.nrc.gov/reading-rm/basic-ref/glossary/neutron-thermal.html + thermal neutron + + + + + + + + + epithermal neutron + a neutron with energy greater than a thermal neutron, but less than a fast neutron. The approximate energy range is 0.025-0.4 eV. + http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670 + https://ns.ph.liv.ac.uk/~ajb/radiometrics/glossary/epithermal_neutron.html + epithermal neutron + + + + + + + + + background radiation + The ambient radiation in a defined environment emanating from natural or anthropogenic sources. + For uses involving experimentation or radiation therapy, use "anthropogenic background radiation" instead. Use this concept to indicate source is a mixture of anthropogenic and naturally occurring (ambient), or unknown or if the discrimination is not sought. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + background radiation + + + + + + + + + non-ionizing background radiation + Background radiation that does not result in ionization of target material + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + non-ionizing background radiation + + + + + + + + + anthropogenic non-ionizing background radiation + Non-ionizing background radiation that is the result of a human planned process. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + anthropogenic non-ionizing background radiation + + + + + + + + + natural non-ionizing background radiation + Non-ionizing background radiation that is not the result of a human planned process. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + natural non-ionizing background radiation + + + + @@ -281211,9 +278091,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -281257,34 +278137,34 @@ Classes for population already exist in IDO ('organism population', I islet of Langerhans http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png - + - + - + - + PMID:16417468 - + PMID:16417468 - + PMID:16417468 @@ -281592,7 +278472,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -281638,7 +278518,7 @@ Classes for population already exist in IDO ('organism population', I sympathetic nervous system http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png - + @@ -281651,7 +278531,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA MA ZFA-modified-from-isa @@ -281851,7 +278731,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -281864,9 +278744,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -281914,19 +278794,19 @@ Classes for population already exist in IDO ('organism population', I endocrine pancreas - + - + - + - + @@ -281939,7 +278819,7 @@ Classes for population already exist in IDO ('organism population', I - + AAO FMA XAO @@ -281947,19 +278827,19 @@ Classes for population already exist in IDO ('organism population', I - + GO - + GO - + GO @@ -282170,7 +279050,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -282198,14 +279078,14 @@ Classes for population already exist in IDO ('organism population', I compound eye https://github.com/obophenotype/uberon/issues/457 - + - + PMID:21062451 @@ -282287,7 +279167,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -282328,14 +279208,14 @@ Classes for population already exist in IDO ('organism population', I camera-type eye - + - + definitional @@ -282773,7 +279653,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a respiratory airway. EMAPA:35877 FMA:265157 @@ -282796,14 +279676,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0000031 lamina propria of trachea - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -283108,8 +279988,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -283160,11 +280040,11 @@ Classes for population already exist in IDO ('organism population', I tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -283177,13 +280057,13 @@ Classes for population already exist in IDO ('organism population', I - + OG - + AEO @@ -283253,8 +280133,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A biological tissue mass, most commonly a mass of nerve cell bodies. TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. @@ -283306,11 +280186,11 @@ Classes for population already exist in IDO ('organism population', I ganglion - + - + @@ -283323,13 +280203,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + Bgee:AN @@ -283968,7 +280848,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -283989,14 +280869,14 @@ Classes for population already exist in IDO ('organism population', I respiratory tract - + - + NCBIBook:NBK10107 @@ -284653,7 +281533,7 @@ Classes for population already exist in IDO ('organism population', I - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) @@ -284679,7 +281559,7 @@ Classes for population already exist in IDO ('organism population', I external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -284692,7 +281572,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -284805,7 +281685,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -284848,14 +281728,14 @@ Classes for population already exist in IDO ('organism population', I morula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png - + - + EHDAA2 @@ -285008,8 +281888,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A mass of cells that develop into the body of the embryo and some extraembryonic tissues. A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG] A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG] @@ -285037,24 +281917,24 @@ Classes for population already exist in IDO ('organism population', I inner cell mass https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg - + - + - + Wikipedia - + Wikipedia @@ -285122,7 +282002,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -285155,14 +282035,14 @@ Classes for population already exist in IDO ('organism population', I trophoblast https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg - + - + MP-def PMID:19829370 @@ -285229,7 +282109,7 @@ Classes for population already exist in IDO ('organism population', I - + A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc. embryonic disc embryonic shield @@ -285249,14 +282129,14 @@ Classes for population already exist in IDO ('organism population', I bilaminar disc http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png - + - + Wikipedia @@ -285357,7 +282237,7 @@ Classes for population already exist in IDO ('organism population', I - + Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]. 2009-07-30T05:19:13Z @@ -285368,14 +282248,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0000094 membrane organ - + - + FMA-def @@ -285398,7 +282278,7 @@ Classes for population already exist in IDO ('organism population', I - + Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]. A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]. ZFA treats this as a subtype of NC. @@ -285415,14 +282295,14 @@ Classes for population already exist in IDO ('organism population', I cardiac neural crest - + - + Wikipedia @@ -285889,7 +282769,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -285925,14 +282805,14 @@ Classes for population already exist in IDO ('organism population', I gastrula stage - + - + BILS @@ -286346,7 +283226,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -286374,7 +283254,7 @@ Classes for population already exist in IDO ('organism population', I lung bud http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png - + @@ -286387,7 +283267,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -286499,7 +283379,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -286525,14 +283405,14 @@ Classes for population already exist in IDO ('organism population', I neural nucleus - + - + we limit this structure by definition to chordate and vertebrate nervous systems @@ -286743,7 +283623,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -286782,14 +283662,14 @@ Classes for population already exist in IDO ('organism population', I anal canal https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png - + - + Wikipathways:WP2062 @@ -286972,8 +283852,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -287006,24 +283886,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -287106,8 +283986,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -287126,24 +284006,24 @@ Classes for population already exist in IDO ('organism population', I embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -287651,7 +284531,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -287697,14 +284577,14 @@ Classes for population already exist in IDO ('organism population', I pair of lungs - + - + FMA-abduced @@ -287880,15 +284760,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. @@ -287932,34 +284812,34 @@ Classes for population already exist in IDO ('organism population', I blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -288075,7 +284955,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -288110,7 +284990,7 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png https://upload.wikimedia.org/wikipedia/commons/5/5b/Frontal_bone.png - + @@ -288123,7 +285003,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -288231,7 +285111,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -288264,14 +285144,14 @@ Classes for population already exist in IDO ('organism population', I atlanto-occipital joint http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png - + - + FMA-abduced-lr @@ -288635,7 +285515,7 @@ Classes for population already exist in IDO ('organism population', I - + The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. BTO:0000503 EMAPA:27181 @@ -288646,7 +285526,7 @@ Classes for population already exist in IDO ('organism population', I gastric gland - + @@ -288659,7 +285539,7 @@ Classes for population already exist in IDO ('organism population', I - + ISBN:0073040584 @@ -289612,7 +286492,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -289639,7 +286519,7 @@ Classes for population already exist in IDO ('organism population', I syncytiotrophoblast http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png - + @@ -289652,7 +286532,7 @@ Classes for population already exist in IDO ('organism population', I - + EMAPA @@ -290772,7 +287652,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -290814,14 +287694,14 @@ Classes for population already exist in IDO ('organism population', I organism substance - + - + this relationship may be too strong and may be weakened in future @@ -291908,7 +288788,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -291952,14 +288832,14 @@ Classes for population already exist in IDO ('organism population', I epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -292560,7 +289440,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -292597,14 +289477,14 @@ Classes for population already exist in IDO ('organism population', I abdomen - + - + MA @@ -292867,7 +289747,7 @@ Classes for population already exist in IDO ('organism population', I - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] @@ -292905,14 +289785,14 @@ Classes for population already exist in IDO ('organism population', I ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -292971,7 +289851,7 @@ Classes for population already exist in IDO ('organism population', I - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal @@ -293008,14 +289888,14 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -293076,7 +289956,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293127,7 +290007,7 @@ Classes for population already exist in IDO ('organism population', I mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + @@ -293140,7 +290020,7 @@ Classes for population already exist in IDO ('organism population', I - + Bgee:AN @@ -293352,7 +290232,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293402,7 +290282,7 @@ Classes for population already exist in IDO ('organism population', I proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -293415,7 +290295,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -293488,7 +290368,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293529,7 +290409,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293609,11 +290489,11 @@ Classes for population already exist in IDO ('organism population', I stomach https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg - + - + @@ -293632,14 +290512,14 @@ Classes for population already exist in IDO ('organism population', I - + absent in lampreys and hagfishes ISBN:0073040584 - + ISBN:0486692132 @@ -293727,7 +290607,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293776,7 +290656,7 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg - + @@ -293789,7 +290669,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -293869,7 +290749,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -293978,14 +290858,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -294181,7 +291061,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -294206,7 +291086,7 @@ Classes for population already exist in IDO ('organism population', I - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion @@ -294270,11 +291150,11 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb - + - + @@ -294287,13 +291167,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + Bgee:AN @@ -294546,9 +291426,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -294573,7 +291453,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -294629,44 +291509,44 @@ Classes for population already exist in IDO ('organism population', I cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + - + MA - + MA - + FMA-isa - + definitional @@ -294856,9 +291736,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -294869,7 +291749,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -294926,44 +291806,44 @@ Classes for population already exist in IDO ('organism population', I retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -295037,8 +291917,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -295074,24 +291954,24 @@ Classes for population already exist in IDO ('organism population', I eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -295262,7 +292142,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -295276,7 +292156,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -295343,14 +292223,14 @@ Classes for population already exist in IDO ('organism population', I pleura http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png - + - + https://github.com/obophenotype/uberon/issues/86 @@ -295525,7 +292405,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -295594,14 +292474,14 @@ Classes for population already exist in IDO ('organism population', I pons http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png - + - + neuronames @@ -297403,7 +294283,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -297470,14 +294350,14 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -297581,7 +294461,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -297636,7 +294516,7 @@ Classes for population already exist in IDO ('organism population', I central nervous system - + @@ -297650,7 +294530,7 @@ Classes for population already exist in IDO ('organism population', I - + Bgee:AN @@ -297877,7 +294757,7 @@ Classes for population already exist in IDO ('organism population', I - + A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. AEO:0000201 EHDAA2:0003200 @@ -297892,14 +294772,14 @@ Classes for population already exist in IDO ('organism population', I sensory nerve - + - + AEO @@ -298056,8 +294936,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]. consider splitting class One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG] @@ -298088,11 +294968,11 @@ Classes for population already exist in IDO ('organism population', I yolk sac http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png - + - + @@ -298111,13 +294991,13 @@ Classes for population already exist in IDO ('organism population', I - + ISBN:0073040584 - + ISBN:0073040584 @@ -298277,7 +295157,7 @@ Classes for population already exist in IDO ('organism population', I - + A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] @@ -298319,14 +295199,14 @@ Classes for population already exist in IDO ('organism population', I Consider generalizing to deuterostome pharynx chordate pharynx - + - + EHDAA2 @@ -298629,7 +295509,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -298666,14 +295546,14 @@ Classes for population already exist in IDO ('organism population', I hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -298929,15 +295809,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + @@ -298991,15 +295871,15 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb - + - + - + @@ -299013,19 +295893,19 @@ Classes for population already exist in IDO ('organism population', I - + MA - + EHDAA2 - + ISBN:0073040584 @@ -299133,7 +296013,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -299180,7 +296060,7 @@ Classes for population already exist in IDO ('organism population', I ventral pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png - + @@ -299193,7 +296073,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -299278,7 +296158,7 @@ Classes for population already exist in IDO ('organism population', I - + A zone of skin that is part of a back [Automatically generated definition]. EMAPA:36392 FMA:10462 @@ -299295,7 +296175,7 @@ Classes for population already exist in IDO ('organism population', I EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of back - + @@ -299308,7 +296188,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -299342,9 +296222,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]. not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO @@ -299377,15 +296257,15 @@ Classes for population already exist in IDO ('organism population', I https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722 http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif - + - + - + @@ -299398,19 +296278,19 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + EHDAA2 - + FMA @@ -299721,14 +296601,14 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -299769,11 +296649,11 @@ Classes for population already exist in IDO ('organism population', I pericardial cavity - + - + @@ -299786,13 +296666,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + Wikipedia @@ -299865,7 +296745,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -299897,14 +296777,14 @@ Classes for population already exist in IDO ('organism population', I endocardium of ventricle - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -300042,7 +296922,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -300070,14 +296950,14 @@ Classes for population already exist in IDO ('organism population', I myocardium of ventricle - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -300521,7 +297401,7 @@ Classes for population already exist in IDO ('organism population', I - + The second vertebral bone in the vertebral column. Vertebra that is posteriorly adjacent to vertebra 1.[TAO] @@ -300557,14 +297437,14 @@ Classes for population already exist in IDO ('organism population', I vertebral bone 2 - + - + FMA @@ -300865,7 +297745,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -300876,7 +297756,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -300922,24 +297802,24 @@ Classes for population already exist in IDO ('organism population', I diaphragm - + - + - + PMID:23586979 - + definitional @@ -301239,7 +298119,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -301320,14 +298200,14 @@ Classes for population already exist in IDO ('organism population', I vertebral column - + - + cjm @@ -302013,7 +298893,7 @@ Classes for population already exist in IDO ('organism population', I - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -302038,14 +298918,14 @@ Classes for population already exist in IDO ('organism population', I mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -302160,7 +299040,7 @@ Classes for population already exist in IDO ('organism population', I - + In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002783 @@ -302183,14 +299063,14 @@ Classes for population already exist in IDO ('organism population', I superior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png - + - + Wikipedia:Vitelline_vein @@ -302249,7 +299129,7 @@ Classes for population already exist in IDO ('organism population', I - + Vein that carries blood away from the liver[ZFA]. todo - add developmental relationships for other taxa @@ -302280,14 +299160,14 @@ Classes for population already exist in IDO ('organism population', I hepatic vein http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png - + - + FMA-abduced-lr @@ -302512,7 +299392,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -302548,7 +299428,7 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png - + @@ -302561,7 +299441,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -302609,7 +299489,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -302664,7 +299544,7 @@ Classes for population already exist in IDO ('organism population', I colon - + @@ -302678,7 +299558,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -302744,7 +299624,7 @@ Classes for population already exist in IDO ('organism population', I - + The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. BTO:0000645 @@ -302776,7 +299656,7 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb - + @@ -302789,7 +299669,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia @@ -302895,7 +299775,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -302949,7 +299829,7 @@ Classes for population already exist in IDO ('organism population', I pyloric antrum http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg - + @@ -302962,7 +299842,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia @@ -303467,7 +300347,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -303484,7 +300364,7 @@ Classes for population already exist in IDO ('organism population', I portal lobule - + @@ -303497,7 +300377,7 @@ Classes for population already exist in IDO ('organism population', I - + MA MP @@ -303521,7 +300401,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -303547,14 +300427,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0001172 hepatic acinus - + - + cjm @@ -303790,10 +300670,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + @@ -303822,19 +300702,19 @@ Classes for population already exist in IDO ('organism population', I common hepatic duct http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg - + - + - + - + @@ -303847,25 +300727,25 @@ Classes for population already exist in IDO ('organism population', I - + MA - + Wikipedia - + Wikipedia - + definitional @@ -304129,7 +301009,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -304171,14 +301051,14 @@ Classes for population already exist in IDO ('organism population', I peritoneal cavity - + - + Wikipedia @@ -305820,8 +302700,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]. currently defined as equivalent to any submucosal gland in the duodenum. Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds @@ -305847,11 +302727,11 @@ Classes for population already exist in IDO ('organism population', I duodenal gland - + - + @@ -305864,13 +302744,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA, modified - + unclear for Aves ISBN:9780521617147 @@ -305927,7 +302807,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -305973,7 +302853,7 @@ Classes for population already exist in IDO ('organism population', I intestinal villus http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg - + @@ -305986,7 +302866,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -306099,7 +302979,7 @@ Classes for population already exist in IDO ('organism population', I - + A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002782 @@ -306123,14 +303003,14 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + FMA/obol @@ -306819,7 +303699,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -306851,7 +303731,7 @@ Classes for population already exist in IDO ('organism population', I interlobular bile duct - + @@ -306865,7 +303745,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA MA MP @@ -307007,7 +303887,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -307039,14 +303919,14 @@ Classes for population already exist in IDO ('organism population', I pancreatic acinus - + - + FMA @@ -307096,9 +303976,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]. Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] @@ -307144,34 +304024,34 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pancreas.glb https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png - + - + - + - + PMID:16417468 - + Wikipedia - + Wikipedia @@ -307236,7 +304116,7 @@ Classes for population already exist in IDO ('organism population', I - + A trabecula that is part of a spleen. EMAPA:35808 @@ -307254,14 +304134,14 @@ Classes for population already exist in IDO ('organism population', I trabecula of spleen - + - + FMA @@ -307847,7 +304727,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -307877,14 +304757,14 @@ Classes for population already exist in IDO ('organism population', I liver parenchyma - + - + XAO @@ -307953,7 +304833,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -308003,14 +304883,14 @@ Classes for population already exist in IDO ('organism population', I hepatic sinusoid - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -308075,8 +304955,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -308119,11 +304999,11 @@ Classes for population already exist in IDO ('organism population', I intralobular bile duct - + - + @@ -308136,13 +305016,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + FMA @@ -308203,7 +305083,7 @@ Classes for population already exist in IDO ('organism population', I - + Muscle (organ) which is a part of the pelvis. Examples: levator ani,. @@ -308221,7 +305101,7 @@ Classes for population already exist in IDO ('organism population', I muscle of pelvis - + @@ -308233,7 +305113,7 @@ Classes for population already exist in IDO ('organism population', I - + FMAdef @@ -308286,7 +305166,7 @@ Classes for population already exist in IDO ('organism population', I - + The anus and surrounding regions. Encompasses both internal and external regions, where present. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EFO:0000847 @@ -308312,14 +305192,14 @@ Classes for population already exist in IDO ('organism population', I https://github.com/obophenotype/uberon/issues/507 http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png - + - + cjm @@ -309178,7 +306058,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -309190,7 +306070,7 @@ Classes for population already exist in IDO ('organism population', I - + Skeletal element that is composed of bone tissue. @@ -309240,14 +306120,14 @@ Classes for population already exist in IDO ('organism population', I bone element - + - + VSAO-modified @@ -309446,7 +306326,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -309490,14 +306370,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + EHDAA2 @@ -309552,7 +306432,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. UBERON:0003271 @@ -309574,14 +306454,14 @@ Classes for population already exist in IDO ('organism population', I muscle of pelvic girdle - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -309651,7 +306531,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -309699,14 +306579,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + left arch 4 in human embryology.ch @@ -309770,7 +306650,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -309806,7 +306686,7 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + @@ -309819,7 +306699,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia @@ -309958,7 +306838,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -310007,14 +306887,14 @@ Classes for population already exist in IDO ('organism population', I abdominal aorta http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png - + - + FMA @@ -310184,7 +307064,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -310222,7 +307102,7 @@ Classes for population already exist in IDO ('organism population', I common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg - + @@ -310235,7 +307115,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia @@ -310307,8 +307187,8 @@ Classes for population already exist in IDO ('organism population', I - - + + One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta. Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO) @@ -310346,24 +307226,24 @@ Classes for population already exist in IDO ('organism population', I subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg - + - + - + EHDAA2 - + EHDAA2 @@ -310547,7 +307427,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -310602,14 +307482,14 @@ Classes for population already exist in IDO ('organism population', I digestive tract - + - + NCBIBook:NBK10107 @@ -311023,7 +307903,7 @@ Classes for population already exist in IDO ('organism population', I - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -311046,7 +307926,7 @@ Classes for population already exist in IDO ('organism population', I ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -311065,7 +307945,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -311183,10 +308063,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + A sphincter muscle that is part of the iris. In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted] WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure @@ -311221,19 +308101,19 @@ Classes for population already exist in IDO ('organism population', I sphincter pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png - + - + - + - + @@ -311246,27 +308126,27 @@ Classes for population already exist in IDO ('organism population', I - + ISBN:0781772214 - + encircles iris dbpedia - + encircles iris dbpedia - + dbpedia @@ -311373,10 +308253,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted]. It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina @@ -311413,19 +308293,19 @@ Classes for population already exist in IDO ('organism population', I dilatator pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png - + - + - + - + @@ -311438,27 +308318,27 @@ Classes for population already exist in IDO ('organism population', I - + ISBN:0781772214 - + outer margins of iris dbpedia - + inner margins of iris dbpedia - + dbpedia @@ -312140,10 +309020,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + The first major branch of the abdominal aorta. EHDAA2:0004519 @@ -312175,44 +309055,44 @@ Classes for population already exist in IDO ('organism population', I celiac artery http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png - + - + - + - + - + ISBN:0073040584 - + ISBN:0073040584 - + ISBN:0073040584 - + ISBN:0073040584 @@ -312333,7 +309213,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -312395,14 +309275,14 @@ Classes for population already exist in IDO ('organism population', I trigeminal nerve https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png - + - + Wikipedia @@ -312669,7 +309549,7 @@ Classes for population already exist in IDO ('organism population', I - + The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] @@ -312693,14 +309573,14 @@ Classes for population already exist in IDO ('organism population', I facial vein http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png - + - + FMA @@ -312776,7 +309656,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -312837,7 +309717,7 @@ Classes for population already exist in IDO ('organism population', I trigeminal ganglion http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png - + @@ -312850,7 +309730,7 @@ Classes for population already exist in IDO ('organism population', I - + Bgee:AN @@ -312974,11 +309854,11 @@ Classes for population already exist in IDO ('organism population', I - - - - - + + + + + @@ -313009,23 +309889,23 @@ Classes for population already exist in IDO ('organism population', I occipital bone http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png - + - + - + - + - + @@ -313038,32 +309918,32 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + basi paired exo and supra occipital bones MA-modified - + interparietal (postparietal) - + WP - + PMID:11523816 @@ -313125,10 +310005,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended. part of viscerocranium (facial skeleton) in FMA @@ -313157,19 +310037,19 @@ Classes for population already exist in IDO ('organism population', I sphenoid bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg - + - + - + - + @@ -313182,25 +310062,25 @@ Classes for population already exist in IDO ('organism population', I - + orbito pre and basi sphenoid - + pterygoid process - + alisphenoid - + cjm @@ -313269,7 +310149,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -313305,7 +310185,7 @@ Classes for population already exist in IDO ('organism population', I ethmoid bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg - + @@ -313318,7 +310198,7 @@ Classes for population already exist in IDO ('organism population', I - + definitional @@ -313401,7 +310281,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -313434,14 +310314,14 @@ Classes for population already exist in IDO ('organism population', I orbit of skull - + - + FMA-abduced-lr @@ -313619,7 +310499,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -313685,14 +310565,14 @@ Classes for population already exist in IDO ('organism population', I jaw skeleton - + - + cjm @@ -313902,7 +310782,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -313937,14 +310817,14 @@ Classes for population already exist in IDO ('organism population', I lower jaw region http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png - + - + Wikipedia:Mandibular_prominence @@ -314127,7 +311007,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -314152,14 +311032,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0001731 cavity of pharynx - + - + XAO @@ -314438,7 +311318,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -314481,14 +311361,14 @@ Classes for population already exist in IDO ('organism population', I iris - + - + XAO @@ -314561,7 +311441,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -314613,14 +311493,14 @@ Classes for population already exist in IDO ('organism population', I corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -314717,15 +311597,15 @@ Classes for population already exist in IDO ('organism population', I - - + + - + @@ -314767,34 +311647,34 @@ Classes for population already exist in IDO ('organism population', I sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + FMA - + ZFA - + ISBN:0781772214 @@ -314845,7 +311725,7 @@ Classes for population already exist in IDO ('organism population', I - + A skeletal muscle organ that is part of the trunk region. Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'. Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here. @@ -314870,14 +311750,14 @@ Classes for population already exist in IDO ('organism population', I skeletal muscle of trunk - + - + prolog @@ -314948,7 +311828,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -314987,14 +311867,14 @@ Classes for population already exist in IDO ('organism population', I ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -315042,14 +311922,14 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -315112,24 +311992,24 @@ Classes for population already exist in IDO ('organism population', I optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -315230,7 +312110,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -315279,14 +312159,14 @@ Classes for population already exist in IDO ('organism population', I substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + cjm ISBN:0781772214 Wikipedia @@ -315354,15 +312234,15 @@ Classes for population already exist in IDO ('organism population', I - + - - - + + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -315382,15 +312262,15 @@ Classes for population already exist in IDO ('organism population', I ciliary epithelium - + - + - + @@ -315403,19 +312283,19 @@ Classes for population already exist in IDO ('organism population', I - + MA - + MP - + Wikipedia @@ -315845,7 +312725,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -315881,14 +312761,14 @@ Classes for population already exist in IDO ('organism population', I aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + FMA def states A and P located_in in EHDAA2 VHOG @@ -316012,8 +312892,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -316046,24 +312926,24 @@ Classes for population already exist in IDO ('organism population', I anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - + - + FMA - + cjm @@ -316115,8 +312995,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -316146,24 +313026,24 @@ Classes for population already exist in IDO ('organism population', I posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + FMA - + cjm @@ -316345,7 +313225,7 @@ Classes for population already exist in IDO ('organism population', I - + The elastic, clear, membrane-like structure, that is outer most layer of the lens. The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] @@ -316371,14 +313251,14 @@ Classes for population already exist in IDO ('organism population', I capsule of lens http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + EHDAA2 @@ -316548,7 +313428,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -316587,14 +313467,14 @@ Classes for population already exist in IDO ('organism population', I sympathetic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png - + - + DOI:10.1101/gr.157586.113 ISBN:0073040584 @@ -316658,7 +313538,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -316669,7 +313549,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -316712,11 +313592,11 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg - + - + @@ -316729,7 +313609,7 @@ Classes for population already exist in IDO ('organism population', I - + BTO FMA-implicit VHOG @@ -316738,7 +313618,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -317058,14 +313938,14 @@ Classes for population already exist in IDO ('organism population', I - + - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised @@ -317118,24 +313998,24 @@ Classes for population already exist in IDO ('organism population', I midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - + - + - + definitional - + Bgee:AN @@ -317350,7 +314230,7 @@ Classes for population already exist in IDO ('organism population', I - + Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]. @@ -317386,14 +314266,14 @@ Classes for population already exist in IDO ('organism population', I metencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + definitional @@ -317655,7 +314535,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that is part of a small intestine [Automatically generated definition]. Intestinal epithelium which lines the lumen of the mid intestine.[TAO] BTO:0001258 @@ -317680,14 +314560,14 @@ Classes for population already exist in IDO ('organism population', I epithelium of small intestine - + - + FMA @@ -318085,7 +314965,7 @@ Classes for population already exist in IDO ('organism population', I - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] @@ -318126,14 +315006,14 @@ Classes for population already exist in IDO ('organism population', I midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -318372,7 +315252,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -318431,14 +315311,14 @@ Classes for population already exist in IDO ('organism population', I bile - + - + 0.3% in humans @@ -318649,7 +315529,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a esophagus [Automatically generated definition]. EMAPA:26987 FMA:63050 @@ -318678,14 +315558,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0001974 lamina propria of esophagus - + - + FMA @@ -318917,7 +315797,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -318958,14 +315838,14 @@ Classes for population already exist in IDO ('organism population', I epithelium of esophagus - + - + FMA @@ -319279,8 +316159,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -319293,7 +316173,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -319352,34 +316232,34 @@ Classes for population already exist in IDO ('organism population', I blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -319912,9 +316792,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. @@ -319956,35 +316836,35 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png - + - + - + - + Wikipedia - + EHDAA2 XAO - + EHDAA2 @@ -320379,7 +317259,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -320392,7 +317272,7 @@ Classes for population already exist in IDO ('organism population', I - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. @@ -320443,25 +317323,25 @@ Classes for population already exist in IDO ('organism population', I hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + - + modified-source-relation ABA - + Bgee:AN @@ -320826,7 +317706,7 @@ Classes for population already exist in IDO ('organism population', I - + The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. @@ -320857,14 +317737,14 @@ Classes for population already exist in IDO ('organism population', I pontine raphe nucleus - + - + Wikipedia @@ -320948,7 +317828,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -321051,14 +317931,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb - + - + some species only have a single lung @@ -321371,9 +318251,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. assume spelling error for ncit EHDAA2:0004143 @@ -321391,15 +318271,15 @@ Classes for population already exist in IDO ('organism population', I truncus arteriosus - + - + - + @@ -321418,19 +318298,19 @@ Classes for population already exist in IDO ('organism population', I - + MA - + EHDAA2 - + EHDAA2 @@ -321461,7 +318341,7 @@ Classes for population already exist in IDO ('organism population', I - + The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO] relationship loss: develops_from endocardial ring (TAO:0005072)[TAO] @@ -321493,14 +318373,14 @@ Classes for population already exist in IDO ('organism population', I endocardial cushion http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png - + - + ZFA @@ -321583,8 +318463,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart. Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO] Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO] @@ -321619,24 +318499,24 @@ Classes for population already exist in IDO ('organism population', I sinus venosus http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png - + - + - + VHOG - + Bgee:AN @@ -321739,7 +318619,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -321770,7 +318650,7 @@ Classes for population already exist in IDO ('organism population', I - + The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. Consider adding a layer-of-skin grouping class for all skin layers @@ -321810,24 +318690,24 @@ Classes for population already exist in IDO ('organism population', I dermis http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg - + - + - + FMA - + definitional @@ -321885,7 +318765,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -321904,7 +318784,7 @@ Classes for population already exist in IDO ('organism population', I - + Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] @@ -321940,24 +318820,24 @@ Classes for population already exist in IDO ('organism population', I hypodermis http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg - + - + - + ZFA - + FMA-modified @@ -322389,8 +319269,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A cardiac ventricle that is in the right side of the heart. The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] @@ -322423,24 +319303,24 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + - + PMID:17276708 - + cjm @@ -322619,7 +319499,7 @@ Classes for population already exist in IDO ('organism population', I - + Cardiac chamber through which blood leaves the heart. A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] One of four heart chambers.[TAO] @@ -322658,14 +319538,14 @@ Classes for population already exist in IDO ('organism population', I cardiac ventricle - + - + Bgee:AN @@ -322740,7 +319620,7 @@ Classes for population already exist in IDO ('organism population', I - + A cardiac ventricle that is in the left side of the heart. Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] @@ -322774,14 +319654,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + GO @@ -323427,7 +320307,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -323473,14 +320353,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb - + - + Wikipathways:WP2062 @@ -323830,7 +320710,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -323882,14 +320762,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spleen.glb https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg - + - + multiple sources - true spleen appear in jawed vertebrates @@ -323947,22 +320827,22 @@ Classes for population already exist in IDO ('organism population', I - + - + - - + + @@ -324042,19 +320922,19 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg - + - + - + - + @@ -324069,25 +320949,25 @@ Classes for population already exist in IDO ('organism population', I - + ZFA - + ZFA-weakened - + EHDAA2 - + http://www.stembook.org/node/512 @@ -324319,7 +321199,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -324390,7 +321270,7 @@ Classes for population already exist in IDO ('organism population', I https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg https://upload.wikimedia.org/wikipedia/commons/f/f4/Abdomal_organs.svg - + @@ -324403,7 +321283,7 @@ Classes for population already exist in IDO ('organism population', I - + definitional @@ -325034,7 +321914,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -325073,14 +321953,14 @@ Classes for population already exist in IDO ('organism population', I superior olivary complex http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png - + - + NIFSTD @@ -325179,7 +322059,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -325237,14 +322117,14 @@ Classes for population already exist in IDO ('organism population', I locus ceruleus http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png - + - + check ZFA NIFSTD @@ -325372,7 +322252,7 @@ Classes for population already exist in IDO ('organism population', I - + Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). @@ -325408,14 +322288,14 @@ Classes for population already exist in IDO ('organism population', I superior salivatory nucleus http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png - + - + definitional @@ -325544,7 +322424,7 @@ Classes for population already exist in IDO ('organism population', I - + The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. Layer that lines the lumen of the heart.[TAO] Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] @@ -325586,14 +322466,14 @@ Classes for population already exist in IDO ('organism population', I endocardium http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png - + - + Bgee:AN @@ -326075,7 +322955,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -326135,7 +323015,7 @@ Classes for population already exist in IDO ('organism population', I integument - + @@ -326148,7 +323028,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -326416,7 +323296,7 @@ Classes for population already exist in IDO ('organism population', I - + Vasculature that is part of the eye region. not part of the eye in ZFA. Note this changed to a blood vessel in ZFA @@ -326439,14 +323319,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + ISBN:0781772214 @@ -326506,7 +323386,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -326547,14 +323427,14 @@ Classes for population already exist in IDO ('organism population', I musculoskeletal system - + - + check ctenophore @@ -326839,15 +323719,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). TODO - add superclass to unify with VNC? @@ -326906,34 +323786,34 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb - + - + - + - + ZFA - + definitional - + definitional @@ -327125,7 +324005,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -327176,14 +324056,14 @@ Classes for population already exist in IDO ('organism population', I ventral horn of spinal cord - + - + FMA-abduced-lr @@ -327483,7 +324363,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -327513,14 +324393,14 @@ Classes for population already exist in IDO ('organism population', I dorsal mesentery http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png - + - + EHDAA2 @@ -327988,7 +324868,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -328029,14 +324909,14 @@ Classes for population already exist in IDO ('organism population', I EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct coelemic cavity lumen - + - + definitional @@ -328142,7 +325022,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a back [Automatically generated definition]. EMAPA:35161 @@ -328156,14 +325036,14 @@ Classes for population already exist in IDO ('organism population', I muscle of back - + - + prolog @@ -328212,9 +325092,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -328271,15 +325151,15 @@ Classes for population already exist in IDO ('organism population', I notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -328298,19 +325178,19 @@ Classes for population already exist in IDO ('organism population', I - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -328396,7 +325276,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -328407,7 +325287,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -328459,11 +325339,11 @@ Classes for population already exist in IDO ('organism population', I somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -328476,13 +325356,13 @@ Classes for population already exist in IDO ('organism population', I - + GOTAX:0000352 - + ZFA @@ -328752,12 +325632,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). @@ -328797,66 +325677,66 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells ISBN:0073040584 - + BTO - + PMID:11523831 - + pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - + PMID:11523831 @@ -329229,15 +326109,15 @@ Classes for population already exist in IDO ('organism population', I - - + + - + A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart. External layer of the heart.[TAO] @@ -329267,34 +326147,34 @@ Classes for population already exist in IDO ('organism population', I EDITOR_NOTE TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer. epicardium - + - + - + - + multiple - + FMA-inferred - + FMA @@ -329481,11 +326361,11 @@ Classes for population already exist in IDO ('organism population', I - - - - - + + + + + @@ -329522,23 +326402,23 @@ Classes for population already exist in IDO ('organism population', I conducting system of heart - + - + - + - + - + @@ -329551,31 +326431,31 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + FMA - + FMA - + FMA - + FMA @@ -329642,7 +326522,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -329706,7 +326586,7 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg - + @@ -329719,7 +326599,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -329996,8 +326876,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -330027,11 +326907,11 @@ Classes for population already exist in IDO ('organism population', I cardiac Purkinje fiber http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png - + - + @@ -330044,7 +326924,7 @@ Classes for population already exist in IDO ('organism population', I - + https://github.com/obophenotype/uberon/issues/1785 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9791-0064 @@ -330052,7 +326932,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -330194,7 +327074,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -330207,7 +327087,7 @@ Classes for population already exist in IDO ('organism population', I - + Serous membrane which is divided into parietal and visceral serous pericardium. EMAPA:19030 FMA:9582 @@ -330221,24 +327101,24 @@ Classes for population already exist in IDO ('organism population', I serous pericardium - + - + - + FMA - + FMA @@ -330279,7 +327159,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -330317,14 +327197,14 @@ Classes for population already exist in IDO ('organism population', I peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png - + - + MP @@ -330378,14 +327258,14 @@ Classes for population already exist in IDO ('organism population', I - + - + Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]. most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium] EMAPA:19029 @@ -330401,11 +327281,11 @@ Classes for population already exist in IDO ('organism population', I fibrous pericardium - + - + @@ -330418,13 +327298,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + WP @@ -330636,7 +327516,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -330694,14 +327574,14 @@ Classes for population already exist in IDO ('organism population', I bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -330773,8 +327653,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -330813,24 +327693,24 @@ Classes for population already exist in IDO ('organism population', I defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984) cranial muscle - + - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships - + EHDAA2-abduced @@ -330905,7 +327785,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle that is part of the cervical (neck) region. EMAPA:36050 @@ -330927,14 +327807,14 @@ Classes for population already exist in IDO ('organism population', I muscle of neck - + - + prolog @@ -330992,7 +327872,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -331024,14 +327904,14 @@ Classes for population already exist in IDO ('organism population', I muscle of abdomen - + - + prolog @@ -331289,14 +328169,14 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -331345,24 +328225,24 @@ Classes for population already exist in IDO ('organism population', I hematopoietic system - + - + - + FMA - + definitional @@ -331418,15 +328298,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + @@ -331473,25 +328353,25 @@ Classes for population already exist in IDO ('organism population', I bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png - + - + - + EMAPA MA - + XAO @@ -331803,7 +328683,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -331848,14 +328728,14 @@ Classes for population already exist in IDO ('organism population', I visceral pleura - + - + FMA @@ -331930,7 +328810,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -331976,14 +328856,14 @@ Classes for population already exist in IDO ('organism population', I pleural cavity http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png - + - + Wikipedia @@ -332154,7 +329034,7 @@ Classes for population already exist in IDO ('organism population', I - + A double-walled sac containing the heart and the roots of the great vessels. FMA:9868 RETIRED_EHDAA2:0001443 @@ -332168,14 +329048,14 @@ Classes for population already exist in IDO ('organism population', I pericardial sac http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png - + - + FMA @@ -332194,7 +329074,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -332253,14 +329133,14 @@ Classes for population already exist in IDO ('organism population', I pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png - + - + MA @@ -332453,7 +329333,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -332509,7 +329389,7 @@ Classes for population already exist in IDO ('organism population', I autonomic nervous system http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png - + @@ -332522,7 +329402,7 @@ Classes for population already exist in IDO ('organism population', I - + EMAPA MA NIFSTD @@ -333490,7 +330370,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues. consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar) The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. @@ -333517,14 +330397,14 @@ Classes for population already exist in IDO ('organism population', I oral epithelium - + - + AAO-modified @@ -333587,8 +330467,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -333616,24 +330496,24 @@ Classes for population already exist in IDO ('organism population', I visceral serous pericardium - + - + - + cjm - + FMA @@ -334238,14 +331118,14 @@ Classes for population already exist in IDO ('organism population', I - + - - + + @@ -334271,11 +331151,11 @@ Classes for population already exist in IDO ('organism population', I iris epithelium - + - + @@ -334288,13 +331168,13 @@ Classes for population already exist in IDO ('organism population', I - + MA - + MP @@ -334361,7 +331241,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -334389,14 +331269,14 @@ Classes for population already exist in IDO ('organism population', I trabecula carnea - + - + WP @@ -334481,7 +331361,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -334515,7 +331395,7 @@ Classes for population already exist in IDO ('organism population', I https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg - + @@ -334528,7 +331408,7 @@ Classes for population already exist in IDO ('organism population', I - + VSAO @@ -334800,8 +331680,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -334827,11 +331707,11 @@ Classes for population already exist in IDO ('organism population', I tunica media https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg - + - + @@ -334844,13 +331724,13 @@ Classes for population already exist in IDO ('organism population', I - + cjm - + cjm @@ -334888,8 +331768,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts @@ -334914,11 +331794,11 @@ Classes for population already exist in IDO ('organism population', I tunica intima https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg - + - + @@ -334931,13 +331811,13 @@ Classes for population already exist in IDO ('organism population', I - + check for exceptions, e.g. capillaries - + ISBN:0073040584 @@ -335329,9 +332209,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] @@ -335367,15 +332247,15 @@ Classes for population already exist in IDO ('organism population', I pharyngeal arch http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png - + - + - + @@ -335388,19 +332268,19 @@ Classes for population already exist in IDO ('organism population', I - + PMID:16313389 - + http://tolweb.org/Chordata/2499 - + PMID:16313389 @@ -335469,7 +332349,7 @@ Classes for population already exist in IDO ('organism population', I - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons @@ -335489,7 +332369,7 @@ Classes for population already exist in IDO ('organism population', I cranial placode - + @@ -335502,7 +332382,7 @@ Classes for population already exist in IDO ('organism population', I - + PMID:11523831 PMID:22512454 @@ -336497,7 +333377,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -336510,7 +333390,7 @@ Classes for population already exist in IDO ('organism population', I - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] @@ -336540,11 +333420,11 @@ Classes for population already exist in IDO ('organism population', I midbrain-hindbrain boundary - + - + @@ -336558,13 +333438,13 @@ Classes for population already exist in IDO ('organism population', I - + ZFA - + ZFA @@ -336610,8 +333490,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] @@ -336640,11 +333520,11 @@ Classes for population already exist in IDO ('organism population', I periderm - + - + @@ -336657,13 +333537,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + ZFA @@ -336829,7 +333709,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -336846,7 +333726,7 @@ Classes for population already exist in IDO ('organism population', I - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] @@ -336871,14 +333751,14 @@ Classes for population already exist in IDO ('organism population', I presomitic mesoderm - + - + Bgee:AN @@ -337043,8 +333923,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue. TODO - check; developmental relationship to anterior hypoblast in ZFA? Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] @@ -337069,24 +333949,24 @@ Classes for population already exist in IDO ('organism population', I prechordal plate - + - + - + ZFA - + PMID:16313393 @@ -337144,9 +334024,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -337188,34 +334068,34 @@ Classes for population already exist in IDO ('organism population', I intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -337528,7 +334408,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -337566,7 +334446,7 @@ Classes for population already exist in IDO ('organism population', I eye primordium - + @@ -337579,7 +334459,7 @@ Classes for population already exist in IDO ('organism population', I - + PMID:16496288 XAO @@ -337635,8 +334515,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -337665,24 +334545,24 @@ Classes for population already exist in IDO ('organism population', I optic cup - + - + - + ZFA - + ZFA @@ -337748,7 +334628,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -337789,7 +334669,7 @@ Classes for population already exist in IDO ('organism population', I lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -337802,7 +334682,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -337866,9 +334746,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] @@ -337900,34 +334780,34 @@ Classes for population already exist in IDO ('organism population', I neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -338047,7 +334927,7 @@ Classes for population already exist in IDO ('organism population', I - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] @@ -338076,7 +334956,7 @@ Classes for population already exist in IDO ('organism population', I paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -338089,7 +334969,7 @@ Classes for population already exist in IDO ('organism population', I - + Bgee:AN @@ -338158,8 +335038,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -338185,11 +335065,11 @@ Classes for population already exist in IDO ('organism population', I epibranchial placode - + - + @@ -338203,13 +335083,13 @@ Classes for population already exist in IDO ('organism population', I - + ZFA - + EHDAA2-abduced @@ -338313,7 +335193,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -338357,7 +335237,7 @@ Classes for population already exist in IDO ('organism population', I lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -338370,7 +335250,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 VHOG @@ -338455,7 +335335,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -338498,7 +335378,7 @@ Classes for population already exist in IDO ('organism population', I myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -338511,7 +335391,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2-abduced @@ -338574,7 +335454,7 @@ Classes for population already exist in IDO ('organism population', I - + Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] @@ -338594,14 +335474,14 @@ Classes for population already exist in IDO ('organism population', I trunk neural crest - + - + ZFA @@ -338645,15 +335525,15 @@ Classes for population already exist in IDO ('organism population', I - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] @@ -338673,15 +335553,15 @@ Classes for population already exist in IDO ('organism population', I heart primordium - + - + - + @@ -338694,19 +335574,19 @@ Classes for population already exist in IDO ('organism population', I - + ZFA - + ZFA - + XAO @@ -338838,8 +335718,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] @@ -338867,11 +335747,11 @@ Classes for population already exist in IDO ('organism population', I sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -338890,13 +335770,13 @@ Classes for population already exist in IDO ('organism population', I - + VHOG:0000680 - + ZFA @@ -341100,8 +337980,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -341133,24 +338013,24 @@ Classes for population already exist in IDO ('organism population', I skeleton of lower jaw - + - + - + EHDAA2 - + VHOG-modified @@ -341226,12 +338106,12 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -341258,7 +338138,7 @@ Classes for population already exist in IDO ('organism population', I mesentery of stomach - + @@ -341271,7 +338151,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -341583,13 +338463,13 @@ Classes for population already exist in IDO ('organism population', I - + - + Racemose mucous glands beneath the mucous membrane of the pharynx. BTO:0004849 EHDAA2:0001461 @@ -341602,14 +338482,14 @@ Classes for population already exist in IDO ('organism population', I pharyngeal gland - + - + BTO @@ -341718,7 +338598,7 @@ Classes for population already exist in IDO ('organism population', I - + A blood island that is part of a mesoderm. in EHDAA2, gives rise to blood and dorsal aorta UBERON:0003305 @@ -341731,7 +338611,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003304 mesoderm blood island - + @@ -341744,7 +338624,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -341797,7 +338677,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -341809,14 +338689,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -342010,7 +338890,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a developing upper jaw [Automatically generated definition]. EHDAA2:0002124 EHDAA:8031 @@ -342023,14 +338903,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003323 mesenchyme of upper jaw - + - + EHDAA2 @@ -342082,7 +338962,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. EHDAA2:0001024 EHDAA:8003 @@ -342095,14 +338975,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003324 mesenchyme of lower jaw - + - + EHDAA2 @@ -343494,15 +340374,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + An epithelium that is part of a pharynx [Automatically generated definition]. Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] BSA:0000112 @@ -343522,24 +340402,24 @@ Classes for population already exist in IDO ('organism population', I pharyngeal epithelium - + - + - + ZFA - + ZFA @@ -343591,12 +340471,12 @@ Classes for population already exist in IDO ('organism population', I - + - + An epithelium that is part of a midgut. BTO:0005053 EHDAA2:0001195 @@ -343609,14 +340489,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003352 epithelium of midgut - + - + BTO @@ -343909,7 +340789,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -343922,7 +340802,7 @@ Classes for population already exist in IDO ('organism population', I - + An unilaminar epithelium that surrounds a pelvic appendage bud. UBERON:0005232 EHDAA2:0001034 @@ -343938,24 +340818,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003371 pelvic appendage bud ectoderm - + - + - + EHDAA2 - + EHDAA2 @@ -344023,7 +340903,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -344036,7 +340916,7 @@ Classes for population already exist in IDO ('organism population', I - + An unilaminar epithelium that surrounds a pectoral appendage bud. UBERON:0005231 UBERON:0005663 @@ -344053,24 +340933,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003372 pectoral appendage bud ectoderm - + - + - + EHDAA2 - + EHDAA2 @@ -346510,13 +343390,13 @@ Classes for population already exist in IDO ('organism population', I - + - + A bone that is part of a facial skeleton [Automatically generated definition]. test whether 'facial bone' is an exact synonym EMAPA:19019 @@ -346537,14 +343417,14 @@ Classes for population already exist in IDO ('organism population', I facial bone - + - + MA @@ -346742,7 +343622,7 @@ Classes for population already exist in IDO ('organism population', I - + The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose. EMAPA:37430 @@ -346759,14 +343639,14 @@ Classes for population already exist in IDO ('organism population', I artery of upper lip - + - + FMA @@ -346832,7 +343712,7 @@ Classes for population already exist in IDO ('organism population', I - + The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. EMAPA:37429 @@ -346850,14 +343730,14 @@ Classes for population already exist in IDO ('organism population', I artery of lower lip - + - + FMA @@ -347367,7 +344247,7 @@ Classes for population already exist in IDO ('organism population', I - + An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37575 MA:0001808 @@ -347398,14 +344278,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003489 respiratory system capillary endothelium - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -347637,7 +344517,7 @@ Classes for population already exist in IDO ('organism population', I - + An arteriole that is part of a respiratory system [Automatically generated definition]. EMAPA:37568 MA:0001803 @@ -347645,14 +344525,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003495 respiratory system arteriole - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -347686,7 +344566,7 @@ Classes for population already exist in IDO ('organism population', I - + A blood vessel that is part of a head [Automatically generated definition]. EMAPA:36610 MA:0000575 @@ -347698,14 +344578,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003496 head blood vessel - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -351740,12 +348620,12 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -351772,7 +348652,7 @@ Classes for population already exist in IDO ('organism population', I intrahepatic bile duct - + @@ -351785,7 +348665,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -352771,7 +349651,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a thorax [Automatically generated definition]. MA:0000561 muscle organ of thorax @@ -352781,14 +349661,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003830 thoracic segment muscle - + - + prolog @@ -352900,7 +349780,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a esophagus [Automatically generated definition]. merge muscle and muscle layer? EMAPA:26983 @@ -352917,14 +349797,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003832 esophagus muscle - + - + MA @@ -353783,12 +350663,12 @@ Classes for population already exist in IDO ('organism population', I - + - + A neural plate that develops_from a future spinal cord. Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] @@ -353801,14 +350681,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003854 spinal cord neural plate - + - + ZFA @@ -354011,7 +350891,7 @@ Classes for population already exist in IDO ('organism population', I - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] @@ -354027,14 +350907,14 @@ Classes for population already exist in IDO ('organism population', I intraembryonic coelom - + - + Wikipedia @@ -354130,8 +351010,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -354165,11 +351045,11 @@ Classes for population already exist in IDO ('organism population', I liver primordium - + - + @@ -354188,13 +351068,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + ventral foregut endoderm Zaret 1996 @@ -354317,7 +351197,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -354337,14 +351217,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0003898 skeletal muscle tissue of trunk - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -354405,7 +351285,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -354422,7 +351302,7 @@ Classes for population already exist in IDO ('organism population', I - + The part of the retina that contains neurons and photoreceptor cells[GO]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] @@ -354454,14 +351334,14 @@ Classes for population already exist in IDO ('organism population', I retinal neural layer - + - + Bgee:AN @@ -354743,7 +351623,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -354773,14 +351653,14 @@ Classes for population already exist in IDO ('organism population', I pancreas primordium http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png - + - + Wikipedia @@ -354822,16 +351702,16 @@ Classes for population already exist in IDO ('organism population', I - - + + - - + + The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. EFO:0003470 EMAPA:35645 @@ -354852,19 +351732,19 @@ Classes for population already exist in IDO ('organism population', I http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png - + - + - + - + @@ -354877,26 +351757,26 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + Wikipedia:Pancreas#Embryological_development - + zebrafish Wikipedia:Pancreatic_bud - + EHDAA2-inferred @@ -354938,8 +351818,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Pancreatic bud that gives rise to the accessory pancreatic duct. The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO] In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] @@ -354967,24 +351847,24 @@ Classes for population already exist in IDO ('organism population', I dorsal pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png - + - + - + EHDAA2 - + XAO @@ -355031,8 +351911,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Pancreatic bud that gives rise to the major pancreatic duct. In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP] @@ -355060,24 +351940,24 @@ Classes for population already exist in IDO ('organism population', I ventral pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png - + - + - + EHDAA2 - + PMID:16417468 WP @@ -355908,7 +352788,7 @@ Classes for population already exist in IDO ('organism population', I - + A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. Not to be confused with 'dermatome segment of skin'. AAO:0011028 @@ -355935,7 +352815,7 @@ Classes for population already exist in IDO ('organism population', I dermatome http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png - + @@ -355948,7 +352828,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2-abduced @@ -356074,7 +352954,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -356101,14 +352981,14 @@ Classes for population already exist in IDO ('organism population', I biliary ductule - + - + BTO @@ -356193,7 +353073,7 @@ Classes for population already exist in IDO ('organism population', I - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure The layer of undifferentiated, proliferating cells that line the neural tube lumen @@ -356211,7 +353091,7 @@ Classes for population already exist in IDO ('organism population', I neural tube ventricular layer - + @@ -356224,7 +353104,7 @@ Classes for population already exist in IDO ('organism population', I - + NCBIBook:NBK10047 @@ -356285,7 +353165,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -356309,7 +353189,7 @@ Classes for population already exist in IDO ('organism population', I neural tube mantle layer - + @@ -356322,7 +353202,7 @@ Classes for population already exist in IDO ('organism population', I - + by division NCBIBook:NBK10047 @@ -356360,7 +353240,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -356377,14 +353257,14 @@ Classes for population already exist in IDO ('organism population', I neural tube marginal layer - + - + forms from axons @@ -356426,7 +353306,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -356451,14 +353331,14 @@ Classes for population already exist in IDO ('organism population', I neural tube basal plate - + - + Shh Swenson @@ -356574,14 +353454,14 @@ Classes for population already exist in IDO ('organism population', I - + - + The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it. Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity. EHDAA2:0001076 @@ -356602,24 +353482,24 @@ Classes for population already exist in IDO ('organism population', I medial nasal prominence http://upload.wikimedia.org/wikipedia/commons/8/85/Gray45.png - + - + - + EHDAA2 - + Wikipedia @@ -357410,7 +354290,7 @@ Classes for population already exist in IDO ('organism population', I - + A myocardium trabecular layer that is part of a cardiac ventricle. TODO - check FMA FMA:83511 @@ -357424,14 +354304,14 @@ Classes for population already exist in IDO ('organism population', I trabecular layer of ventricle - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -357466,9 +354346,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -357501,34 +354381,34 @@ Classes for population already exist in IDO ('organism population', I optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -357678,8 +354558,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 @@ -357692,24 +354572,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -357768,7 +354648,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelial tube that will give rise to the mature heart. the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 @@ -357788,14 +354668,14 @@ Classes for population already exist in IDO ('organism population', I heart tube - + - + ZFA-modified @@ -357940,8 +354820,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles. the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles. HPS @@ -357952,11 +354832,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004146 His-Purkinje system - + - + @@ -357969,13 +354849,13 @@ Classes for population already exist in IDO ('organism population', I - + GO - + PMID:12626327 PMID:21234997 github:michaelerice @@ -358150,8 +355030,8 @@ Classes for population already exist in IDO ('organism population', I - - + + An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium. propepicardial Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA] @@ -358163,24 +355043,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004160 proepicardium - + - + - + todo check other taxa - + ZFA @@ -358661,8 +355541,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35469 @@ -358678,24 +355558,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004220 large intestine smooth muscle - + - + - + MA - + consider merging @@ -358776,7 +355656,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -358813,14 +355693,14 @@ Classes for population already exist in IDO ('organism population', I intestine smooth muscle - + - + consider merging @@ -359872,7 +356752,7 @@ Classes for population already exist in IDO ('organism population', I - + A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35783 @@ -359897,14 +356777,14 @@ Classes for population already exist in IDO ('organism population', I small intestine smooth muscle - + - + consider merging @@ -360671,13 +357551,13 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -360693,14 +357573,14 @@ Classes for population already exist in IDO ('organism population', I eye muscle - + - + MA @@ -360790,7 +357670,7 @@ Classes for population already exist in IDO ('organism population', I - + The bilaminar epithelium formed from the myotome and dermatome. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] @@ -360813,7 +357693,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004290 dermomyotome - + @@ -360832,7 +357712,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 ZFA @@ -361116,14 +357996,14 @@ Classes for population already exist in IDO ('organism population', I - + - + Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition. distinction between trophectoderm and trophoblast unclear/inconsistent in many sources The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG] @@ -361141,11 +358021,11 @@ Classes for population already exist in IDO ('organism population', I trophectoderm - + - + @@ -361158,13 +358038,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 @@ -361567,7 +358447,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -361623,14 +358503,14 @@ Classes for population already exist in IDO ('organism population', I pharyngeal arch artery http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png - + - + ZFA @@ -361882,7 +358762,7 @@ Classes for population already exist in IDO ('organism population', I - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] @@ -361914,14 +358794,14 @@ Classes for population already exist in IDO ('organism population', I Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -363322,12 +360202,12 @@ Classes for population already exist in IDO ('organism population', I - + - + A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. Note placement of MA class based on parthood relationship EMAPA:32688 @@ -363338,14 +360218,14 @@ Classes for population already exist in IDO ('organism population', I cardiac muscle tissue of myocardium - + - + MA @@ -363532,21 +360412,21 @@ Classes for population already exist in IDO ('organism population', I - + A portion of trabecula carnea cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. FMA:84429 uberon UBERON:0004525 cardiac muscle tissue of trabecula carnea of right ventricle - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -363575,21 +360455,21 @@ Classes for population already exist in IDO ('organism population', I - + A portion of trabecula carnea cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. FMA:84430 uberon UBERON:0004526 cardiac muscle tissue of trabecula carnea of left ventricle - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -364286,7 +361166,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -364320,7 +361200,7 @@ Classes for population already exist in IDO ('organism population', I liver lobule - + @@ -364333,7 +361213,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA MA @@ -364522,7 +361402,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -364554,14 +361434,14 @@ Classes for population already exist in IDO ('organism population', I interventricular septum membranous part - + - + Wikipedia @@ -364768,8 +361648,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. BAMS:RA EMAPA:35721 @@ -364798,25 +361678,25 @@ Classes for population already exist in IDO ('organism population', I raphe nuclei http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png - + - + - + GO Wikipedia - + Wikipedia @@ -365322,14 +362202,14 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -365360,7 +362240,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -365383,11 +362263,11 @@ Classes for population already exist in IDO ('organism population', I paired limb/fin - + - + @@ -365400,13 +362280,13 @@ Classes for population already exist in IDO ('organism population', I - + VSAO - + definitional @@ -365488,7 +362368,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -365510,14 +362390,14 @@ Classes for population already exist in IDO ('organism population', I pelvic appendage - + - + definitional @@ -365586,7 +362466,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -365610,14 +362490,14 @@ Classes for population already exist in IDO ('organism population', I pectoral appendage - + - + definitional @@ -366150,7 +363030,7 @@ Classes for population already exist in IDO ('organism population', I - + A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 @@ -366164,7 +363044,7 @@ Classes for population already exist in IDO ('organism population', I Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue - + @@ -366177,7 +363057,7 @@ Classes for population already exist in IDO ('organism population', I - + 2012-08-14 VSAO:0000015 VSAO @@ -366356,7 +363236,7 @@ Classes for population already exist in IDO ('organism population', I - + The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) AAO:0000094 @@ -366378,7 +363258,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004761 cartilaginous neurocranium - + @@ -366391,7 +363271,7 @@ Classes for population already exist in IDO ('organism population', I - + PMC1571569 @@ -366488,7 +363368,7 @@ Classes for population already exist in IDO ('organism population', I - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] @@ -366504,14 +363384,14 @@ Classes for population already exist in IDO ('organism population', I skeletal element - + - + VSAO @@ -366640,7 +363520,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -366679,14 +363559,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004770 articular system - + - + FMA @@ -366801,7 +363681,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a respiratory system [Automatically generated definition]. EMAPA:37576 MA:0001821 @@ -366816,14 +363696,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004779 respiratory system lamina propria - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -366899,7 +363779,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a gastrointestinal system. MA:0001899 NCIT:C49299 @@ -366908,14 +363788,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004780 gastrointestinal system lamina propria - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -366950,7 +363830,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a gallbladder [Automatically generated definition]. EMAPA:35371 FMA:278594 @@ -366969,14 +363849,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004781 gallbladder lamina propria - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -367571,10 +364451,10 @@ Classes for population already exist in IDO ('organism population', I - - - - + + + + A mucosa that is part of a gastrointestinal system. BTO:0000546 BTO:0005568 @@ -367590,44 +364470,44 @@ Classes for population already exist in IDO ('organism population', I The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 gastrointestinal system mucosa - + - + - + - + - + PMID:16417468 - + PMID:16417468 - + PMID:16417468 - + BTO-modified @@ -368971,7 +365851,7 @@ Classes for population already exist in IDO ('organism population', I - + An endothelium of artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37566 @@ -368992,14 +365872,14 @@ Classes for population already exist in IDO ('organism population', I respiratory system arterial endothelium - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -369881,7 +366761,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -369904,14 +366784,14 @@ Classes for population already exist in IDO ('organism population', I splanchnopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -369939,7 +366819,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -369962,14 +366842,14 @@ Classes for population already exist in IDO ('organism population', I somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -370517,8 +367397,8 @@ Classes for population already exist in IDO ('organism population', I - - + + EHDAA2:0000171 EMAPA:16561 EMAPA_RETIRED:16565 @@ -370529,11 +367409,11 @@ Classes for population already exist in IDO ('organism population', I biliary bud http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png - + - + @@ -370546,13 +367426,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2-modified @@ -372113,7 +368993,7 @@ Classes for population already exist in IDO ('organism population', I - + A mucosa that is part of a pyloric antrum [Automatically generated definition]. BTO:0004107 FMA:17055 @@ -372146,14 +369026,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0004997 mucosa of pyloric antrum - + - + BTO @@ -373797,20 +370677,20 @@ Classes for population already exist in IDO ('organism population', I - + Missing definition for term UBERON:0005064. Please replace it using linked reference. uberon UBERON:0005064 left ventricular trabecular myocardium - + - + GO @@ -373837,20 +370717,20 @@ Classes for population already exist in IDO ('organism population', I - + Missing definition for term UBERON:0005066. Please replace it using linked reference. uberon UBERON:0005066 right ventricular trabecular myocardium - + - + GO @@ -374829,7 +371709,7 @@ Classes for population already exist in IDO ('organism population', I - + An external ectoderm that is part of a optic eminence [Automatically generated definition]. EMAPA:16539 RETIRED_EHDAA2:0001311 @@ -374838,14 +371718,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005216 optic eminence surface ectoderm - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -375294,7 +372174,7 @@ Classes for population already exist in IDO ('organism population', I - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] EFO:0003492 @@ -375316,14 +372196,14 @@ Classes for population already exist in IDO ('organism population', I head mesenchyme - + - + EHDAA2 @@ -375390,7 +372270,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -375406,14 +372286,14 @@ Classes for population already exist in IDO ('organism population', I trunk mesenchyme - + - + EHDAA2 @@ -375435,7 +372315,7 @@ Classes for population already exist in IDO ('organism population', I - + The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] @@ -375460,14 +372340,14 @@ Classes for population already exist in IDO ('organism population', I myelencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + definitional @@ -376445,7 +373325,7 @@ Classes for population already exist in IDO ('organism population', I - + An apical ectodermal ridge that is part of a pectoral appendage bud. An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pectoral fin bud.[TAO] @@ -376472,14 +373352,14 @@ Classes for population already exist in IDO ('organism population', I pectoral appendage apical ectodermal ridge - + - + EHDAA2 @@ -376597,7 +373477,7 @@ Classes for population already exist in IDO ('organism population', I - + An apical ectodermal ridge that is part of a pelvic appendage bud. An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] @@ -376620,14 +373500,14 @@ Classes for population already exist in IDO ('organism population', I pelvic appendage apical ectodermal ridge - + - + EHDAA2 @@ -376953,7 +373833,7 @@ Classes for population already exist in IDO ('organism population', I - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -376961,7 +373841,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005427 corneal primordium - + @@ -376980,7 +373860,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -377080,7 +373960,7 @@ Classes for population already exist in IDO ('organism population', I - + The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates. the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. EHDAA2:0004145 @@ -377095,7 +373975,7 @@ Classes for population already exist in IDO ('organism population', I aortic sac - + @@ -377108,7 +373988,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -377436,7 +374316,7 @@ Classes for population already exist in IDO ('organism population', I - + A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. sulcus limitans BAMS:slim @@ -377447,14 +374327,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005478 sulcus limitans of neural tube - + - + EHDAA2 @@ -377722,7 +374602,7 @@ Classes for population already exist in IDO ('organism population', I - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. BTO:0006179 EHDAA2:0001512 @@ -377741,14 +374621,14 @@ Classes for population already exist in IDO ('organism population', I primitive heart tube - + - + ZFA @@ -377830,7 +374710,7 @@ Classes for population already exist in IDO ('organism population', I - + Cranial neural crest which gives rise to the trigeminal ganglion. todo - compare ZFA and EHDAA2 representation We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] @@ -377847,7 +374727,7 @@ Classes for population already exist in IDO ('organism population', I trigeminal neural crest - + @@ -377866,7 +374746,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -377893,7 +374773,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -377922,7 +374802,7 @@ Classes for population already exist in IDO ('organism population', I gonad primordium - + @@ -377935,7 +374815,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -377993,15 +374873,15 @@ Classes for population already exist in IDO ('organism population', I - + - - + + Somite located in the head region, caudal to the otic vesicle. in humans this includes somites 1-4 They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) @@ -378015,24 +374895,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005594 head somite - + - + - + EHDAA2 - + EHDAA2 @@ -378080,7 +374960,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -378100,7 +374980,7 @@ Classes for population already exist in IDO ('organism population', I lung primordium - + @@ -378113,7 +374993,7 @@ Classes for population already exist in IDO ('organism population', I - + XAO @@ -378186,8 +375066,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum. The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG] EHDAA2:0000416 @@ -378203,11 +375083,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005602 dorsal mesogastrium - + - + @@ -378220,13 +375100,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 @@ -378264,8 +375144,8 @@ Classes for population already exist in IDO ('organism population', I - - + + EMAPA:16844 MA:0001636 VHOG:0000215 @@ -378275,24 +375155,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005604 extrahepatic part of hepatic duct - + - + - + MA - + MA @@ -379403,7 +376283,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0000474 EMAPA:31862 EMAPA:31863 @@ -379415,7 +376295,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005728 extraembryonic mesoderm - + @@ -379428,7 +376308,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -379566,7 +376446,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -379582,14 +376462,14 @@ Classes for population already exist in IDO ('organism population', I paired limb/fin field - + - + ISBN:9780878932504 ZFA-inferred @@ -380381,7 +377261,7 @@ Classes for population already exist in IDO ('organism population', I - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -380391,7 +377271,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005856 developing mesenchymal condensation - + @@ -380410,7 +377290,7 @@ Classes for population already exist in IDO ('organism population', I - + AEO-modified-relation @@ -380432,7 +377312,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -380453,7 +377333,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005863 cartilaginous condensation - + @@ -380466,7 +377346,7 @@ Classes for population already exist in IDO ('organism population', I - + AEO @@ -380517,7 +377397,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -380539,14 +377419,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005865 pre-muscle condensation - + - + AEO @@ -380557,7 +377437,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -380577,7 +377457,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005866 pre-cartilage condensation - + @@ -380590,7 +377470,7 @@ Classes for population already exist in IDO ('organism population', I - + AEO @@ -381022,7 +377902,7 @@ Classes for population already exist in IDO ('organism population', I - + trabecula trabecular cartilage EFO:0003677 @@ -381034,7 +377914,7 @@ Classes for population already exist in IDO ('organism population', I neurocranial trabecula - + @@ -381047,7 +377927,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -381149,7 +378029,7 @@ Classes for population already exist in IDO ('organism population', I - + Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk. infundibulum EMAPA:37926 @@ -381172,14 +378052,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0005953 outflow part of right ventricle - + - + PMID:17276708 @@ -381661,7 +378541,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -381681,14 +378561,14 @@ Classes for population already exist in IDO ('organism population', I atrium myocardial trabecula - + - + ZFA @@ -381740,7 +378620,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -381764,14 +378644,14 @@ Classes for population already exist in IDO ('organism population', I atrioventricular septum - + - + PMID:15797462 Wikipedia @@ -381818,7 +378698,7 @@ Classes for population already exist in IDO ('organism population', I - + The paired arteries that carry blood to the yolk sac from the dorsal aorta. EHDAA2:0002208 EMAPA:16207 @@ -381830,14 +378710,14 @@ Classes for population already exist in IDO ('organism population', I vitelline artery http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png - + - + ventral branch @@ -382109,7 +378989,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -382140,14 +379020,14 @@ Classes for population already exist in IDO ('organism population', I cervical region of vertebral column - + - + FMA @@ -382225,7 +379105,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -382259,14 +379139,14 @@ Classes for population already exist in IDO ('organism population', I thoracic region of vertebral column - + - + FMA @@ -382447,7 +379327,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -382467,14 +379347,14 @@ Classes for population already exist in IDO ('organism population', I subdivision of vertebral column - + - + FMA @@ -382518,7 +379398,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -382551,14 +379431,14 @@ Classes for population already exist in IDO ('organism population', I aortico-pulmonary spiral septum http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png - + - + PMID:6844926 Wikipedia @@ -382614,7 +379494,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -382658,14 +379538,14 @@ Classes for population already exist in IDO ('organism population', I buccopharyngeal membrane http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png - + - + EHDAA2 @@ -382739,9 +379619,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -382758,34 +379638,34 @@ Classes for population already exist in IDO ('organism population', I ethmoid bone primordium - + - + - + - + FMA - + AAO - + EHDAA2 @@ -382995,8 +379875,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -383015,24 +379895,24 @@ Classes for population already exist in IDO ('organism population', I future central tendon - + - + - + EHDAA2 - + mesenchyme cranial part Wikipedia @@ -383068,7 +379948,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -383092,14 +379972,14 @@ Classes for population already exist in IDO ('organism population', I future spinal cord - + - + EHDAA2 @@ -383145,8 +380025,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -383164,24 +380044,24 @@ Classes for population already exist in IDO ('organism population', I gallbladder primordium - + - + - + EMAPA - + EHDAA2 @@ -383257,7 +380137,7 @@ Classes for population already exist in IDO ('organism population', I - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] @@ -383272,7 +380152,7 @@ Classes for population already exist in IDO ('organism population', I notochordal plate - + @@ -383285,7 +380165,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -383323,7 +380203,7 @@ Classes for population already exist in IDO ('organism population', I - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -383340,14 +380220,14 @@ Classes for population already exist in IDO ('organism population', I The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -383426,7 +380306,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -383459,7 +380339,7 @@ Classes for population already exist in IDO ('organism population', I pleuroperitoneal canal - + @@ -383472,7 +380352,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -383504,8 +380384,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -383536,24 +380416,24 @@ Classes for population already exist in IDO ('organism population', I The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP] future cardiac ventricle - + - + - + ZFA - + EMAPA @@ -383603,8 +380483,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP]. check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme UBERON:0009750 @@ -383621,11 +380501,11 @@ Classes for population already exist in IDO ('organism population', I spleen primordium - + - + @@ -383638,13 +380518,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2-modified - + XAO @@ -383703,7 +380583,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA:924 EMAPA:16663 RETIRED_EHDAA2:0002089 @@ -383715,14 +380595,14 @@ Classes for population already exist in IDO ('organism population', I See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model future trigeminal ganglion - + - + EHDAA2 @@ -385057,14 +381937,14 @@ Classes for population already exist in IDO ('organism population', I - + - + The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers. In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] EMAPA:17702 @@ -385082,24 +381962,24 @@ Classes for population already exist in IDO ('organism population', I central tendon of diaphragm - + - + - + VHOG - + definitional @@ -385580,7 +382460,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -385601,7 +382481,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0006815 areolar connective tissue - + @@ -385614,7 +382494,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -386054,7 +382934,7 @@ Classes for population already exist in IDO ('organism population', I - + A head mesenchyme that develops_from a mesoderm. merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme AAO:0011051 @@ -386082,7 +382962,7 @@ Classes for population already exist in IDO ('organism population', I head mesenchyme from mesoderm - + @@ -386095,7 +382975,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 XAO @@ -386823,7 +383703,7 @@ Classes for population already exist in IDO ('organism population', I - + The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis. CALOHA:TS-1246 @@ -386845,14 +383725,14 @@ Classes for population already exist in IDO ('organism population', I ovary stroma - + - + FMA @@ -387274,7 +384154,7 @@ Classes for population already exist in IDO ('organism population', I - + Cranial neural crest that migrates into the mandibular arch. TAO:0007064 XAO:0000024 @@ -387283,7 +384163,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007098 mandibular neural crest - + @@ -387296,7 +384176,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -387315,7 +384195,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -387326,7 +384206,7 @@ Classes for population already exist in IDO ('organism population', I - + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis SPD:0000130 @@ -387341,14 +384221,14 @@ Classes for population already exist in IDO ('organism population', I Gene notes: Bmp, Nkx, Gata primary circulatory organ - + - + GO uses blood circulation generically to include the haemolymphatic fluid of arthropods @@ -388061,7 +384941,7 @@ Classes for population already exist in IDO ('organism population', I - + relationship to Meckel's cartilage to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000031 @@ -388075,14 +384955,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007237 1st arch mandibular component - + - + EHDAA2 @@ -388120,7 +385000,7 @@ Classes for population already exist in IDO ('organism population', I - + relationship to palatoquadrate to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000038 @@ -388131,14 +385011,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007238 1st arch maxillary component - + - + EHDAA2 @@ -388236,7 +385116,7 @@ Classes for population already exist in IDO ('organism population', I - + A tunica adventitia that is part of a artery. EMAPA:36295 EV:0100030 @@ -388248,14 +385128,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007240 tunica adventitia of artery - + - + FMA @@ -388701,7 +385581,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -388722,14 +385602,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007272 pectoral appendage skeleton - + - + VSAO @@ -388764,7 +385644,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -388782,14 +385662,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007273 pelvic appendage skeleton - + - + VSAO @@ -388822,8 +385702,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -388850,24 +385730,24 @@ Classes for population already exist in IDO ('organism population', I presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -388924,7 +385804,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -388938,14 +385818,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007278 presumptive sinus venosus - + - + ZFA @@ -389031,7 +385911,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -389050,14 +385930,14 @@ Classes for population already exist in IDO ('organism population', I presumptive midbrain hindbrain boundary - + - + ZFA @@ -389096,7 +385976,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -389113,14 +385993,14 @@ Classes for population already exist in IDO ('organism population', I presumptive segmental plate - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 @@ -389219,7 +386099,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -389245,7 +386125,7 @@ Classes for population already exist in IDO ('organism population', I presumptive paraxial mesoderm - + @@ -389261,7 +386141,7 @@ Classes for population already exist in IDO ('organism population', I - + https://github.com/obophenotype/uberon/issues/1277 @@ -389603,7 +386483,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -389649,7 +386529,7 @@ Classes for population already exist in IDO ('organism population', I pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png - + @@ -389662,7 +386542,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -389797,7 +386677,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -389824,14 +386704,14 @@ Classes for population already exist in IDO ('organism population', I outer epithelium - + - + Wikipedia:Epidermis_(zoology) @@ -390433,7 +387313,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -390441,7 +387321,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007524 dense mesenchyme tissue - + @@ -390454,7 +387334,7 @@ Classes for population already exist in IDO ('organism population', I - + AEO @@ -390593,7 +387473,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -390613,14 +387493,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007616 layer of synovial tissue - + - + BTO @@ -390821,7 +387701,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -390847,7 +387727,7 @@ Classes for population already exist in IDO ('organism population', I trigeminal nuclear complex http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png - + @@ -390860,7 +387740,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -391030,7 +387910,7 @@ Classes for population already exist in IDO ('organism population', I - + EFO:0003626 EHDAA2:0001457 EHDAA:962 @@ -391049,14 +387929,14 @@ Classes for population already exist in IDO ('organism population', I early pharyngeal endoderm http://dev.biologists.org/content/128/22/4573.full - + - + cjm @@ -391300,7 +388180,7 @@ Classes for population already exist in IDO ('organism population', I - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -391319,14 +388199,14 @@ Classes for population already exist in IDO ('organism population', I vascular system - + - + MA @@ -391531,7 +388411,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -391583,14 +388463,14 @@ Classes for population already exist in IDO ('organism population', I post-anal tail - + - + possible exception in hemichordates cjm @@ -391755,7 +388635,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesentery that is located in the peritoneum. FMA:20570 TAO:0005129 @@ -391765,14 +388645,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007826 peritoneal mesentery - + - + FMA @@ -392139,7 +389019,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -392182,14 +389062,14 @@ Classes for population already exist in IDO ('organism population', I pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -392354,8 +389234,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -392381,11 +389261,11 @@ Classes for population already exist in IDO ('organism population', I cartilage element - + - + @@ -392398,13 +389278,13 @@ Classes for population already exist in IDO ('organism population', I - + VSAO - + VSAO @@ -392614,12 +389494,12 @@ Classes for population already exist in IDO ('organism population', I - + - + A bone that is part of a craniocervical region. EMAPA:37245 MA:0000569 @@ -392629,7 +389509,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0007914 bone of craniocervical region - + @@ -392642,7 +389522,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -393009,12 +389889,12 @@ Classes for population already exist in IDO ('organism population', I - + - + Musculature system of the pharyngeal and head regions. in MA this is restricted to skeletal muscles EMAPA:37259 @@ -393028,7 +389908,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0008229 craniocervical region musculature - + @@ -393041,7 +389921,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -393088,8 +389968,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax. EMAPA:37234 FMA:24217 @@ -393105,25 +389985,25 @@ Classes for population already exist in IDO ('organism population', I UBERON:0008231 dorsal thoracic segment of trunk - + - + - + FMA MA - + FMA @@ -393184,13 +390064,13 @@ Classes for population already exist in IDO ('organism population', I - + - + A muscle of back that is part of a dorsal thoracic segment of trunk. EMAPA:37261 MA:0000508 @@ -393199,7 +390079,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0008243 upper back muscle - + @@ -393212,7 +390092,7 @@ Classes for population already exist in IDO ('organism population', I - + MA @@ -393355,7 +390235,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that is part of a duodenum. CALOHA:TS-2087 @@ -393369,14 +390249,14 @@ Classes for population already exist in IDO ('organism population', I duodenal epithelium - + - + FMA @@ -393477,7 +390357,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -393489,7 +390369,7 @@ Classes for population already exist in IDO ('organism population', I - + An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers. EHDAA2:0000444 EHDAA:42 @@ -393505,14 +390385,14 @@ Classes for population already exist in IDO ('organism population', I The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5. inner cell mass derived epiblast - + - + Wikipedia @@ -393664,7 +390544,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -393679,7 +390559,7 @@ Classes for population already exist in IDO ('organism population', I neural tube derived brain https://github.com/obophenotype/uberon/issues/338 - + @@ -393692,7 +390572,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -393713,8 +390593,8 @@ Classes for population already exist in IDO ('organism population', I - - + + An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10 The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut. @@ -393733,11 +390613,11 @@ Classes for population already exist in IDO ('organism population', I hepatic diverticulum http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png - + - + @@ -393750,14 +390630,14 @@ Classes for population already exist in IDO ('organism population', I - + caudal part EHDAA2 - + EHDAA2 @@ -393796,13 +390676,13 @@ Classes for population already exist in IDO ('organism population', I - + BTO:0001642 uberon UBERON:0008836 liver bud - + @@ -393815,7 +390695,7 @@ Classes for population already exist in IDO ('organism population', I - + http://www.stembook.org/node/512 @@ -393896,7 +390776,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -393923,14 +390803,14 @@ Classes for population already exist in IDO ('organism population', I stomach muscularis externa - + - + MA-abduced @@ -393976,7 +390856,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -394008,7 +390888,7 @@ Classes for population already exist in IDO ('organism population', I pyloric canal https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg - + @@ -394021,7 +390901,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia @@ -394075,7 +390955,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -394100,7 +390980,7 @@ Classes for population already exist in IDO ('organism population', I pyloric gastric gland http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png - + @@ -394113,7 +390993,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia:Tubular_gland @@ -394173,7 +391053,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -394206,14 +391086,14 @@ Classes for population already exist in IDO ('organism population', I hypodermis skeletal muscle layer - + - + MP-def @@ -394314,8 +391194,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Subdivision of endoskeleton derived from pharyngeal arches. @@ -394348,24 +391228,24 @@ Classes for population already exist in IDO ('organism population', I splanchnocranium http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg - + - + - + https://github.com/obophenotype/uberon/issues/83 - + redundant Grays PMID:11237469 @@ -394483,13 +391363,13 @@ Classes for population already exist in IDO ('organism population', I - + - + Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. Intramembranous bone that forms superficially in the organism.[TAO] other AOs are not yet in sync with this classification @@ -394504,7 +391384,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0008907 dermal bone - + @@ -394523,7 +391403,7 @@ Classes for population already exist in IDO ('organism population', I - + VSAO @@ -394635,13 +391515,13 @@ Classes for population already exist in IDO ('organism population', I - + - + A parenchyma that is part of a lung. EMAPA:35522 FMA:27360 @@ -394654,7 +391534,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0008946 lung parenchyma - + @@ -394667,7 +391547,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -395131,13 +392011,13 @@ Classes for population already exist in IDO ('organism population', I - + - + Cranial ganglion which develops from an epibranchial placode. BTO:0006250 TAO:0001555 @@ -395148,7 +392028,7 @@ Classes for population already exist in IDO ('organism population', I Epibranchial ganglia orchestrate the development of the cranial neurogenic crest epibranchial ganglion - + @@ -395161,7 +392041,7 @@ Classes for population already exist in IDO ('organism population', I - + NCBIBook:NBK53175 @@ -395213,8 +392093,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Endocardium that is part of the right atrium. EHDAA2:0000274 FMA:7281 @@ -395228,24 +392108,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009129 right atrium endocardium - + - + - + EHDAA2 - + EHDAA2 @@ -395410,7 +392290,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -395427,14 +392307,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -395450,7 +392330,7 @@ Classes for population already exist in IDO ('organism population', I - + EMAPA:16549 RETIRED_EHDAA2:0001454 pharyngeal region @@ -395458,14 +392338,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009145 pharyngeal region of foregut - + - + EHDAA2 @@ -395496,8 +392376,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -395511,11 +392391,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009191 sphenoid bone pre-cartilage condensation - + - + @@ -395534,13 +392414,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 @@ -395637,12 +392517,12 @@ Classes for population already exist in IDO ('organism population', I - + - + Mesenchyme that is part of a medial nasal prominence. EHDAA2:0001077 EMAPA:16810 @@ -395651,14 +392531,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009204 medial nasal process mesenchyme - + - + EHDAA2 @@ -395893,7 +392773,7 @@ Classes for population already exist in IDO ('organism population', I - + A portion of mesenchymal tissue associated with an individual pharyngeal arch. this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. EMAPA:32755 @@ -395905,7 +392785,7 @@ Classes for population already exist in IDO ('organism population', I pharyngeal arch mesenchymal region - + @@ -395918,7 +392798,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -395965,14 +392845,14 @@ Classes for population already exist in IDO ('organism population', I - + - + An epithelium that is part of a foregut-midgut junction. EHDAA2:0000573 EMAPA:16564 @@ -395981,24 +392861,24 @@ Classes for population already exist in IDO ('organism population', I epithelium of foregut-midgut junction - + - + - + EHDAA2 - + EHDAA2 @@ -396369,7 +393249,7 @@ Classes for population already exist in IDO ('organism population', I - + A submucosa that is part of a intestine. FMA:15696 submucosa of intestine @@ -396377,14 +393257,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009566 intestinal submucosa - + - + FMA @@ -396598,7 +393478,7 @@ Classes for population already exist in IDO ('organism population', I - + A sulcus limitans of neural tube that is part of a future medulla oblongata. EHDAA2:0001100 EMAPA:17561 @@ -396606,14 +393486,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009576 medulla oblongata sulcus limitans - + - + EHDAA2 @@ -396789,12 +393669,12 @@ Classes for population already exist in IDO ('organism population', I - + - + Mesenchyme that is part of a 1st arch mandibular component. UBERON:0010043 EHDAA2:0000034 @@ -396807,14 +393687,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009584 1st arch mandibular mesenchyme - + - + EMAPA @@ -396930,9 +393810,9 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -396946,7 +393826,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009611 midbrain neural plate - + @@ -396955,20 +393835,20 @@ Classes for population already exist in IDO ('organism population', I - + - + ZFA - + ZFA @@ -396983,9 +393863,9 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -396999,7 +393879,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009614 hindbrain neural plate - + @@ -397008,20 +393888,20 @@ Classes for population already exist in IDO ('organism population', I - + - + ZFA - + ZFA @@ -397037,8 +393917,8 @@ Classes for population already exist in IDO ('organism population', I - - + + TODO - developmental relationships for lines TAO:0007044 ZFA:0007044 @@ -397048,24 +393928,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009615 midbrain hindbrain boundary neural plate - + - + - + ZFA - + https://github.com/obophenotype/uberon/issues/438 Bgee:AN @@ -397099,14 +393979,14 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -397131,24 +394011,24 @@ Classes for population already exist in IDO ('organism population', I presumptive midbrain - + - + - + ZFA - + ZFA @@ -397194,7 +394074,7 @@ Classes for population already exist in IDO ('organism population', I - + Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. A major contributor to neurocranium [PMID:16313393] EHDAA2:0000736 @@ -397211,14 +394091,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009617 head paraxial mesoderm - + - + EHDAA2 @@ -397271,7 +394151,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -397279,14 +394159,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -397472,7 +394352,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0004566 EMAPA:32911 MA:0003203 @@ -397483,14 +394363,14 @@ Classes for population already exist in IDO ('organism population', I gut mesentery https://github.com/obophenotype/uberon/issues/509 - + - + EHDAA2 @@ -397578,8 +394458,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -397596,24 +394476,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009670 rectal lumen - + - + - + cjm - + EHDAA2 @@ -397637,9 +394517,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + EHDAA2:0001371 uberon @@ -397649,15 +394529,15 @@ Classes for population already exist in IDO ('organism population', I dorsal pancreas - + - + - + @@ -397670,19 +394550,19 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 - + cjm @@ -397694,9 +394574,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + EHDAA2:0001393 uberon @@ -397706,15 +394586,15 @@ Classes for population already exist in IDO ('organism population', I ventral pancreas - + - + - + @@ -397727,19 +394607,19 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 - + cjm @@ -397766,8 +394646,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Any endocardium that is part of the right ventricle of the heart. Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. EHDAA2:0002188 @@ -397784,24 +394664,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009712 endocardium of right ventricle - + - + - + EHDAA2 - + FMA @@ -397864,7 +394744,7 @@ Classes for population already exist in IDO ('organism population', I - + Any endocardium that is part of the left ventricle of the heart. Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. EHDAA2:0002182 @@ -397880,14 +394760,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009713 endocardium of left ventricle - + - + FMA @@ -397973,7 +394853,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -397988,14 +394868,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009722 entire pharyngeal arch endoderm - + - + EHDAA2 @@ -398152,7 +395032,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -398165,7 +395045,7 @@ Classes for population already exist in IDO ('organism population', I - + A serous sac that has the pleura and the pleural cavity as parts. despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac EHDAA2:0004737 @@ -398176,24 +395056,24 @@ Classes for population already exist in IDO ('organism population', I pleural sac - + - + - + FMA - + FMA-abduced-lr @@ -398308,8 +395188,8 @@ Classes for population already exist in IDO ('organism population', I - - + + An epithelium that is part of a embryonic cloaca. cloacal epithelium EHDAA2:0004585 @@ -398317,24 +395197,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009846 embryonic cloacal epithelium - + - + - + EHDAA2 - + EHDAA2 @@ -398523,7 +395403,7 @@ Classes for population already exist in IDO ('organism population', I - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -398533,14 +395413,14 @@ Classes for population already exist in IDO ('organism population', I anterior lateral plate mesoderm - + - + ZFA @@ -398559,9 +395439,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -398581,34 +395461,34 @@ Classes for population already exist in IDO ('organism population', I UBERON:0009889 secondary heart field - + - + - + - + GO:0003129 - + PMID:17276708 - + PMID:17276708 @@ -398777,14 +395657,14 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -398797,7 +395677,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -399313,8 +396193,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. EHDAA2:0001459 EMAPA:16550 @@ -399326,11 +396206,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010046 entire pharyngeal arch associated mesenchyme - + - + @@ -399343,13 +396223,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + cjm @@ -399531,9 +396411,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -399547,34 +396427,34 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010083 future dermis - + - + - + - + EHDAA2 - + EHDAA2 - + XAO @@ -399601,9 +396481,9 @@ Classes for population already exist in IDO ('organism population', I - - - + + + @@ -399616,34 +396496,34 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010084 future diaphragm - + - + - + - + EHDAA2 - + PMID:23586979 - + PMID:23586979 @@ -399929,7 +396809,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -399947,14 +396827,14 @@ Classes for population already exist in IDO ('organism population', I post-anal tail tip - + - + MA @@ -400063,7 +396943,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400080,7 +396960,7 @@ Classes for population already exist in IDO ('organism population', I pair of dorsal aortae - + @@ -400093,7 +396973,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -400116,7 +396996,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400128,14 +397008,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010191 aortic system - + - + Wikipedia @@ -400318,7 +397198,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400336,14 +397216,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010227 future cardiac atrium - + - + ZFA @@ -400378,7 +397258,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400403,14 +397283,14 @@ Classes for population already exist in IDO ('organism population', I eyeball of camera-type eye - + - + FMA @@ -400496,7 +397376,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400506,8 +397386,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -400520,11 +397400,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010252 1st arch mandibular mesenchyme from neural crest - + - + @@ -400537,13 +397417,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 @@ -400562,7 +397442,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400572,32 +397452,32 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme. EHDAA2:0000044 uberon UBERON:0010253 1st arch maxillary mesenchyme from neural crest - + - + - + EHDAA2 - + EHDAA2 @@ -400616,7 +397496,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400627,8 +397507,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000098 @@ -400643,24 +397523,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010256 4th arch mesenchyme from neural crest - + - + - + EHDAA2 - + EHDAA2 @@ -400701,7 +397581,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400712,8 +397592,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. EHDAA2:0004077 neural crest derived arch 6 mesenchyme @@ -400723,24 +397603,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010257 6th arch mesenchyme from neural crest - + - + - + EHDAA2 - + EHDAA2 @@ -400767,7 +397647,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -400780,14 +397660,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010258 mesenchyme from rhombencephalic neural crest - + - + EHDAA2 @@ -400899,8 +397779,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -400914,11 +397794,11 @@ Classes for population already exist in IDO ('organism population', I midbrain basal plate - + - + @@ -400931,13 +397811,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + ZFA @@ -400966,7 +397846,7 @@ Classes for population already exist in IDO ('organism population', I - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -400975,14 +397855,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010286 midbrain neural tube - + - + ZFA @@ -400999,20 +397879,20 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia:Sclera#Histology uberon UBERON:0010291 layer of sclera - + - + cjm @@ -401284,7 +398164,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401300,14 +398180,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010312 immature eye - + - + definitional @@ -401561,20 +398441,20 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a limb/fin bud. uberon UBERON:0010329 paired limb/fin bud mesenchyme - + - + EHDAA2-abduced @@ -401609,20 +398489,20 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that is part of a extraembryonic membrane. uberon UBERON:0010333 extraembryonic membrane mesenchyme - + - + EHDAA2-abduced @@ -401641,7 +398521,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401651,32 +398531,32 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme. EHDAA2:0004601 uberon UBERON:0010334 maxillary process mesenchyme from neural crest - + - + - + EHDAA2 - + EHDAA2 @@ -401695,7 +398575,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401705,32 +398585,32 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme. EHDAA2:0004602 uberon UBERON:0010335 maxillary process mesenchyme from head mesenchyme - + - + - + EHDAA2 - + EHDAA2 @@ -401749,7 +398629,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401759,32 +398639,32 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. EHDAA2:0004603 uberon UBERON:0010336 mandibular process mesenchyme from neural crest - + - + - + EHDAA2 - + EHDAA2 @@ -401803,7 +398683,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401813,32 +398693,32 @@ Classes for population already exist in IDO ('organism population', I - - + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. EHDAA2:0004604 uberon UBERON:0010337 mandibular process mesenchyme from head mesenchyme - + - + - + EHDAA2 - + EHDAA2 @@ -401857,7 +398737,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401867,21 +398747,21 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme. EHDAA2:0000043 uberon UBERON:0010338 1st arch maxillary mesenchyme from head mesenchyme - + - + EHDAA2 @@ -401900,7 +398780,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401910,21 +398790,21 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000036 uberon UBERON:0010339 1st arch mandibular mesenchyme from head mesenchyme - + - + EHDAA2 @@ -401943,7 +398823,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -401954,7 +398834,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. EMAPA:16130 mesenchyme derived from head mesoderm of mesenchyme of 1st arch @@ -401962,14 +398842,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010341 1st arch mesenchyme from head mesenchyme - + - + EMAPA @@ -401994,7 +398874,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402005,7 +398885,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. EHDAA2:0000097 EMAPA:16771 @@ -402017,14 +398897,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010345 4th arch mesenchyme from head mesenchyme - + - + EHDAA2 @@ -402049,7 +398929,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402060,7 +398940,7 @@ Classes for population already exist in IDO ('organism population', I - + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. EHDAA2:0004078 head mesenchyme derived arch 6 mesenchyme @@ -402070,14 +398950,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010347 6th arch mesenchyme from head mesenchyme - + - + EHDAA2 @@ -402444,7 +399324,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402459,14 +399339,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010375 pancreas dorsal primordium - + - + EHDAA2 @@ -402495,7 +399375,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402510,14 +399390,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010376 pancreas ventral primordium - + - + EHDAA2 @@ -402551,7 +399431,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402565,7 +399445,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010377 mesenchyme from somatopleure - + @@ -402578,7 +399458,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -402611,7 +399491,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402624,7 +399504,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010378 mesenchyme from splanchnopleure - + @@ -402637,7 +399517,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -402671,7 +399551,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -402692,14 +399572,14 @@ Classes for population already exist in IDO ('organism population', I spleen trabecular artery - + - + MP @@ -403112,7 +399992,7 @@ Classes for population already exist in IDO ('organism population', I - + Skeletal element that forms as a replacement or substitution of another element or tissue. VSAO:0000135 XAO:0004016 @@ -403121,7 +400001,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010522 replacement element - + @@ -403134,7 +400014,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -403153,7 +400033,7 @@ Classes for population already exist in IDO ('organism population', I - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -403163,14 +400043,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -403706,7 +400586,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -403729,14 +400609,14 @@ Classes for population already exist in IDO ('organism population', I bone of appendage girdle complex - + - + UBERONREF:0000003 @@ -403911,7 +400791,7 @@ Classes for population already exist in IDO ('organism population', I - + Muscles of the pelvic girdle, hindlimb or pelvic fin. Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] AAO:0000218 @@ -403929,14 +400809,14 @@ Classes for population already exist in IDO ('organism population', I pelvic complex muscle - + - + prolog @@ -404004,7 +400884,7 @@ Classes for population already exist in IDO ('organism population', I - + A muscle of a pectoral girdle, pectoral fin or anterior limb. the MA class belongs here, based on its current child classes Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO] @@ -404021,14 +400901,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010891 pectoral complex muscle - + - + prolog @@ -404080,8 +400960,8 @@ Classes for population already exist in IDO ('organism population', I - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 @@ -404094,11 +400974,11 @@ Classes for population already exist in IDO ('organism population', I subdivision of skeleton - + - + @@ -404111,13 +400991,13 @@ Classes for population already exist in IDO ('organism population', I - + UBERONREF:0000003 - + VSAO @@ -404157,7 +401037,7 @@ Classes for population already exist in IDO ('organism population', I - + Skeletal element that forms around the notochord and is part of the vertebral column. we include a distinct subclass for bony vertebra In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG] @@ -404174,7 +401054,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010913 vertebral element - + @@ -404188,7 +401068,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -404252,7 +401132,7 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of either the head or the neck. NCIT:C32716 UMLS:C0448281 @@ -404262,14 +401142,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0010959 craniocervical muscle - + - + prolog @@ -404294,12 +401174,12 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -404318,7 +401198,7 @@ Classes for population already exist in IDO ('organism population', I pharyngeal arch cartilage - + @@ -404331,7 +401211,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -404375,7 +401255,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -404403,7 +401283,7 @@ Classes for population already exist in IDO ('organism population', I palatoquadrate arch - + @@ -404416,7 +401296,7 @@ Classes for population already exist in IDO ('organism population', I - + VHOG @@ -404970,7 +401850,7 @@ Classes for population already exist in IDO ('organism population', I - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system @@ -404981,7 +401861,7 @@ Classes for population already exist in IDO ('organism population', I postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -404994,7 +401874,7 @@ Classes for population already exist in IDO ('organism population', I - + cjm @@ -405034,7 +401914,7 @@ Classes for population already exist in IDO ('organism population', I - + Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. BTO:0003751 EMAPA:37970 @@ -405043,14 +401923,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011148 submucosal gland - + - + perforates @@ -405074,7 +401954,7 @@ Classes for population already exist in IDO ('organism population', I - + Subdivision of skull that consists of the facial bones. EHDAA2:0002206 EHDAA:8361 @@ -405093,7 +401973,7 @@ Classes for population already exist in IDO ('organism population', I facial skeleton http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg - + @@ -405106,7 +401986,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -405391,7 +402271,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a large intestine. FMA:15654 @@ -405405,14 +402285,14 @@ Classes for population already exist in IDO ('organism population', I lamina propria of large intestine - + - + FMA @@ -405457,7 +402337,7 @@ Classes for population already exist in IDO ('organism population', I - + A muscle layer that is part of a large intestine. FMA:14971 NCIT:C32927 @@ -405470,14 +402350,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011198 muscle layer of large intestine - + - + FMA @@ -405535,7 +402415,7 @@ Classes for population already exist in IDO ('organism population', I - + A muscle layer that is part of a small intestine. FMA:14932 NCIT:C33569 @@ -405551,14 +402431,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011201 muscle layer of small intestine - + - + FMA @@ -405716,7 +402596,7 @@ Classes for population already exist in IDO ('organism population', I - + Muscles within the eye (bulbus oculi).[AAO] AAO:0010038 EMAPA:18808 @@ -405727,14 +402607,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -405924,7 +402804,7 @@ Classes for population already exist in IDO ('organism population', I - + The part of the trunk that is in the dorsum[cjm]. In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA] EMAPA:35162 @@ -405939,7 +402819,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011270 dorsal trunk - + @@ -405952,7 +402832,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -405988,8 +402868,8 @@ Classes for population already exist in IDO ('organism population', I - - + + compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' EHDAA2:0001845 uberon @@ -405998,11 +402878,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011272 embryonic skin basal layer - + - + @@ -406015,13 +402895,13 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 - + EHDAA2 @@ -406147,7 +403027,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -406171,14 +403051,14 @@ Classes for population already exist in IDO ('organism population', I lumen of esophagus - + - + FMA @@ -406242,7 +403122,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -406260,14 +403140,14 @@ Classes for population already exist in IDO ('organism population', I paired limb/fin skeleton - + - + ISBN:9780878932504 @@ -406330,19 +403210,19 @@ Classes for population already exist in IDO ('organism population', I - - + + EHDAA2:0002120 upper jaw future lip uberon UBERON:0011592 future upper lip - + - + @@ -406355,13 +403235,13 @@ Classes for population already exist in IDO ('organism population', I - + fusion - + fusion @@ -406389,7 +403269,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -406410,14 +403290,14 @@ Classes for population already exist in IDO ('organism population', I jaw region http://eol.org/collections/11578 - + - + EMAPA FMA-abduced ZFA-abduced @@ -406437,14 +403317,14 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0001020 lower jaw future lip uberon UBERON:0011596 future lower lip - + @@ -406457,7 +403337,7 @@ Classes for population already exist in IDO ('organism population', I - + Wikipedia:Mandibular_prominence @@ -406534,14 +403414,14 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that develops_from a ectoderm and is part of a oral epithelium. EHDAA2:0004137 uberon UBERON:0011642 oral epithelium from ectoderm - + @@ -406554,7 +403434,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -407548,7 +404428,7 @@ Classes for population already exist in IDO ('organism population', I - + A muscle layer that is part of a wall of esophagus. In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle FMA:62998 @@ -407562,14 +404442,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011878 muscle layer of esophagus - + - + upper part Wikipedia:Muscular_layer @@ -407632,7 +404512,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -407674,7 +404554,7 @@ Classes for population already exist in IDO ('organism population', I anterior uvea - + @@ -407687,7 +404567,7 @@ Classes for population already exist in IDO ('organism population', I - + MP @@ -407728,7 +404608,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -407753,7 +404633,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0011899 epimysium - + @@ -407766,7 +404646,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -407819,7 +404699,7 @@ Classes for population already exist in IDO ('organism population', I - + Masses of developing blood cells attached to endothelium in the yolk sac. EHDAA2:0000177 EMAPA:16115 @@ -407830,14 +404710,14 @@ Classes for population already exist in IDO ('organism population', I yolk sac blood island - + - + EHDAA2 @@ -408698,7 +405578,7 @@ Classes for population already exist in IDO ('organism population', I - + The deep cervical artery (Profunda cervicalis) is an artery of the neck. FMA:10659 @@ -408710,14 +405590,14 @@ Classes for population already exist in IDO ('organism population', I deep cervical artery - + - + FMA @@ -408861,20 +405741,20 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -408895,7 +405775,7 @@ Classes for population already exist in IDO ('organism population', I - + A muscle layer that is part of an intestine. FMA:15697 intestinal muscularis propria @@ -408905,14 +405785,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0012367 muscle layer of intestine - + - + FMA @@ -409202,7 +406082,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -409224,7 +406104,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0012429 hematopoietic tissue - + @@ -409237,7 +406117,7 @@ Classes for population already exist in IDO ('organism population', I - + defitional @@ -409383,7 +406263,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -409400,14 +406280,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0012463 cloacal lumen - + - + cjm @@ -409597,20 +406477,20 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -409637,7 +406517,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -409657,14 +406537,14 @@ Classes for population already exist in IDO ('organism population', I skeleton of pectoral complex - + - + FMA @@ -409733,7 +406613,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -409753,14 +406633,14 @@ Classes for population already exist in IDO ('organism population', I skeleton of pelvic complex - + - + FMA @@ -409812,8 +406692,8 @@ Classes for population already exist in IDO ('organism population', I - - + + The posterior region of the neck, including the suboccipital region. nuchal nape @@ -409836,11 +406716,11 @@ Classes for population already exist in IDO ('organism population', I dorsal part of neck - + - + @@ -409853,13 +406733,13 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + FMA @@ -410688,7 +407568,7 @@ Classes for population already exist in IDO ('organism population', I - + A vein that drains a lip. SCTID:367664002 labial vein of face @@ -410699,14 +407579,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0013136 vein of lip - + - + FMA @@ -410885,7 +407765,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -410909,14 +407789,14 @@ Classes for population already exist in IDO ('organism population', I cranial cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg - + - + Wikipedia @@ -411409,7 +408289,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -411426,14 +408306,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0013525 stomach lumen - + - + FMA @@ -411484,7 +408364,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that is part of a intestinal villus. FMA:63587 intestinal villus epithelium @@ -411494,14 +408374,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0013636 epithelium of intestinal villus - + - + FMA @@ -413043,7 +409923,7 @@ Classes for population already exist in IDO ('organism population', I - + An epithelium that is part of a frontonasal prominence. EHDAA2:0004108 EMAPA:32918 @@ -413051,7 +409931,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0014702 frontonasal process epithelium - + @@ -413064,7 +409944,7 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2 @@ -413134,7 +410014,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -413149,14 +410029,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0014704 pleuroperitoneal canal lumen - + - + EHDAA2 @@ -413358,8 +410238,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -413388,24 +410268,24 @@ Classes for population already exist in IDO ('organism population', I Classification notes: May be considered an external sphincter[PMID:8224664] crus of diaphragm - + - + - + PMID:23586979 - + PMID:23586979 @@ -413894,20 +410774,20 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). uberon UBERON:0014794 pectoral appendage muscle - + - + prolog @@ -413934,20 +410814,20 @@ Classes for population already exist in IDO ('organism population', I - + Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). uberon UBERON:0014795 pelvic appendage muscle - + - + prolog @@ -414108,7 +410988,7 @@ Classes for population already exist in IDO ('organism population', I - + One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites. Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4]. EFO:0003664 @@ -414126,7 +411006,7 @@ Classes for population already exist in IDO ('organism population', I intersomitic vessel - + @@ -414139,7 +411019,7 @@ Classes for population already exist in IDO ('organism population', I - + ZFA @@ -414366,7 +411246,7 @@ Classes for population already exist in IDO ('organism population', I - + consider merging into myocardial compact layer FMA:83105 perimysial connective tissue of subepicardium @@ -414375,14 +411255,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0015128 subepicardial layer of epicardium - + - + FMA @@ -414482,7 +411362,7 @@ Classes for population already exist in IDO ('organism population', I - + A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104] the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648] @@ -414493,14 +411373,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0015152 gland of ocular region - + - + inferred @@ -414957,7 +411837,7 @@ Classes for population already exist in IDO ('organism population', I - + A basement membrane of epithelium that is part of a respiratory system. EMAPA:37570 MA:0001815 @@ -414965,14 +411845,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0015329 respiratory system basement membrane - + - + MA @@ -415034,7 +411914,7 @@ Classes for population already exist in IDO ('organism population', I - + The hepatic artery proper (also proper hepatic artery), arises from the common hepatic artery and runs alongside the portal vein and the common bile duct to form the portal triad. The hepatic artery proper gives off a small supraduodenal artery to the duodenal bulb. Then the right gastric artery comes off and runs to the left along the lesser curvature of the stomach to meet the left gastric artery, which is a branch of the celiac trunk. It subsequently gives off the cystic artery, which feeds the gallbladder, before bifurcating into the right and left hepatic arteries. Of note, the right and left hepatic arteries may demonstrate variant anatomy. A replaced right hepatic artery may arise from the superior mesenteric artery (SMA) and a replaced left hepatic artery may arise from the left gastric artery. EMAPA:37217 @@ -415049,7 +411929,7 @@ Classes for population already exist in IDO ('organism population', I proper hepatic artery - + @@ -415062,7 +411942,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -415099,13 +411979,13 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -415125,14 +412005,14 @@ Classes for population already exist in IDO ('organism population', I left hepatic artery - + - + FMA @@ -415177,13 +412057,13 @@ Classes for population already exist in IDO ('organism population', I - + - + @@ -415203,14 +412083,14 @@ Classes for population already exist in IDO ('organism population', I right hepatic artery - + - + FMA @@ -415574,7 +412454,7 @@ Classes for population already exist in IDO ('organism population', I - + A lamina propria that is part of a duodenum. EMAPA:27255 @@ -415588,14 +412468,14 @@ Classes for population already exist in IDO ('organism population', I duodenum lamina propria - + - + FMA @@ -416574,7 +413454,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -416597,7 +413477,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0016887 entire extraembryonic component - + @@ -416610,7 +413490,7 @@ Classes for population already exist in IDO ('organism population', I - + AEO @@ -417118,7 +413998,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -417136,14 +414016,14 @@ Classes for population already exist in IDO ('organism population', I skeletal musculature - + - + MA @@ -418514,7 +415394,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -418528,14 +415408,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0034710 spinal cord ventricular layer - + - + EHDAA2 @@ -419781,7 +416661,7 @@ Classes for population already exist in IDO ('organism population', I - + Any of several arteries that arise from the aorta and supply blood to the esophagus. FMA:4149 @@ -419795,7 +416675,7 @@ Classes for population already exist in IDO ('organism population', I esophageal artery - + @@ -419808,7 +416688,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -420286,7 +417166,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -420302,14 +417182,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0035763 cavity of cardiac chamber - + - + FMA @@ -420680,8 +417560,8 @@ Classes for population already exist in IDO ('organism population', I - - + + @@ -420697,24 +417577,24 @@ Classes for population already exist in IDO ('organism population', I UBERON:0035831 costal diaphragm - + - + - + PMID:23586979 - + PMID:23586979 @@ -420822,20 +417702,20 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0004070 uberon UBERON:0036072 respiratory primordium epithelium - + - + EHDAA2 @@ -420863,21 +417743,21 @@ Classes for population already exist in IDO ('organism population', I - + EHDAA2:0004071 respiratory primordium associated mesenchyme uberon UBERON:0036073 respiratory primordium mesenchyme - + - + EHDAA2 @@ -421343,12 +418223,12 @@ Classes for population already exist in IDO ('organism population', I - + - + Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall @@ -421356,7 +418236,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0036285 wall of left ventricle - + @@ -421369,7 +418249,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421394,12 +418274,12 @@ Classes for population already exist in IDO ('organism population', I - + - + Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 right ventricular wall @@ -421407,7 +418287,7 @@ Classes for population already exist in IDO ('organism population', I UBERON:0036286 wall of right ventricle - + @@ -421420,7 +418300,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421453,7 +418333,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -421465,14 +418345,14 @@ Classes for population already exist in IDO ('organism population', I UBERON:0036288 anterior wall of left ventricle - + - + FMA @@ -421707,27 +418587,27 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:14657 gallbladder wall uberon UBERON:0036343 wall of gallbladder - + - + FMA @@ -421746,19 +418626,19 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:15089 brachiocephalic arterial wall uberon UBERON:0036351 wall of brachiocephalic artery - + @@ -421771,7 +418651,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421790,19 +418670,19 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:15090 subclavian arterial wall uberon UBERON:0036352 wall of subclavian artery - + @@ -421815,7 +418695,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421834,7 +418714,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -421844,21 +418724,21 @@ Classes for population already exist in IDO ('organism population', I - + FMA:15704 anal canal wall uberon UBERON:0036362 wall of anal canal - + - + FMA @@ -421877,19 +418757,19 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:18211 pulmonary arterial wall uberon UBERON:0036422 wall of pulmonary artery - + @@ -421902,7 +418782,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421921,19 +418801,19 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:231590 uberon UBERON:0036553 wall of synovial tendon sheath - + @@ -421946,7 +418826,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -421959,20 +418839,20 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:58098 eyeball wall uberon UBERON:0036925 wall of eyeball - + @@ -421985,7 +418865,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -422004,21 +418884,21 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:63144 orbit wall uberon UBERON:0037089 wall of orbit - + @@ -422031,7 +418911,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -422050,19 +418930,19 @@ Classes for population already exist in IDO ('organism population', I - + - + FMA:66284 common carotid arterial wall uberon UBERON:0037094 wall of common carotid artery - + @@ -422075,7 +418955,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -422094,15 +418974,15 @@ Classes for population already exist in IDO ('organism population', I - + - - - + + + Wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees. FMA:7274 cardiac wall @@ -422110,15 +418990,15 @@ Classes for population already exist in IDO ('organism population', I UBERON:0037144 wall of heart - + - + - + @@ -422131,19 +419011,19 @@ Classes for population already exist in IDO ('organism population', I - + FMA - + FMA - + FMA @@ -422177,7 +419057,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -422193,14 +419073,14 @@ Classes for population already exist in IDO ('organism population', I https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + FMA Wikipedia @@ -422241,20 +419121,20 @@ Classes for population already exist in IDO ('organism population', I - + FMA:15395 uberon UBERON:0039228 sigmoid vein - + - + FMA @@ -422316,14 +419196,14 @@ Classes for population already exist in IDO ('organism population', I - + Ovarian vein, each instance of which is a tributary of some inferior vena cava that drains the right pampiniform plexus of some broad ligament. FMA:14342 uberon UBERON:0039856 right ovarian vein - + @@ -422336,7 +419216,7 @@ Classes for population already exist in IDO ('organism population', I - + FMA @@ -423272,8 +420152,8 @@ Classes for population already exist in IDO ('organism population', I - - + + A collection of Purkinje fibers that receives signals from the right and left bundle branches and innervates the ventricular cardiac muscle. The Purkinje fiber network creates synchronized contractions of the heart ventricles. Purkinje fibre network @@ -423281,11 +420161,11 @@ Classes for population already exist in IDO ('organism population', I UBERON:8000009 Purkinje fiber network - + - + @@ -423300,7 +420180,7 @@ Classes for population already exist in IDO ('organism population', I - + https://github.com/obophenotype/uberon/issues/1785 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9791-0064 @@ -423308,7 +420188,7 @@ Classes for population already exist in IDO ('organism population', I - + https://github.com/obophenotype/uberon/issues/1785 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9791-0064 @@ -424490,7 +421370,6 @@ Classes for population already exist in IDO ('organism population', I length unit - A unit which is a standard measure of the distance between two points. "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] length unit @@ -424504,7 +421383,6 @@ Classes for population already exist in IDO ('organism population', I mass unit - A unit which is a standard measure of the amount of matter/energy of a physical object. "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia] mass unit @@ -424518,7 +421396,6 @@ Classes for population already exist in IDO ('organism population', I time unit - A unit which is a standard measure of the dimension in which events occur in sequence. time derived unit "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia] @@ -431665,6 +428542,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim + + + + Obsolete Class + + + + @@ -432639,7 +429524,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Affymetrix Affymetrix supplied microarray - An organization which supplies technology, tools and protocols for use in high throughput applications + An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix @@ -432759,7 +429644,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module SVM - GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. + GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. James Malone Ryan Brinkman GenePattern module SVM @@ -432821,7 +429706,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module KMeansClustering - GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. + GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. James Malone PERSON: James Malone GenePattern module KMeansClustering @@ -432849,7 +429734,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module CARTXValidation - GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. + GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. GenePattern module CARTXValidation @@ -432885,7 +429770,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module KNNXValidation - GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. + GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. James Malone PERSON: James Malone GenePattern module KNNXValidation @@ -432912,7 +429797,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module KNN - GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. + GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module KNN @@ -432926,7 +429811,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module HierarchicalClustering - GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. + GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. James Malone PERSON: James Malone GenePattern module HierarchicalClustering @@ -432965,7 +429850,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module PCA - GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. + GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. James Malone PERSON: James Malone GenePattern module PCA @@ -433004,7 +429889,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern HeatMapViewer data visualization - The GenePattern process of generating Heat Maps from clustered data. + The GenePattern process of generating Heat Maps from clustered data. James Malone GenePattern HeatMapViewer data visualization @@ -433017,7 +429902,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern HierarchicalClusteringViewer data visualization - The GenePattern process of generating hierarchical clustering visualization from clustered data. + The GenePattern process of generating hierarchical clustering visualization from clustered data. James Malone GenePattern HierarchicalClusteringViewer data visualization @@ -433031,7 +429916,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module HeatMapViewer - A GenePattern software module which is used to generate a heatmap view of data. + A GenePattern software module which is used to generate a heatmap view of data. James Malone GenePattern module HeatMapViewer @@ -433045,7 +429930,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim GenePattern module HierarchicalClusteringViewer - A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. + A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. James Malone GenePattern module HierarchicalClusteringViewer @@ -433365,7 +430250,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Nimblegen - An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. + An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Person: Jie Zheng Nimblegen @@ -433378,7 +430263,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Pacific Biosciences - An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. + An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. Person: Jie Zheng Pacific Biosciences @@ -433391,7 +430276,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim NanoString Technologies - An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. + An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. NanoString Technologies @@ -433403,7 +430288,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Thermo Fisher Scientific - An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. + An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific Thermo Fisher Scientific @@ -433417,7 +430302,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G1: Well differentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. + A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. Chris Stoeckert, Helena Ellis G1 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet @@ -433433,7 +430318,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G2: Moderately differentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. + A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. Chris Stoeckert, Helena Ellis G2 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet @@ -433449,7 +430334,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G3: Poorly differentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. + A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G3 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet @@ -433465,7 +430350,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G4: Undifferentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. + A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G4 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet @@ -433481,7 +430366,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G1 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. Chris Stoeckert, Helena Ellis Grade 1 NCI BBRB, OBI @@ -433497,7 +430382,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G2 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. Chris Stoeckert, Helena Ellis Grade 2 NCI BBRB, OBI @@ -433513,7 +430398,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G3 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. Chris Stoeckert, Helena Ellis Grade 3 NCI BBRB, OBI @@ -433529,7 +430414,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G4 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. Chris Stoeckert, Helena Ellis Grade 4 NCI BBRB, OBI @@ -433545,7 +430430,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Low grade ovarian tumor - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. Chris Stoeckert, Helena Ellis Low grade NCI BBRB, OBI @@ -433561,7 +430446,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim High grade ovarian tumor - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. Chris Stoeckert, Helena Ellis High grade NCI BBRB, OBI @@ -433577,7 +430462,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G1 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. Chris Stoeckert, Helena Ellis G1 NCI BBRB, OBI @@ -433593,7 +430478,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G2 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. Chris Stoeckert, Helena Ellis G2 NCI BBRB, OBI @@ -433609,7 +430494,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G3 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. Chris Stoeckert, Helena Ellis G3 NCI BBRB, OBI @@ -433625,7 +430510,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim G4 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. Chris Stoeckert, Helena Ellis G4 NCI BBRB, OBI @@ -433641,7 +430526,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT0 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433656,7 +430541,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pTis (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433671,7 +430556,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433686,7 +430571,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433701,7 +430586,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433716,7 +430601,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT4a (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433731,7 +430616,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT4b (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB @@ -433746,7 +430631,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT0 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433761,7 +430646,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pTis (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433776,7 +430661,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433791,7 +430676,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1a (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433806,7 +430691,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1b (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433821,7 +430706,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433836,7 +430721,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2a (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433851,7 +430736,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2b (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433866,7 +430751,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433881,7 +430766,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT4 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB @@ -433896,7 +430781,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT0 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433911,7 +430796,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433926,7 +430811,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1a (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433941,7 +430826,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1b (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433956,7 +430841,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433971,7 +430856,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2a (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -433986,7 +430871,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2b (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434001,7 +430886,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434016,7 +430901,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3a (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434031,7 +430916,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3b (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434046,7 +430931,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3c (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434061,7 +430946,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT4 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB @@ -434076,7 +430961,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT0 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434091,7 +430976,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434106,7 +430991,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1a (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434121,7 +431006,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1b (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434136,7 +431021,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT1c (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434151,7 +431036,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434166,7 +431051,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2a (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434181,7 +431066,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2b (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434196,7 +431081,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT2c (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434211,7 +431096,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434226,7 +431111,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3a (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434241,7 +431126,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3b (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434256,7 +431141,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pT3c (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB @@ -434271,7 +431156,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN0 (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434286,7 +431171,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1 (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434301,7 +431186,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1a (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434316,7 +431201,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1b (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434331,7 +431216,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1c (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434346,7 +431231,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN2 (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434361,7 +431246,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN2a (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434376,7 +431261,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN2b (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB @@ -434391,7 +431276,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN0 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. + A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB @@ -434406,7 +431291,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB @@ -434421,7 +431306,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN2 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB @@ -434436,7 +431321,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN3 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB @@ -434451,7 +431336,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN0 (kidney) - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB @@ -434466,7 +431351,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1 (kidney) - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB @@ -434481,7 +431366,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN0 (ovary) - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB @@ -434496,7 +431381,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pN1 (ovary) - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB @@ -434511,7 +431396,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM0 (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB @@ -434526,7 +431411,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1 (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB @@ -434541,7 +431426,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1a (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB @@ -434556,7 +431441,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1b (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB @@ -434571,7 +431456,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1 (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB @@ -434586,7 +431471,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1a (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB @@ -434601,7 +431486,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1b (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB @@ -434616,7 +431501,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM0 (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434631,7 +431516,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1 (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434646,7 +431531,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1a (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434661,7 +431546,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1b (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434676,7 +431561,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1 (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434691,7 +431576,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1a (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434706,7 +431591,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1b (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB @@ -434721,7 +431606,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM0 (kidney) - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB @@ -434736,7 +431621,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1 (kidney) - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB @@ -434751,7 +431636,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1 (kidney) - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB @@ -434766,7 +431651,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM0 (ovary) - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB @@ -434781,7 +431666,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim cM1 (ovary) - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB @@ -434796,7 +431681,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim pM1 (ovary) - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB @@ -434811,7 +431696,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Occult Carcinoma (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. + A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. Chris Stoeckert, Helena Ellis Occult Carcinoma http://www.medilexicon.com/dictionary/14371 @@ -434827,7 +431712,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 0 (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. + A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. Chris Stoeckert, Helena Ellis Stage 0 https://en.wikipedia.org/wiki/Cancer_staging @@ -434843,7 +431728,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage I (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. + A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. Chris Stoeckert, Helena Ellis Stage I https://en.wikipedia.org/wiki/Cancer_staging @@ -434859,7 +431744,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIA (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cancer_staging @@ -434875,7 +431760,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIB (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cancer_staging @@ -434891,7 +431776,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIC (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. Chris Stoeckert, Helena Ellis Stage IIC https://en.wikipedia.org/wiki/Cancer_staging @@ -434907,7 +431792,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIIA (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cancer_staging @@ -434923,7 +431808,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIIB (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cancer_staging @@ -434939,7 +431824,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIIC (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. Chris Stoeckert, Helena Ellis Stage IIIC https://en.wikipedia.org/wiki/Cancer_staging @@ -434955,7 +431840,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IVA (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cancer_staging @@ -434971,7 +431856,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IVB (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cancer_staging @@ -434987,7 +431872,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. Chris Stoeckert, Helena Ellis Stage IA https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435003,7 +431888,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IA1 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. Chris Stoeckert, Helena Ellis Stage IA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435019,7 +431904,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IA2 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. Chris Stoeckert, Helena Ellis Stage IA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435035,7 +431920,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA Chris Stoeckert, Helena Ellis Stage IB https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435051,7 +431936,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IB1 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB1 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435067,7 +431952,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IB2 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB2 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435083,7 +431968,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435099,7 +431984,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIA1 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435115,7 +432000,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIA2 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435131,7 +432016,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435147,7 +432032,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIIA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435163,7 +432048,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IIIB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435179,7 +432064,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IVA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435195,7 +432080,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage IVB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cervical_cancer_staging @@ -435211,7 +432096,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 1 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435227,7 +432112,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 1A (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435243,7 +432128,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 1B (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435259,7 +432144,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 1C (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435275,7 +432160,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 2 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435291,7 +432176,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 2A (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435307,7 +432192,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 2B (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435323,7 +432208,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 2C (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435339,7 +432224,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 3 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). Chris Stoeckert, Helena Ellis Stage 3 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435355,7 +432240,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 3A (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435371,7 +432256,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 3B (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435387,7 +432272,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 3C (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). Chris Stoeckert, Helena Ellis Stage 3C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435403,7 +432288,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage 4 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. Chris Stoeckert, Helena Ellis Stage 4 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435419,7 +432304,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Stage Unknown (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). Chris Stoeckert, Helena Ellis Stage Unknown https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ @@ -435435,7 +432320,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 3: symptomatic in bed more than 50% of the day but not bed ridden - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435450,7 +432335,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 2: symptomatic but in bed less than 50% of the day - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435465,7 +432350,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 4: bed ridden - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435480,7 +432365,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 0: asymptomatic - An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. + An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435495,7 +432380,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 1: symptomatic but fully ambulatory - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435510,7 +432395,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 100: asymptomatic - A Karnofsky score vaue specification indicating that a patient is asymptomatic. + A Karnofsky score vaue specification indicating that a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435525,7 +432410,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 80-90: symptomatic but fully ambulatory - A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. + A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435540,7 +432425,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 60-70: symptomatic but in bed less than 50% of the day - A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. + A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435555,7 +432440,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden - A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. + A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -435570,7 +432455,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Oxford Nanopore Technologies - An organization that is developing and selling nanopore sequencing products and is based in the UK. + An organization that is developing and selling nanopore sequencing products and is based in the UK. James A. Overton https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies Oxford Nanopore Technologies @@ -435584,7 +432469,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim BioGents - An organization that manufactures mosquito traps and other mosquito control products. + An organization that manufactures mosquito traps and other mosquito control products. John Judkins WEB:https://eu.biogents.com/about-biogents/ BioGents @@ -435598,7 +432483,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim Abbott - A manufacturer of rapid point-of-care assay devices. + A manufacturer of rapid point-of-care assay devices. John Judkins ORCID:0000-0001-6595-0902 WEB:https://www.globalpointofcare.abbott/en/about.html https://github.com/obi-ontology/obi/issues/1456 @@ -435613,7 +432498,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim J. Mitra - A manufacturer of in vitro diagnostic assay kits in India. + A manufacturer of in vitro diagnostic assay kits in India. John Judkins ORCID:0000-0001-6595-0902 WEB:https://jmitra.co.in/about-us/ https://github.com/obi-ontology/obi/issues/1456 @@ -435628,7 +432513,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim InBios - A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases. + A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases. John Judkins ORCID:0000-0001-6595-0902 WEB:https://inbios.com/about/ https://github.com/obi-ontology/obi/issues/1456 @@ -435640,6 +432525,7 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. @@ -435650,6 +432536,20 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim + + + + + The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. + This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). + + https://github.com/information-artifact-ontology/ontology-metadata/issues/136 + https://orcid.org/0000-0002-4142-7153 + domain entity does not exist + + + + @@ -436922,9 +433822,6 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim "A dosage unit which is equal to 1 milligram per day of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC] milligram per kilogram per day - - - @@ -437398,14 +434295,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + - + @@ -437419,14 +434316,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + PMID:16417468 - + @@ -437545,14 +434442,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -437566,14 +434463,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -437767,14 +434664,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA-abduced-lr - + @@ -437788,14 +434685,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + definitional - + @@ -437809,14 +434706,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest - + @@ -437875,14 +434772,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + only in species that have a stomach - + @@ -437926,14 +434823,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + Wikipedia:Vitelline_vein - + @@ -437977,14 +434874,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438013,14 +434910,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + Wikipedia:Vitelline_vein - + @@ -438034,15 +434931,15 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + may be present in other parts in other species FMA - + @@ -438116,15 +435013,15 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + right arch 4 in human embryology.ch - + @@ -438138,14 +435035,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438159,14 +435056,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + Wikipedia:Vitelline_vein - + @@ -438180,14 +435077,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + Wikipedia - + @@ -438201,14 +435098,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + PMID:22179203 - + @@ -438222,14 +435119,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438243,14 +435140,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438264,14 +435161,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438285,14 +435182,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438306,14 +435203,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438327,14 +435224,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438348,14 +435245,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438369,14 +435266,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438390,14 +435287,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438438,14 +435335,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438519,14 +435416,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + https://github.com/obophenotype/uberon/wiki/The-neural-crest - + @@ -438540,14 +435437,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438561,14 +435458,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438582,14 +435479,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + @@ -438620,14 +435517,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + cjm - + @@ -438673,14 +435570,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + PMID:16417468 - + @@ -438694,14 +435591,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + PMID:16417468 - + @@ -438715,15 +435612,15 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + AAO https://github.com/geneontology/go-ontology/issues/16143 - + @@ -438752,14 +435649,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + teleosts - + @@ -438773,14 +435670,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + Mammals - + @@ -438794,14 +435691,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + conservatively place at deuterostome, excluding acoelomates - + @@ -438890,14 +435787,14 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim - + - + FMA - + diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 9062c31..d5f28e6 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for rbo # Generated using ontology-development-kit -# ODK Version: v1.3.0 +# ODK Version: v1.4.3 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use rbo.Makefile instead @@ -15,11 +15,13 @@ # ---------------------------------------- # these can be overwritten on the command line +OBOBASE= http://purl.obolibrary.org/obo URIBASE= http://purl.obolibrary.org/obo ONT= rbo -ONTBASE= $(URIBASE)/$(ONT) +ONTBASE= http://purl.obolibrary.org/obo/rbo EDIT_FORMAT= owl SRC = $(ONT)-edit.$(EDIT_FORMAT) +MAKE_FAST= $(MAKE) IMP=false PAT=false COMP=false MIR=false CATALOG= catalog-v001.xml ROBOT= robot --catalog $(CATALOG) @@ -32,26 +34,29 @@ MIRRORDIR= mirror IMPORTDIR= imports SUBSETDIR= subsets SCRIPTSDIR= ../scripts +UPDATEREPODIR= target SPARQLDIR = ../sparql COMPONENTSDIR = components REPORT_FAIL_ON = None REPORT_LABEL = -l true REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = -SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri +SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms -ODK_VERSION_MAKEFILE = v1.3.0 +ODK_VERSION_MAKEFILE = v1.4.3 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') VERSION= $(TODAY) ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION) +ANNOTATE_CONVERT_FILE = annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@ OTHER_SRC = $(COMPONENTSDIR)/all_templates.owl ONTOLOGYTERMS = $(TMPDIR)/ontologyterms.txt +EDIT_PREPROCESSED = $(TMPDIR)/$(ONT)-preprocess.owl FORMATS = $(sort owl owl) FORMATS_INCL_TSV = $(sort $(FORMATS) tsv) -RELEASE_ARTEFACTS = $(sort $(ONT)-full $(ONT)-base $(ONT)-base $(ONT)-full) +RELEASE_ARTEFACTS = $(sort $(ONT)-full $(ONT)-base ) # ---------------------------------------- # Top-level targets @@ -60,15 +65,27 @@ RELEASE_ARTEFACTS = $(sort $(ONT)-full $(ONT)-base $(ONT)-base $(ONT)-full) .PHONY: .FORCE .PHONY: all -all: odkversion test all_assets +all: all_odk + +.PHONY: all_odk +all_odk: odkversion test all_assets .PHONY: test -test: odkversion sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt - $(ROBOT) reason --input $(SRC) --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural --output test.owl && rm test.owl && echo "Success" +test: odkversion reason_test sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt + echo "Finished running all tests successfully." + +.PHONY: release_diff +release_diff: $(REPORTDIR)/release-diff.md + +.PHONY: reason_test +reason_test: $(EDIT_PREPROCESSED) + $(ROBOT) reason --input $< --reasoner ELK --equivalent-classes-allowed all \ + --exclude-tautologies structural --output test.owl && rm test.owl .PHONY: odkversion odkversion: - echo "ODK Makefile version: $(ODK_VERSION_MAKEFILE) (this is the version of the ODK with which this Makefile was generated, not the version of the ODK you are running)" &&\ + echo "ODK Makefile version: $(ODK_VERSION_MAKEFILE) (this is the version of the ODK with which this Makefile was generated, \ + not the version of the ODK you are running)" &&\ echo "ROBOT version (ODK): " && $(ROBOT) --version $(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR): @@ -91,7 +108,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = ro bfo chebi pato chmo envo pco obi uo doid uberon cob go efo ncbitaxon +IMPORTS = ro bfo chebi pato chmo envo pco obi uo doid uberon cob go efo IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -114,6 +131,19 @@ SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n .PHONY: all_subsets all_subsets: $(SUBSET_FILES) +# ---------------------------------------- +# Mapping assets +# ---------------------------------------- + + +MAPPINGS = + +MAPPING_FILES = $(patsubst %, $(MAPPINGDIR)/%.sssom.tsv, $(MAPPINGS)) + +.PHONY: all_mappings +all_mappings: $(MAPPING_FILES) + + # ---------------------------------------- # QC Reports & Utilities # ---------------------------------------- @@ -132,7 +162,7 @@ all_reports: custom_reports robot_reports # ROBOT OWL Profile checking # ---------------------------------------- -# The conversion to functional syntax is necessary to avoid undeclared entity violations. +# The merge step is necessary to avoid undeclared entity violations. $(REPORTDIR)/validate_profile_owl2dl_%.txt: % | $(REPORTDIR) $(TMPDIR) $(ROBOT) merge -i $< convert -f ofn -o $(TMPDIR)/validate.ofn $(ROBOT) validate-profile --profile DL -i $(TMPDIR)/validate.ofn -o $@ || { cat $@ && exit 1; } @@ -150,9 +180,10 @@ validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql) -sparql_test: $(SRC) catalog-v001.xml | $(REPORTDIR) +sparql_test: $(EDIT_PREPROCESSED) catalog-v001.xml | $(REPORTDIR) ifneq ($(SPARQL_VALIDATION_QUERIES),) - $(ROBOT) verify --catalog catalog-v001.xml -i $< --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) + + $(ROBOT) verify --catalog catalog-v001.xml -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) endif # ---------------------------------------- @@ -173,33 +204,41 @@ ASSETS = \ $(IMPORT_FILES) \ $(MAIN_FILES) \ $(REPORT_FILES) \ - $(SUBSET_FILES) + $(SUBSET_FILES) \ + $(MAPPING_FILES) RELEASE_ASSETS = \ $(MAIN_FILES) \ $(SUBSET_FILES) .PHONY: all_assets -all_assets: $(ASSETS) +all_assets: $(ASSETS) .PHONY: show_assets show_assets: echo $(ASSETS) du -sh $(ASSETS) +check_rdfxml_%: % + @check-rdfxml $< + +.PHONY: check_rdfxml_assets +check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl) + # ---------------------------------------- # Release Management # ---------------------------------------- -CLEANFILES=$(MAIN_FILES) $(SRCMERGED) +CLEANFILES=$(MAIN_FILES) $(SRCMERGED) $(EDIT_PREPROCESSED) # This should be executed by the release manager whenever time comes to make a release. # It will ensure that all assets/files are fresh, and will copy to release folder .PHONY: prepare_release -prepare_release: all +prepare_release: all_odk rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\ rm -f $(CLEANFILES) &&\ - echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab" + echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release \ + on your git hosting site such as GitHub or GitLab" .PHONY: prepare_initial_release prepare_initial_release: all_assets @@ -207,6 +246,18 @@ prepare_initial_release: all_assets rm -f $(patsubst %, ./%, $(CLEANFILES)) &&\ cd $(RELEASEDIR) && git add $(RELEASE_ASSETS) +.PHONY: prepare_release_fast +prepare_release_fast: + $(MAKE) prepare_release IMP=false PAT=false MIR=false COMP=false + +CURRENT_RELEASE=$(ONTBASE).owl + +$(TMPDIR)/current-release.owl: + wget $(CURRENT_RELEASE) -O $@ + +$(REPORTDIR)/release-diff.md: $(ONT).owl $(TMPDIR)/current-release.owl + $(ROBOT) diff --labels true --left $(TMPDIR)/current-release.owl --right $(ONT).owl -f markdown -o $@ + # ------------------------ # Imports: Seeding system # ------------------------ @@ -215,10 +266,13 @@ prepare_initial_release: all_assets IMPORTSEED=$(TMPDIR)/seed.txt PRESEED=$(TMPDIR)/pre_seed.txt -$(SRCMERGED): $(SRC) $(OTHER_SRC) +$(SRCMERGED): $(EDIT_PREPROCESSED) $(OTHER_SRC) $(ROBOT) remove --input $< --select imports --trim false \ merge $(patsubst %, -i %, $(OTHER_SRC)) -o $@ +$(EDIT_PREPROCESSED): $(SRC) + $(ROBOT) convert --input $< --format ofn --output $@ + $(PRESEED): $(SRCMERGED) $(ROBOT) query -f csv -i $< --query ../sparql/terms.sparql $@.tmp &&\ cat $@.tmp | sort | uniq > $@ @@ -250,8 +304,8 @@ $(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \ - query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \ - annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ + $(ANNOTATE_CONVERT_FILE); fi .PRECIOUS: $(IMPORTDIR)/%_import.owl @@ -263,6 +317,10 @@ $(IMPORTDIR)/chebi_import.owl: $(MIRRORDIR)/chebi.owl $(IMPORTDIR)/pato_import.owl: $(MIRRORDIR)/pato.owl echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in rbo.Makefile!" && false +## Module for ontology: chmo + +$(IMPORTDIR)/chmo_import.owl: $(MIRRORDIR)/chmo.owl + echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in rbo.Makefile!" && false ## Module for ontology: envo $(IMPORTDIR)/envo_import.owl: $(MIRRORDIR)/envo.owl @@ -285,38 +343,32 @@ $(IMPORTDIR)/cob_import.owl: $(MIRRORDIR)/cob.owl echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in rbo.Makefile!" && false ## Module for ontology: go -$(IMPORTDIR)/go_import.owl: $(MIRRORDIR)/go.owl $(IMPORTDIR)/go_terms_combined.txt - if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T $(IMPORTDIR)/go_terms_combined.txt --force true --individuals include --method BOT \ - query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \ - annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi - +$(IMPORTDIR)/go_import.owl: $(MIRRORDIR)/go.owl + echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in rbo.Makefile!" && false ## Module for ontology: efo $(IMPORTDIR)/efo_import.owl: $(MIRRORDIR)/efo.owl echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in rbo.Makefile!" && false -## Module for ontology: ncbitaxon -$(IMPORTDIR)/ncbitaxon_import.owl: $(MIRRORDIR)/ncbitaxon.owl - echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in rbo.Makefile!" && false .PHONY: refresh-imports refresh-imports: - make IMP=true MIR=true PAT=false IMP_LARGE=true all_imports -B + $(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=true all_imports -B .PHONY: no-mirror-refresh-imports no-mirror-refresh-imports: - make IMP=true MIR=false PAT=false IMP_LARGE=true all_imports -B + $(MAKE) IMP=true MIR=false PAT=false IMP_LARGE=true all_imports -B .PHONY: refresh-imports-excluding-large refresh-imports-excluding-large: - make IMP=true MIR=true PAT=false IMP_LARGE=false all_imports -B + $(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=false all_imports -B .PHONY: refresh-% refresh-%: - make IMP=true IMP_LARGE=true MIR=true PAT=false $(IMPORTDIR)/$*_import.owl -B + $(MAKE) IMP=true IMP_LARGE=true MIR=true PAT=false $(IMPORTDIR)/$*_import.owl -B .PHONY: no-mirror-refresh-% no-mirror-refresh-%: - make IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B + $(MAKE) IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B # ---------------------------------------- @@ -326,19 +378,35 @@ no-mirror-refresh-%: COMP=true # Global parameter to bypass component generation -$(COMPONENTSDIR)/%: | $(COMPONENTSDIR) - touch $@ -.PRECIOUS: $(COMPONENTSDIR)/% +.PHONY: all_components +all_components: $(OTHER_SRC) +.PHONY: recreate-components +recreate-components: + $(MAKE) COMP=true IMP=false MIR=true PAT=true IMP_LARGE=false all_components -B +.PHONY: no-mirror-recreate-components +no-mirror-recreate-components: + $(MAKE) COMP=true IMP=false MIR=false PAT=true IMP_LARGE=false all_components -B +.PHONY: recreate-% +recreate-%: + $(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=true PAT=true $(COMPONENTSDIR)/$*.owl -B + +.PHONY: no-mirror-recreate-% +no-mirror-recreate-%: + $(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=false PAT=true $(COMPONENTSDIR)/$*.owl -B + +$(COMPONENTSDIR)/%: | $(COMPONENTSDIR) + touch $@ +.PRECIOUS: $(COMPONENTSDIR)/% # ---------------------------------------- # Mirroring upstream ontologies # ---------------------------------------- -IMP=false# Global parameter to bypass import generation +IMP=true # Global parameter to bypass import generation MIR=false # Global parameter to bypass mirror generation IMP_LARGE=false # Global parameter to bypass handling of large imports @@ -348,109 +416,129 @@ IMP_LARGE=false # Global parameter to bypass handling of large imports .PHONY: mirror-ro .PRECIOUS: $(MIRRORDIR)/ro.owl mirror-ro: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ro.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: bfo .PHONY: mirror-bfo .PRECIOUS: $(MIRRORDIR)/bfo.owl mirror-bfo: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/bfo.owl --create-dirs -o $(MIRRORDIR)/bfo.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/bfo.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/bfo.owl --create-dirs -o $(MIRRORDIR)/bfo.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/bfo.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: chebi .PHONY: mirror-chebi .PRECIOUS: $(MIRRORDIR)/chebi.owl mirror-chebi: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L --connect-timeout 500.0 --max-time 36000 $(URIBASE)/chebi.owl --create-dirs -o $(MIRRORDIR)/chebi.owl && $(ROBOT) convert -i $(MIRRORDIR)/chebi.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/chebi.owl --create-dirs -o $(MIRRORDIR)/chebi.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/chebi.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: pato .PHONY: mirror-pato .PRECIOUS: $(MIRRORDIR)/pato.owl mirror-pato: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/pato.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pato.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: chmo .PHONY: mirror-chmo .PRECIOUS: $(MIRRORDIR)/chmo.owl mirror-chmo: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/chmo.owl --create-dirs -o $(MIRRORDIR)/chmo.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/chmo.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/chmo.owl --create-dirs -o $(MIRRORDIR)/chmo.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/chmo.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: envo .PHONY: mirror-envo .PRECIOUS: $(MIRRORDIR)/envo.owl mirror-envo: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/envo.owl --create-dirs -o $(MIRRORDIR)/envo.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/envo.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/envo.owl --create-dirs -o $(MIRRORDIR)/envo.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/envo.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: pco .PHONY: mirror-pco .PRECIOUS: $(MIRRORDIR)/pco.owl mirror-pco: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/pco.owl --create-dirs -o $(MIRRORDIR)/pco.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/pco.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pco.owl --create-dirs -o $(MIRRORDIR)/pco.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/pco.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: obi .PHONY: mirror-obi .PRECIOUS: $(MIRRORDIR)/obi.owl mirror-obi: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: uo .PHONY: mirror-uo .PRECIOUS: $(MIRRORDIR)/uo.owl mirror-uo: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/uo.owl --create-dirs -o $(MIRRORDIR)/uo.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/uo.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/uo.owl --create-dirs -o $(MIRRORDIR)/uo.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/uo.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: doid .PHONY: mirror-doid .PRECIOUS: $(MIRRORDIR)/doid.owl mirror-doid: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/doid/subsets/DO_RAD_slim.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/doid/subsets/DO_RAD_slim.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: uberon .PHONY: mirror-uberon .PRECIOUS: $(MIRRORDIR)/uberon.owl mirror-uberon: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/uberon.owl --create-dirs -o $(MIRRORDIR)/uberon.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/uberon.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/uberon.owl --create-dirs -o $(MIRRORDIR)/uberon.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/uberon.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: cob .PHONY: mirror-cob .PRECIOUS: $(MIRRORDIR)/cob.owl mirror-cob: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/cob.owl --create-dirs -o $(MIRRORDIR)/cob.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/cob.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cob.owl --create-dirs -o $(MIRRORDIR)/cob.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/cob.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: go .PHONY: mirror-go .PRECIOUS: $(MIRRORDIR)/go.owl mirror-go: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(URIBASE)/go.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(OBOBASE)/go.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: efo .PHONY: mirror-efo .PRECIOUS: $(MIRRORDIR)/efo.owl mirror-efo: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://www.ebi.ac.uk/efo/efo.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi - - -## ONTOLOGY: ncbitaxon -.PHONY: mirror-ncbitaxon -.PRECIOUS: $(MIRRORDIR)/ncbitaxon.owl -mirror-ncbitaxon: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ncbitaxon.owl --create-dirs -o $(MIRRORDIR)/ncbitaxon.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/ncbitaxon.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://www.ebi.ac.uk/efo/efo.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) - if [ $(IMP) = true ] && [ $(MIR) = true ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." && cp $(TMPDIR)/mirror-$*.owl $@; fi; fi + if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ + cp $(TMPDIR)/mirror-$*.owl $@; fi; fi @@ -468,9 +556,6 @@ $(SUBSETDIR)/%.owl: $(ONT).owl | $(SUBSETDIR) .PRECIOUS: $(SUBSETDIR)/%.owl -$(SUBSETDIR)/%.obo: $(SUBSETDIR)/%.owl - $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo - # --------------------------------------------- # Sparql queries: Table exports / Query Reports @@ -480,9 +565,9 @@ SPARQL_EXPORTS_ARGS = $(foreach V,$(SPARQL_EXPORTS),-s $(SPARQLDIR)/$(V).sparql # This combines all into one single command .PHONY: custom_reports -custom_reports: $(SRC) | $(REPORTDIR) +custom_reports: $(EDIT_PREPROCESSED) | $(REPORTDIR) ifneq ($(SPARQL_EXPORTS_ARGS),) - $(ROBOT) query -f tsv -i $< $(SPARQL_EXPORTS_ARGS) + $(ROBOT) query -f tsv --use-graphs true -i $< $(SPARQL_EXPORTS_ARGS) endif # ---------------------------------------- @@ -490,12 +575,6 @@ endif # ---------------------------------------- -$(ONT)-full.obo: $(ONT)-full.owl - $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo -$(ONT)-base.obo: $(ONT)-base.owl - $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo -# We always want a base - even if it is not explicitly configured.. -# We always want a full release - even if it is not explicitly configured.. # ---------------------------------------- # Release artefacts: main release artefacts # ---------------------------------------- @@ -504,48 +583,51 @@ $(ONT).owl: $(ONT)-full.owl $(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ convert -o $@.tmp.owl && mv $@.tmp.owl $@ -$(ONT).obo: $(ONT).owl - $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo # ----------------------------------------------------- # Release artefacts: variants (base, full, simple, etc) # ----------------------------------------------------- SHARED_ROBOT_COMMANDS = -$(ONTOLOGYTERMS): $(SRC) $(OTHER_SRC) - touch $(ONTOLOGYTERMS) && \ - $(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/rbo_terms.sparql $@ - - - - - +$(ONTOLOGYTERMS): $(SRCMERGED) + $(ROBOT) query -f csv -i $< --query ../sparql/rbo_terms.sparql $@ +# ROBOT pipeline that merges imports, including components. +ROBOT_RELEASE_IMPORT_MODE=$(ROBOT) merge --input $< +# ROBOT pipeline that removes imports, then merges components. This is for release artefacts that start from "base" +ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --trim false merge $(patsubst %, -i %, $(OTHER_SRC)) -# base: OTHER sources of interest, such as definitions owl -$(ONT)-base.owl: $(SRC) $(OTHER_SRC) - $(ROBOT) remove --input $< --select imports --trim false \ - merge $(patsubst %, -i %, $(OTHER_SRC)) \ - $(SHARED_ROBOT_COMMANDS) annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ +# base: All the axioms as they are editted by the editors, excluding reasoning +$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) + $(ROBOT_RELEASE_IMPORT_MODE_BASE) \ + $(SHARED_ROBOT_COMMANDS) \ + annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ --output $@.tmp.owl && mv $@.tmp.owl $@ - -# Full: The full artefacts with imports merged, reasoned -$(ONT)-full.owl: $(SRC) $(OTHER_SRC) $(IMPORT_FILES) - $(ROBOT) merge --input $< \ +# Full: The full artefacts with imports merged, reasoned. +$(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural \ relax \ reduce -r ELK \ $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@ - # ---------------------------------------- # Debugging Tools # ---------------------------------------- -explain_unsat: $(SRC) - $(ROBOT) explain -i $(SRC) -M unsatisfiability --unsatisfiable random:10 --explanation $(TMPDIR)/$@.md +explain_unsat: $(EDIT_PREPROCESSED) + $(ROBOT) explain -i $< -M unsatisfiability --unsatisfiable random:10 --explanation $(TMPDIR)/$@.md + + +RELEASE_ASSETS_AFTER_RELEASE=$(foreach n,$(RELEASE_ASSETS), ../../$(n)) +GHVERSION=v$(VERSION) +.PHONY: public_release +public_release: + @test $(GHVERSION) + ls -alt $(RELEASE_ASSETS_AFTER_RELEASE) + gh release create $(GHVERSION) --title "$(VERSION) Release" --draft $(RELEASE_ASSETS_AFTER_RELEASE) --generate-notes # ---------------------------------------- # General Validation @@ -560,7 +642,7 @@ validate-tsv: $(TSV) | $(TMPDIR) done validate-all-tsv: $(ALL_TSV_FILES) - make validate-tsv TSV="$^" + $(MAKE) validate-tsv TSV="$^" # ---------------------------------------- # Editors Utilities @@ -588,6 +670,7 @@ update_repo: clean: [ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/* [ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/* + [ -n "$(UPDATEREPODIR)" ] && [ $(UPDATEREPODIR) != "." ] && [ $(UPDATEREPODIR) != "/" ] && [ $(UPDATEREPODIR) != ".." ] && [ -d ./$(UPDATEREPODIR) ] && rm -rf ./$(UPDATEREPODIR)/* rm -f $(CLEANFILES) .PHONY: help @@ -603,15 +686,18 @@ Usage: [IMAGE=(odklite|odkfull)] [ODK_DEBUG=yes] sh run.sh make [(IMP|MIR|IMP_LA Core commands: * prepare_release: Run the entire release pipeline. Use make IMP=false prepare_release to avoid rerunning the imports +* prepare_release_fast: Run the entire release pipeline without refreshing imports, recreating components or recompiling patterns. * update_repo: Update the ODK repository setup using the config file rbo-odk.yaml * test: Running all validation tests * odkversion: Show the current version of the ODK Makefile and ROBOT. * clean: Delete all temporary files * help: Print ODK Usage information +* public_release: Uploads the release file to a release management system, such as GitHub releases. Must be configured. Imports management: * refresh-imports: Refresh all imports and mirrors. +* recreate-components: Recreate all components. * no-mirror-refresh-imports: Refresh all imports without downloading mirrors. * refresh-imports-excluding-large: Refresh all imports and mirrors, but skipping the ones labelled as 'is_large'. * refresh-%: Refresh a single import, i.e. refresh-go will refresh 'imports/go_import.owl'. @@ -624,6 +710,7 @@ Editor utilities: * explain_unsat: If you have unsatisfiable classes, this command will create a markdown file (tmp/explain_unsat.md) which will explain all your unsatisfiable classes * validate-all-tsv: Check all your tsv files for possible problems in syntax. Use ALL_TSV_FILES variable to list files * validate-tsv: Check a tsv file for syntactic problems with tsvalid. Use TSV variable to pass filepath, e.g. make TSV=../my.tsv validate-tsv. +* release_diff: Create a diff between the current release and the new release Additional build commands (advanced users) * all: Run the entire pipeline (like prepare_release), but without copying the release files to the release directory. @@ -631,10 +718,12 @@ Additional build commands (advanced users) * custom_reports: Generate all custom sparql reports you have configured in your rbo-odk.yaml file. * all_assets: Build all assets * show_assets: Print a list of all assets that would be build by the release pipeline +* all_mappings: Update all SSSOM mapping sets Additional QC commands (advanced users) * robot_reports: Run all configured ROBOT reports * validate_profile_%: Run an OWL2 DL profile validation check, for example validate_profile_rbo-edit.owl. +* reason_test: Run a basic reasoning test Examples: * sh run.sh make IMP=false prepare_release diff --git a/src/ontology/components/all_templates.owl b/src/ontology/components/all_templates.owl index fbdc170..74a25ca 100644 --- a/src/ontology/components/all_templates.owl +++ b/src/ontology/components/all_templates.owl @@ -9,7 +9,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -43,6 +43,12 @@ + + + + + + @@ -90,9 +96,9 @@ - + - + has atomic number @@ -472,9 +478,9 @@ - + The amount of ionizing radiation to which a member of the population on Earth is exposed from natural sources, such as terrestrial radiation from naturally-occurring radionuclides in the soil, cosmic radiation originating in outer space, and naturally-occurring ra - background ionizing radiation + ionizing background radiation @@ -2965,7 +2971,16 @@ - Atomic nuclei, with atomic number 2 or greater and kinetic energy imparted by natural or artificial means + A type of ionizing radiation consisting of charged particles that are relatively massive compared to other types of radiation, such as alpha, beta, and gamma radiation. Heavy ion radiation is composed of atomic nuclei that have been stripped of their electrons, resulting in positively charged particles. + Heavy ion radiation has several notable characteristics and contexts: + +High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. + +Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation. + +Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. + +In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. heavy ion radiation @@ -4011,7 +4026,7 @@ https://orcid.org/0000-0001-9227-0670 ambient radiation background radiation - anthropogenic background radiation + anthropogenic ionizing background radiation @@ -4023,7 +4038,7 @@ Radiation originating in the terrestrial or extra-terrestrial environment. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 - natural background radiation + natural ionizing background radiation @@ -4087,6 +4102,81 @@ + + + + + thermal neutron + A neutron that has (by collision with other particles) reached an energy state equal to that of its surroundings, typically on the order of 0.025 eV. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + https://www.nrc.gov/reading-rm/basic-ref/glossary/neutron-thermal.html + thermal neutron + + + + + + + + + epithermal neutron + a neutron with energy greater than a thermal neutron, but less than a fast neutron. The approximate energy range is 0.025-0.4 eV. + http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670 + https://ns.ph.liv.ac.uk/~ajb/radiometrics/glossary/epithermal_neutron.html + epithermal neutron + + + + + + + + + background radiation + The ambient radiation in a defined environment emanating from natural or anthropogenic sources. + For uses involving experimentation or radiation therapy, use "anthropogenic background radiation" instead. Use this concept to indicate source is a mixture of anthropogenic and naturally occurring (ambient), or unknown or if the discrimination is not sought. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + background radiation + + + + + + + + + non-ionizing background radiation + Background radiation that does not result in ionization of target material + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + non-ionizing background radiation + + + + + + + + + anthropogenic non-ionizing background radiation + Non-ionizing background radiation that is the result of a human planned process. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + anthropogenic non-ionizing background radiation + + + + + + + + + natural non-ionizing background radiation + Non-ionizing background radiation that is not the result of a human planned process. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + natural non-ionizing background radiation + + + + diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl index 6718d52..fcd28ed 100644 --- a/src/ontology/imports/bfo_import.owl +++ b/src/ontology/imports/bfo_import.owl @@ -1,764 +1,349 @@ - - - - - - 2024-02-06 - - - - - - - - - - - - - - - - - - - - - - - - - - editor preferred term - - - - - - - - - example of usage - - - - - - - - - definition - - - - - - - - - - - - - - - term editor - - - - - - - - - alternative term - - - - - - - - - definition source - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - continuant - Continuant - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - - - - - occurrent - Occurrent - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - - - - - - - +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-10-23") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (editor preferred term) + +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "editor preferred term"@en) + +# Annotation Property: (example of usage) + +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "example of usage"@en) + +# Annotation Property: (definition) + +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition"@en) + +# Annotation Property: (editor note) + +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "editor note"@en) + +# Annotation Property: (term editor) + +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "term editor"@en) + +# Annotation Property: (alternative term) + +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "alternative term"@en) + +# Annotation Property: (definition source) + +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition source"@en) + + + +############################ +# Classes +############################ + +# Class: (entity) + +AnnotationAssertion( "entity") +AnnotationAssertion( "Entity") +AnnotationAssertion( "Julius Caesar"@en) +AnnotationAssertion( "Verdi’s Requiem"@en) +AnnotationAssertion( "the Second World War"@en) +AnnotationAssertion( "your body mass index"@en) +AnnotationAssertion( "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") Annotation(rdfs:seeAlso ) "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"@en) +AnnotationAssertion(Annotation( ) "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "entity"@en) + +# Class: (continuant) + +AnnotationAssertion( "continuant") +AnnotationAssertion( "Continuant") +AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) +AnnotationAssertion(Annotation( ) "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en) +AnnotationAssertion(Annotation( ) "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ") +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (occurrent) + +AnnotationAssertion( "occurrent") +AnnotationAssertion( "Occurrent") +AnnotationAssertion( "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) +AnnotationAssertion( "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process."@en) +AnnotationAssertion(Annotation( ) "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.") +AnnotationAssertion(Annotation( ) "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])"@en) +AnnotationAssertion(Annotation( ) "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])"@en) +AnnotationAssertion(Annotation( ) "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ) + +# Class: (independent continuant) + +AnnotationAssertion( "ic") +AnnotationAssertion( "IndependentContinuant") +AnnotationAssertion( "a chair"@en) +AnnotationAssertion( "a heart"@en) +AnnotationAssertion( "a leg"@en) +AnnotationAssertion( "a molecule"@en) +AnnotationAssertion( "a spatial region"@en) +AnnotationAssertion( "an atom"@en) +AnnotationAssertion( "an orchestra."@en) +AnnotationAssertion( "an organism"@en) +AnnotationAssertion( "the bottom right portion of a human torso"@en) +AnnotationAssertion( "the interior of your mouth"@en) +AnnotationAssertion(Annotation( ) "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(Annotation( ) "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])"@en) +AnnotationAssertion(Annotation( ) "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") +AnnotationAssertion(Annotation( ) "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (spatial region) + +AnnotationAssertion( "s-region") +AnnotationAssertion( "SpatialRegion") +AnnotationAssertion( "BFO 2 Reference: Spatial regions do not participate in processes."@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional."@en) +AnnotationAssertion(Annotation( ) "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])"@en) +AnnotationAssertion(Annotation( ) "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "spatial region"@en) +SubClassOf( ) + +# Class: (process) + +AnnotationAssertion( "process") +AnnotationAssertion( "Process") +AnnotationAssertion( "a process of cell-division, \\ a beating of the heart"@en) +AnnotationAssertion( "a process of meiosis"@en) +AnnotationAssertion( "a process of sleeping"@en) +AnnotationAssertion( "the course of a disease"@en) +AnnotationAssertion( "the flight of a bird"@en) +AnnotationAssertion( "the life of an organism"@en) +AnnotationAssertion( "your process of aging."@en) +AnnotationAssertion(Annotation( ) "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) +AnnotationAssertion(Annotation( ) "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) + +# Class: (disposition) + +AnnotationAssertion( "disposition") +AnnotationAssertion( "Disposition") +AnnotationAssertion( "an atom of element X has the disposition to decay to an atom of element Y"@en) +AnnotationAssertion( "certain people have a predisposition to colon cancer"@en) +AnnotationAssertion( "children are innately disposed to categorize objects in certain ways."@en) +AnnotationAssertion( "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en) +AnnotationAssertion( "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type."@en) +AnnotationAssertion(Annotation( ) "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])"@en) +AnnotationAssertion(Annotation( ) "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (realizable entity) + +AnnotationAssertion( "realizable") +AnnotationAssertion( "RealizableEntity") +AnnotationAssertion( "the disposition of this piece of metal to conduct electricity."@en) +AnnotationAssertion( "the disposition of your blood to coagulate"@en) +AnnotationAssertion( "the function of your reproductive organs"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the role of this boundary to delineate where Utah and Colorado meet"@en) +AnnotationAssertion(Annotation( ) "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])"@en) +AnnotationAssertion(Annotation( ) "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) + +# Class: (specifically dependent continuant) + +AnnotationAssertion( "sdc") +AnnotationAssertion( "SpecificallyDependentContinuant") +AnnotationAssertion( "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"@en) +AnnotationAssertion( "of one-sided specifically dependent continuants: the mass of this tomato"@en) +AnnotationAssertion( "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."@en) +AnnotationAssertion( "the disposition of this fish to decay"@en) +AnnotationAssertion( "the function of this heart: to pump blood"@en) +AnnotationAssertion( "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en) +AnnotationAssertion( "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en) +AnnotationAssertion( "the pink color of a medium rare piece of grilled filet mignon at its center"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the shape of this hole."@en) +AnnotationAssertion( "the smell of this portion of mozzarella"@en) +AnnotationAssertion(Annotation( ) "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."@en) +AnnotationAssertion(Annotation( ) "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +SubClassOf( ) + +# Class: (role) + +AnnotationAssertion( "role") +AnnotationAssertion( "Role") +AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) +AnnotationAssertion( "the priest role"@en) +AnnotationAssertion( "the role of a boundary to demarcate two neighboring administrative territories"@en) +AnnotationAssertion( "the role of a building in serving as a military target"@en) +AnnotationAssertion( "the role of a stone in marking a property boundary"@en) +AnnotationAssertion( "the role of subject in a clinical trial"@en) +AnnotationAssertion( "the student role"@en) +AnnotationAssertion( "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) +AnnotationAssertion(Annotation( ) "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (object aggregate) + +AnnotationAssertion( "object-aggregate") +AnnotationAssertion( "ObjectAggregate") +AnnotationAssertion( "a collection of cells in a blood biobank."@en) +AnnotationAssertion( "a swarm of bees is an aggregate of members who are linked together through natural bonds"@en) +AnnotationAssertion( "a symphony orchestra"@en) +AnnotationAssertion( "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)"@en) +AnnotationAssertion( "defined by fiat: the aggregate of members of an organization"@en) +AnnotationAssertion( "defined through physical attachment: the aggregate of atoms in a lump of granite"@en) +AnnotationAssertion( "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container"@en) +AnnotationAssertion( "defined via attributive delimitations such as: the patients in this hospital"@en) +AnnotationAssertion( "the aggregate of bearings in a constant velocity axle joint"@en) +AnnotationAssertion( "the aggregate of blood cells in your body"@en) +AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) +AnnotationAssertion( "the restaurants in Palo Alto"@en) +AnnotationAssertion( "your collection of Meissen ceramic plates."@en) +AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) +AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") +AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") +AnnotationAssertion(Annotation( ) "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.") +AnnotationAssertion(Annotation( ) "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "object aggregate"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "material") +AnnotationAssertion( "MaterialEntity") +AnnotationAssertion( "a flame"@en) +AnnotationAssertion( "a forest fire"@en) +AnnotationAssertion( "a human being"@en) +AnnotationAssertion( "a hurricane"@en) +AnnotationAssertion( "a photon"@en) +AnnotationAssertion( "a puff of smoke"@en) +AnnotationAssertion( "a sea wave"@en) +AnnotationAssertion( "a tornado"@en) +AnnotationAssertion( "an aggregate of human beings."@en) +AnnotationAssertion( "an energy wave"@en) +AnnotationAssertion( "an epidemic"@en) +AnnotationAssertion( "the undetached arm of a human being"@en) +AnnotationAssertion( "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"@en) +AnnotationAssertion( "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."@en) +AnnotationAssertion( "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."@en) +AnnotationAssertion(Annotation( ) "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"@en) +AnnotationAssertion(Annotation( ) "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])"@en) +AnnotationAssertion(Annotation( ) "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (immaterial entity) + +AnnotationAssertion( "immaterial") +AnnotationAssertion( "ImmaterialEntity") +AnnotationAssertion( "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "immaterial entity"@en) +SubClassOf( ) + +# Class: (history) + +AnnotationAssertion( "history") +AnnotationAssertion( "History") +AnnotationAssertion(Annotation( ) "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "history"@en) +SubClassOf( ) + + +) \ No newline at end of file diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl index c240cec..fad860f 100644 --- a/src/ontology/imports/chebi_import.owl +++ b/src/ontology/imports/chebi_import.owl @@ -10,8 +10,8 @@ xmlns:chebi="http://purl.obolibrary.org/obo/chebi/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2024-02-06 + + 2024-10-23 diff --git a/src/ontology/imports/chebi_terms_combined.txt b/src/ontology/imports/chebi_terms_combined.txt index a2434f7..1f72f5c 100644 --- a/src/ontology/imports/chebi_terms_combined.txt +++ b/src/ontology/imports/chebi_terms_combined.txt @@ -7,7 +7,6 @@ CHEBI:36080 CHEBI:36347 # nuclear particle CHEBI:36348 # pi meson CHEBI:36356 # muon -COB:0000800 http://creativecommons.org/licenses/by/3.0/ http://purl.obolibrary.org/obo/BFO_0000003 http://purl.obolibrary.org/obo/BFO_0000004 @@ -15,6 +14,7 @@ http://purl.obolibrary.org/obo/BFO_0000015 http://purl.obolibrary.org/obo/BFO_0000016 http://purl.obolibrary.org/obo/BFO_0000017 http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/BFO_0000027 http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000182 @@ -31,7 +31,7 @@ http://purl.obolibrary.org/obo/CL_0000000 http://purl.obolibrary.org/obo/CL_0017502 http://purl.obolibrary.org/obo/CL_0017503 http://purl.obolibrary.org/obo/CL_0017504 -http://purl.obolibrary.org/obo/COB_0000082 +http://purl.obolibrary.org/obo/COB_0000800 http://purl.obolibrary.org/obo/DOID_4 http://purl.obolibrary.org/obo/ENVO_01000254 http://purl.obolibrary.org/obo/ENVO_01000637 @@ -52,13 +52,13 @@ http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.obolibrary.org/obo/IAO_0000116 http://purl.obolibrary.org/obo/IAO_0000117 http://purl.obolibrary.org/obo/IAO_0000118 http://purl.obolibrary.org/obo/IAO_0000119 http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/OBI_0000272 -http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/OBI_0000984 @@ -66,11 +66,14 @@ http://purl.obolibrary.org/obo/OBI_0001138 http://purl.obolibrary.org/obo/OBI_0001909 http://purl.obolibrary.org/obo/OBI_0002983 http://purl.obolibrary.org/obo/OBI_0302889 +http://purl.obolibrary.org/obo/PATO_0000025 http://purl.obolibrary.org/obo/PATO_0001018 http://purl.obolibrary.org/obo/PATO_0001236 http://purl.obolibrary.org/obo/PATO_0001241 +http://purl.obolibrary.org/obo/PATO_0001739 http://purl.obolibrary.org/obo/PATO_0002062 http://purl.obolibrary.org/obo/PO_0009012 +http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RBO_00000001 http://purl.obolibrary.org/obo/RBO_00000002 http://purl.obolibrary.org/obo/RBO_00000003 @@ -426,6 +429,18 @@ http://purl.obolibrary.org/obo/RBO_00015026 http://purl.obolibrary.org/obo/RBO_00015027 http://purl.obolibrary.org/obo/RBO_00015028 http://purl.obolibrary.org/obo/RBO_00015029 +http://purl.obolibrary.org/obo/RBO_00015030 +http://purl.obolibrary.org/obo/RBO_00015031 +http://purl.obolibrary.org/obo/RBO_00015032 +http://purl.obolibrary.org/obo/RBO_00015033 +http://purl.obolibrary.org/obo/RBO_00015034 +http://purl.obolibrary.org/obo/RBO_00015035 +http://purl.obolibrary.org/obo/RBO_00015036 +http://purl.obolibrary.org/obo/RBO_00015037 +http://purl.obolibrary.org/obo/RBO_00015038 +http://purl.obolibrary.org/obo/RBO_00015039 +http://purl.obolibrary.org/obo/RBO_00015040 +http://purl.obolibrary.org/obo/RBO_00015041 http://purl.obolibrary.org/obo/RBO_010000 http://purl.obolibrary.org/obo/RBO_010001 http://purl.obolibrary.org/obo/RBO_010002 @@ -447,7 +462,6 @@ http://purl.obolibrary.org/obo/RBO_010019 http://purl.obolibrary.org/obo/RBO_010020 http://purl.obolibrary.org/obo/RBO_2000 http://purl.obolibrary.org/obo/RBO_2001 -http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RO_0000086 http://purl.obolibrary.org/obo/RO_0002180 http://purl.obolibrary.org/obo/RO_0002233 @@ -457,12 +471,12 @@ http://purl.obolibrary.org/obo/RO_0002493 http://purl.obolibrary.org/obo/RO_0002608 http://purl.obolibrary.org/obo/SO_0000704 http://purl.obolibrary.org/obo/UBERON_0000000 -http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.obolibrary.org/obo/UO_0000127 http://purl.obolibrary.org/obo/UO_0000129 http://purl.obolibrary.org/obo/UO_0000160 http://purl.obolibrary.org/obo/UO_0000219 http://purl.obolibrary.org/obo/UO_1000135 +http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/description diff --git a/src/ontology/imports/chmo_import.owl b/src/ontology/imports/chmo_import.owl index 8c714a6..eab37b0 100644 --- a/src/ontology/imports/chmo_import.owl +++ b/src/ontology/imports/chmo_import.owl @@ -12,9 +12,9 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - 2024-02-06 + 2024-10-23 @@ -206,16 +206,6 @@ - - - - - OBI:0000293 - has_specified_input - - - - diff --git a/src/ontology/imports/chmo_terms_combined.txt b/src/ontology/imports/chmo_terms_combined.txt index 3bab942..7296d70 100644 --- a/src/ontology/imports/chmo_terms_combined.txt +++ b/src/ontology/imports/chmo_terms_combined.txt @@ -1,4 +1,3 @@ -COB:0000800 http://creativecommons.org/licenses/by/3.0/ http://purl.obolibrary.org/obo/BFO_0000003 http://purl.obolibrary.org/obo/BFO_0000004 @@ -6,6 +5,7 @@ http://purl.obolibrary.org/obo/BFO_0000015 http://purl.obolibrary.org/obo/BFO_0000016 http://purl.obolibrary.org/obo/BFO_0000017 http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/BFO_0000027 http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000182 @@ -22,7 +22,7 @@ http://purl.obolibrary.org/obo/CL_0000000 http://purl.obolibrary.org/obo/CL_0017502 http://purl.obolibrary.org/obo/CL_0017503 http://purl.obolibrary.org/obo/CL_0017504 -http://purl.obolibrary.org/obo/COB_0000082 +http://purl.obolibrary.org/obo/COB_0000800 http://purl.obolibrary.org/obo/DOID_4 http://purl.obolibrary.org/obo/ENVO_01000254 http://purl.obolibrary.org/obo/ENVO_01000637 @@ -43,13 +43,13 @@ http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.obolibrary.org/obo/IAO_0000116 http://purl.obolibrary.org/obo/IAO_0000117 http://purl.obolibrary.org/obo/IAO_0000118 http://purl.obolibrary.org/obo/IAO_0000119 http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/OBI_0000272 -http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/OBI_0000984 @@ -57,11 +57,14 @@ http://purl.obolibrary.org/obo/OBI_0001138 http://purl.obolibrary.org/obo/OBI_0001909 http://purl.obolibrary.org/obo/OBI_0002983 http://purl.obolibrary.org/obo/OBI_0302889 +http://purl.obolibrary.org/obo/PATO_0000025 http://purl.obolibrary.org/obo/PATO_0001018 http://purl.obolibrary.org/obo/PATO_0001236 http://purl.obolibrary.org/obo/PATO_0001241 +http://purl.obolibrary.org/obo/PATO_0001739 http://purl.obolibrary.org/obo/PATO_0002062 http://purl.obolibrary.org/obo/PO_0009012 +http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RBO_00000001 http://purl.obolibrary.org/obo/RBO_00000002 http://purl.obolibrary.org/obo/RBO_00000003 @@ -417,6 +420,18 @@ http://purl.obolibrary.org/obo/RBO_00015026 http://purl.obolibrary.org/obo/RBO_00015027 http://purl.obolibrary.org/obo/RBO_00015028 http://purl.obolibrary.org/obo/RBO_00015029 +http://purl.obolibrary.org/obo/RBO_00015030 +http://purl.obolibrary.org/obo/RBO_00015031 +http://purl.obolibrary.org/obo/RBO_00015032 +http://purl.obolibrary.org/obo/RBO_00015033 +http://purl.obolibrary.org/obo/RBO_00015034 +http://purl.obolibrary.org/obo/RBO_00015035 +http://purl.obolibrary.org/obo/RBO_00015036 +http://purl.obolibrary.org/obo/RBO_00015037 +http://purl.obolibrary.org/obo/RBO_00015038 +http://purl.obolibrary.org/obo/RBO_00015039 +http://purl.obolibrary.org/obo/RBO_00015040 +http://purl.obolibrary.org/obo/RBO_00015041 http://purl.obolibrary.org/obo/RBO_010000 http://purl.obolibrary.org/obo/RBO_010001 http://purl.obolibrary.org/obo/RBO_010002 @@ -438,7 +453,6 @@ http://purl.obolibrary.org/obo/RBO_010019 http://purl.obolibrary.org/obo/RBO_010020 http://purl.obolibrary.org/obo/RBO_2000 http://purl.obolibrary.org/obo/RBO_2001 -http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RO_0000086 http://purl.obolibrary.org/obo/RO_0002180 http://purl.obolibrary.org/obo/RO_0002233 @@ -448,12 +462,12 @@ http://purl.obolibrary.org/obo/RO_0002493 http://purl.obolibrary.org/obo/RO_0002608 http://purl.obolibrary.org/obo/SO_0000704 http://purl.obolibrary.org/obo/UBERON_0000000 -http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.obolibrary.org/obo/UO_0000127 http://purl.obolibrary.org/obo/UO_0000129 http://purl.obolibrary.org/obo/UO_0000160 http://purl.obolibrary.org/obo/UO_0000219 http://purl.obolibrary.org/obo/UO_1000135 +http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/description diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl index e9d2b8e..9ebe4f1 100644 --- a/src/ontology/imports/cob_import.owl +++ b/src/ontology/imports/cob_import.owl @@ -10,8 +10,8 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/"> - - 2024-02-06 + + 2024-10-23 @@ -142,26 +142,6 @@ - - - - - - - has specified input - - - - - - - - - is specified input of - - - - diff --git a/src/ontology/imports/cob_terms_combined.txt b/src/ontology/imports/cob_terms_combined.txt index 7074f8e..71635bb 100644 --- a/src/ontology/imports/cob_terms_combined.txt +++ b/src/ontology/imports/cob_terms_combined.txt @@ -1,5 +1,4 @@ -COB:0000800 http://creativecommons.org/licenses/by/3.0/ http://purl.obolibrary.org/obo/BFO_0000003 http://purl.obolibrary.org/obo/BFO_0000004 @@ -7,6 +6,7 @@ http://purl.obolibrary.org/obo/BFO_0000015 http://purl.obolibrary.org/obo/BFO_0000016 http://purl.obolibrary.org/obo/BFO_0000017 http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/BFO_0000027 http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000182 @@ -23,7 +23,7 @@ http://purl.obolibrary.org/obo/CL_0000000 http://purl.obolibrary.org/obo/CL_0017502 http://purl.obolibrary.org/obo/CL_0017503 http://purl.obolibrary.org/obo/CL_0017504 -http://purl.obolibrary.org/obo/COB_0000082 +http://purl.obolibrary.org/obo/COB_0000800 http://purl.obolibrary.org/obo/COB_0000800 # has_atomic_number http://purl.obolibrary.org/obo/DOID_4 http://purl.obolibrary.org/obo/ENVO_01000254 @@ -45,13 +45,13 @@ http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.obolibrary.org/obo/IAO_0000116 http://purl.obolibrary.org/obo/IAO_0000117 http://purl.obolibrary.org/obo/IAO_0000118 http://purl.obolibrary.org/obo/IAO_0000119 http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/OBI_0000272 -http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/OBI_0000984 @@ -59,11 +59,14 @@ http://purl.obolibrary.org/obo/OBI_0001138 http://purl.obolibrary.org/obo/OBI_0001909 http://purl.obolibrary.org/obo/OBI_0002983 http://purl.obolibrary.org/obo/OBI_0302889 +http://purl.obolibrary.org/obo/PATO_0000025 http://purl.obolibrary.org/obo/PATO_0001018 http://purl.obolibrary.org/obo/PATO_0001236 http://purl.obolibrary.org/obo/PATO_0001241 +http://purl.obolibrary.org/obo/PATO_0001739 http://purl.obolibrary.org/obo/PATO_0002062 http://purl.obolibrary.org/obo/PO_0009012 +http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RBO_00000001 http://purl.obolibrary.org/obo/RBO_00000002 http://purl.obolibrary.org/obo/RBO_00000003 @@ -419,6 +422,18 @@ http://purl.obolibrary.org/obo/RBO_00015026 http://purl.obolibrary.org/obo/RBO_00015027 http://purl.obolibrary.org/obo/RBO_00015028 http://purl.obolibrary.org/obo/RBO_00015029 +http://purl.obolibrary.org/obo/RBO_00015030 +http://purl.obolibrary.org/obo/RBO_00015031 +http://purl.obolibrary.org/obo/RBO_00015032 +http://purl.obolibrary.org/obo/RBO_00015033 +http://purl.obolibrary.org/obo/RBO_00015034 +http://purl.obolibrary.org/obo/RBO_00015035 +http://purl.obolibrary.org/obo/RBO_00015036 +http://purl.obolibrary.org/obo/RBO_00015037 +http://purl.obolibrary.org/obo/RBO_00015038 +http://purl.obolibrary.org/obo/RBO_00015039 +http://purl.obolibrary.org/obo/RBO_00015040 +http://purl.obolibrary.org/obo/RBO_00015041 http://purl.obolibrary.org/obo/RBO_010000 http://purl.obolibrary.org/obo/RBO_010001 http://purl.obolibrary.org/obo/RBO_010002 @@ -440,7 +455,6 @@ http://purl.obolibrary.org/obo/RBO_010019 http://purl.obolibrary.org/obo/RBO_010020 http://purl.obolibrary.org/obo/RBO_2000 http://purl.obolibrary.org/obo/RBO_2001 -http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RO_0000086 http://purl.obolibrary.org/obo/RO_0002180 http://purl.obolibrary.org/obo/RO_0002233 @@ -450,12 +464,12 @@ http://purl.obolibrary.org/obo/RO_0002493 http://purl.obolibrary.org/obo/RO_0002608 http://purl.obolibrary.org/obo/SO_0000704 http://purl.obolibrary.org/obo/UBERON_0000000 -http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.obolibrary.org/obo/UO_0000127 http://purl.obolibrary.org/obo/UO_0000129 http://purl.obolibrary.org/obo/UO_0000160 http://purl.obolibrary.org/obo/UO_0000219 http://purl.obolibrary.org/obo/UO_1000135 +http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/description diff --git a/src/ontology/imports/efo_import.owl b/src/ontology/imports/efo_import.owl index 6b212c0..7785959 100644 --- a/src/ontology/imports/efo_import.owl +++ b/src/ontology/imports/efo_import.owl @@ -1,7 +1,6 @@ - - 2024-05-16 + + 2024-10-23 @@ -64,7 +63,9 @@ - + + editor note + @@ -164,17 +165,17 @@ - + - + - + - + @@ -244,14 +245,6 @@ - - - - - - - - @@ -260,25 +253,17 @@ - - - - - - - - - + - + - + - + @@ -492,8 +477,8 @@ my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) - For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) a core relation that holds between a part and its whole + For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime @@ -523,13 +508,13 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of EFO_0000822 - part of part of + part of part_of - http://www.obofoundry.org/ro/#OBO_REL:part_of https://wiki.geneontology.org/Part_of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -555,59 +540,12 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - - - - - - - - - - - - has_specified_input - has_specified_input - see is_input_of example_of_usage - - The inverse property of is_specified_input_of - 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Coutot - - http://www.ebi.ac.uk/efo/has_input - has_input - has_specified_input - - - - - - - - - - is_specified_input_of - some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. - Alan Ruttenberg - PERSON:Bjoern Peters - http://www.ebi.ac.uk/efo/is_input_of - is_input_of - is_specified_input_of - - - - - has_specified_output has_specified_output + has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg @@ -615,8 +553,8 @@ A continuant cannot be part of an occurrent: use 'participates in'. An PERSON: Larry Hunter PERSON: Melanie Courtot - has_output has_specified_output + has_output @@ -643,8 +581,8 @@ A continuant cannot be part of an occurrent: use 'participates in'. An inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of - inheres in inheres in + inheres in inheres_in @@ -850,7 +788,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An chemical entity - UniProt + UniProt @@ -870,7 +808,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An biological function - ChEBI + ChEBI @@ -898,48 +836,48 @@ A continuant cannot be part of an occurrent: use 'participates in'. An atom - - - - atoms - ChEBI - - - - - atomus - ChEBI - element - ChEBI + ChEBI elements - ChEBI + ChEBI atom - IUPAC + IUPAC atome - IUPAC + IUPAC atomo - IUPAC + IUPAC + + + + + atoms + ChEBI + + + + + atomus + ChEBI @@ -967,7 +905,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An proteins - IUPAC + IUPAC @@ -1030,7 +968,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An XAO:0003012 - The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell @@ -1048,7 +985,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). + A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 GO:0008372 NIF_Subcellular:sao1337158144 @@ -1069,7 +1006,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). + A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). GOC:pdt @@ -1146,10 +1083,8 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - - - + cytoplasm @@ -1234,7 +1169,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An response to abiotic stress biological_process GO:0009628 - + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. @@ -1292,13 +1227,12 @@ A continuant cannot be part of an occurrent: use 'participates in'. An physiological response to stimulus biological_process GO:0050896 - + - - + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus @@ -1320,7 +1254,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. biological_process GO:0051716 - + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stimulus @@ -1574,12 +1508,12 @@ A continuant cannot be part of an occurrent: use 'participates in'. An population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. - A population is a group of material entities consisting of individuals which share a particular characteristic such as inhabiting a particular region or area or ability to interbreed. a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area + A population is a group of material entities consisting of individuals which share a particular characteristic such as inhabiting a particular region or area or ability to interbreed. 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/ - James Malone modified from original OBI definition PERSON: Philippe Rocca-Serra + James Malone modified from original OBI definition Tomasz Adamusiak modified from original OBI definition adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process @@ -1588,8 +1522,8 @@ http://code.google.com/p/popcomm-ontology/ MeSH:D011153 NIFSTD:sao2254405550 SNOMEDCT:385436007 - population population + population @@ -1604,9 +1538,9 @@ http://code.google.com/p/popcomm-ontology/ A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. A protocol is an information entity which is a set of instructions that describe an how an experiment is done. a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process. + PlanAndPlannedProcess Branch James Malone Jie Zheng - PlanAndPlannedProcess Branch Tomasz Adamusiak OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol @@ -1618,8 +1552,8 @@ http://code.google.com/p/popcomm-ontology/ method method used in an experiment plan specification - protocol protocol + protocol @@ -1629,14 +1563,14 @@ http://code.google.com/p/popcomm-ontology/ organism - Drosophila melanogaster animal fungus plant virus + Drosophila melanogaster - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. E.g Drosophila melanogaster 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: @@ -1654,8 +1588,8 @@ This issue is outside the scope of OBI. NIFSTD:birnlex_376 SNOMEDCT:410607006 species - organism organism + organism @@ -2183,13 +2117,13 @@ The CBA/J inbred mouse strain is used to study granulomatous experimental autoim --> - absorbed dose unit - A unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue. A derived unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue. + A unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue. + absorbed dose unit - + diff --git a/src/ontology/imports/efo_terms_combined.txt b/src/ontology/imports/efo_terms_combined.txt index 2196090..08d48dc 100644 --- a/src/ontology/imports/efo_terms_combined.txt +++ b/src/ontology/imports/efo_terms_combined.txt @@ -1,4 +1,3 @@ -COB:0000800 http://creativecommons.org/licenses/by/3.0/ http://purl.obolibrary.org/obo/BFO_0000003 http://purl.obolibrary.org/obo/BFO_0000004 @@ -23,7 +22,7 @@ http://purl.obolibrary.org/obo/CL_0000000 http://purl.obolibrary.org/obo/CL_0017502 http://purl.obolibrary.org/obo/CL_0017503 http://purl.obolibrary.org/obo/CL_0017504 -http://purl.obolibrary.org/obo/COB_0000082 +http://purl.obolibrary.org/obo/COB_0000800 http://purl.obolibrary.org/obo/DOID_4 http://purl.obolibrary.org/obo/ENVO_01000254 http://purl.obolibrary.org/obo/ENVO_01000637 @@ -45,13 +44,13 @@ http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.obolibrary.org/obo/IAO_0000116 http://purl.obolibrary.org/obo/IAO_0000117 http://purl.obolibrary.org/obo/IAO_0000118 http://purl.obolibrary.org/obo/IAO_0000119 http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/OBI_0000272 -http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/OBI_0000984 @@ -66,6 +65,7 @@ http://purl.obolibrary.org/obo/PATO_0001241 http://purl.obolibrary.org/obo/PATO_0001739 http://purl.obolibrary.org/obo/PATO_0002062 http://purl.obolibrary.org/obo/PO_0009012 +http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RBO_00000001 http://purl.obolibrary.org/obo/RBO_00000002 http://purl.obolibrary.org/obo/RBO_00000003 @@ -427,6 +427,12 @@ http://purl.obolibrary.org/obo/RBO_00015032 http://purl.obolibrary.org/obo/RBO_00015033 http://purl.obolibrary.org/obo/RBO_00015034 http://purl.obolibrary.org/obo/RBO_00015035 +http://purl.obolibrary.org/obo/RBO_00015036 +http://purl.obolibrary.org/obo/RBO_00015037 +http://purl.obolibrary.org/obo/RBO_00015038 +http://purl.obolibrary.org/obo/RBO_00015039 +http://purl.obolibrary.org/obo/RBO_00015040 +http://purl.obolibrary.org/obo/RBO_00015041 http://purl.obolibrary.org/obo/RBO_010000 http://purl.obolibrary.org/obo/RBO_010001 http://purl.obolibrary.org/obo/RBO_010002 @@ -448,7 +454,6 @@ http://purl.obolibrary.org/obo/RBO_010019 http://purl.obolibrary.org/obo/RBO_010020 http://purl.obolibrary.org/obo/RBO_2000 http://purl.obolibrary.org/obo/RBO_2001 -http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RO_0000086 http://purl.obolibrary.org/obo/RO_0002180 http://purl.obolibrary.org/obo/RO_0002233 @@ -458,12 +463,12 @@ http://purl.obolibrary.org/obo/RO_0002493 http://purl.obolibrary.org/obo/RO_0002608 http://purl.obolibrary.org/obo/SO_0000704 http://purl.obolibrary.org/obo/UBERON_0000000 -http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.obolibrary.org/obo/UO_0000127 http://purl.obolibrary.org/obo/UO_0000129 http://purl.obolibrary.org/obo/UO_0000160 http://purl.obolibrary.org/obo/UO_0000219 http://purl.obolibrary.org/obo/UO_1000135 +http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/description diff --git a/src/ontology/imports/envo_import.owl b/src/ontology/imports/envo_import.owl index 27d030a..b5db1cf 100644 --- a/src/ontology/imports/envo_import.owl +++ b/src/ontology/imports/envo_import.owl @@ -19,8 +19,8 @@ xmlns:taxslim="http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2024-02-08 + + 2024-10-23 diff --git a/src/ontology/imports/envo_terms_combined.txt b/src/ontology/imports/envo_terms_combined.txt index ee002f7..ed8e07c 100644 --- a/src/ontology/imports/envo_terms_combined.txt +++ b/src/ontology/imports/envo_terms_combined.txt @@ -1,5 +1,4 @@ -COB:0000800 http://creativecommons.org/licenses/by/3.0/ http://purl.obolibrary.org/obo/BFO_0000003 http://purl.obolibrary.org/obo/BFO_0000004 @@ -7,6 +6,7 @@ http://purl.obolibrary.org/obo/BFO_0000015 http://purl.obolibrary.org/obo/BFO_0000016 http://purl.obolibrary.org/obo/BFO_0000017 http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/BFO_0000027 http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000182 @@ -23,7 +23,7 @@ http://purl.obolibrary.org/obo/CL_0000000 http://purl.obolibrary.org/obo/CL_0017502 http://purl.obolibrary.org/obo/CL_0017503 http://purl.obolibrary.org/obo/CL_0017504 -http://purl.obolibrary.org/obo/COB_0000082 +http://purl.obolibrary.org/obo/COB_0000800 http://purl.obolibrary.org/obo/DOID_4 http://purl.obolibrary.org/obo/ENVO_00000070 http://purl.obolibrary.org/obo/ENVO_00000073 @@ -192,13 +192,13 @@ http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.obolibrary.org/obo/IAO_0000116 http://purl.obolibrary.org/obo/IAO_0000117 http://purl.obolibrary.org/obo/IAO_0000118 http://purl.obolibrary.org/obo/IAO_0000119 http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/OBI_0000272 -http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/OBI_0000984 @@ -206,9 +206,11 @@ http://purl.obolibrary.org/obo/OBI_0001138 http://purl.obolibrary.org/obo/OBI_0001909 http://purl.obolibrary.org/obo/OBI_0002983 http://purl.obolibrary.org/obo/OBI_0302889 +http://purl.obolibrary.org/obo/PATO_0000025 http://purl.obolibrary.org/obo/PATO_0001018 http://purl.obolibrary.org/obo/PATO_0001236 http://purl.obolibrary.org/obo/PATO_0001241 +http://purl.obolibrary.org/obo/PATO_0001739 http://purl.obolibrary.org/obo/PATO_0002062 http://purl.obolibrary.org/obo/PO_0000003 http://purl.obolibrary.org/obo/PO_0009005 @@ -217,6 +219,7 @@ http://purl.obolibrary.org/obo/PO_0009012 http://purl.obolibrary.org/obo/PO_0025025 http://purl.obolibrary.org/obo/PO_0025034 http://purl.obolibrary.org/obo/PO_0025131 +http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RBO_00000001 http://purl.obolibrary.org/obo/RBO_00000002 http://purl.obolibrary.org/obo/RBO_00000003 @@ -572,6 +575,18 @@ http://purl.obolibrary.org/obo/RBO_00015026 http://purl.obolibrary.org/obo/RBO_00015027 http://purl.obolibrary.org/obo/RBO_00015028 http://purl.obolibrary.org/obo/RBO_00015029 +http://purl.obolibrary.org/obo/RBO_00015030 +http://purl.obolibrary.org/obo/RBO_00015031 +http://purl.obolibrary.org/obo/RBO_00015032 +http://purl.obolibrary.org/obo/RBO_00015033 +http://purl.obolibrary.org/obo/RBO_00015034 +http://purl.obolibrary.org/obo/RBO_00015035 +http://purl.obolibrary.org/obo/RBO_00015036 +http://purl.obolibrary.org/obo/RBO_00015037 +http://purl.obolibrary.org/obo/RBO_00015038 +http://purl.obolibrary.org/obo/RBO_00015039 +http://purl.obolibrary.org/obo/RBO_00015040 +http://purl.obolibrary.org/obo/RBO_00015041 http://purl.obolibrary.org/obo/RBO_010000 http://purl.obolibrary.org/obo/RBO_010001 http://purl.obolibrary.org/obo/RBO_010002 @@ -593,7 +608,6 @@ http://purl.obolibrary.org/obo/RBO_010019 http://purl.obolibrary.org/obo/RBO_010020 http://purl.obolibrary.org/obo/RBO_2000 http://purl.obolibrary.org/obo/RBO_2001 -http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RO_0000086 http://purl.obolibrary.org/obo/RO_0002180 http://purl.obolibrary.org/obo/RO_0002233 @@ -603,12 +617,12 @@ http://purl.obolibrary.org/obo/RO_0002493 http://purl.obolibrary.org/obo/RO_0002608 http://purl.obolibrary.org/obo/SO_0000704 http://purl.obolibrary.org/obo/UBERON_0000000 -http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.obolibrary.org/obo/UO_0000127 http://purl.obolibrary.org/obo/UO_0000129 http://purl.obolibrary.org/obo/UO_0000160 http://purl.obolibrary.org/obo/UO_0000219 http://purl.obolibrary.org/obo/UO_1000135 +http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/description diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index 3402bff..203d609 100644 --- a/src/ontology/imports/go_import.owl +++ b/src/ontology/imports/go_import.owl @@ -12,9 +12,9 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - 2024-02-06 + 2024-10-23 @@ -38,6 +38,12 @@ + + + + + + diff --git a/src/ontology/imports/go_terms_combined.txt b/src/ontology/imports/go_terms_combined.txt index 75038c4..ec75183 100644 --- a/src/ontology/imports/go_terms_combined.txt +++ b/src/ontology/imports/go_terms_combined.txt @@ -1,5 +1,4 @@ -COB:0000800 http://creativecommons.org/licenses/by/3.0/ http://purl.obolibrary.org/obo/BFO_0000003 http://purl.obolibrary.org/obo/BFO_0000004 @@ -7,6 +6,7 @@ http://purl.obolibrary.org/obo/BFO_0000015 http://purl.obolibrary.org/obo/BFO_0000016 http://purl.obolibrary.org/obo/BFO_0000017 http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/BFO_0000027 http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000182 @@ -23,7 +23,7 @@ http://purl.obolibrary.org/obo/CL_0000000 http://purl.obolibrary.org/obo/CL_0017502 http://purl.obolibrary.org/obo/CL_0017503 http://purl.obolibrary.org/obo/CL_0017504 -http://purl.obolibrary.org/obo/COB_0000082 +http://purl.obolibrary.org/obo/COB_0000800 http://purl.obolibrary.org/obo/DOID_4 http://purl.obolibrary.org/obo/ENVO_01000254 http://purl.obolibrary.org/obo/ENVO_01000637 @@ -49,13 +49,13 @@ http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.obolibrary.org/obo/IAO_0000116 http://purl.obolibrary.org/obo/IAO_0000117 http://purl.obolibrary.org/obo/IAO_0000118 http://purl.obolibrary.org/obo/IAO_0000119 http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/OBI_0000272 -http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/OBI_0000984 @@ -63,11 +63,14 @@ http://purl.obolibrary.org/obo/OBI_0001138 http://purl.obolibrary.org/obo/OBI_0001909 http://purl.obolibrary.org/obo/OBI_0002983 http://purl.obolibrary.org/obo/OBI_0302889 +http://purl.obolibrary.org/obo/PATO_0000025 http://purl.obolibrary.org/obo/PATO_0001018 http://purl.obolibrary.org/obo/PATO_0001236 http://purl.obolibrary.org/obo/PATO_0001241 +http://purl.obolibrary.org/obo/PATO_0001739 http://purl.obolibrary.org/obo/PATO_0002062 http://purl.obolibrary.org/obo/PO_0009012 +http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RBO_00000001 http://purl.obolibrary.org/obo/RBO_00000002 http://purl.obolibrary.org/obo/RBO_00000003 @@ -423,6 +426,18 @@ http://purl.obolibrary.org/obo/RBO_00015026 http://purl.obolibrary.org/obo/RBO_00015027 http://purl.obolibrary.org/obo/RBO_00015028 http://purl.obolibrary.org/obo/RBO_00015029 +http://purl.obolibrary.org/obo/RBO_00015030 +http://purl.obolibrary.org/obo/RBO_00015031 +http://purl.obolibrary.org/obo/RBO_00015032 +http://purl.obolibrary.org/obo/RBO_00015033 +http://purl.obolibrary.org/obo/RBO_00015034 +http://purl.obolibrary.org/obo/RBO_00015035 +http://purl.obolibrary.org/obo/RBO_00015036 +http://purl.obolibrary.org/obo/RBO_00015037 +http://purl.obolibrary.org/obo/RBO_00015038 +http://purl.obolibrary.org/obo/RBO_00015039 +http://purl.obolibrary.org/obo/RBO_00015040 +http://purl.obolibrary.org/obo/RBO_00015041 http://purl.obolibrary.org/obo/RBO_010000 http://purl.obolibrary.org/obo/RBO_010001 http://purl.obolibrary.org/obo/RBO_010002 @@ -444,7 +459,6 @@ http://purl.obolibrary.org/obo/RBO_010019 http://purl.obolibrary.org/obo/RBO_010020 http://purl.obolibrary.org/obo/RBO_2000 http://purl.obolibrary.org/obo/RBO_2001 -http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RO_0000086 http://purl.obolibrary.org/obo/RO_0002180 http://purl.obolibrary.org/obo/RO_0002233 @@ -454,12 +468,12 @@ http://purl.obolibrary.org/obo/RO_0002493 http://purl.obolibrary.org/obo/RO_0002608 http://purl.obolibrary.org/obo/SO_0000704 http://purl.obolibrary.org/obo/UBERON_0000000 -http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.obolibrary.org/obo/UO_0000127 http://purl.obolibrary.org/obo/UO_0000129 http://purl.obolibrary.org/obo/UO_0000160 http://purl.obolibrary.org/obo/UO_0000219 http://purl.obolibrary.org/obo/UO_1000135 +http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/description diff --git a/src/ontology/imports/ncbitaxon_import.owl b/src/ontology/imports/ncbitaxon_import.owl index ff7d9ec..110bcac 100644 --- a/src/ontology/imports/ncbitaxon_import.owl +++ b/src/ontology/imports/ncbitaxon_import.owl @@ -11,8 +11,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-02-06 + + 2024-08-23 diff --git a/src/ontology/imports/ncbitaxon_terms_combined.txt b/src/ontology/imports/ncbitaxon_terms_combined.txt index b92846d..a77b31c 100644 --- a/src/ontology/imports/ncbitaxon_terms_combined.txt +++ b/src/ontology/imports/ncbitaxon_terms_combined.txt @@ -1,4 +1,3 @@ -COB:0000800 http://creativecommons.org/licenses/by/3.0/ http://purl.obolibrary.org/obo/BFO_0000003 http://purl.obolibrary.org/obo/BFO_0000004 @@ -6,6 +5,7 @@ http://purl.obolibrary.org/obo/BFO_0000015 http://purl.obolibrary.org/obo/BFO_0000016 http://purl.obolibrary.org/obo/BFO_0000017 http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/BFO_0000027 http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000182 @@ -22,7 +22,7 @@ http://purl.obolibrary.org/obo/CL_0000000 http://purl.obolibrary.org/obo/CL_0017502 http://purl.obolibrary.org/obo/CL_0017503 http://purl.obolibrary.org/obo/CL_0017504 -http://purl.obolibrary.org/obo/COB_0000082 +http://purl.obolibrary.org/obo/COB_0000800 http://purl.obolibrary.org/obo/DOID_4 http://purl.obolibrary.org/obo/ENVO_01000254 http://purl.obolibrary.org/obo/ENVO_01000637 @@ -43,6 +43,7 @@ http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.obolibrary.org/obo/IAO_0000116 http://purl.obolibrary.org/obo/IAO_0000117 http://purl.obolibrary.org/obo/IAO_0000118 http://purl.obolibrary.org/obo/IAO_0000119 @@ -118,7 +119,6 @@ http://purl.obolibrary.org/obo/NCIT_C61398 http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/OBI_0000272 -http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/OBI_0000984 @@ -126,11 +126,14 @@ http://purl.obolibrary.org/obo/OBI_0001138 http://purl.obolibrary.org/obo/OBI_0001909 http://purl.obolibrary.org/obo/OBI_0002983 http://purl.obolibrary.org/obo/OBI_0302889 +http://purl.obolibrary.org/obo/PATO_0000025 http://purl.obolibrary.org/obo/PATO_0001018 http://purl.obolibrary.org/obo/PATO_0001236 http://purl.obolibrary.org/obo/PATO_0001241 +http://purl.obolibrary.org/obo/PATO_0001739 http://purl.obolibrary.org/obo/PATO_0002062 http://purl.obolibrary.org/obo/PO_0009012 +http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RBO_00000001 http://purl.obolibrary.org/obo/RBO_00000002 http://purl.obolibrary.org/obo/RBO_00000003 @@ -486,6 +489,18 @@ http://purl.obolibrary.org/obo/RBO_00015026 http://purl.obolibrary.org/obo/RBO_00015027 http://purl.obolibrary.org/obo/RBO_00015028 http://purl.obolibrary.org/obo/RBO_00015029 +http://purl.obolibrary.org/obo/RBO_00015030 +http://purl.obolibrary.org/obo/RBO_00015031 +http://purl.obolibrary.org/obo/RBO_00015032 +http://purl.obolibrary.org/obo/RBO_00015033 +http://purl.obolibrary.org/obo/RBO_00015034 +http://purl.obolibrary.org/obo/RBO_00015035 +http://purl.obolibrary.org/obo/RBO_00015036 +http://purl.obolibrary.org/obo/RBO_00015037 +http://purl.obolibrary.org/obo/RBO_00015038 +http://purl.obolibrary.org/obo/RBO_00015039 +http://purl.obolibrary.org/obo/RBO_00015040 +http://purl.obolibrary.org/obo/RBO_00015041 http://purl.obolibrary.org/obo/RBO_010000 http://purl.obolibrary.org/obo/RBO_010001 http://purl.obolibrary.org/obo/RBO_010002 @@ -507,7 +522,6 @@ http://purl.obolibrary.org/obo/RBO_010019 http://purl.obolibrary.org/obo/RBO_010020 http://purl.obolibrary.org/obo/RBO_2000 http://purl.obolibrary.org/obo/RBO_2001 -http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RO_0000086 http://purl.obolibrary.org/obo/RO_0002180 http://purl.obolibrary.org/obo/RO_0002233 @@ -517,12 +531,12 @@ http://purl.obolibrary.org/obo/RO_0002493 http://purl.obolibrary.org/obo/RO_0002608 http://purl.obolibrary.org/obo/SO_0000704 http://purl.obolibrary.org/obo/UBERON_0000000 -http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.obolibrary.org/obo/UO_0000127 http://purl.obolibrary.org/obo/UO_0000129 http://purl.obolibrary.org/obo/UO_0000160 http://purl.obolibrary.org/obo/UO_0000219 http://purl.obolibrary.org/obo/UO_1000135 +http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/description diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index b13c358..3be8f44 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -1,108 +1,580 @@ - - - - - - 2024-02-06 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - editor preferred label - editor preferred term - editor preferred label - editor preferred term - editor preferred term~editor preferred label - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - editor preferred label - editor preferred term - editor preferred label - editor preferred term - editor preferred term~editor preferred label - - - - - - - - example of usage - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - example of usage - - - - - - - - - - - - - - definition - definition - textual definition - - The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-10-23") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class(owl:Thing)) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(rdfs:comment)) +Declaration(Datatype(rdfs:Literal)) +Declaration(Datatype(xsd:date)) +Declaration(Datatype(xsd:integer)) +Declaration(Datatype(xsd:nonNegativeInteger)) +Declaration(Datatype(xsd:string)) +############################ +# Annotation Properties +############################ + +# Annotation Property: (editor preferred term) + +AnnotationAssertion( "editor preferred label"@en) +AnnotationAssertion( "editor preferred term"@en) +AnnotationAssertion( "editor preferred term") +AnnotationAssertion( "editor preferred term~editor preferred label") +AnnotationAssertion( ) +AnnotationAssertion( "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "editor preferred label"@en) +AnnotationAssertion(rdfs:label "editor preferred term"@en) +AnnotationAssertion(rdfs:label "editor preferred term") +AnnotationAssertion(rdfs:label "editor preferred term~editor preferred label") + +# Annotation Property: (example of usage) + +AnnotationAssertion( "example of usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "example of usage"@en) + +# Annotation Property: (definition) + +AnnotationAssertion( "definition"@en) +AnnotationAssertion( "definition") +AnnotationAssertion( "textual definition") +AnnotationAssertion( ) +AnnotationAssertion( "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "2012-04-05: Barry Smith -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: @@ -110,2750 +582,1025 @@ A statement of necessary and sufficient conditions explaining the meaning of an Alan Ruttenberg -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition - definition - textual definition - - - - - - - - - - - - - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - term editor - - - - - - - - alternative term - - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - alternative term - - - - - - - - definition source - - Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition source - - - - - - - - - - - - - - - +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") +AnnotationAssertion(rdfs:label "textual definition") + +# Annotation Property: (editor note) + +AnnotationAssertion( "editor note"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "editor note"@en) + +# Annotation Property: (term editor) + +AnnotationAssertion( "term editor"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) +AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "term editor"@en) + +# Annotation Property: (alternative label) + +AnnotationAssertion( "alternative label"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "OBO Operations committee") +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:comment "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") +AnnotationAssertion(rdfs:label "alternative label"@en) + +# Annotation Property: (definition source) + +AnnotationAssertion( "definition source"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "definition source"@en) + +# Annotation Property: (Creator) + +AnnotationAssertion( "Examples of a Creator include a person, an organisation, + or a service. Typically, the name of a Creator should + be used to indicate the entity."@en-us) +AnnotationAssertion(rdfs:comment "An entity primarily responsible for making the content + of the resource."@en-us) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "Creator"@en-us) +AnnotationAssertion(rdfs:label "Creator") - +# Annotation Property: (Date) - - +AnnotationAssertion( "Typically, Date will be associated with the creation or + availability of the resource. Recommended best practice + for encoding the date value is defined in a profile of + ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format."@en-us) +AnnotationAssertion(rdfs:comment "A date associated with an event in the life cycle of the + resource."@en-us) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "Date"@en-us) +AnnotationAssertion(rdfs:label "Date") +# Annotation Property: (Description) - +AnnotationAssertion( "Description may include but is not limited to: an abstract, + table of contents, reference to a graphical representation + of content or a free-text account of the content."@en-us) +AnnotationAssertion(rdfs:comment "An account of the content of the resource."@en-us) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "Description"@en-us) +AnnotationAssertion(rdfs:label "Description") - - +# Annotation Property: (Title) +AnnotationAssertion( " + Typically, a Title will be a name by which the resource is + formally known. + "@en-us) +AnnotationAssertion(rdfs:comment "A name given to the resource."@en-us) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "Title"@en-us) +AnnotationAssertion(rdfs:label "Title") - +# Annotation Property: () - - +AnnotationAssertion( "Mark Miller") +AnnotationAssertion( "2018-05-11T13:47:29Z"^^xsd:dateTime) +# Annotation Property: (has broad synonym) - +AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") +AnnotationAssertion(rdfs:label "has broad synonym"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") - - +# Annotation Property: (has exact synonym) +AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") +AnnotationAssertion(rdfs:label "has exact synonym"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") - - - +############################ +# Object Properties +############################ +# Object Property: (part of) - +AnnotationAssertion(rdfs:label "part of") +InverseObjectProperties( ) +TransitiveObjectProperty() - - +# Object Property: (has part) + +AnnotationAssertion( "has part"@en) +AnnotationAssertion( "a core relation that holds between a whole and its part"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part"@en) +AnnotationAssertion(rdfs:label "has part") +TransitiveObjectProperty() +# Object Property: (realized in) + +AnnotationAssertion(rdfs:label "realized in"@en) +InverseObjectProperties( ) + +# Object Property: (executed by) + +AnnotationAssertion(rdfs:label "executed by"@en) +InverseObjectProperties( ) + +# Object Property: (concretizes) + +AnnotationAssertion(rdfs:label "concretizes") +InverseObjectProperties( ) + +# Object Property: (intended to realize) + +AnnotationAssertion(rdfs:label "intended to realize") + +# Object Property: (realizes) + +AnnotationAssertion(rdfs:label "realizes") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has measurement unit label) + +AnnotationAssertion( "has measurement unit label"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has measurement unit label"@en) +SubObjectPropertyOf( ) +FunctionalObjectProperty() + +# Object Property: (is about) + +AnnotationAssertion( "http://purl.obolibrary.org/obo/IAO_0000136") +AnnotationAssertion( "is about"@en) +AnnotationAssertion( "A (currently) primitive relation that relates an information artifact to an entity."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "is about"@en) +AnnotationAssertion(rdfs:label "is about") + +# Object Property: (is_supported_by_data) + +AnnotationAssertion( "is_supported_by_data") +AnnotationAssertion( "The relation between the conclusion \"Gene tpbA is involved in EPS production\" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.") +AnnotationAssertion( ) +AnnotationAssertion( "The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process"@en) +AnnotationAssertion( "OBI") +AnnotationAssertion( "OBI") +AnnotationAssertion( "Philly 2011 workshop") +AnnotationAssertion(rdfs:label "is_supported_by_data") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has specified input) + +AnnotationAssertion( "has specified input"@en) +AnnotationAssertion( "see is_input_of example_of_usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is_specified_input_of"@en) +AnnotationAssertion( "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Coutot") +AnnotationAssertion(rdfs:label "has specified input"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (is specified input of) + +AnnotationAssertion( "is specified input of"@en) +AnnotationAssertion( "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "is specified input of"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (has specified output) + +AnnotationAssertion( "has specified output"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is_specified_output_of"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion(rdfs:label "has specified output"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (is specified output of) + +AnnotationAssertion( "is specified output of"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "is specified output of"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (achieves_planned_objective) + +AnnotationAssertion( "achieves_planned_objective") +AnnotationAssertion( "A cell sorting process achieves the objective specification 'material separation objective'") +AnnotationAssertion( ) +AnnotationAssertion( "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process."@en) +AnnotationAssertion( "BP, AR, PPPB branch") +AnnotationAssertion( "PPPB branch derived") +AnnotationAssertion( "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch") +AnnotationAssertion(rdfs:label "achieves_planned_objective") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (objective_achieved_by) + +AnnotationAssertion( "objective_achieved_by") +AnnotationAssertion( ) +AnnotationAssertion( "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process."@en) +AnnotationAssertion( "OBI") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "objective_achieved_by") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has value specification) + +AnnotationAssertion( "has value specification") +AnnotationAssertion( ) +AnnotationAssertion( "A relation between an information content entity and a value specification that specifies its value."@en) +AnnotationAssertion( "PERSON: James A. Overton") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "has value specification") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (characteristic of) + +AnnotationAssertion(rdfs:label "characteristic of"@en) +InverseObjectProperties( ) + +# Object Property: (has characteristic) + +AnnotationAssertion(rdfs:label "has characteristic") +AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") +InverseFunctionalObjectProperty() +ObjectPropertyRange( ) + +# Object Property: (participates in) + +AnnotationAssertion(rdfs:label "participates in"@en) +InverseObjectProperties( ) + +# Object Property: (has participant) - +AnnotationAssertion(rdfs:label "has participant") +ObjectPropertyDomain( ) - - +# Object Property: (is concretized as) +AnnotationAssertion(rdfs:label "is concretized as"@en) - +# Object Property: (has function) - - +AnnotationAssertion( "has function"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has function"@en) +# Object Property: (has quality) - +AnnotationAssertion( "has quality"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has quality"@en) - - +# Object Property: (has role) +AnnotationAssertion( "has role"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has role"@en) - +# Object Property: (has component) - - +AnnotationAssertion( "has component"@en) +AnnotationAssertion( "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has component"@en) +# Object Property: (has member) - +AnnotationAssertion( "has member"@en) +AnnotationAssertion( "has member is a mereological relation between a collection and an item.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has member"@en) +IrreflexiveObjectProperty() - - Examples of a Creator include a person, an organisation, - or a service. Typically, the name of a Creator should - be used to indicate the entity. - An entity primarily responsible for making the content - of the resource. - - Creator - Creator - - +# Object Property: (executes) +AnnotationAssertion(rdfs:label "executes") - - - Typically, Date will be associated with the creation or - availability of the resource. Recommended best practice - for encoding the date value is defined in a profile of - ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. - A date associated with an event in the life cycle of the - resource. - - Date - Date - - +############################ +# Data Properties +############################ +# Data Property: (has atomic number) - +AnnotationAssertion( "Number of protons in an atomic nucleus") +AnnotationAssertion(rdfs:comment "We are undecided as to whether to ultimately model this as a data property of object property + cardinality, but for now we are using DPs as these are faster for reasoning") +AnnotationAssertion(rdfs:label "has atomic number"@en) +DataPropertyDomain( ) +DataPropertyRange( xsd:nonNegativeInteger) - - Description may include but is not limited to: an abstract, - table of contents, reference to a graphical representation - of content or a free-text account of the content. - An account of the content of the resource. - - Description - Description - - +# Data Property: (has number of atomic nuclei) +AnnotationAssertion(rdfs:label "has number of atomic nuclei"@en) +DataPropertyDomain( ) +DataPropertyRange( xsd:nonNegativeInteger) - +# Data Property: (has specified numeric value) - - +AnnotationAssertion( "has specified numeric value") +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a value specification and a number that quantifies it."@en) +AnnotationAssertion( "A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.") +AnnotationAssertion( "PERSON: James A. Overton") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "has specified numeric value") +SubDataPropertyOf( ) +DataPropertyDomain( ) +DataPropertyRange( owl:real) +# Data Property: (has specified value) - +AnnotationAssertion( "has specified value"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a value specification and a literal."@en) +AnnotationAssertion( "This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "has specified value"@en) +DataPropertyDomain( ) - - - +############################ +# Classes +############################ - - +# Class: (process) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ObjectAllValuesFrom( )) - +# Class: (disposition) - - - Typically, a Title will be a name by which the resource is - formally known. - - A name given to the resource. - - Title - Title - - +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +# Class: (realizable) - +AnnotationAssertion(rdfs:label "realizable"@en) +SubClassOf( ) - - Mark Miller - 2018-05-11T13:47:29Z - - +# Class: (characteristic) +AnnotationAssertion( "characteristic"@en) +AnnotationAssertion( "specifically dependent continuant"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "characteristic"@en) +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/OBOFoundry/COB/issues/65") +AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") +SubClassOf(Annotation(rdfs:comment "We should name the inverse in COB and avoid the confusing inverse(..) construct") ObjectSomeValuesFrom(ObjectInverseOf() owl:Thing)) +SubClassOf( ObjectAllValuesFrom( )) - +# Class: (role) - - +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) +# Class: (function) - +AnnotationAssertion(rdfs:label "function"@en) +SubClassOf( ) - - +# Class: (material entity) +AnnotationAssertion( "material entity"@en) +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "material entity"@en) - +# Class: (uncharged atom) - - +AnnotationAssertion(rdfs:label "uncharged atom") +SubClassOf( ) +# Class: (atomic nucleus) - +AnnotationAssertion(rdfs:comment "Some people may be uncomfortable calling every proton an atomic nucleus") +AnnotationAssertion(rdfs:comment "This is equivalent to CHEBI:33252") +AnnotationAssertion(rdfs:label "atomic nucleus"@en) +SubClassOf( ) - +# Class: (subatomic particle) +AnnotationAssertion(rdfs:label "subatomic particle"@en) +SubClassOf( ) - +# Class: (cell) - - +AnnotationAssertion( "cell") +AnnotationAssertion( "PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. \"...Epithelial cells were harvested from histologically confirmed adenocarcinomas ..\""@en) +AnnotationAssertion( "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.") +AnnotationAssertion( "A material entity that has a plasma membrane and results from cellular division.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.") +AnnotationAssertion(rdfs:comment "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.") +AnnotationAssertion(rdfs:label "cell"@en) +AnnotationAssertion(rdfs:label "cell") +SubClassOf( ) +# Class: (atom) - +AnnotationAssertion( "A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.") +AnnotationAssertion(rdfs:comment "This atom is closely related to ChEBI's atom, but not exactly equivalent to.") +AnnotationAssertion(rdfs:label "atom"@en) +EquivalentClasses( DataHasValue( "1"^^xsd:integer)) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) - - +# Class: (action specification) +AnnotationAssertion(rdfs:label "action specification") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) - +# Class: (planned process) - - +AnnotationAssertion( "A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification.") +AnnotationAssertion(rdfs:label "planned process") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +# Class: (information representation) - +AnnotationAssertion( "http://purl.obolibrary.org/obo/IAO_0000015") +AnnotationAssertion(rdfs:comment "Pier 'representational entity'") +AnnotationAssertion(rdfs:comment "This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc") +AnnotationAssertion(rdfs:label "information representation") +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) - +# Class: (measurement datum) +AnnotationAssertion( "http://purl.obolibrary.org/obo/IAO_0000109") +AnnotationAssertion(rdfs:label "measurement datum") +SubClassOf( ) - +# Class: (physical information carrier) - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) +AnnotationAssertion(rdfs:label "physical information carrier") +EquivalentClasses( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) +SubClassOf( ) -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - +# Class: (device) +AnnotationAssertion( "A processed material entity which is designed to perform a function."@en) +AnnotationAssertion( ) +AnnotationAssertion( "2023-03-24T16:04:27+00:00"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "In this definition we assume devices are made of processed material, not natural artifacts, so we involve artifactual function rather than biological function, but align with a general BFO function sense where functions such as pumping, lifting can occur in both contexts. Thus we can compare a biological arm with a robotic arm device. - +We say \"designed\" to emphasize a device's primary function rather than all the other possible dispositions a device may have that may also be useful. E.g. one can use a hammer for a paper weight. - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) +Regarding usage then, we don't say a naturally formed rock is a hammering device - it wasn't designed to bear a hammering function per se. However, a given rock may still happen to have the disposition to bear a hammering function, and so we could say it is a hammering \"tool\", which does not necessarily convey intentional design. -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - +Example of use: A whole device like an engine; a component like a bolt is also a device."@en) +AnnotationAssertion(rdfs:label "device"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +# Class: (cellular_component) - +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cellular_component") +SubClassOf( ) - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - +# Class: (measurement unit label) +AnnotationAssertion( "measurement unit label"@en) +AnnotationAssertion( "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "measurement unit label"@en) +SubClassOf( ) + +# Class: (objective specification) + +AnnotationAssertion( "objective specification"@en) +AnnotationAssertion( "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "objective specification"@en) +AnnotationAssertion(rdfs:label "objective specification") +SubClassOf( ) + +# Class: (datum label) + +AnnotationAssertion( "datum label"@en) +AnnotationAssertion( "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "datum label"@en) +SubClassOf( ) + +# Class: (software) + +AnnotationAssertion( "software"@en) +AnnotationAssertion( "Software is a plan specification composed of a series of instructions that can be +interpreted by or directly executed by a processing unit."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "software"@en) +SubClassOf( ) + +# Class: (data item) + +AnnotationAssertion( "data item"@en) +AnnotationAssertion( "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) + +# Class: (information) + +AnnotationAssertion( "information content entity"@en) +AnnotationAssertion( "A generically dependent continuant that is about some thing."@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Pier: 'data, information or knowledge'. OR 'representation") +AnnotationAssertion(rdfs:label "information content entity"@en) +AnnotationAssertion(rdfs:label "information") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( owl:Thing)) +SubClassOf( ObjectSomeValuesFrom(ObjectInverseOf() )) + +# Class: (scalar measurement datum) + +AnnotationAssertion( "scalar measurement datum"@en) +AnnotationAssertion( "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "scalar measurement datum"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (directive information entity) + +AnnotationAssertion( "directive information entity"@en) +AnnotationAssertion( "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "directive information entity"@en) +AnnotationAssertion(rdfs:label "directive information entity") +SubClassOf( ) + +# Class: (dot plot) + +AnnotationAssertion( "dot plot"@en) +AnnotationAssertion( "A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "dot plot"@en) +SubClassOf( ) + +# Class: (graph) + +AnnotationAssertion( "graph"@en) +AnnotationAssertion( "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "graph"@en) +SubClassOf( ) + +# Class: (algorithm) + +AnnotationAssertion( "algorithm"@en) +AnnotationAssertion( "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "algorithm"@en) +SubClassOf( ) + +# Class: (curation status specification) + +AnnotationAssertion( "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "OBI_0000266"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "curation status specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (data format specification) + +AnnotationAssertion( "data format specification"@en) +AnnotationAssertion( "A data format specification is the information content borne by the document published defining the specification. +Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "data format specification"@en) +SubClassOf( ) + +# Class: (data set) + +AnnotationAssertion( "data set"@en) +AnnotationAssertion( "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "data set"@en) +SubClassOf( ) + +# Class: (image) + +AnnotationAssertion( "image"@en) +AnnotationAssertion( "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "image"@en) +SubClassOf( ) + +# Class: (data about an ontology part) + +AnnotationAssertion( "data about an ontology part"@en) +AnnotationAssertion( "Data about an ontology part is a data item about a part of an ontology, for example a term"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "data about an ontology part"@en) +SubClassOf( ) + +# Class: (plan specification) + +AnnotationAssertion( "plan specification"@en) +AnnotationAssertion( "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "plan specification"@en) +AnnotationAssertion(rdfs:label "plan specification") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (histogram) + +AnnotationAssertion( "histogram"@en) +AnnotationAssertion( "A histogram is a report graph which is a statistical description of a +distribution in terms of occurrence frequencies of different event classes."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "histogram"@en) +SubClassOf( ) + +# Class: (heatmap) + +AnnotationAssertion( "heatmap"@en) +AnnotationAssertion( "A heatmap is a report graph which is a graphical representation of data +where the values taken by a variable(s) are shown as colors in a +two-dimensional map."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "heatmap"@en) +SubClassOf( ) - +# Class: (dendrogram) - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - - - has measurement unit label - - - - - - - - - This document is about information artifacts and their representations - - A (currently) primitive relation that relates an information artifact to an entity. - 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. - person:Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - is about - - - - - - - - - - - - m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later - From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] - -This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. --- -From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] - -unit of measure is a quality, e.g. the length of a ruler. - -[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] - -[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] - -a represents b means either a denotes b or a describes - -describe: -a describes b means a is about b and a allows an inference of at least one quality of b - -We have had a long discussion about denotes versus describes. - From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. - -a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. - From the second meeting on IAO: - -An attempt at defining assay using Barry's "reliability" wording - -assay: -process and has_input some material entity -and has_output some information content entity -and which is such that instances of this process type reliably generate -outputs that describes the input. - This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. - Alan Ruttenberg - is quality measurement of - - - - - - - - - inverse of the relation of is quality measurement of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - is quality measured as - - - - - - - - - - is_supported_by_data - The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. - - The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process - OBI - OBI - Philly 2011 workshop - is_supported_by_data - - - - - - - - - - - - - - - - has_specified_input - has_specified_input - see is_input_of example_of_usage - - The inverse property of is_specified_input_of - 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Coutot - - has_specified_input - - - - - - - - - - is_specified_input_of - some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. - Alan Ruttenberg - PERSON:Bjoern Peters - is_specified_input_of - - - - - - - - - - - - - - - - has_specified_output - has_specified_output - - The inverse property of is_specified_output_of - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Courtot - - has_specified_output - - - - - - - - - - is_specified_output_of - is_specified_output_of - - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - Alan Ruttenberg - PERSON:Bjoern Peters - - is_specified_output_of - - - - - - - - - - - achieves_planned_objective - A cell sorting process achieves the objective specification 'material separation objective' - - This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. - BP, AR, PPPB branch - PPPB branch derived - modified according to email thread from 1/23/09 in accordince with DT and PPPB branch - achieves_planned_objective - - - - - - - - - - objective_achieved_by - - This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. - OBI - OBI - objective_achieved_by - - - - - - - - - - - has value specification - - A relation between an information content entity and a value specification that specifies its value. - PERSON: James A. Overton - OBI - has value specification - - - - - - - - - inheres in - this fragility inheres in this vase - this red color inheres in this apple - a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence - A dependent inheres in its bearer at all times for which the dependent exists. - inheres_in - - inheres in - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - bearer of - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. - is concretized as - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - has component - - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - - - - - - - has measurement value - - - - - - - - - - - has specified numeric value - - A relation between a value specification and a number that quantifies it. - A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. - PERSON: James A. Overton - OBI - has specified numeric value - - - - - - - - - has specified value - - A relation between a value specification and a literal. - This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. - OBI - has specified value - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A planned process that has specified output a software product and that involves the creation of source code. - Mathias Brochhausen - William R. Hogan - http://en.wikipedia.org/wiki/Software_development - A planned process resulting in a software product involving the creation of source code. - software development - - - - - - - - - - - - - - - - - - - - creating a data set - A planned process that has a data set as its specified output. - William R. Hogan - data set creation - dataset creation - dataset creating - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - quality - Quality - quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - specifically dependent continuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - material - MaterialEntity - material entity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - - - - - - - - - atom - A chemical entity constituting the smallest component of an element having the chemical properties of the element. - - atom - - - - - - - - - cell - PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - - cell - - - - - - - - - cellular_component - A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). - - cellular_component - - - - - - - - - measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - measurement unit label - - - - - - - - - objective specification - In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." - 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - goal specification - OBI Plan and Planned Process/Roles Branch - OBI_0000217 - objective specification - - - - - - - - - Pour the contents of flask 1 into flask 2 - - A directive information entity that describes an action the bearer will take. - Alan Ruttenberg - OBI Plan and Planned Process branch - action specification - - - - - - - - - datum label - - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - - datum label - - - - - - - - - software - - Software is a plan specification composed of a series of instructions that can be -interpreted by or directly executed by a processing unit. - see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI - software - - - - - - - - - - - - - - - - - - - - information carrier - In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. - - A quality of an information bearer that imparts the information content - 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. - 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. - PERSON: Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - information carrier - - - - - - - - - data item - Data items include counts of things, analyte concentrations, and statistical summaries. - - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - JAR: datum -- well, this will be very tricky to define, but maybe some -information-like stuff that might be put into a computer and that is -meant, by someone, to denote and/or to be interpreted by some -process... I would include lists, tables, sentences... I think I might -defer to Barry, or to Brian Cantwell Smith - -JAR: A data item is an approximately justified approximately true approximate belief - 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Jonathan Rees - data - - data item - - - - - - - - - - - - - - - information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - - A generically dependent continuant that is about some thing. - 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert - OBI_0000142 - - information content entity - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - 10 feet. 3 ml. - - A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form - Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - scalar measurement datum - - - - - - - - - - - - - - - - An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - directive information entity - - - - - - - - - dot plot - Dot plot of SSC-H and FSC-H. - - A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000123 - group:OBI - dot plot - - - - - - - - - graph - - A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - PERSON: Lawrence Hunter - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000240 - group:OBI - graph - - - - - - - - - algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - - A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) - algorithm - - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - source code module - The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. - - A source code module is a directive information entity that specifies, using a programming language, some algorithm. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000039 - group:OBI - source code module - - - - - - - - - data format specification - - A data format specification is the information content borne by the document published defining the specification. -Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes -information. Example: The ISO document specifying what encompasses an -XML document; The instructions in a XSD file" - PERSON: Alan Ruttenberg - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000187 - data format specification - - - - - - - - - data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI - data set - - - - - - - - - image - - An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - person:Alan Ruttenberg - person:Allyson - person:Chris Stoeckert - OBI_0000030 - group:OBI - image - - - - - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - - - - - - - - - - - - - - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2014-03-31: A plan specification can have other parts, such as conditional specifications. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - OBI Plan and Planned Process branch - OBI_0000344 - 2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them - plan specification - - - - - - - - - - - - - - - measurement datum - Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - 2/2/2009 is_specified_output of some assay? - person:Chris Stoeckert - OBI_0000305 - group:OBI - measurement datum - - - - - - - - - - - - - - - - - - - - - - - - - material information bearer - A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. - a brain - a hard drive - - A material entity in which a concretization of an information content entity inheres. - GROUP: IAO - material information bearer - - - - - - - - - histogram - - A histogram is a report graph which is a statistical description of a -distribution in terms of occurrence frequencies of different event classes. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - histogram - - - - - - - - - heatmap - - A heatmap is a report graph which is a graphical representation of data -where the values taken by a variable(s) are shown as colors in a -two-dimensional map. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - heatmap - - - - - - - - - dendrogram - Dendrograms are often used in computational biology to -illustrate the clustering of genes. - - A dendrogram is a report graph which is a tree diagram +AnnotationAssertion( "dendrogram"@en) +AnnotationAssertion( "A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a -clustering algorithm. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Dendrogram - dendrogram - - - - - - - - - scatter plot - Comparison of gene expression values in two samples can be displayed in a scatter plot - - A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - scattergraph - WEB: http://en.wikipedia.org/wiki/Scatterplot - scatter plot - - - - - - - - - - - - - - - - - - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - - - - - - - figure - Any picture, diagram or table - - An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - PERSON: Lawrence Hunter - figure - - - - - - - - - diagram - A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. - - A figure that expresses one or more propositions - PERSON: Lawrence Hunter - diagram - - - - - - - - - document - A journal article, patent application, laboratory notebook, or a book - - A collection of information content entities intended to be understood together as a whole - PERSON: Lawrence Hunter - document - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measurement of length quality - Alan Ruttenberg - length measurement datum - - - - - - - - - - - - - - - - - - denotator type - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - - - - - - - Viruses - - Viruses - - - - - - - - - Euteleostomi - bony vertebrates - - Euteleostomi - - - - - - - - - Bacteria - eubacteria - - Bacteria - - - - - - - - - Archaea - - Archaea - - - - - - - - - Eukaryota - eucaryotes - eukaryotes - - Eukaryota - - - - - - - - - Euarchontoglires - - Euarchontoglires - - - - - - - - - Tetrapoda - tetrapods - - Tetrapoda - - - - - - - - - Amniota - amniotes - - Amniota - - - - - - - - - Opisthokonta - - Opisthokonta - - - - - - - - - Metazoa - metazoans - multicellular animals - - Metazoa - - - - - - - - - Bilateria - - Bilateria - - - - - - - - - Mammalia - mammals - - Mammalia - - - - - - - - - Vertebrata <vertebrates> - Vertebrata - vertebrates - - Vertebrata <vertebrates> - - - - - - - - - Homo sapiens - human - human being - - Homo sapiens - - - - - - - - - - - - - - - - - - - - planned process - planned process - Injecting mice with a vaccine in order to test its efficacy - - A process that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. - Bjoern Peters - branch derived - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - 6/11/9: Edited at workshop. Used to include: is initiated by an agent - - planned process - - - - - - - - - regulator role - Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 - - a regulatory role involved with making and/or enforcing relevant legislation and governmental orders - Person:Jennifer Fostel - regulator - OBI - regulator role - - - - - - - - - regulatory role - Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 - - a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. - GROUP: Role branch - OBI, CDISC - govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent - regulatory role - - - - - - - - - material supplier role - Jackson Labs is an organization which provide mice as experimental material - - a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. - Supplier role is a special kind of service, e.g. biobank - PERSON:Jennifer Fostel - material provider role - supplier - material supplier role - - - - - - - - - - - - - - - classified data set - - A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. - PERSON: James Malone - PERSON: Monnie McGee - data set with assigned class labels - classified data set - - - - - - - - - - - - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - - Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material - - - - - - - - - - - - - - - - - - - - - - - - - - - material processing - A cell lysis, production of a cloning vector, creating a buffer. - - A planned process which results in physical changes in a specified input material - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca Serra - material transformation - OBI branch derived - material processing - - - - - - - - - - - - - - - - - - - - - - - - - specimen role - liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. - - a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation - blood taken from animal: animal continues in study, whereas blood has role specimen. -something taken from study subject, leaves the study and becomes the specimen. - parasite example +clustering algorithm."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "dendrogram"@en) +SubClassOf( ) + +# Class: (scatter plot) + +AnnotationAssertion( "scatter plot"@en) +AnnotationAssertion( "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "scatter plot"@en) +SubClassOf( ) + +# Class: (obsolescence reason specification) + +AnnotationAssertion( "obsolescence reason specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (figure) + +AnnotationAssertion( "figure"@en) +AnnotationAssertion( "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "figure"@en) +SubClassOf( ) + +# Class: (document) + +AnnotationAssertion( "document"@en) +AnnotationAssertion( "A collection of information content entities intended to be understood together as a whole"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "document"@en) +SubClassOf( ) + +# Class: (length measurement datum) + +AnnotationAssertion( "length measurement datum"@en) +AnnotationAssertion( "A scalar measurement datum that is the result of measurement of length quality"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "length measurement datum"@en) +SubClassOf( ) + +# Class: (denotator type) + +AnnotationAssertion( "denotator type"@en) +AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en) +AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Barry Smith, Werner Ceusters"@en) +AnnotationAssertion(rdfs:label "denotator type"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (Viruses) + +AnnotationAssertion( "Viruses") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Viruses") +SubClassOf( ) + +# Class: (Euteleostomi) + +AnnotationAssertion( "Euteleostomi") +AnnotationAssertion( "bony vertebrates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Euteleostomi") +SubClassOf( ) + +# Class: (Bacteria) + +AnnotationAssertion( "Bacteria") +AnnotationAssertion( "eubacteria") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Bacteria") +SubClassOf( ) + +# Class: (Archaea) + +AnnotationAssertion( "Archaea") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Archaea") +SubClassOf( ) + +# Class: (Eukaryota) + +AnnotationAssertion( "Eukaryota") +AnnotationAssertion( "eucaryotes") +AnnotationAssertion( "eukaryotes") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Eukaryota") +SubClassOf( ) + +# Class: (Euarchontoglires) + +AnnotationAssertion( "Euarchontoglires") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Euarchontoglires") +SubClassOf( ) + +# Class: (Tetrapoda) + +AnnotationAssertion( "Tetrapoda") +AnnotationAssertion( "tetrapods") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Tetrapoda") +SubClassOf( ) + +# Class: (Amniota) + +AnnotationAssertion( "Amniota") +AnnotationAssertion( "amniotes") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Amniota") +SubClassOf( ) + +# Class: (Opisthokonta) + +AnnotationAssertion( "Opisthokonta") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Opisthokonta") +SubClassOf( ) + +# Class: (Metazoa) + +AnnotationAssertion( "Metazoa") +AnnotationAssertion( "metazoans") +AnnotationAssertion( "multicellular animals") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Metazoa") +SubClassOf( ) + +# Class: (Bilateria) + +AnnotationAssertion( "Bilateria") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Bilateria") +SubClassOf( ) + +# Class: (Mammalia) + +AnnotationAssertion( "Mammalia") +AnnotationAssertion( "mammals") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Mammalia") +SubClassOf( ) + +# Class: (Vertebrata ) + +AnnotationAssertion( "Vertebrata ") +AnnotationAssertion( "Vertebrata") +AnnotationAssertion( "vertebrates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Vertebrata ") +SubClassOf( ) + +# Class: (Homo sapiens) + +AnnotationAssertion( "Homo sapiens") +AnnotationAssertion( "human") +AnnotationAssertion( "human being") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Homo sapiens") +SubClassOf( ) + +# Class: (completely executed planned process) + +AnnotationAssertion( "completely executed planned process"@en) +AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") +AnnotationAssertion( ) +AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) +AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") +AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "branch derived") +AnnotationAssertion( "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en) +AnnotationAssertion( "6/11/9: Edited at workshop. Used to include: is initiated by an agent") +AnnotationAssertion(rdfs:label "completely executed planned process"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulator role) + +AnnotationAssertion( "regulator role") +AnnotationAssertion( "Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805"@en) +AnnotationAssertion( ) +AnnotationAssertion( "a regulatory role involved with making and/or enforcing relevant legislation and governmental orders"@en) +AnnotationAssertion( "Person:Jennifer Fostel"@en) +AnnotationAssertion( "regulator") +AnnotationAssertion( "OBI"@en) +AnnotationAssertion(rdfs:label "regulator role"@en) +SubClassOf( ) + +# Class: (regulatory role) + +AnnotationAssertion( "regulatory role"@en) +AnnotationAssertion( "Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008"@en) +AnnotationAssertion( ) +AnnotationAssertion( "a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body."@en) +AnnotationAssertion( "GROUP: Role branch"@en) +AnnotationAssertion( "OBI, CDISC"@en) +AnnotationAssertion( "govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent"@en) +AnnotationAssertion(rdfs:label "regulatory role"@en) +SubClassOf( ) + +# Class: (material supplier role) + +AnnotationAssertion( "material supplier role") +AnnotationAssertion( "Jackson Labs is an organization which provide mice as experimental material") +AnnotationAssertion( ) +AnnotationAssertion( "a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation."@en) +AnnotationAssertion( "Supplier role is a special kind of service, e.g. biobank") +AnnotationAssertion( "PERSON:Jennifer Fostel"@en) +AnnotationAssertion( "material provider role") +AnnotationAssertion( "supplier") +AnnotationAssertion(rdfs:label "material supplier role"@en) +SubClassOf( ) + +# Class: (classified data set) + +AnnotationAssertion( "classified data set") +AnnotationAssertion( ) +AnnotationAssertion( "A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels."@en) +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion( "PERSON: Monnie McGee") +AnnotationAssertion( "data set with assigned class labels") +AnnotationAssertion(rdfs:label "classified data set"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (processed material entity) + +AnnotationAssertion( "processed material entity"@en) +AnnotationAssertion( "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity processed by human activity with an intent to produce") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "processed material entity"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (material processing) + +AnnotationAssertion( "material processing") +AnnotationAssertion( "A cell lysis, production of a cloning vector, creating a buffer.") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process which results in physical changes in a specified input material"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca Serra") +AnnotationAssertion( "material transformation"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion(rdfs:label "material processing"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (specimen role) + +AnnotationAssertion( "specimen role") +AnnotationAssertion( "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.") +AnnotationAssertion( ) +AnnotationAssertion( "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation"@en) +AnnotationAssertion( "blood taken from animal: animal continues in study, whereas blood has role specimen. +something taken from study subject, leaves the study and becomes the specimen."@en) +AnnotationAssertion( "parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study -specimen can later be subject. - 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. - GROUP: Role Branch - OBI - - specimen role - - - - - - - - - organization - PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. - - An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. - BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: +specimen can later be subject."@en) +AnnotationAssertion( "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.") +AnnotationAssertion( "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "GROUP: Role Branch") +AnnotationAssertion( "OBI") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "specimen role"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) + +# Class: (organization) + +AnnotationAssertion( "organization"@en) +AnnotationAssertion( "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods."@en) +AnnotationAssertion( ) +AnnotationAssertion( "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members."@en) +AnnotationAssertion( "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers @@ -2866,8 +1613,8 @@ charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the -bearer of organization_roles' are. My personal favorite is still to define -organization as a kind of 'legal entity', but thinking it through leads to +bearer of organization_roles' are. My personal favorite is still to define +organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place @@ -2876,6041 +1623,4085 @@ Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - -3 above, but without an 'is a' statement for now. We can leave it in its +3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to -'continuant'. We leave further clarifications to BFO, and close this issue -for now. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra - PERSON: Susanna Sansone - GROUP: OBI - organization - - - - - - - - - protocol - PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. - - A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. - PlanAndPlannedProcess Branch - OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) - study protocol - protocol - - - - - - - - - - - - - - - - - - - - - interpreting data - Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. - - A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - Bjoern Peters - drawing a conclusion based on data - - - - - - - - - light emission function - - A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - light emission function - - - - - - - - - excitation function - - A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - excitation function - - - - - - - - - - - - - - - - - - - - regulatory agency - The US Environmental Protection Agency - - A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. - GROUP: OBI Biomaterial Branch - WEB: en.wikipedia.org/wiki/Regulator - regulatory agency - - - - - - - - - material transformation objective - The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. - - an objective specifiction that creates an specific output object from input materials. - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - artifact creation objective - GROUP: OBI PlanAndPlannedProcess Branch - material transformation objective - - - - - - - - - - - - - - - - - - - - - - - - - - - manufacturing - - A planned process with the objective to produce a processed material which will have a function for future use. - This includes a single scientist making a processed material for personal use. - A person or organization (having manufacturer role) is a participant in this process - Manufacturing implies reproducibility and responsibility AR - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - GROUP: OBI PlanAndPlannedProcess Branch - manufacturing - - - - - - - - - manufacturing objective - - is the objective to manufacture a material of a certain function (device) - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - GROUP: OBI PlanAndPlannedProcess Branch - manufacturing objective - - - - - - - - - - - - - - - - - - - - - - - - - - - - manufacturer role - With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. - - Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. - GROUP: Role Branch - OBI - manufacturer role - - - - - - - - - - - - - - - clustered data set - A clustered data set is the output of a K means clustering data transformation - - A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. - PERSON: James Malone - PERSON: Monnie McGee - data set with assigned discovered class labels - AR thinks could be a data item instead - clustered data set - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - specimen collection process - drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation - - A planned process with the objective of collecting a specimen. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. - Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. - Philly2013: The specimen_role for the specimen is created during the specimen collection process. - label changed to 'specimen collection process' on 10/27/2014, details see tracker: -http://sourceforge.net/p/obi/obi-terms/716/ - Bjoern Peters - specimen collection - 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession - 6/9/09: used at workshop - specimen collection process - - - - - - - - - - - - - - - - - - - - - - - class prediction data transformation - - A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. - James Malone - supervised classification data transformation - PERSON: James Malone - class prediction data transformation - - - - - - - - - specimen collection objective - The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. - - A objective specification to obtain a material entity for potential use as an input during an investigation. - Bjoern Peters - Bjoern Peters - specimen collection objective - - - - - - - - - - - - - - - support vector machine - - A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. - James Malone - Ryan Brinkman - SVM - PERSON: Ryan Brinkman - support vector machine - - - - - - - - - decision tree induction objective - - A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. - James Malone - decision tree induction objective - - - - - - - - - - - - - - - decision tree building data transformation - - A decision tree building data transformation is a data transformation that has objective decision tree induction. - James Malone - PERSON: James Malone - decision tree building data transformation - - - - - - - - - GenePattern software - - a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. - James Malone - Person:Helen Parkinson - WEB: http://www.broadinstitute.org/cancer/software/genepattern/ - GenePattern software - - - - - - - - - peak matching - - Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold - James Malone - Ryan Brinkman - PERSON: Ryan Brinkman - peak matching - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - k-nearest neighbors - - A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. - James Malone - k-NN - PERSON: James Malone - k-nearest neighbors - - - - - - - - - - - - - - - CART - - A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. - James Malone - classification and regression trees - BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. - CART - - - - - - - - - - - - - - - statistical model validation - Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia - - A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. - Helen Parkinson - http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 - statistical model validation - - - - - - - - - - - - - - - - - - - - - - - - - manufacturer - - A person or organization that has a manufacturer role. - manufacturer - - - - - - - - - - - - - - - - - - - - - - - - - - - - service provider role - Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. - - is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person - PERSON:Helen Parkinson - service provider role - - - - - - - - - - - - - - - - - - processed specimen - A tissue sample that has been sliced and stained for a histology study. -A blood specimen that has been centrifuged to obtain the white blood cells. - - A specimen that has been intentionally physically modified. - Bjoern Peters - Bjoern Peters - A tissue sample that has been sliced and stained for a histology study. - processed specimen - - - - - - - - - categorical label - The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. - - A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. - Bjoern Peters - Bjoern Peters - categorical label - - - - - - - - - - - - - - - - - - - - - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device - - - - - - - - - dose - An organism has been injected 1ml of vaccine - - A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. - dose - - - - - - - - - questionnaire - - A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. - JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. -JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. - Need to clarify if this is a document or a directive information entity (or what their connection is)) - PERSON: Jessica Turner - Merriam-Webster - questionnaire - - - - - - - - - - - - - - - - - - - - light emission device - A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) - - A device which has a function to emit light. - Person:Helen Parkinson - OBI - light emission device - - - - - - - - - - - - - - - X-ray source - - A device that is used to generate X-rays. - PERSON: Erik Segerdell - x-ray generator - http://en.wikipedia.org/wiki/X-ray_generator - X-ray source - - - - - - - - - - - - - - - - - - - - - conclusion based on data - The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. -The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". - - An information content entity that is inferred from data. - In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. - Group:2013 Philly Workshop group - Group:2013 Philly Workshop group - conclusion based on data - - - - - - - - - categorical value specification - - A value specification that is specifies one category out of a fixed number of nominal categories - PERSON:Bjoern Peters - categorical value specification - - - - - - - - - - - - 1 - - - - - - 1 - - - scalar value specification - - A value specification that consists of two parts: a numeral and a unit label - PERSON:Bjoern Peters - scalar value specification - - - - - - - - - value specification - The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. - - An information content entity that specifies a value within a classification scheme or on a quantitative scale. - This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. - PERSON:Bjoern Peters - value specification - - - - - - - - - - - - - - - - - - - - collection of specimens - Blood cells collected from multiple donors over the course of a study. - - A material entity that has two or more specimens as its parts. - Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ - Person: Chris Stoeckert, Jie Zheng - OBIB, OBI - Biobank - collection of specimens - - - - - - - - - histologic grade according to AJCC 7th edition - G1:Well differentiated - G4: Undifferentiated - - A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - histologic grade according to AJCC 7th edition - - - - - - - - - histologic grade according to the Fuhrman Nuclear Grading System - - A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. - Chris Stoeckert, Helena Ellis - Histologic Grade (Fuhrman Nuclear Grading System) - NCI BBRB, OBI - NCI BBRB - histologic grade according to the Fuhrman Nuclear Grading System - - - - - - - - - histologic grade for ovarian tumor - - A categorical value specification that is a histologic grade assigned to a ovarian tumor. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - histologic grade for ovarian tumor - - - - - - - - - histologic grade for ovarian tumor according to a two-tier grading system - - A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - histologic grade for ovarian tumor according to a two-tier grading system - - - - - - - - - histologic grade for ovarian tumor according to the World Health Organization - - A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - histologic grade for ovarian tumor according to the World Health Organization - - - - - - - - - pathologic primary tumor stage for colon and rectum according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic primary tumor stage for colon and rectum according to AJCC 7th edition - - - - - - - - - pathologic primary tumor stage for lung according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread lung primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic primary tumor stage for lung according to AJCC 7th edition - - - - - - - - - pathologic primary tumor stage for kidney according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic primary tumor stage for kidney according to AJCC 7th edition - - - - - - - - - pathologic primary tumor stage for ovary according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic primary tumor stage for ovary according to AJCC 7th edition - - - - - - - - - pathologic lymph node stage for colon and rectum according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic lymph node stage for colon and rectum according to AJCC 7th edition - - - - - - - - - pathologic lymph node stage for lung according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic lymph node stage for lung according to AJCC 7th edition - - - - - - - - - pathologic lymph node stage for kidney according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic lymph node stage for kidney according to AJCC 7th edition - - - - - - - - - pathologic lymph node stage for ovary according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic lymph node stage for ovary according to AJCC 7th edition - - - - - - - - - pathologic distant metastases stage for colon according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: colon distant metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic distant metastases stage for colon according to AJCC 7th edition - - - - - - - - - pathologic distant metastases stage for lung according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: lung distant metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic distant metastases stage for lung according to AJCC 7th edition - - - - - - - - - pathologic distant metastases stage for kidney according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: kidney distant Metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic distant metastases stage for kidney according to AJCC 7th edition - - - - - - - - - pathologic distant metastases stage for ovary according to AJCC 7th edition - - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: ovarian distant metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic distant metastases stage for ovary according to AJCC 7th edition - - - - - - - - - clinical tumor stage group according to AJCC 7th edition - - A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. - Chris Stoeckert, Helena Ellis - Clinical tumor stage group (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - clinical tumor stage group according to AJCC 7th edition - - - - - - - - - International Federation of Gynecology and Obstetrics cervical cancer stage value specification - - A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. - Chris Stoeckert, Helena Ellis - Clinical FIGO stage - NCI BBRB, OBI - NCI BBRB - International Federation of Gynecology and Obstetrics cervical cancer stage value specification - - - - - - - - - International Federation of Gynecology and Obstetrics ovarian cancer stage value specification - - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. - Chris Stoeckert, Helena Ellis - Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) - NCI BBRB, OBI - NCI BBRB - International Federation of Gynecology and Obstetrics ovarian cancer stage value specification - - - - - - - - - performance status value specification - - A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). - Chris Stoeckert, Helena Ellis - Performance Status Scale - https://en.wikipedia.org/wiki/Performance_status - NCI BBRB - performance status value specification - - - - - - - - - Eastern Cooperative Oncology Group score value specification - - A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. - Chris Stoeckert, Helena Ellis - ECOG score - NCI BBRB, OBI - NCI BBRB - Eastern Cooperative Oncology Group score value specification - - - - - - - - - Karnofsky score vaue specification - - A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. - Chris Stoeckert, Helena Ellis - Karnofsky Score - NCI BBRB, OBI - NCI BBRB - Karnofsky score vaue specification - - - - - - - - - altitude measurement datum - - A length measurement datum between a point at sea or ground level and some point above it. - Chris Stoeckert - Adapted from https://www.merriam-webster.com/dictionary/altitude - altitude measurement datum - - - - - - - - - - - - - - - - - - - - - - - - - material supplier - - A person or organization that provides material supplies to other people or organizations. - Rebecca Jackson - https://github.com/obi-ontology/obi/issues/1289 - material supplier - - - - - - - - - - - - - - - - - - - organism - animal - fungus - plant - virus - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism - - - - - - - - - - - - - - - - - - - - specimen - Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. - - A material entity that has the specimen role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. - PERSON: James Malone - PERSON: Philippe Rocca-Serra - GROUP: OBI Biomaterial Branch - - specimen - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data transformation - The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. - - A planned process that produces output data from input data. - Elisabetta Manduchi - Helen Parkinson - James Malone - Melanie Courtot - Richard Scheuermann - Ryan Brinkman - Tina Hernandez-Boussard - Philippe Rocca-Serra - data analysis - data processing - Branch editors - - data transformation - - - - - - - - - - - - - - - leave one out cross validation method - The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 - - is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data - 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 - Person:Helen Parkinson - leave one out cross validation method - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - k-means clustering - - A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). - James Malone - Elisabetta Manduchi - Philippe Rocca-Serra - WEB: http://en.wikipedia.org/wiki/K-means - k-means clustering - - - - - - - - - - - - - - - - - - - - - - - - hierarchical clustering - - A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). - James Malone - WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering - hierarchical clustering - - - - - - - - - - - - - - - - - - - - - - - - dimensionality reduction - - A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. - Elisabetta Manduchi - James Malone - Melanie Courtot - Philippe Rocca-Serra - data projection - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - dimensionality reduction - - - - - - - - - principal components analysis dimensionality reduction - - A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. - Elisabetta Manduchi - James Malone - Melanie Courtot - Philippe Rocca-Serra - pca data reduction - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - principal components analysis dimensionality reduction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data visualization - Generation of a heatmap from a microarray dataset - - A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations. - Elisabetta Manduchi - James Malone - Melanie Courtot - Tina Boussard - visualization - data encoding as image - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - PERSON: Tina Boussard - Possible future hierarchy might include this: +'continuant'. We leave further clarifications to BFO, and close this issue +for now."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg") +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "PERSON: Susanna Sansone") +AnnotationAssertion( "GROUP: OBI") +AnnotationAssertion(rdfs:comment "Should revisit if we can place outside of material entity - a collection of roles.") +AnnotationAssertion(rdfs:label "organization"@en) +SubClassOf( ) + +# Class: (plan) + +AnnotationAssertion( "plan"@en) +AnnotationAssertion( "The plan of researcher X to perform an experiment according to a protocol.") +AnnotationAssertion( ) +AnnotationAssertion( "A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process."@en) +AnnotationAssertion( "This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.") +AnnotationAssertion( "AR, BP, JM, MC, PRS"@en) +AnnotationAssertion( "branch derived"@en) +AnnotationAssertion(rdfs:label "plan"@en) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom(ObjectInverseOf() )) + +# Class: (protocol) + +AnnotationAssertion( "protocol"@en) +AnnotationAssertion( "PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process."@en) +AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion( "OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)"@en) +AnnotationAssertion( "study protocol") +AnnotationAssertion(rdfs:label "protocol"@en) +SubClassOf( ) + +# Class: (drawing a conclusion based on data) + +AnnotationAssertion( "interpreting data") +AnnotationAssertion( "Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion(rdfs:label "drawing a conclusion based on data"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (light emission function) + +AnnotationAssertion( "light emission function"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A light emission function is an excitation function to excite a material to a specific excitation state that it emits light."@en) +AnnotationAssertion( "Bill Bug") +AnnotationAssertion( "Daniel Schober") +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "Melanie Courtot") +AnnotationAssertion(rdfs:label "light emission function"@en) +SubClassOf( ) + +# Class: (excitation function) + +AnnotationAssertion( "excitation function"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons."@en) +AnnotationAssertion( "Bill Bug") +AnnotationAssertion( "Daniel Schober") +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "Melanie Courtot") +AnnotationAssertion(rdfs:label "excitation function"@en) +SubClassOf( ) + +# Class: (regulatory agency) + +AnnotationAssertion( "regulatory agency"@en) +AnnotationAssertion( "The US Environmental Protection Agency") +AnnotationAssertion( ) +AnnotationAssertion( "A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government."@en) +AnnotationAssertion( "GROUP: OBI Biomaterial Branch") +AnnotationAssertion( "WEB: en.wikipedia.org/wiki/Regulator") +AnnotationAssertion(rdfs:label "regulatory agency"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (material transformation objective) + +AnnotationAssertion( "material transformation objective") +AnnotationAssertion( "The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.") +AnnotationAssertion( ) +AnnotationAssertion( "an objective specifiction that creates an specific output object from input materials."@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "artifact creation objective"@en) +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "material transformation objective"@en) +SubClassOf( ) + +# Class: (manufacturing) + +AnnotationAssertion( "manufacturing") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective to produce a processed material which will have a function for future use."@en) +AnnotationAssertion( "This includes a single scientist making a processed material for personal use."@en) +AnnotationAssertion( "A person or organization (having manufacturer role) is a participant in this process") +AnnotationAssertion( "Manufacturing implies reproducibility and responsibility AR") +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "manufacturing"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (manufacturing objective) + +AnnotationAssertion( "manufacturing objective") +AnnotationAssertion( ) +AnnotationAssertion( "is the objective to manufacture a material of a certain function (device)"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "manufacturing objective"@en) +SubClassOf( ) + +# Class: (manufacturer role) + +AnnotationAssertion( "manufacturer role") +AnnotationAssertion( "With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.") +AnnotationAssertion( ) +AnnotationAssertion( "Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process."@en) +AnnotationAssertion( "GROUP: Role Branch") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "manufacturer role") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (clustered data set) + +AnnotationAssertion( "clustered data set") +AnnotationAssertion( "A clustered data set is the output of a K means clustering data transformation") +AnnotationAssertion( ) +AnnotationAssertion( "A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels."@en) +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion( "PERSON: Monnie McGee") +AnnotationAssertion( "data set with assigned discovered class labels") +AnnotationAssertion( "AR thinks could be a data item instead") +AnnotationAssertion(rdfs:label "clustered data set"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (specimen collection process) + +AnnotationAssertion( "specimen collection process") +AnnotationAssertion( "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective of collecting a specimen."@en) +AnnotationAssertion( "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.") +AnnotationAssertion( "Philly2013: The specimen_role for the specimen is created during the specimen collection process.") +AnnotationAssertion( "label changed to 'specimen collection process' on 10/27/2014, details see tracker: +http://sourceforge.net/p/obi/obi-terms/716/") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "specimen collection") +AnnotationAssertion( "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession") +AnnotationAssertion( "6/9/09: used at workshop") +AnnotationAssertion(rdfs:label "specimen collection process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (class prediction data transformation) + +AnnotationAssertion( "class prediction data transformation"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "supervised classification data transformation") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "class prediction data transformation"@en) +EquivalentClasses( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (specimen collection objective) + +AnnotationAssertion( "specimen collection objective") +AnnotationAssertion( "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.") +AnnotationAssertion( ) +AnnotationAssertion( "A objective specification to obtain a material entity for potential use as an input during an investigation."@en) +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion(rdfs:label "specimen collection objective") +SubClassOf( ) + +# Class: (support vector machine) + +AnnotationAssertion( "support vector machine") +AnnotationAssertion( ) +AnnotationAssertion( "A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "Ryan Brinkman") +AnnotationAssertion( "SVM") +AnnotationAssertion( "PERSON: Ryan Brinkman") +AnnotationAssertion(rdfs:label "support vector machine") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (decision tree induction objective) + +AnnotationAssertion( "decision tree induction objective") +AnnotationAssertion( ) +AnnotationAssertion( "A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "decision tree induction objective") +SubClassOf( ) + +# Class: (decision tree building data transformation) + +AnnotationAssertion( "decision tree building data transformation"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A decision tree building data transformation is a data transformation that has objective decision tree induction."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "decision tree building data transformation"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (GenePattern software) + +AnnotationAssertion( "GenePattern software") +AnnotationAssertion( ) +AnnotationAssertion( "a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "Person:Helen Parkinson") +AnnotationAssertion( "WEB: http://www.broadinstitute.org/cancer/software/genepattern/") +AnnotationAssertion(rdfs:label "GenePattern software") +SubClassOf( ) + +# Class: (peak matching) + +AnnotationAssertion( "peak matching") +AnnotationAssertion( ) +AnnotationAssertion( "Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold"@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "Ryan Brinkman") +AnnotationAssertion( "PERSON: Ryan Brinkman") +AnnotationAssertion(rdfs:label "peak matching") +SubClassOf( ) + +# Class: (k-nearest neighbors) + +AnnotationAssertion( "k-nearest neighbors"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "k-NN") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "k-nearest neighbors"@en) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (CART) + +AnnotationAssertion( "CART"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "classification and regression trees") +AnnotationAssertion( "BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining."@en) +AnnotationAssertion(rdfs:label "CART"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (statistical model validation) + +AnnotationAssertion( "statistical model validation") +AnnotationAssertion( "Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia") +AnnotationAssertion( ) +AnnotationAssertion( "A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set."@en) +AnnotationAssertion( "Helen Parkinson") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29") +AnnotationAssertion(rdfs:label "statistical model validation") +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (manufacturer) + +AnnotationAssertion( "manufacturer") +AnnotationAssertion( ) +AnnotationAssertion( "A person or organization that has a manufacturer role."@en) +AnnotationAssertion(rdfs:label "manufacturer") +EquivalentClasses( ObjectIntersectionOf(ObjectUnionOf( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (service provider role) + +AnnotationAssertion( "service provider role") +AnnotationAssertion( "Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.") +AnnotationAssertion( ) +AnnotationAssertion( "is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person"@en) +AnnotationAssertion( "PERSON:Helen Parkinson") +AnnotationAssertion(rdfs:label "service provider role") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (processed specimen) + +AnnotationAssertion( "processed specimen") +AnnotationAssertion( "A tissue sample that has been sliced and stained for a histology study. +A blood specimen that has been centrifuged to obtain the white blood cells.") +AnnotationAssertion( ) +AnnotationAssertion( "A specimen that has been intentionally physically modified."@en) +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion(rdfs:comment "A tissue sample that has been sliced and stained for a histology study.") +AnnotationAssertion(rdfs:label "processed specimen") +EquivalentClasses( ObjectIntersectionOf( )) +SubClassOf( ) +SubClassOf( ) + +# Class: (categorical label) + +AnnotationAssertion( "categorical label") +AnnotationAssertion( "The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.") +AnnotationAssertion( ) +AnnotationAssertion( "A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale."@en) +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion(rdfs:label "categorical label") +SubClassOf( ) + +# Class: (obsolete_device) + +AnnotationAssertion( "obsolete_device") +AnnotationAssertion( "A voltmeter is a measurement device which is intended to perform some measure function.") +AnnotationAssertion( "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.") +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent."@en) +AnnotationAssertion( "PERSON: Helen Parkinson") +AnnotationAssertion( "instrument") +AnnotationAssertion( "OBI development call 2012-12-17") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "obsolete_device") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) +SubClassOf( ) + +# Class: (dose) + +AnnotationAssertion( "dose") +AnnotationAssertion( "An organism has been injected 1ml of vaccine") +AnnotationAssertion( ) +AnnotationAssertion( "A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses."@en) +AnnotationAssertion(rdfs:label "dose") +SubClassOf( ) + +# Class: (questionnaire) + +AnnotationAssertion( "questionnaire") +AnnotationAssertion( ) +AnnotationAssertion( "A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study."@en) +AnnotationAssertion( "JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. +JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not."@en) +AnnotationAssertion( "Need to clarify if this is a document or a directive information entity (or what their connection is))") +AnnotationAssertion( "PERSON: Jessica Turner"@en) +AnnotationAssertion( "Merriam-Webster"@en) +AnnotationAssertion(rdfs:label "questionnaire") +SubClassOf( ) + +# Class: (light emission device) + +AnnotationAssertion( "light emission device") +AnnotationAssertion( "A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)") +AnnotationAssertion( ) +AnnotationAssertion( "A device which has a function to emit light."@en) +AnnotationAssertion( "Person:Helen Parkinson") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "light emission device") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (X-ray source) + +AnnotationAssertion( "X-ray source") +AnnotationAssertion( ) +AnnotationAssertion( "A device that is used to generate X-rays."@en) +AnnotationAssertion( "PERSON: Erik Segerdell") +AnnotationAssertion( "x-ray generator") +AnnotationAssertion( "http://en.wikipedia.org/wiki/X-ray_generator") +AnnotationAssertion(rdfs:label "X-ray source") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (conclusion based on data) + +AnnotationAssertion( "conclusion based on data") +AnnotationAssertion( "The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. +The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. \"13 is prime\".") +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that is inferred from data."@en) +AnnotationAssertion( "In the Philly 2013 workshop, we recognized the limitations of \"conclusion textual entity\", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.") +AnnotationAssertion( "Group:2013 Philly Workshop group") +AnnotationAssertion( "Group:2013 Philly Workshop group") +AnnotationAssertion(rdfs:label "conclusion based on data") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (categorical value specification) + +AnnotationAssertion( "categorical value specification") +AnnotationAssertion( ) +AnnotationAssertion( "A value specification that is specifies one category out of a fixed number of nominal categories"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "categorical value specification") +SubClassOf( ) + +# Class: (scalar value specification) + +AnnotationAssertion( "scalar value specification") +AnnotationAssertion( ) +AnnotationAssertion( "A value specification that consists of two parts: a numeral and a unit label"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "scalar value specification") +SubClassOf( ) +SubClassOf( ObjectMinCardinality(1 )) +SubClassOf( DataMinCardinality(1 )) + +# Class: (value specification) + +AnnotationAssertion( "value specification") +AnnotationAssertion( "The value of 'positive' in a classification scheme of \"positive or negative\"; the value of '20g' on the quantitative scale of mass.") +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that specifies a value within a classification scheme or on a quantitative scale."@en) +AnnotationAssertion( "This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.") +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "value specification") +SubClassOf( ) + +# Class: (collection of specimens) + +AnnotationAssertion( "collection of specimens"@en) +AnnotationAssertion( "Blood cells collected from multiple donors over the course of a study."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that has two or more specimens as its parts."@en) +AnnotationAssertion( "Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/") +AnnotationAssertion( "Person: Chris Stoeckert, Jie Zheng"@en) +AnnotationAssertion( "OBIB, OBI") +AnnotationAssertion( "Biobank") +AnnotationAssertion(rdfs:label "collection of specimens"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) +SubClassOf( ) + +# Class: (histologic grade according to AJCC 7th edition) + +AnnotationAssertion( "histologic grade according to AJCC 7th edition") +AnnotationAssertion( "G1:Well differentiated") +AnnotationAssertion( "G4: Undifferentiated") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "histologic grade according to AJCC 7th edition") +SubClassOf( ) + +# Class: (histologic grade according to the Fuhrman Nuclear Grading System) + +AnnotationAssertion( "histologic grade according to the Fuhrman Nuclear Grading System") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Histologic Grade (Fuhrman Nuclear Grading System)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "histologic grade according to the Fuhrman Nuclear Grading System") +SubClassOf( ) + +# Class: (histologic grade for ovarian tumor) + +AnnotationAssertion( "histologic grade for ovarian tumor") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a histologic grade assigned to a ovarian tumor."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "histologic grade for ovarian tumor") +SubClassOf( ) + +# Class: (histologic grade for ovarian tumor according to a two-tier grading system) + +AnnotationAssertion( "histologic grade for ovarian tumor according to a two-tier grading system") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "histologic grade for ovarian tumor according to a two-tier grading system") +SubClassOf( ) + +# Class: (histologic grade for ovarian tumor according to the World Health Organization) + +AnnotationAssertion( "histologic grade for ovarian tumor according to the World Health Organization") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "histologic grade for ovarian tumor according to the World Health Organization") +SubClassOf( ) + +# Class: (pathologic primary tumor stage for colon and rectum according to AJCC 7th edition) + +AnnotationAssertion( "pathologic primary tumor stage for colon and rectum according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic primary tumor stage for colon and rectum according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic primary tumor stage for lung according to AJCC 7th edition) + +AnnotationAssertion( "pathologic primary tumor stage for lung according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pT: Pathologic spread lung primary tumor (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic primary tumor stage for lung according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic primary tumor stage for kidney according to AJCC 7th edition) + +AnnotationAssertion( "pathologic primary tumor stage for kidney according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic primary tumor stage for kidney according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic primary tumor stage for ovary according to AJCC 7th edition) + +AnnotationAssertion( "pathologic primary tumor stage for ovary according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic primary tumor stage for ovary according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic lymph node stage for colon and rectum according to AJCC 7th edition) + +AnnotationAssertion( "pathologic lymph node stage for colon and rectum according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic lymph node stage for colon and rectum according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic lymph node stage for lung according to AJCC 7th edition) + +AnnotationAssertion( "pathologic lymph node stage for lung according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic lymph node stage for lung according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic lymph node stage for kidney according to AJCC 7th edition) + +AnnotationAssertion( "pathologic lymph node stage for kidney according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic lymph node stage for kidney according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic lymph node stage for ovary according to AJCC 7th edition) + +AnnotationAssertion( "pathologic lymph node stage for ovary according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic lymph node stage for ovary according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic distant metastases stage for colon according to AJCC 7th edition) + +AnnotationAssertion( "pathologic distant metastases stage for colon according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "M: colon distant metastases (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic distant metastases stage for colon according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic distant metastases stage for lung according to AJCC 7th edition) + +AnnotationAssertion( "pathologic distant metastases stage for lung according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "M: lung distant metastases (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic distant metastases stage for lung according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic distant metastases stage for kidney according to AJCC 7th edition) + +AnnotationAssertion( "pathologic distant metastases stage for kidney according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "M: kidney distant Metastases (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic distant metastases stage for kidney according to AJCC 7th edition") +SubClassOf( ) + +# Class: (pathologic distant metastases stage for ovary according to AJCC 7th edition) + +AnnotationAssertion( "pathologic distant metastases stage for ovary according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "M: ovarian distant metastases (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pathologic distant metastases stage for ovary according to AJCC 7th edition") +SubClassOf( ) + +# Class: (clinical tumor stage group according to AJCC 7th edition) + +AnnotationAssertion( "clinical tumor stage group according to AJCC 7th edition") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Clinical tumor stage group (AJCC 7th Edition)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "clinical tumor stage group according to AJCC 7th edition") +SubClassOf( ) + +# Class: (International Federation of Gynecology and Obstetrics cervical cancer stage value specification) + +AnnotationAssertion( "International Federation of Gynecology and Obstetrics cervical cancer stage value specification") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Clinical FIGO stage") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "International Federation of Gynecology and Obstetrics cervical cancer stage value specification") +SubClassOf( ) + +# Class: (International Federation of Gynecology and Obstetrics ovarian cancer stage value specification) + +AnnotationAssertion( "International Federation of Gynecology and Obstetrics ovarian cancer stage value specification") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "International Federation of Gynecology and Obstetrics ovarian cancer stage value specification") +SubClassOf( ) + +# Class: (performance status value specification) + +AnnotationAssertion( "performance status value specification") +AnnotationAssertion( ) +AnnotationAssertion( "A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Performance Status Scale") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Performance_status") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "performance status value specification") +SubClassOf( ) + +# Class: (Eastern Cooperative Oncology Group score value specification) + +AnnotationAssertion( "Eastern Cooperative Oncology Group score value specification") +AnnotationAssertion( ) +AnnotationAssertion( "A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "ECOG score") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Eastern Cooperative Oncology Group score value specification") +SubClassOf( ) + +# Class: (Karnofsky score vaue specification) + +AnnotationAssertion( "Karnofsky score vaue specification") +AnnotationAssertion( ) +AnnotationAssertion( "A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Karnofsky Score") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Karnofsky score vaue specification") +SubClassOf( ) + +# Class: (altitude measurement datum) + +AnnotationAssertion( "altitude measurement datum") +AnnotationAssertion( ) +AnnotationAssertion( "A length measurement datum between a point at sea or ground level and some point above it."@en) +AnnotationAssertion( "Chris Stoeckert") +AnnotationAssertion( "Adapted from https://www.merriam-webster.com/dictionary/altitude") +AnnotationAssertion(rdfs:label "altitude measurement datum") +SubClassOf( ) + +# Class: (material supplier) + +AnnotationAssertion( "material supplier") +AnnotationAssertion( ) +AnnotationAssertion( "A person or organization that provides material supplies to other people or organizations."@en) +AnnotationAssertion( "Rebecca Jackson") +AnnotationAssertion( "https://github.com/obi-ontology/obi/issues/1289") +AnnotationAssertion(rdfs:label "material supplier") +EquivalentClasses( ObjectIntersectionOf(ObjectUnionOf( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (organism) + +AnnotationAssertion( "organism"@en) +AnnotationAssertion( "animal"@en) +AnnotationAssertion( "fungus"@en) +AnnotationAssertion( "plant"@en) +AnnotationAssertion( "virus"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) +AnnotationAssertion( "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')") +AnnotationAssertion( "13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI.") +AnnotationAssertion( "GROUP: OBI Biomaterial Branch") +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Organism"@en) +AnnotationAssertion(rdfs:label "organism"@en) +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (specimen) + +AnnotationAssertion( "specimen"@en) +AnnotationAssertion( "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.") +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that has the specimen role."@en) +AnnotationAssertion( "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI Biomaterial Branch"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "specimen"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (data transformation) + +AnnotationAssertion( "data transformation"@en) +AnnotationAssertion( "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process that produces output data from input data."@en) +AnnotationAssertion( "Elisabetta Manduchi"@en) +AnnotationAssertion( "Helen Parkinson"@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Melanie Courtot"@en) +AnnotationAssertion( "Richard Scheuermann"@en) +AnnotationAssertion( "Ryan Brinkman"@en) +AnnotationAssertion( "Tina Hernandez-Boussard"@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "data analysis"@en) +AnnotationAssertion( "data processing"@en) +AnnotationAssertion( "Branch editors"@en) +AnnotationAssertion(rdfs:label "data transformation"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (leave one out cross validation method) + +AnnotationAssertion( "leave one out cross validation method"@en) +AnnotationAssertion( "The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368") +AnnotationAssertion( ) +AnnotationAssertion( "is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data"@en) +AnnotationAssertion( "2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178") +AnnotationAssertion( "Person:Helen Parkinson") +AnnotationAssertion(rdfs:label "leave one out cross validation method"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (k-means clustering) + +AnnotationAssertion( "k-means clustering"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed)."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Elisabetta Manduchi") +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/K-means"@en) +AnnotationAssertion(rdfs:label "k-means clustering"@en) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hierarchical clustering) + +AnnotationAssertion( "hierarchical clustering"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root)."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering"@en) +AnnotationAssertion(rdfs:label "hierarchical clustering"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (dimensionality reduction) + +AnnotationAssertion( "dimensionality reduction"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m."@en) +AnnotationAssertion( "Elisabetta Manduchi"@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Melanie Courtot"@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "data projection") +AnnotationAssertion( "PERSON: Elisabetta Manduchi"@en) +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "dimensionality reduction"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (principal components analysis dimensionality reduction) + +AnnotationAssertion( "principal components analysis dimensionality reduction"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones."@en) +AnnotationAssertion( "Elisabetta Manduchi"@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Melanie Courtot"@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "pca data reduction"@en) +AnnotationAssertion( "PERSON: Elisabetta Manduchi"@en) +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "principal components analysis dimensionality reduction"@en) +SubClassOf( ) + +# Class: (data visualization) + +AnnotationAssertion( "data visualization") +AnnotationAssertion( "Generation of a heatmap from a microarray dataset") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations."@en) +AnnotationAssertion( "Elisabetta Manduchi"@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Melanie Courtot"@en) +AnnotationAssertion( "Tina Boussard"@en) +AnnotationAssertion( "visualization"@en) +AnnotationAssertion( "data encoding as image") +AnnotationAssertion( "PERSON: Elisabetta Manduchi"@en) +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "PERSON: Tina Boussard"@en) +AnnotationAssertion( "Possible future hierarchy might include this: information_encoding ->data_encoding ->>image_encoding - data visualization - - - - - - - - - data transformation objective - normalize objective - - An objective specification to transformation input data into output data - Modified definition in 2013 Philly OBI workshop - James Malone - PERSON: James Malone - data transformation objective - - - - - - - - - - - - - - - partitioning data transformation - - A partitioning data transformation is a data transformation that has objective partitioning. - James Malone - PERSON: James Malone - partitioning data transformation - - - - - - - - - partitioning objective - A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. - - A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. - James Malone - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - partitioning objective - - - - - - - - - - - - - - - - - - - - - - - class discovery data transformation - - A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. - James Malone - clustering data transformation - unsupervised classification data transformation - PERSON: James Malone - class discovery data transformation - - - - - - - - - class discovery objective - - A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. - James Malone - discriminant analysis objective - unsupervised classification objective - clustering objective - PERSON: Elisabetta Manduchi - PERSON: James Malone - class discovery objective - - - - - - - - - class prediction objective - - A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and -class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. - James Malone - supervised classification objective - classification objective - PERSON: Elisabetta Manduchi - PERSON: James Malone - class prediction objective - - - - - - - - - cross validation objective - - A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. - James Malone - rotation estimation objective - WEB: http://en.wikipedia.org/wiki/Cross_validation - cross validation objective - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - clustered data visualization - - A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. - James Malone - clustered data visualization - - - - - - - - - - - - - - - - - - - - - - - - - - - planned irradiation - PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370. - - A planned process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays, X-rays, charged particles or neutrons) or non-ionizing radiation (such as UV light or microwaves) - Philippe Rocca-Serra - adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) - planned irradiation - - - - - - - - - - - - - - - light source - - A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. - Elizabeth M. Goralczyk - John Quinn - Olga Tchuvatkina - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - light source - - - - - - - - - morphology - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - - morphology - - - - - - - - - length - A 1-D extent quality which is equal to the distance between two points. - - length - - - - - - - - - physical quality - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - - physical quality - - - - - - - - - physical object quality - A quality which inheres in a continuant. - - physical object quality - - - - - - - - - length unit - A unit which is a standard measure of the distance between two points. - - length unit - - - - - - - - - mass unit - A unit which is a standard measure of the amount of matter/energy of a physical object. - - mass unit - - - - - - - - - time unit - A unit which is a standard measure of the dimension in which events occur in sequence. - - time unit - - - - - - - - - temperature unit - - temperature unit - - - - - - - - - substance unit - - substance unit - - - - - - - - - concentration unit - - concentration unit - - - - - - - - - volume unit - - volume unit - - - - - - - - - frequency unit - - frequency unit - - - - - - - - - volumetric flow rate unit - - volumetric flow rate unit - - - - - - - - - rate unit - - rate unit - - - - - - - - +>data_encoding +>>image_encoding") +AnnotationAssertion(rdfs:label "data visualization"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectAllValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( ObjectUnionOf( ))) + +# Class: (data transformation objective) + +AnnotationAssertion( "data transformation objective"@en) +AnnotationAssertion( "normalize objective"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An objective specification to transformation input data into output data"@en) +AnnotationAssertion( "Modified definition in 2013 Philly OBI workshop") +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "data transformation objective"@en) +SubClassOf( ) + +# Class: (partitioning data transformation) + +AnnotationAssertion( "partitioning data transformation"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A partitioning data transformation is a data transformation that has objective partitioning."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "partitioning data transformation"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) + +# Class: (partitioning objective) + +AnnotationAssertion( "partitioning objective"@en) +AnnotationAssertion( "A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Elisabetta Manduchi") +AnnotationAssertion( "PERSON: Elisabetta Manduchi") +AnnotationAssertion(rdfs:label "partitioning objective"@en) +SubClassOf( ) + +# Class: (class discovery data transformation) + +AnnotationAssertion( "class discovery data transformation"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "clustering data transformation") +AnnotationAssertion( "unsupervised classification data transformation") +AnnotationAssertion( "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label "class discovery data transformation"@en) +EquivalentClasses( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (class discovery objective) + +AnnotationAssertion( "class discovery objective"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "discriminant analysis objective"@en) +AnnotationAssertion( "unsupervised classification objective"@en) +AnnotationAssertion( "clustering objective") +AnnotationAssertion( "PERSON: Elisabetta Manduchi") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "class discovery objective"@en) +SubClassOf( ) + +# Class: (class prediction objective) + +AnnotationAssertion( "class prediction objective"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and +class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "supervised classification objective"@en) +AnnotationAssertion( "classification objective") +AnnotationAssertion( "PERSON: Elisabetta Manduchi") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "class prediction objective"@en) +SubClassOf( ) + +# Class: (cross validation objective) + +AnnotationAssertion( "cross validation objective"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis."@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "rotation estimation objective"@en) +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Cross_validation") +AnnotationAssertion(rdfs:label "cross validation objective"@en) +SubClassOf( ) + +# Class: (clustered data visualization) + +AnnotationAssertion( "clustered data visualization") +AnnotationAssertion( ) +AnnotationAssertion( "A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "clustered data visualization") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (planned irradiation) + +AnnotationAssertion( "planned irradiation") +AnnotationAssertion( "PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A planned process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays, X-rays, charged particles or neutrons) or non-ionizing radiation (such as UV light or microwaves)"@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation)") +AnnotationAssertion(rdfs:label "planned irradiation"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (light source) + +AnnotationAssertion( "light source") +AnnotationAssertion( ) +AnnotationAssertion( "A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser."@en) +AnnotationAssertion( "Elizabeth M. Goralczyk") +AnnotationAssertion( "John Quinn") +AnnotationAssertion( "Olga Tchuvatkina") +AnnotationAssertion( "Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253") +AnnotationAssertion(rdfs:label "light source") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (composition) + +AnnotationAssertion( "composition") +AnnotationAssertion( "A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "composition") +SubClassOf( ) + +# Class: (morphology) + +AnnotationAssertion( "morphology") +AnnotationAssertion( "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "morphology") +SubClassOf( ) + +# Class: (structure) + +AnnotationAssertion( "structure") +AnnotationAssertion( "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "structure") +SubClassOf( ) + +# Class: (physical quality) + +AnnotationAssertion( "physical quality") +AnnotationAssertion( "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "physical quality") +SubClassOf( ) + +# Class: (physical object quality) +AnnotationAssertion( "physical object quality") +AnnotationAssertion( "A quality which inheres in a continuant.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "physical object quality") +SubClassOf( ) + +# Class: (agent role) - +AnnotationAssertion( "A role realized by a participant in a process such that the participant causes the process.") +AnnotationAssertion(rdfs:label "agent role") +SubClassOf( ) - +# Class: (length unit) +AnnotationAssertion( "length unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "length unit") +SubClassOf( ) - +# Class: (mass unit) - - - example to be eventually removed - example to be eventually removed - - +AnnotationAssertion( "mass unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mass unit") +SubClassOf( ) +# Class: (time unit) - +AnnotationAssertion( "time unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "time unit") +SubClassOf( ) - - - failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - +# Class: (temperature unit) +AnnotationAssertion( "temperature unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "temperature unit") +SubClassOf( ) - +# Class: (substance unit) - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - +AnnotationAssertion( "substance unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "substance unit") +SubClassOf( ) +# Class: (concentration unit) - +AnnotationAssertion( "concentration unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "concentration unit") +SubClassOf( ) - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - PERSON:Alan Ruttenberg - organizational term - - +# Class: (volume unit) +AnnotationAssertion( "volume unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "volume unit") +SubClassOf( ) - +# Class: (frequency unit) - - - ready for release - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - +AnnotationAssertion( "frequency unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "frequency unit") +SubClassOf( ) +# Class: (volumetric flow rate unit) - +AnnotationAssertion( "volumetric flow rate unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "volumetric flow rate unit") +SubClassOf( ) - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - +# Class: (rate unit) +AnnotationAssertion( "rate unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "rate unit") +SubClassOf( ) - +# Class: (Obsolete Class) - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - +AnnotationAssertion(rdfs:label "Obsolete Class") - +############################ +# Named Individuals +############################ - - - pending final vetting - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - +# Individual: (example to be eventually removed) +AnnotationAssertion( "example to be eventually removed"@en) +AnnotationAssertion(rdfs:label "example to be eventually removed"@en) +ClassAssertion( ) - +# Individual: (failed exploratory term) - - - placeholder removed - placeholder removed - - +AnnotationAssertion( "failed exploratory term"@en) +AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "failed exploratory term"@en) +ClassAssertion( ) +# Individual: (metadata complete) - +AnnotationAssertion( "metadata complete"@en) +AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) +AnnotationAssertion(rdfs:label "metadata complete"@en) +ClassAssertion( ) - - - terms merged - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - +# Individual: (organizational term) +AnnotationAssertion( "organizational term"@en) +AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg") +AnnotationAssertion(rdfs:label "organizational term"@en) +ClassAssertion( ) - +# Individual: (ready for release) - - - term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - +AnnotationAssertion( "ready for release"@en) +AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) +AnnotationAssertion(rdfs:label "ready for release"@en) +ClassAssertion( ) +# Individual: (metadata incomplete) - - - - - term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - +AnnotationAssertion( "metadata incomplete"@en) +AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) +AnnotationAssertion(rdfs:label "metadata incomplete"@en) +ClassAssertion( ) +# Individual: (uncurated) - - - - - universal - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - +AnnotationAssertion( "uncurated"@en) +AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) +AnnotationAssertion(rdfs:label "uncurated"@en) +ClassAssertion( ) +# Individual: (pending final vetting) - - - - - defined class - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - - - - - - - named class expression - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - - Transformation-ML - Transformation-ML file describing parameter transformations used in a GvHD experiment. - - Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) - person:Jennifer Fostel - web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf - Transformation-ML - - - - - - - - - ACS - d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment. - - ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) - person:Jennifer Fostel - web-page:http://www.isac-net.org/content/view/607/150/ - ACS - - - - - - - - - XML - RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document - - XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) - person:Jennifer Fostel - web-page:http://www.w3.org/XML/ - XML - - - - - - - - - RDF - A FOAF file, a SKOS file, an OWL file. - - RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) - person:Jennifer Fostel - web-page:http://www.w3.org/RDF/ - RDF - - - - - - - - - zip - MagicDraw MDZIP archive, Java JAR file. - - zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) - person:Jennifer Fostel - web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ - zip - - - - - - - - - tar - Example.tar file. - - tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) - person:Jennifer Fostel - web-page:http://www.gnu.org/software/tar/manual/ - tar - - - - - - - - - FCS - d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment. - - FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) - person:Jennifer Fostel - web-page:http://www.fcspress.com/ - FCS - - - - - - - - - Compensation-ML - compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment - - Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) - person:Jennifer Fostel - web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf - Compensation-ML - - - - - - - - - Gating-ML - foogate.xml, Gating-ML file describing gates used in a GvHD experiment. - - Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) - person:Jennifer Fostel - web-page:http://www.flowcyt.org/gating/ - Gating-ML - - - - - - - - - OWL - OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file. - - OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) - person:Jennifer Fostel - web-page:http://www.w3.org/2004/OWL/ - OWL - - - - - - - - - - Affymetrix - Affymetrix supplied microarray - - An organization which supplies technology, tools and protocols for use in high throughput applications - Affymetrix - - - - - - - - - Thermo - - Philippe Rocca-Serra - Thermo - - - - - - - - - Waters - - Philippe Rocca-Serra - Waters - - - - - - - - - BIO-RAD - - Philippe Rocca-Serra - BIO-RAD - - - - - - - - - GenePattern hierarchical clustering - - James Malone - GenePattern hierarchical clustering - - - - - - - - - Ambion - - Philippe Rocca-Serra - Ambion - - - - - - - - - Helicos - - Philippe Rocca-Serra - Helicos - - - - - - - - - Roche - - Philippe Rocca-Serra - Roche - - +AnnotationAssertion( "pending final vetting"@en) +AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) +AnnotationAssertion(rdfs:label "pending final vetting"@en) +ClassAssertion( ) +# Individual: (placeholder removed) - - - - - Illumina - - Philippe Rocca-Serra - Illumina - - +AnnotationAssertion( "placeholder removed"@en) +AnnotationAssertion(rdfs:label "placeholder removed"@en) +ClassAssertion( ) +# Individual: (terms merged) - - - - - GenePattern PCA - - GenePattern PCA - - - - - - - - - - GenePattern module SVM - - GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. - James Malone - Ryan Brinkman - GenePattern module SVM - - +AnnotationAssertion( "terms merged"@en) +AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(rdfs:label "terms merged"@en) +ClassAssertion( ) +# Individual: (term imported) - - - - - GenePattern k-nearest neighbors - - James Malone - GenePattern k-nearest neighbors - - +AnnotationAssertion( "term imported"@en) +AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) +AnnotationAssertion(rdfs:label "term imported"@en) +ClassAssertion( ) +# Individual: (term split) - +AnnotationAssertion( "term split"@en) +AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) +AnnotationAssertion(rdfs:label "term split"@en) +ClassAssertion( ) - - - GenePattern LOOCV - - GenePattern LOOCV - - - - - - - - - GenePattern k-means clustering - - James Malone - GenePattern k-means clustering - - - - - - - - - Agilent - - Philippe Rocca-Serra - Agilent - - - - - - - - - - GenePattern module KMeansClustering - - GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. - James Malone - PERSON: James Malone - GenePattern module KMeansClustering - - - - - - - - - GenePattern CART - - James Malone - GenePattern CART - - - - - - - - - - - GenePattern module CARTXValidation - - GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. - GenePattern module CARTXValidation - - - - - - - - - Li-Cor - - Philippe Rocca-Serra - Li-Cor - - - - - - - - - Bruker Corporation - - Philippe Rocca-Serra - Bruker Corporation - - - - - - - - - GenePattern module KNNXValidation - - GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. - James Malone - PERSON: James Malone - GenePattern module KNNXValidation - - - - - - - - - - GenePattern module PeakMatch - - GenePattern module PeakMatch - - - - - - - - - - GenePattern module KNN - - GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. - James Malone - GenePattern module KNN - - - - - - - - - - GenePattern module HierarchicalClustering - - GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. - James Malone - PERSON: James Malone - GenePattern module HierarchicalClustering - - - - - - - - - GenePattern SVM - - James Malone - GenePattern SVM - - - - - - - - - Applied Biosystems - - Philippe Rocca-Serra - Applied Biosystems - - - - - - - - - - GenePattern module PCA - - GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. - James Malone - PERSON: James Malone - GenePattern module PCA - - - - - - - - - GenePattern peak matching - - James Malone - Ryan Brinkman - GenePattern peak matching - - - - - - - - - Bruker Daltonics - - Philippe Rocca-Serra - Bruker Daltonics - - - - - - - - - GenePattern HeatMapViewer data visualization - - The GenePattern process of generating Heat Maps from clustered data. - James Malone - GenePattern HeatMapViewer data visualization - - - - - - - - - GenePattern HierarchicalClusteringViewer data visualization - - The GenePattern process of generating hierarchical clustering visualization from clustered data. - James Malone - GenePattern HierarchicalClusteringViewer data visualization - - - - - - - - - - GenePattern module HeatMapViewer - - A GenePattern software module which is used to generate a heatmap view of data. - James Malone - GenePattern module HeatMapViewer - - - - - - - - - - GenePattern module HierarchicalClusteringViewer - - A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. - James Malone - GenePattern module HierarchicalClusteringViewer - - - - - - - - - Sysmex Corporation, Kobe, Japan - - WEB:http://www.sysmex.com/@2009/08/06 - Sysmex Corporation, Kobe, Japan - - - - - - - - - U.S. Food and Drug Administration - - FDA - U.S. Food and Drug Administration - - - - - - - - - right handed - - right handed - - - - - - - - - ambidexterous - - ambidexterous - - - - - - - - - left handed - - left handed - - - - - - - - - Edingburgh handedness inventory - - The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. - PERSON:Alan Ruttenberg - PERSON:Jessica Turner - PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 - WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html - Edingburgh handedness inventory - - - - - - - - - eBioscience - - Karin Breuer - WEB:http://www.ebioscience.com/@2011/04/11 - eBioscience - - - - - - - - - Cytopeia - - Karin Breuer - WEB:http://www.cytopeia.com/@2011/04/11 - Cytopeia - - - - - - - - - Exalpha Biological - - Karin Breuer - WEB:http://www.exalpha.com/@2011/04/11 - Exalpha Biological - - - - - - - - - Apogee Flow Systems - - Karin Breuer - WEB:http://www.apogeeflow.com/@2011/04/11 - Apogee Flow Systems - - - - - - - - - Exbio Antibodies - - Karin Breuer - WEB:http://www.exbio.cz/@2011/04/11 - Exbio Antibodies - - - - - - - - - Becton Dickinson (BD Biosciences) - - Karin Breuer - WEB:http://www.bdbiosciences.com/@2011/04/11 - Becton Dickinson (BD Biosciences) - - - - - - - - - Dako Cytomation - - Karin Breuer - WEB:http://www.dakousa.com/@2011/04/11 - Dako Cytomation - - - - - - - - - Millipore - - Karin Breuer - WEB:http://www.guavatechnologies.com/@2011/04/11 - Millipore - - - - - - - - - Antigenix - - Karin Breuer - WEB:http://www.antigenix.com/@2011/04/11 - Antigenix - - - - - - - - - Partec - - Karin Breuer - WEB:http://www.partec.de/@2011/04/11 - Partec - - - - - - - - - Beckman Coulter - - Karin Breuer - WEB:http://www.beckmancoulter.com/@2011/04/11 - Beckman Coulter - - - - - - - - - Advanced Instruments Inc. (AI Companies) - - Karin Breuer - WEB:http://www.aicompanies.com/@2011/04/11 - Advanced Instruments Inc. (AI Companies) - - - - - - - - - Miltenyi Biotec - - Karin Breuer - WEB:http://www.miltenyibiotec.com/@2011/04/11 - Miltenyi Biotec - - - - - - - - - AES Chemunex - - Karin Breuer - WEB:http://www.aeschemunex.com/@2011/04/11 - AES Chemunex - - - - - - - - - Bentley Instruments - - Karin Breuer - WEB:http://bentleyinstruments.com/@2011/04/11 - Bentley Instruments - - - - - - - - - Invitrogen - - Karin Breuer - WEB:http://www.invitrogen.com/@2011/04/11 - Invitrogen - - - - - - - - - Luminex - - Karin Breuer - WEB:http://www.luminexcorp.com/@2011/04/11 - Luminex - - - - - - - - - CytoBuoy - - Karin Breuer - WEB:http://www.cytobuoy.com/@2011/04/11 - CytoBuoy - - - - - - - - - Nimblegen - - An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. - Person: Jie Zheng - Nimblegen - - - - - - - - - Pacific Biosciences - - An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. - Person: Jie Zheng - Pacific Biosciences - - - - - - - - - NanoString Technologies - - An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. - NanoString Technologies - - - - - - - - - Thermo Fisher Scientific - - An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. - Chris Stoeckert, Helena Ellis - https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific - Thermo Fisher Scientific - - - - - - - - - G1: Well differentiated - - A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. - Chris Stoeckert, Helena Ellis - G1 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB - G1: Well differentiated - - - - - - - - - G2: Moderately differentiated - - A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. - Chris Stoeckert, Helena Ellis - G2 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB - G2: Moderately differentiated - - - - - - - - - G3: Poorly differentiated - - A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. - Chris Stoeckert, Helena Ellis - G3 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB - G3: Poorly differentiated - - - - - - - - - G4: Undifferentiated - - A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. - Chris Stoeckert, Helena Ellis - G4 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB - G4: Undifferentiated - - - - - - - - - G1 (Fuhrman) - - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. - Chris Stoeckert, Helena Ellis - Grade 1 - NCI BBRB, OBI - NCI BBRB - G1 (Fuhrman) - - - - - - - - - G2 (Fuhrman) - - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. - Chris Stoeckert, Helena Ellis - Grade 2 - NCI BBRB, OBI - NCI BBRB - G2 (Fuhrman) - - - - - - - - - G3 (Fuhrman) - - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. - Chris Stoeckert, Helena Ellis - Grade 3 - NCI BBRB, OBI - NCI BBRB - G3 (Fuhrman) - - - - - - - - - G4 (Fuhrman) - - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. - Chris Stoeckert, Helena Ellis - Grade 4 - NCI BBRB, OBI - NCI BBRB - G4 (Fuhrman) - - - - - - - - - Low grade ovarian tumor - - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. - Chris Stoeckert, Helena Ellis - Low grade - NCI BBRB, OBI - NCI BBRB - Low grade ovarian tumor - - - - - - - - - High grade ovarian tumor - - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. - Chris Stoeckert, Helena Ellis - High grade - NCI BBRB, OBI - NCI BBRB - High grade ovarian tumor - - - - - - - - - G1 (WHO) - - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. - Chris Stoeckert, Helena Ellis - G1 - NCI BBRB, OBI - NCI BBRB - G1 (WHO) - - - - - - - - - G2 (WHO) - - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. - Chris Stoeckert, Helena Ellis - G2 - NCI BBRB, OBI - NCI BBRB - G2 (WHO) - - - - - - - - - G3 (WHO) - - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. - Chris Stoeckert, Helena Ellis - G3 - NCI BBRB, OBI - NCI BBRB - G3 (WHO) - - - - - - - - - G4 (WHO) - - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. - Chris Stoeckert, Helena Ellis - G4 - NCI BBRB, OBI - NCI BBRB - G4 (WHO) - - - - - - - - - pT0 (colon) - - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT0 (colon) - - - - - - - - - pTis (colon) - - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pTis (colon) - - - - - - - - - pT1 (colon) - - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT1 (colon) - - - - - - - - - pT2 (colon) - - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT2 (colon) - - - - - - - - - pT3 (colon) - - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT3 (colon) - - - - - - - - - pT4a (colon) - - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT4a (colon) - - - - - - - - - pT4b (colon) - - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT4b (colon) - - - - - - - - - pT0 (lung) - - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT0 (lung) - - - - - - - - - pTis (lung) - - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pTis (lung) - - - - - - - - - pT1 (lung) - - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT1 (lung) - - - - - - - - - pT1a (lung) - - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT1a (lung) - - - - - - - - - pT1b (lung) - - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT1b (lung) - - - - - - - - - pT2 (lung) - - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT2 (lung) - - - - - - - - - pT2a (lung) - - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT2a (lung) - - - - - - - - - pT2b (lung) - - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT2b (lung) - - - - - - - - - pT3 (lung) - - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT3 (lung) - - - - - - - - - pT4 (lung) - - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT4 (lung) - - - - - - - - - pT0 (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT0 (kidney) - - - - - - - - - pT1 (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT1 (kidney) - - - - - - - - - pT1a (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT1a (kidney) - - - - - - - - - pT1b (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT1b (kidney) - - - - - - - - - pT2 (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT2 (kidney) - - - - - - - - - pT2a (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT2a (kidney) - - - - - - - - - pT2b (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT2b (kidney) - - - - - - - - - pT3 (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT3 (kidney) - - - - - - - - - pT3a (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT3a (kidney) - - - - - - - - - pT3b (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT3b (kidney) - - - - - - - - - pT3c (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT3c (kidney) - - - - - - - - - pT4 (kidney) - - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT4 (kidney) - - - - - - - - - pT0 (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT0 (ovary) - - - - - - - - - pT1 (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT1 (ovary) - - - - - - - - - pT1a (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT1a (ovary) - - - - - - - - - pT1b (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT1b (ovary) - - - - - - - - - pT1c (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT1c (ovary) - - - - - - - - - pT2 (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT2 (ovary) - - - - - - - - - pT2a (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT2a (ovary) - - - - - - - - - pT2b (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT2b (ovary) - - - - - - - - - pT2c (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT2c (ovary) - - - - - - - - - pT3 (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT3 (ovary) - - - - - - - - - pT3a (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT3a (ovary) - - - - - - - - - pT3b (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT3b (ovary) - - - - - - - - - pT3c (ovary) - - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT3c (ovary) - - - - - - - - - pN0 (colon) - - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN0 (colon) - - - - - - - - - pN1 (colon) - - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN1 (colon) - - - - - - - - - pN1a (colon) - - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN1a (colon) - - - - - - - - - pN1b (colon) - - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN1b (colon) - - - - - - - - - pN1c (colon) - - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN1c (colon) - - - - - - - - - pN2 (colon) - - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN2 (colon) - - - - - - - - - pN2a (colon) - - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN2a (colon) - - - - - - - - - pN2b (colon) - - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN2b (colon) - - - - - - - - - pN0 (lung) - - A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB - pN0 (lung) - - - - - - - - - pN1 (lung) - - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB - pN1 (lung) - - - - - - - - - pN2 (lung) - - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB - pN2 (lung) - - - - - - - - - pN3 (lung) - - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB - pN3 (lung) - - - - - - - - - pN0 (kidney) - - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ - NCI BBRB - pN0 (kidney) - - - - - - - - - pN1 (kidney) - - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ - NCI BBRB - pN1 (kidney) - - - - - - - - - pN0 (ovary) - - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ - NCI BBRB - pN0 (ovary) - - - - - - - - - pN1 (ovary) - - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ - NCI BBRB - pN1 (ovary) - - - - - - - - - cM0 (colon) - - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. - Chris Stoeckert, Helena Ellis - https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 - NCI BBRB - cM0 (colon) - - - - - - - - - cM1 (colon) - - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. - Chris Stoeckert, Helena Ellis - https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 - NCI BBRB - cM1 (colon) - - - - - - - - - cM1a (colon) - - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB - cM1a (colon) - - - - - - - - - cM1b (colon) - - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB - cM1b (colon) - - - - - - - - - pM1 (colon) - - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB - pM1 (colon) - - - - - - - - - pM1a (colon) - - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB - pM1a (colon) - - - - - - - - - pM1b (colon) - - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB - pM1b (colon) - - - - - - - - - cM0 (lung) - - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - cM0 (lung) - - - - - - - - - cM1 (lung) - - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - cM1 (lung) - - - - - - - - - cM1a (lung) - - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - cM1a (lung) - - - - - - - - - cM1b (lung) - - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - cM1b (lung) - - - - - - - - - pM1 (lung) - - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - pM1 (lung) - - - - - - - - - pM1a (lung) - - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - pM1a (lung) - - - - - - - - - pM1b (lung) - - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - pM1b (lung) - - - - - - - - - cM0 (kidney) - - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ - NCI BBRB - cM0 (kidney) - - - - - - - - - cM1 (kidney) - - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ - NCI BBRB - cM1 (kidney) - - - - - - - - - pM1 (kidney) - - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ - NCI BBRB - pM1 (kidney) - - - - - - - - - cM0 (ovary) - - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ - NCI BBRB - cM0 (ovary) - - - - - - - - - cM1 (ovary) - - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ - NCI BBRB - cM1 (ovary) - - - - - - - - - pM1 (ovary) - - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ - NCI BBRB - pM1 (ovary) - - - - - - - - - Occult Carcinoma (AJCC 7th) - - A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. - Chris Stoeckert, Helena Ellis - Occult Carcinoma - http://www.medilexicon.com/dictionary/14371 - NCI BBRB - Occult Carcinoma (AJCC 7th) - - - - - - - - - Stage 0 (AJCC 7th) - - A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. - Chris Stoeckert, Helena Ellis - Stage 0 - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage 0 (AJCC 7th) - - - - - - - - - Stage I (AJCC 7th) - - A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. - Chris Stoeckert, Helena Ellis - Stage I - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage I (AJCC 7th) - - - - - - - - - Stage IIA (AJCC 7th) - - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. - Chris Stoeckert, Helena Ellis - Stage IIA - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIA (AJCC 7th) - - - - - - - - - Stage IIB (AJCC 7th) - - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. - Chris Stoeckert, Helena Ellis - Stage IIB - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIB (AJCC 7th) - - - - - - - - - Stage IIC (AJCC 7th) - - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. - Chris Stoeckert, Helena Ellis - Stage IIC - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIC (AJCC 7th) - - - - - - - - - Stage IIIA (AJCC 7th) - - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. - Chris Stoeckert, Helena Ellis - Stage IIIA - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIIA (AJCC 7th) - - - - - - - - - Stage IIIB (AJCC 7th) - - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. - Chris Stoeckert, Helena Ellis - Stage IIIB - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIIB (AJCC 7th) - - - - - - - - - Stage IIIC (AJCC 7th) - - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. - Chris Stoeckert, Helena Ellis - Stage IIIC - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIIC (AJCC 7th) - - - - - - - - - Stage IVA (AJCC 7th) - - A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. - Chris Stoeckert, Helena Ellis - Stage IVA - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IVA (AJCC 7th) - - - - - - - - - Stage IVB (AJCC 7th) - - A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. - Chris Stoeckert, Helena Ellis - Stage IVB - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IVB (AJCC 7th) - - - - - - - - - Stage IA (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. - Chris Stoeckert, Helena Ellis - Stage IA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IA (FIGO) - - - - - - - - - Stage IA1 (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. - Chris Stoeckert, Helena Ellis - Stage IA1 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IA1 (FIGO) - - - - - - - - - Stage IA2 (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. - Chris Stoeckert, Helena Ellis - Stage IA2 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IA2 (FIGO) - - - - - - - - - Stage IB (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA - Chris Stoeckert, Helena Ellis - Stage IB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IB (FIGO) - - - - - - - - - Stage IB1 (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IB1 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IB1 (FIGO) - - - - - - - - - Stage IB2 (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IB2 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IB2 (FIGO) - - - - - - - - - Stage IIA (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. - Chris Stoeckert, Helena Ellis - Stage IIA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIA (FIGO) - - - - - - - - - Stage IIA1 (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IIA1 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIA1 (FIGO) - - - - - - - - - Stage IIA2 (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IIA2 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIA2 (FIGO) - - - - - - - - - Stage IIB (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. - Chris Stoeckert, Helena Ellis - Stage IIB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIB (FIGO) - - - - - - - - - Stage IIIA (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. - Chris Stoeckert, Helena Ellis - Stage IIIA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIIA (FIGO) - - - - - - - - - Stage IIIB (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. - Chris Stoeckert, Helena Ellis - Stage IIIB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIIB (FIGO) - - - - - - - - - Stage IVA (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. - Chris Stoeckert, Helena Ellis - Stage IVA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IVA (FIGO) - - - - - - - - - Stage IVB (FIGO) - - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. - Chris Stoeckert, Helena Ellis - Stage IVB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IVB (FIGO) - - - - - - - - - Stage 1 (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 1 (FIGO) - - - - - - - - - Stage 1A (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1A - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 1A (FIGO) - - - - - - - - - Stage 1B (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1B - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 1B (FIGO) - - - - - - - - - Stage 1C (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1C - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 1C (FIGO) - - - - - - - - - Stage 2 (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 2 (FIGO) - - - - - - - - - Stage 2A (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2A - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 2A (FIGO) - - - - - - - - - Stage 2B (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2B - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 2B (FIGO) - - - - - - - - - Stage 2C (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2C - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 2C (FIGO) - - - - - - - - - Stage 3 (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). - Chris Stoeckert, Helena Ellis - Stage 3 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 3 (FIGO) - - - - - - - - - Stage 3A (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . - Chris Stoeckert, Helena Ellis - Stage 3A - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 3A (FIGO) - - - - - - - - - Stage 3B (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . - Chris Stoeckert, Helena Ellis - Stage 3B - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 3B (FIGO) - - - - - - - - - Stage 3C (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). - Chris Stoeckert, Helena Ellis - Stage 3C - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 3C (FIGO) - - - - - - - - - Stage 4 (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. - Chris Stoeckert, Helena Ellis - Stage 4 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 4 (FIGO) - - - - - - - - - Stage Unknown (FIGO) - - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). - Chris Stoeckert, Helena Ellis - Stage Unknown - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage Unknown (FIGO) - - - - - - - - - 3: symptomatic in bed more than 50% of the day but not bed ridden - - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 3: symptomatic in bed more than 50% of the day but not bed ridden - - - - - - - - - 2: symptomatic but in bed less than 50% of the day - - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 2: symptomatic but in bed less than 50% of the day - - - - - - - - - 4: bed ridden - - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 4: bed ridden - - - - - - - - - 0: asymptomatic - - An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 0: asymptomatic - - - - - - - - - 1: symptomatic but fully ambulatory - - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 1: symptomatic but fully ambulatory - - - - - - - - - 100: asymptomatic - - A Karnofsky score vaue specification indicating that a patient is asymptomatic. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 100: asymptomatic - - - - - - - - - 80-90: symptomatic but fully ambulatory - - A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 80-90: symptomatic but fully ambulatory - - - - - - - - - 60-70: symptomatic but in bed less than 50% of the day - - A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 60-70: symptomatic but in bed less than 50% of the day - - - - - - - - - 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden - - A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden - - - - - - - - - Oxford Nanopore Technologies - - An organization that is developing and selling nanopore sequencing products and is based in the UK. - James A. Overton - https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies - Oxford Nanopore Technologies - - - - - - - - - BioGents - - An organization that manufactures mosquito traps and other mosquito control products. - John Judkins - WEB:https://eu.biogents.com/about-biogents/ - BioGents - - - - - - - - - Abbott - - A manufacturer of rapid point-of-care assay devices. - John Judkins ORCID:0000-0001-6595-0902 - WEB:https://www.globalpointofcare.abbott/en/about.html - https://github.com/obi-ontology/obi/issues/1456 - Abbott - - - - - - - - - J. Mitra - - A manufacturer of in vitro diagnostic assay kits in India. - John Judkins ORCID:0000-0001-6595-0902 - WEB:https://jmitra.co.in/about-us/ - https://github.com/obi-ontology/obi/issues/1456 - J. Mitra - - - - - - - - - InBios - - A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases. - John Judkins ORCID:0000-0001-6595-0902 - WEB:https://inbios.com/about/ - https://github.com/obi-ontology/obi/issues/1456 - InBios - - - - - - - - - meter - A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. - m - - meter - - - - - - - - - kilogram - A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. - kg - - kilogram - - - - - - - - - second - A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. - s - sec - - second - - - - - - - - - centimeter - A length unit which is equal to one hundredth of a meter or 10^[-2] m. - cm - - centimeter - - - - - - - - - millimeter - A length unit which is equal to one thousandth of a meter or 10^[-3] m. - mm - - millimeter - - - - - - - - - micrometer - A length unit which is equal to one millionth of a meter or 10^[-6] m. - um - - micrometer - - - - - - - - - nanometer - A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. - nm - - nanometer - - - - - - - - - angstrom - A length unit which is equal to 10 [-10] m. - - angstrom - - - - - - - - - gram - A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. - g - - gram - - - - - - - - - milligram - A mass unit which is equal to one thousandth of a gram or 10^[-3] g. - mg - - milligram - - - - - - - - - microgram - A mass unit which is equal to one millionth of a gram or 10^[-6] g. - ug - - microgram - - - - - - - - - nanogram - A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. - ng - - nanogram - - - - - - - - - picogram - A mass unit which is equal to 10^[-12] g. - pg - - picogram - - - - - - - - - degree Celsius - A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. - C - degree C - - degree Celsius - - - - - - - - - minute - A time unit which is equal to 60 seconds. - min - - minute - - - - - - - - - hour - A time unit which is equal to 3600 seconds or 60 minutes. - h - hr - - hour - - - - - - - - - day - A time unit which is equal to 24 hours. - - day - - - - - - - - - week - A time unit which is equal to 7 days. - - week - - - - - - - - - month - A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. - - month - - - - - - - - - year - A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. - - year - - - - - - - - - micromole - A substance unit equal to a millionth of a mol or 10^[-6] mol. - umol - - micromole - - - - - - - - - nanomole - A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. - nmol - - nanomole - - - - - - - - - picomole - A substance unit equal to 10^[-12] mol. - pmol - - picomole - - - - - - - - - molar - A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). - M - - molar - - - - - - - - - millimolar - A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. - mM - - millimolar - - - - - - - - - micromolar - A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. - uM - - micromolar - - - - - - - - - nanomolar - A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. - nM - - nanomolar - - - - - - - - - picomolar - A unit of molarity which is equal to 10^[-12] M. - pM - - picomolar - - - - - - - - - cubic centimeter - A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. - cc - - cubic centimeter - - - - - - - - - milliliter - A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. - ml - - milliliter - - - - - - - - - liter - A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. - L - - liter - - - - - - - - - cubic decimeter - A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. - - cubic decimeter - - - - - - - - - microliter - A volume unit which is equal to one millionth of a liter or 10^[-6] L. - ul - - microliter - - - - - - - - - nanoliter - A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. - nl - - nanoliter - - - - - - - - - picoliter - A volume unit which is equal to 10^[-12] L. - pl - - picoliter - - - - - - - - - hertz - A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. - - hertz - - - - - - - - - mass percentage - A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. - % w/w - percent weight pr weight - - mass percentage - - - - - - - - - mass volume percentage - A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. - % w/v - percent vol per vol - - mass volume percentage - - - - - - - - - volume percentage - A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. - % v/v - percent vol per vol - - volume percentage - - - - - - - - - gram per liter - A mass unit density which is equal to mass of an object in grams divided by the volume in liters. - g per L - g/L - - gram per liter - - - - - - - - - milligram per milliliter - A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. - mg per ml - mg/ml - - milligram per milliliter - - - - - - - - - degree Fahrenheit - A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. - - degree Fahrenheit - - - - - - - - - pH - A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). - - pH - - - - - - - - - milliliter per liter - A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. - ml per L - ml/l - - milliliter per liter - - - - - - - - - gram per deciliter - A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. - g/dl - - gram per deciliter - - - - - - - - - colony forming unit per volume - A concentration unit which a measure of viable bacterial numbers in a given volume. - - colony forming unit per volume - - - - - - - - - microliters per minute - A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. - - microliters per minute - - - - - - - - - count per nanomolar second - A rate unit which is equal to one over one nanomolar second. - - count per nanomolar second - - - - - - - - - count per molar second - A rate unit which is equal to one over one molar second. - - count per molar second - - - - - - - - - count per nanomolar - A rate unit which is equal to one over one nanomolar. - - count per nanomolar - - - - - - - - - count per molar - A rate unit which is equal to one over one molar. - - count per molar - - - - - - - - - microgram per liter - A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. - ng/ml - ug/L - - microgram per liter - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# Individual: (universal) +AnnotationAssertion( "universal"@en) +AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en) +AnnotationAssertion(rdfs:label "universal"@en) +ClassAssertion( ) + +# Individual: (defined class) + +AnnotationAssertion( "defined class"@en) +AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en) +AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "defined class"@en) +ClassAssertion( ) + +# Individual: (named class expression) + +AnnotationAssertion( "named class expression"@en) +AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en) +AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "named class expression"@en) +ClassAssertion( ) + +# Individual: (to be replaced with external ontology term) + +AnnotationAssertion( "to be replaced with external ontology term"@en) +AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) +ClassAssertion( ) + +# Individual: (requires discussion) + +AnnotationAssertion( "requires discussion"@en) +AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "requires discussion"@en) +ClassAssertion( ) + +# Individual: (Transformation-ML) + +AnnotationAssertion( "Transformation-ML"@en) +AnnotationAssertion( "Transformation-ML file describing parameter transformations used in a GvHD experiment."@en) +AnnotationAssertion( ) +AnnotationAssertion( "Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf") +AnnotationAssertion(rdfs:label "Transformation-ML"@en) +ClassAssertion( ) + +# Individual: (ACS) + +AnnotationAssertion( "ACS"@en) +AnnotationAssertion( "d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment."@en) +AnnotationAssertion( ) +AnnotationAssertion( "ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.isac-net.org/content/view/607/150/") +AnnotationAssertion(rdfs:label "ACS"@en) +ClassAssertion( ) + +# Individual: (XML) + +AnnotationAssertion( "XML"@en) +AnnotationAssertion( "RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document"@en) +AnnotationAssertion( ) +AnnotationAssertion( "XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.w3.org/XML/") +AnnotationAssertion(rdfs:label "XML"@en) +ClassAssertion( ) + +# Individual: (RDF) + +AnnotationAssertion( "RDF"@en) +AnnotationAssertion( "A FOAF file, a SKOS file, an OWL file."@en) +AnnotationAssertion( ) +AnnotationAssertion( "RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.w3.org/RDF/") +AnnotationAssertion(rdfs:label "RDF"@en) +ClassAssertion( ) + +# Individual: (zip) + +AnnotationAssertion( "zip"@en) +AnnotationAssertion( "MagicDraw MDZIP archive, Java JAR file."@en) +AnnotationAssertion( ) +AnnotationAssertion( "zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/") +AnnotationAssertion(rdfs:label "zip"@en) +ClassAssertion( ) + +# Individual: (tar) + +AnnotationAssertion( "tar"@en) +AnnotationAssertion( "Example.tar file."@en) +AnnotationAssertion( ) +AnnotationAssertion( "tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.gnu.org/software/tar/manual/") +AnnotationAssertion(rdfs:label "tar"@en) +ClassAssertion( ) + +# Individual: (FCS) + +AnnotationAssertion( "FCS"@en) +AnnotationAssertion( "d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment."@en) +AnnotationAssertion( ) +AnnotationAssertion( "FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.fcspress.com/") +AnnotationAssertion(rdfs:label "FCS"@en) +ClassAssertion( ) + +# Individual: (Compensation-ML) + +AnnotationAssertion( "Compensation-ML"@en) +AnnotationAssertion( "compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf") +AnnotationAssertion(rdfs:label "Compensation-ML"@en) +ClassAssertion( ) + +# Individual: (Gating-ML) + +AnnotationAssertion( "Gating-ML"@en) +AnnotationAssertion( "foogate.xml, Gating-ML file describing gates used in a GvHD experiment."@en) +AnnotationAssertion( ) +AnnotationAssertion( "Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.flowcyt.org/gating/") +AnnotationAssertion(rdfs:label "Gating-ML"@en) +ClassAssertion( ) + +# Individual: (OWL) + +AnnotationAssertion( "OWL"@en) +AnnotationAssertion( "OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file."@en) +AnnotationAssertion( ) +AnnotationAssertion( "OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)"@en) +AnnotationAssertion( "person:Jennifer Fostel"@en) +AnnotationAssertion( "web-page:http://www.w3.org/2004/OWL/") +AnnotationAssertion(rdfs:label "OWL"@en) +ClassAssertion( ) + +# Individual: (Affymetrix) + +AnnotationAssertion( "Affymetrix") +AnnotationAssertion( "Affymetrix supplied microarray") +AnnotationAssertion( ) +AnnotationAssertion( "An organization which supplies technology, tools and protocols for use in high throughput applications"@en) +AnnotationAssertion(rdfs:label "Affymetrix") +ClassAssertion( ) +ClassAssertion( ) + +# Individual: (Thermo) + +AnnotationAssertion( "Thermo") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Thermo") +ClassAssertion( ) + +# Individual: (Waters) + +AnnotationAssertion( "Waters") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Waters") +ClassAssertion( ) + +# Individual: (BIO-RAD) + +AnnotationAssertion( "BIO-RAD") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "BIO-RAD") +ClassAssertion( ) + +# Individual: (GenePattern hierarchical clustering) + +AnnotationAssertion( "GenePattern hierarchical clustering") +AnnotationAssertion( ) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern hierarchical clustering") +ClassAssertion( ) + +# Individual: (Ambion) + +AnnotationAssertion( "Ambion") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Ambion") +ClassAssertion( ) + +# Individual: (Helicos) + +AnnotationAssertion( "Helicos") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Helicos") +ClassAssertion( ) + +# Individual: (Roche) + +AnnotationAssertion( "Roche") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Roche") +ClassAssertion( ) + +# Individual: (Illumina) + +AnnotationAssertion( "Illumina") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Illumina") +ClassAssertion( ) + +# Individual: (GenePattern PCA) + +AnnotationAssertion( "GenePattern PCA") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "GenePattern PCA") +ClassAssertion( ) + +# Individual: (GenePattern module SVM) + +AnnotationAssertion( "GenePattern module SVM") +AnnotationAssertion( ) +AnnotationAssertion( "GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "Ryan Brinkman") +AnnotationAssertion(rdfs:label "GenePattern module SVM") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern k-nearest neighbors) + +AnnotationAssertion( "GenePattern k-nearest neighbors") +AnnotationAssertion( ) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern k-nearest neighbors") +ClassAssertion( ) + +# Individual: (GenePattern LOOCV) + +AnnotationAssertion( "GenePattern LOOCV") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "GenePattern LOOCV") +ClassAssertion( ) + +# Individual: (GenePattern k-means clustering) + +AnnotationAssertion( "GenePattern k-means clustering") +AnnotationAssertion( ) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern k-means clustering") +ClassAssertion( ) + +# Individual: (Agilent) + +AnnotationAssertion( "Agilent") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Agilent") +ClassAssertion( ) + +# Individual: (GenePattern module KMeansClustering) + +AnnotationAssertion( "GenePattern module KMeansClustering") +AnnotationAssertion( ) +AnnotationAssertion( "GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "GenePattern module KMeansClustering") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern CART) + +AnnotationAssertion( "GenePattern CART") +AnnotationAssertion( ) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern CART") +ClassAssertion( ) + +# Individual: (GenePattern module CARTXValidation) + +AnnotationAssertion( "GenePattern module CARTXValidation") +AnnotationAssertion( ) +AnnotationAssertion( "GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations."@en) +AnnotationAssertion(rdfs:label "GenePattern module CARTXValidation") +ClassAssertion( ) +ObjectPropertyAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (Li-Cor) + +AnnotationAssertion( "Li-Cor") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Li-Cor") +ClassAssertion( ) + +# Individual: (Bruker Corporation) + +AnnotationAssertion( "Bruker Corporation") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Bruker Corporation") +ClassAssertion( ) + +# Individual: (GenePattern module KNNXValidation) + +AnnotationAssertion( "GenePattern module KNNXValidation") +AnnotationAssertion( ) +AnnotationAssertion( "GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "GenePattern module KNNXValidation") +ClassAssertion( ) + +# Individual: (GenePattern module PeakMatch) + +AnnotationAssertion( "GenePattern module PeakMatch") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "GenePattern module PeakMatch") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern module KNN) + +AnnotationAssertion( "GenePattern module KNN") +AnnotationAssertion( ) +AnnotationAssertion( "GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern module KNN") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern module HierarchicalClustering) + +AnnotationAssertion( "GenePattern module HierarchicalClustering") +AnnotationAssertion( ) +AnnotationAssertion( "GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "GenePattern module HierarchicalClustering") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern SVM) + +AnnotationAssertion( "GenePattern SVM") +AnnotationAssertion( ) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern SVM") +ClassAssertion( ) + +# Individual: (Applied Biosystems) + +AnnotationAssertion( "Applied Biosystems") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Applied Biosystems") +ClassAssertion( ) + +# Individual: (GenePattern module PCA) + +AnnotationAssertion( "GenePattern module PCA") +AnnotationAssertion( ) +AnnotationAssertion( "GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion(rdfs:label "GenePattern module PCA") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern peak matching) + +AnnotationAssertion( "GenePattern peak matching") +AnnotationAssertion( ) +AnnotationAssertion( "James Malone") +AnnotationAssertion( "Ryan Brinkman") +AnnotationAssertion(rdfs:label "GenePattern peak matching") +ClassAssertion( ) + +# Individual: (Bruker Daltonics) + +AnnotationAssertion( "Bruker Daltonics") +AnnotationAssertion( ) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion(rdfs:label "Bruker Daltonics") +ClassAssertion( ) + +# Individual: (GenePattern HeatMapViewer data visualization) + +AnnotationAssertion( "GenePattern HeatMapViewer data visualization") +AnnotationAssertion( ) +AnnotationAssertion( "The GenePattern process of generating Heat Maps from clustered data."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern HeatMapViewer data visualization") +ClassAssertion( ) + +# Individual: (GenePattern HierarchicalClusteringViewer data visualization) + +AnnotationAssertion( "GenePattern HierarchicalClusteringViewer data visualization") +AnnotationAssertion( ) +AnnotationAssertion( "The GenePattern process of generating hierarchical clustering visualization from clustered data."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern HierarchicalClusteringViewer data visualization") +ClassAssertion( ) + +# Individual: (GenePattern module HeatMapViewer) + +AnnotationAssertion( "GenePattern module HeatMapViewer") +AnnotationAssertion( ) +AnnotationAssertion( "A GenePattern software module which is used to generate a heatmap view of data."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern module HeatMapViewer") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (GenePattern module HierarchicalClusteringViewer) + +AnnotationAssertion( "GenePattern module HierarchicalClusteringViewer") +AnnotationAssertion( ) +AnnotationAssertion( "A GenePattern software module which is used to generate a view of data that has been hierarchically clustered."@en) +AnnotationAssertion( "James Malone") +AnnotationAssertion(rdfs:label "GenePattern module HierarchicalClusteringViewer") +ClassAssertion( ) +ObjectPropertyAssertion( ) + +# Individual: (Sysmex Corporation, Kobe, Japan) + +AnnotationAssertion( "Sysmex Corporation, Kobe, Japan") +AnnotationAssertion( ) +AnnotationAssertion( "WEB:http://www.sysmex.com/@2009/08/06") +AnnotationAssertion(rdfs:label "Sysmex Corporation, Kobe, Japan") +ClassAssertion( ) + +# Individual: (U.S. Food and Drug Administration) + +AnnotationAssertion( "U.S. Food and Drug Administration") +AnnotationAssertion( ) +AnnotationAssertion( "FDA") +AnnotationAssertion(rdfs:label "U.S. Food and Drug Administration") +ClassAssertion( ) + +# Individual: (right handed) + +AnnotationAssertion( "right handed") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "right handed") +ClassAssertion( ) + +# Individual: (ambidexterous) + +AnnotationAssertion( "ambidexterous") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "ambidexterous") +ClassAssertion( ) + +# Individual: (left handed) + +AnnotationAssertion( "left handed") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "left handed") +ClassAssertion( ) + +# Individual: (Edingburgh handedness inventory) + +AnnotationAssertion( "Edingburgh handedness inventory") +AnnotationAssertion( ) +AnnotationAssertion( "The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities."@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg") +AnnotationAssertion( "PERSON:Jessica Turner") +AnnotationAssertion( "PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113") +AnnotationAssertion( "WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html") +AnnotationAssertion(rdfs:label "Edingburgh handedness inventory") +ClassAssertion( ) + +# Individual: (eBioscience) + +AnnotationAssertion( "eBioscience") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.ebioscience.com/@2011/04/11") +AnnotationAssertion(rdfs:label "eBioscience") +ClassAssertion( ) + +# Individual: (Cytopeia) + +AnnotationAssertion( "Cytopeia") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.cytopeia.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Cytopeia") +ClassAssertion( ) + +# Individual: (Exalpha Biological) + +AnnotationAssertion( "Exalpha Biological") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.exalpha.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Exalpha Biological") +ClassAssertion( ) + +# Individual: (Apogee Flow Systems) + +AnnotationAssertion( "Apogee Flow Systems") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.apogeeflow.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Apogee Flow Systems") +ClassAssertion( ) + +# Individual: (Exbio Antibodies) + +AnnotationAssertion( "Exbio Antibodies") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.exbio.cz/@2011/04/11") +AnnotationAssertion(rdfs:label "Exbio Antibodies") +ClassAssertion( ) + +# Individual: (Becton Dickinson (BD Biosciences)) + +AnnotationAssertion( "Becton Dickinson (BD Biosciences)") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.bdbiosciences.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Becton Dickinson (BD Biosciences)") +ClassAssertion( ) + +# Individual: (Dako Cytomation) + +AnnotationAssertion( "Dako Cytomation") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.dakousa.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Dako Cytomation") +ClassAssertion( ) + +# Individual: (Millipore) + +AnnotationAssertion( "Millipore") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.guavatechnologies.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Millipore") +ClassAssertion( ) + +# Individual: (Antigenix) + +AnnotationAssertion( "Antigenix") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.antigenix.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Antigenix") +ClassAssertion( ) + +# Individual: (Partec) + +AnnotationAssertion( "Partec") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.partec.de/@2011/04/11") +AnnotationAssertion(rdfs:label "Partec") +ClassAssertion( ) + +# Individual: (Beckman Coulter) + +AnnotationAssertion( "Beckman Coulter") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.beckmancoulter.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Beckman Coulter") +ClassAssertion( ) + +# Individual: (Advanced Instruments Inc. (AI Companies)) + +AnnotationAssertion( "Advanced Instruments Inc. (AI Companies)") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.aicompanies.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Advanced Instruments Inc. (AI Companies)") +ClassAssertion( ) + +# Individual: (Miltenyi Biotec) + +AnnotationAssertion( "Miltenyi Biotec") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.miltenyibiotec.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Miltenyi Biotec") +ClassAssertion( ) + +# Individual: (AES Chemunex) + +AnnotationAssertion( "AES Chemunex") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.aeschemunex.com/@2011/04/11") +AnnotationAssertion(rdfs:label "AES Chemunex") +ClassAssertion( ) + +# Individual: (Bentley Instruments) + +AnnotationAssertion( "Bentley Instruments") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://bentleyinstruments.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Bentley Instruments") +ClassAssertion( ) + +# Individual: (Invitrogen) + +AnnotationAssertion( "Invitrogen") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.invitrogen.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Invitrogen") +ClassAssertion( ) + +# Individual: (Luminex) + +AnnotationAssertion( "Luminex") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.luminexcorp.com/@2011/04/11") +AnnotationAssertion(rdfs:label "Luminex") +ClassAssertion( ) + +# Individual: (CytoBuoy) + +AnnotationAssertion( "CytoBuoy") +AnnotationAssertion( ) +AnnotationAssertion( "Karin Breuer") +AnnotationAssertion( "WEB:http://www.cytobuoy.com/@2011/04/11") +AnnotationAssertion(rdfs:label "CytoBuoy") +ClassAssertion( ) + +# Individual: (Nimblegen) + +AnnotationAssertion( "Nimblegen") +AnnotationAssertion( ) +AnnotationAssertion( "An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing."@en) +AnnotationAssertion( "Person: Jie Zheng") +AnnotationAssertion(rdfs:label "Nimblegen") +ClassAssertion( ) + +# Individual: (Pacific Biosciences) + +AnnotationAssertion( "Pacific Biosciences") +AnnotationAssertion( ) +AnnotationAssertion( "An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution."@en) +AnnotationAssertion( "Person: Jie Zheng") +AnnotationAssertion(rdfs:label "Pacific Biosciences") +ClassAssertion( ) + +# Individual: (NanoString Technologies) + +AnnotationAssertion( "NanoString Technologies") +AnnotationAssertion( ) +AnnotationAssertion( "An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules."@en) +AnnotationAssertion(rdfs:label "NanoString Technologies") +ClassAssertion( ) + +# Individual: (Thermo Fisher Scientific) + +AnnotationAssertion( "Thermo Fisher Scientific") +AnnotationAssertion( ) +AnnotationAssertion( "An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific") +AnnotationAssertion(rdfs:label "Thermo Fisher Scientific") +ClassAssertion( ) + +# Individual: (G1: Well differentiated) + +AnnotationAssertion( "G1: Well differentiated") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G1") +AnnotationAssertion( "https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G1: Well differentiated") +ClassAssertion( ) + +# Individual: (G2: Moderately differentiated) + +AnnotationAssertion( "G2: Moderately differentiated") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G2") +AnnotationAssertion( "https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G2: Moderately differentiated") +ClassAssertion( ) + +# Individual: (G3: Poorly differentiated) + +AnnotationAssertion( "G3: Poorly differentiated") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G3") +AnnotationAssertion( "https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G3: Poorly differentiated") +ClassAssertion( ) + +# Individual: (G4: Undifferentiated) + +AnnotationAssertion( "G4: Undifferentiated") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G4") +AnnotationAssertion( "https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G4: Undifferentiated") +ClassAssertion( ) + +# Individual: (G1 (Fuhrman)) + +AnnotationAssertion( "G1 (Fuhrman)") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Grade 1") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G1 (Fuhrman)") +ClassAssertion( ) + +# Individual: (G2 (Fuhrman)) + +AnnotationAssertion( "G2 (Fuhrman)") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Grade 2") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G2 (Fuhrman)") +ClassAssertion( ) + +# Individual: (G3 (Fuhrman)) + +AnnotationAssertion( "G3 (Fuhrman)") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Grade 3") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G3 (Fuhrman)") +ClassAssertion( ) + +# Individual: (G4 (Fuhrman)) + +AnnotationAssertion( "G4 (Fuhrman)") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Grade 4") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G4 (Fuhrman)") +ClassAssertion( ) + +# Individual: (Low grade ovarian tumor) + +AnnotationAssertion( "Low grade ovarian tumor") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Low grade") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Low grade ovarian tumor") +ClassAssertion( ) + +# Individual: (High grade ovarian tumor) + +AnnotationAssertion( "High grade ovarian tumor") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "High grade") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "High grade ovarian tumor") +ClassAssertion( ) + +# Individual: (G1 (WHO)) + +AnnotationAssertion( "G1 (WHO)") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G1") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G1 (WHO)") +ClassAssertion( ) + +# Individual: (G2 (WHO)) + +AnnotationAssertion( "G2 (WHO)") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G2") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G2 (WHO)") +ClassAssertion( ) + +# Individual: (G3 (WHO)) + +AnnotationAssertion( "G3 (WHO)") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G3") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G3 (WHO)") +ClassAssertion( ) + +# Individual: (G4 (WHO)) + +AnnotationAssertion( "G4 (WHO)") +AnnotationAssertion( ) +AnnotationAssertion( "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "G4") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "G4 (WHO)") +ClassAssertion( ) + +# Individual: (pT0 (colon)) + +AnnotationAssertion( "pT0 (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT0 (colon)") +ClassAssertion( ) + +# Individual: (pTis (colon)) + +AnnotationAssertion( "pTis (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pTis (colon)") +ClassAssertion( ) + +# Individual: (pT1 (colon)) + +AnnotationAssertion( "pT1 (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT1 (colon)") +ClassAssertion( ) + +# Individual: (pT2 (colon)) + +AnnotationAssertion( "pT2 (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT2 (colon)") +ClassAssertion( ) + +# Individual: (pT3 (colon)) + +AnnotationAssertion( "pT3 (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT3 (colon)") +ClassAssertion( ) + +# Individual: (pT4a (colon)) + +AnnotationAssertion( "pT4a (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT4a (colon)") +ClassAssertion( ) + +# Individual: (pT4b (colon)) + +AnnotationAssertion( "pT4b (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT4b (colon)") +ClassAssertion( ) + +# Individual: (pT0 (lung)) + +AnnotationAssertion( "pT0 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT0 (lung)") +ClassAssertion( ) + +# Individual: (pTis (lung)) + +AnnotationAssertion( "pTis (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pTis (lung)") +ClassAssertion( ) + +# Individual: (pT1 (lung)) + +AnnotationAssertion( "pT1 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT1 (lung)") +ClassAssertion( ) + +# Individual: (pT1a (lung)) + +AnnotationAssertion( "pT1a (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT1a (lung)") +ClassAssertion( ) + +# Individual: (pT1b (lung)) + +AnnotationAssertion( "pT1b (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT1b (lung)") +ClassAssertion( ) + +# Individual: (pT2 (lung)) + +AnnotationAssertion( "pT2 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT2 (lung)") +ClassAssertion( ) + +# Individual: (pT2a (lung)) + +AnnotationAssertion( "pT2a (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT2a (lung)") +ClassAssertion( ) + +# Individual: (pT2b (lung)) + +AnnotationAssertion( "pT2b (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT2b (lung)") +ClassAssertion( ) + +# Individual: (pT3 (lung)) + +AnnotationAssertion( "pT3 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT3 (lung)") +ClassAssertion( ) + +# Individual: (pT4 (lung)) + +AnnotationAssertion( "pT4 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT4 (lung)") +ClassAssertion( ) + +# Individual: (pT0 (kidney)) + +AnnotationAssertion( "pT0 (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT0 (kidney)") +ClassAssertion( ) + +# Individual: (pT1 (kidney)) + +AnnotationAssertion( "pT1 (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT1 (kidney)") +ClassAssertion( ) + +# Individual: (pT1a (kidney)) + +AnnotationAssertion( "pT1a (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT1a (kidney)") +ClassAssertion( ) + +# Individual: (pT1b (kidney)) + +AnnotationAssertion( "pT1b (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT1b (kidney)") +ClassAssertion( ) + +# Individual: (pT2 (kidney)) + +AnnotationAssertion( "pT2 (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT2 (kidney)") +ClassAssertion( ) + +# Individual: (pT2a (kidney)) + +AnnotationAssertion( "pT2a (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT2a (kidney)") +ClassAssertion( ) + +# Individual: (pT2b (kidney)) + +AnnotationAssertion( "pT2b (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT2b (kidney)") +ClassAssertion( ) + +# Individual: (pT3 (kidney)) + +AnnotationAssertion( "pT3 (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT3 (kidney)") +ClassAssertion( ) + +# Individual: (pT3a (kidney)) + +AnnotationAssertion( "pT3a (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT3a (kidney)") +ClassAssertion( ) + +# Individual: (pT3b (kidney)) + +AnnotationAssertion( "pT3b (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT3b (kidney)") +ClassAssertion( ) + +# Individual: (pT3c (kidney)) + +AnnotationAssertion( "pT3c (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT3c (kidney)") +ClassAssertion( ) + +# Individual: (pT4 (kidney)) + +AnnotationAssertion( "pT4 (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT4 (kidney)") +ClassAssertion( ) + +# Individual: (pT0 (ovary)) + +AnnotationAssertion( "pT0 (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT0 (ovary)") +ClassAssertion( ) + +# Individual: (pT1 (ovary)) + +AnnotationAssertion( "pT1 (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT1 (ovary)") +ClassAssertion( ) + +# Individual: (pT1a (ovary)) + +AnnotationAssertion( "pT1a (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT1a (ovary)") +ClassAssertion( ) + +# Individual: (pT1b (ovary)) + +AnnotationAssertion( "pT1b (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT1b (ovary)") +ClassAssertion( ) + +# Individual: (pT1c (ovary)) + +AnnotationAssertion( "pT1c (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT1c (ovary)") +ClassAssertion( ) + +# Individual: (pT2 (ovary)) + +AnnotationAssertion( "pT2 (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT2 (ovary)") +ClassAssertion( ) + +# Individual: (pT2a (ovary)) + +AnnotationAssertion( "pT2a (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT2a (ovary)") +ClassAssertion( ) + +# Individual: (pT2b (ovary)) + +AnnotationAssertion( "pT2b (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT2b (ovary)") +ClassAssertion( ) + +# Individual: (pT2c (ovary)) + +AnnotationAssertion( "pT2c (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT2c (ovary)") +ClassAssertion( ) + +# Individual: (pT3 (ovary)) + +AnnotationAssertion( "pT3 (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT3 (ovary)") +ClassAssertion( ) + +# Individual: (pT3a (ovary)) + +AnnotationAssertion( "pT3a (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT3a (ovary)") +ClassAssertion( ) + +# Individual: (pT3b (ovary)) + +AnnotationAssertion( "pT3b (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT3b (ovary)") +ClassAssertion( ) + +# Individual: (pT3c (ovary)) + +AnnotationAssertion( "pT3c (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pT3c (ovary)") +ClassAssertion( ) + +# Individual: (pN0 (colon)) + +AnnotationAssertion( "pN0 (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN0 (colon)") +ClassAssertion( ) + +# Individual: (pN1 (colon)) + +AnnotationAssertion( "pN1 (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN1 (colon)") +ClassAssertion( ) + +# Individual: (pN1a (colon)) + +AnnotationAssertion( "pN1a (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN1a (colon)") +ClassAssertion( ) + +# Individual: (pN1b (colon)) + +AnnotationAssertion( "pN1b (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN1b (colon)") +ClassAssertion( ) + +# Individual: (pN1c (colon)) + +AnnotationAssertion( "pN1c (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN1c (colon)") +ClassAssertion( ) + +# Individual: (pN2 (colon)) + +AnnotationAssertion( "pN2 (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN2 (colon)") +ClassAssertion( ) + +# Individual: (pN2a (colon)) + +AnnotationAssertion( "pN2a (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN2a (colon)") +ClassAssertion( ) + +# Individual: (pN2b (colon)) + +AnnotationAssertion( "pN2b (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN2b (colon)") +ClassAssertion( ) + +# Individual: (pN0 (lung)) + +AnnotationAssertion( "pN0 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN0 (lung)") +ClassAssertion( ) + +# Individual: (pN1 (lung)) + +AnnotationAssertion( "pN1 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN1 (lung)") +ClassAssertion( ) + +# Individual: (pN2 (lung)) + +AnnotationAssertion( "pN2 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN2 (lung)") +ClassAssertion( ) + +# Individual: (pN3 (lung)) + +AnnotationAssertion( "pN3 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN3 (lung)") +ClassAssertion( ) + +# Individual: (pN0 (kidney)) + +AnnotationAssertion( "pN0 (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN0 (kidney)") +ClassAssertion( ) + +# Individual: (pN1 (kidney)) + +AnnotationAssertion( "pN1 (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN1 (kidney)") +ClassAssertion( ) + +# Individual: (pN0 (ovary)) + +AnnotationAssertion( "pN0 (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN0 (ovary)") +ClassAssertion( ) + +# Individual: (pN1 (ovary)) + +AnnotationAssertion( "pN1 (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pN1 (ovary)") +ClassAssertion( ) + +# Individual: (cM0 (colon)) + +AnnotationAssertion( "cM0 (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM0 (colon)") +ClassAssertion( ) + +# Individual: (cM1 (colon)) + +AnnotationAssertion( "cM1 (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM1 (colon)") +ClassAssertion( ) + +# Individual: (cM1a (colon)) + +AnnotationAssertion( "cM1a (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM1a (colon)") +ClassAssertion( ) + +# Individual: (cM1b (colon)) + +AnnotationAssertion( "cM1b (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM1b (colon)") +ClassAssertion( ) + +# Individual: (pM1 (colon)) + +AnnotationAssertion( "pM1 (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pM1 (colon)") +ClassAssertion( ) + +# Individual: (pM1a (colon)) + +AnnotationAssertion( "pM1a (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pM1a (colon)") +ClassAssertion( ) + +# Individual: (pM1b (colon)) + +AnnotationAssertion( "pM1b (colon)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pM1b (colon)") +ClassAssertion( ) + +# Individual: (cM0 (lung)) + +AnnotationAssertion( "cM0 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM0 (lung)") +ClassAssertion( ) + +# Individual: (cM1 (lung)) + +AnnotationAssertion( "cM1 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM1 (lung)") +ClassAssertion( ) + +# Individual: (cM1a (lung)) + +AnnotationAssertion( "cM1a (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM1a (lung)") +ClassAssertion( ) + +# Individual: (cM1b (lung)) + +AnnotationAssertion( "cM1b (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM1b (lung)") +ClassAssertion( ) + +# Individual: (pM1 (lung)) + +AnnotationAssertion( "pM1 (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pM1 (lung)") +ClassAssertion( ) + +# Individual: (pM1a (lung)) + +AnnotationAssertion( "pM1a (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pM1a (lung)") +ClassAssertion( ) + +# Individual: (pM1b (lung)) + +AnnotationAssertion( "pM1b (lung)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pM1b (lung)") +ClassAssertion( ) + +# Individual: (cM0 (kidney)) + +AnnotationAssertion( "cM0 (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM0 (kidney)") +ClassAssertion( ) + +# Individual: (cM1 (kidney)) + +AnnotationAssertion( "cM1 (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM1 (kidney)") +ClassAssertion( ) + +# Individual: (pM1 (kidney)) + +AnnotationAssertion( "pM1 (kidney)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pM1 (kidney)") +ClassAssertion( ) + +# Individual: (cM0 (ovary)) + +AnnotationAssertion( "cM0 (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM0 (ovary)") +ClassAssertion( ) + +# Individual: (cM1 (ovary)) + +AnnotationAssertion( "cM1 (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "cM1 (ovary)") +ClassAssertion( ) + +# Individual: (pM1 (ovary)) + +AnnotationAssertion( "pM1 (ovary)") +AnnotationAssertion( ) +AnnotationAssertion( "A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "pM1 (ovary)") +ClassAssertion( ) + +# Individual: (Occult Carcinoma (AJCC 7th)) + +AnnotationAssertion( "Occult Carcinoma (AJCC 7th)") +AnnotationAssertion( ) +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Occult Carcinoma") +AnnotationAssertion( "http://www.medilexicon.com/dictionary/14371") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Occult Carcinoma (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage 0 (AJCC 7th)) + +AnnotationAssertion( "Stage 0 (AJCC 7th)") +AnnotationAssertion( ) +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 0") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 0 (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage I (AJCC 7th)) + +AnnotationAssertion( "Stage I (AJCC 7th)") +AnnotationAssertion( ) +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage I") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage I (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIA (AJCC 7th)) + +AnnotationAssertion( "Stage IIA (AJCC 7th)") +AnnotationAssertion( ) +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIA (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIB (AJCC 7th)) + +AnnotationAssertion( "Stage IIB (AJCC 7th)") +AnnotationAssertion( ) +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIB (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIC (AJCC 7th)) + +AnnotationAssertion( "Stage IIC (AJCC 7th)") +AnnotationAssertion( ) +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIC") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIC (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIIA (AJCC 7th)) + +AnnotationAssertion( "Stage IIIA (AJCC 7th)") +AnnotationAssertion( ) +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIIA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIIA (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIIB (AJCC 7th)) + +AnnotationAssertion( "Stage IIIB (AJCC 7th)") +AnnotationAssertion( ) +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIIB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIIB (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IIIC (AJCC 7th)) + +AnnotationAssertion( "Stage IIIC (AJCC 7th)") +AnnotationAssertion( ) +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIIC") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIIC (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IVA (AJCC 7th)) + +AnnotationAssertion( "Stage IVA (AJCC 7th)") +AnnotationAssertion( ) +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IVA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IVA (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IVB (AJCC 7th)) + +AnnotationAssertion( "Stage IVB (AJCC 7th)") +AnnotationAssertion( ) +AnnotationAssertion( "A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IVB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IVB (AJCC 7th)") +ClassAssertion( ) + +# Individual: (Stage IA (FIGO)) + +AnnotationAssertion( "Stage IA (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IA (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IA1 (FIGO)) + +AnnotationAssertion( "Stage IA1 (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IA1") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IA1 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IA2 (FIGO)) + +AnnotationAssertion( "Stage IA2 (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IA2") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IA2 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IB (FIGO)) + +AnnotationAssertion( "Stage IB (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA"@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IB (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IB1 (FIGO)) + +AnnotationAssertion( "Stage IB1 (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IB1") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IB1 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IB2 (FIGO)) + +AnnotationAssertion( "Stage IB2 (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IB2") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IB2 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIA (FIGO)) + +AnnotationAssertion( "Stage IIA (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIA (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIA1 (FIGO)) + +AnnotationAssertion( "Stage IIA1 (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIA1") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIA1 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIA2 (FIGO)) + +AnnotationAssertion( "Stage IIA2 (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIA2") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIA2 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIB (FIGO)) + +AnnotationAssertion( "Stage IIB (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIB (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIIA (FIGO)) + +AnnotationAssertion( "Stage IIIA (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIIA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIIA (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IIIB (FIGO)) + +AnnotationAssertion( "Stage IIIB (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IIIB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IIIB (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IVA (FIGO)) + +AnnotationAssertion( "Stage IVA (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IVA") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IVA (FIGO)") +ClassAssertion( ) + +# Individual: (Stage IVB (FIGO)) + +AnnotationAssertion( "Stage IVB (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage IVB") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Cervical_cancer_staging") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage IVB (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 1 (FIGO)) + +AnnotationAssertion( "Stage 1 (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 1") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 1 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 1A (FIGO)) + +AnnotationAssertion( "Stage 1A (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 1A") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 1A (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 1B (FIGO)) + +AnnotationAssertion( "Stage 1B (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 1B") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 1B (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 1C (FIGO)) + +AnnotationAssertion( "Stage 1C (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 1C") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 1C (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 2 (FIGO)) + +AnnotationAssertion( "Stage 2 (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 2") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 2 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 2A (FIGO)) + +AnnotationAssertion( "Stage 2A (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 2A") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 2A (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 2B (FIGO)) + +AnnotationAssertion( "Stage 2B (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 2B") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 2B (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 2C (FIGO)) + +AnnotationAssertion( "Stage 2C (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 2C") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 2C (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 3 (FIGO)) + +AnnotationAssertion( "Stage 3 (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 3") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 3 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 3A (FIGO)) + +AnnotationAssertion( "Stage 3A (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 ."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 3A") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 3A (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 3B (FIGO)) + +AnnotationAssertion( "Stage 3B (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 ."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 3B") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 3B (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 3C (FIGO)) + +AnnotationAssertion( "Stage 3C (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 3C") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 3C (FIGO)") +ClassAssertion( ) + +# Individual: (Stage 4 (FIGO)) + +AnnotationAssertion( "Stage 4 (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage 4") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage 4 (FIGO)") +ClassAssertion( ) + +# Individual: (Stage Unknown (FIGO)) + +AnnotationAssertion( "Stage Unknown (FIGO)") +AnnotationAssertion( ) +AnnotationAssertion( "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0)."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "Stage Unknown") +AnnotationAssertion( "https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "Stage Unknown (FIGO)") +ClassAssertion( ) + +# Individual: (3: symptomatic in bed more than 50% of the day but not bed ridden) + +AnnotationAssertion( "3: symptomatic in bed more than 50% of the day but not bed ridden") +AnnotationAssertion( ) +AnnotationAssertion( "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "3: symptomatic in bed more than 50% of the day but not bed ridden") +ClassAssertion( ) + +# Individual: (2: symptomatic but in bed less than 50% of the day) + +AnnotationAssertion( "2: symptomatic but in bed less than 50% of the day") +AnnotationAssertion( ) +AnnotationAssertion( "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "2: symptomatic but in bed less than 50% of the day") +ClassAssertion( ) + +# Individual: (4: bed ridden) + +AnnotationAssertion( "4: bed ridden") +AnnotationAssertion( ) +AnnotationAssertion( "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "4: bed ridden") +ClassAssertion( ) + +# Individual: (0: asymptomatic) + +AnnotationAssertion( "0: asymptomatic") +AnnotationAssertion( ) +AnnotationAssertion( "An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "0: asymptomatic") +ClassAssertion( ) + +# Individual: (1: symptomatic but fully ambulatory) + +AnnotationAssertion( "1: symptomatic but fully ambulatory") +AnnotationAssertion( ) +AnnotationAssertion( "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "1: symptomatic but fully ambulatory") +ClassAssertion( ) + +# Individual: (100: asymptomatic) + +AnnotationAssertion( "100: asymptomatic") +AnnotationAssertion( ) +AnnotationAssertion( "A Karnofsky score vaue specification indicating that a patient is asymptomatic."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "100: asymptomatic") +ClassAssertion( ) + +# Individual: (80-90: symptomatic but fully ambulatory) + +AnnotationAssertion( "80-90: symptomatic but fully ambulatory") +AnnotationAssertion( ) +AnnotationAssertion( "A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "80-90: symptomatic but fully ambulatory") +ClassAssertion( ) + +# Individual: (60-70: symptomatic but in bed less than 50% of the day) + +AnnotationAssertion( "60-70: symptomatic but in bed less than 50% of the day") +AnnotationAssertion( ) +AnnotationAssertion( "A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "60-70: symptomatic but in bed less than 50% of the day") +ClassAssertion( ) + +# Individual: (40-50: symptomatic, in bed more than 50% of the day, but not bed ridden) + +AnnotationAssertion( "40-50: symptomatic, in bed more than 50% of the day, but not bed ridden") +AnnotationAssertion( ) +AnnotationAssertion( "A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden."@en) +AnnotationAssertion( "Chris Stoeckert, Helena Ellis") +AnnotationAssertion( "NCI BBRB, OBI") +AnnotationAssertion( "NCI BBRB") +AnnotationAssertion(rdfs:label "40-50: symptomatic, in bed more than 50% of the day, but not bed ridden") +ClassAssertion( ) + +# Individual: (Oxford Nanopore Technologies) + +AnnotationAssertion( "Oxford Nanopore Technologies") +AnnotationAssertion( ) +AnnotationAssertion( "An organization that is developing and selling nanopore sequencing products and is based in the UK."@en) +AnnotationAssertion( "James A. Overton") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies") +AnnotationAssertion(rdfs:label "Oxford Nanopore Technologies") +ClassAssertion( ) + +# Individual: (BioGents) + +AnnotationAssertion( "BioGents") +AnnotationAssertion( ) +AnnotationAssertion( "An organization that manufactures mosquito traps and other mosquito control products."@en) +AnnotationAssertion( "John Judkins") +AnnotationAssertion( "WEB:https://eu.biogents.com/about-biogents/") +AnnotationAssertion(rdfs:label "BioGents") +ClassAssertion( ) + +# Individual: (Abbott) + +AnnotationAssertion( "Abbott") +AnnotationAssertion( ) +AnnotationAssertion( "A manufacturer of rapid point-of-care assay devices."@en) +AnnotationAssertion( "John Judkins ORCID:0000-0001-6595-0902") +AnnotationAssertion( "WEB:https://www.globalpointofcare.abbott/en/about.html") +AnnotationAssertion( "https://github.com/obi-ontology/obi/issues/1456") +AnnotationAssertion(rdfs:label "Abbott") +ClassAssertion( ) + +# Individual: (J. Mitra) + +AnnotationAssertion( "J. Mitra") +AnnotationAssertion( ) +AnnotationAssertion( "A manufacturer of in vitro diagnostic assay kits in India."@en) +AnnotationAssertion( "John Judkins ORCID:0000-0001-6595-0902") +AnnotationAssertion( "WEB:https://jmitra.co.in/about-us/") +AnnotationAssertion( "https://github.com/obi-ontology/obi/issues/1456") +AnnotationAssertion(rdfs:label "J. Mitra") +ClassAssertion( ) + +# Individual: (InBios) + +AnnotationAssertion( "InBios") +AnnotationAssertion( ) +AnnotationAssertion( "A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases."@en) +AnnotationAssertion( "John Judkins ORCID:0000-0001-6595-0902") +AnnotationAssertion( "WEB:https://inbios.com/about/") +AnnotationAssertion( "https://github.com/obi-ontology/obi/issues/1456") +AnnotationAssertion(rdfs:label "InBios") +ClassAssertion( ) + +# Individual: (out of scope) + +AnnotationAssertion( "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) +AnnotationAssertion( "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") +AnnotationAssertion( "https://orcid.org/0000-0001-5208-3432") +AnnotationAssertion(rdfs:label "out of scope") +ClassAssertion( ) + +# Individual: (domain entity does not exist) + +AnnotationAssertion( "The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality."@en) +AnnotationAssertion( "This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). "@en) +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/136") +AnnotationAssertion( "https://orcid.org/0000-0002-4142-7153") +AnnotationAssertion(rdfs:label "domain entity does not exist") +ClassAssertion( ) + +# Individual: (meter) + +AnnotationAssertion( "meter") +AnnotationAssertion( "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.") +AnnotationAssertion( "m") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "meter") +ClassAssertion( ) + +# Individual: (kilogram) + +AnnotationAssertion( "kilogram") +AnnotationAssertion( "A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.") +AnnotationAssertion( "kg") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "kilogram") +ClassAssertion( ) + +# Individual: (second) + +AnnotationAssertion( "second") +AnnotationAssertion( "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.") +AnnotationAssertion( "s") +AnnotationAssertion( "sec") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "second") +ClassAssertion( ) + +# Individual: (centimeter) + +AnnotationAssertion( "centimeter") +AnnotationAssertion( "A length unit which is equal to one hundredth of a meter or 10^[-2] m.") +AnnotationAssertion( "cm") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "centimeter") +ClassAssertion( ) + +# Individual: (millimeter) + +AnnotationAssertion( "millimeter") +AnnotationAssertion( "A length unit which is equal to one thousandth of a meter or 10^[-3] m.") +AnnotationAssertion( "mm") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "millimeter") +ClassAssertion( ) + +# Individual: (micrometer) + +AnnotationAssertion( "micrometer") +AnnotationAssertion( "A length unit which is equal to one millionth of a meter or 10^[-6] m.") +AnnotationAssertion( "um") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "micrometer") +ClassAssertion( ) + +# Individual: (nanometer) + +AnnotationAssertion( "nanometer") +AnnotationAssertion( "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.") +AnnotationAssertion( "nm") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nanometer") +ClassAssertion( ) + +# Individual: (angstrom) + +AnnotationAssertion( "angstrom") +AnnotationAssertion( "A length unit which is equal to 10 [-10] m.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "angstrom") +ClassAssertion( ) + +# Individual: (gram) + +AnnotationAssertion( "gram") +AnnotationAssertion( "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.") +AnnotationAssertion( "g") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "gram") +ClassAssertion( ) + +# Individual: (milligram) + +AnnotationAssertion( "milligram") +AnnotationAssertion( "A mass unit which is equal to one thousandth of a gram or 10^[-3] g.") +AnnotationAssertion( "mg") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "milligram") +ClassAssertion( ) + +# Individual: (microgram) + +AnnotationAssertion( "microgram") +AnnotationAssertion( "A mass unit which is equal to one millionth of a gram or 10^[-6] g.") +AnnotationAssertion( "ug") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "microgram") +ClassAssertion( ) + +# Individual: (nanogram) + +AnnotationAssertion( "nanogram") +AnnotationAssertion( "A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.") +AnnotationAssertion( "ng") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nanogram") +ClassAssertion( ) + +# Individual: (picogram) + +AnnotationAssertion( "picogram") +AnnotationAssertion( "A mass unit which is equal to 10^[-12] g.") +AnnotationAssertion( "pg") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "picogram") +ClassAssertion( ) + +# Individual: (degree Celsius) + +AnnotationAssertion( "degree Celsius") +AnnotationAssertion( "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.") +AnnotationAssertion( "C") +AnnotationAssertion( "degree C") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "degree Celsius") +ClassAssertion( ) + +# Individual: (minute) + +AnnotationAssertion( "minute") +AnnotationAssertion( "A time unit which is equal to 60 seconds.") +AnnotationAssertion( "min") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "minute") +ClassAssertion( ) + +# Individual: (hour) + +AnnotationAssertion( "hour") +AnnotationAssertion( "A time unit which is equal to 3600 seconds or 60 minutes.") +AnnotationAssertion( "h") +AnnotationAssertion( "hr") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "hour") +ClassAssertion( ) + +# Individual: (day) + +AnnotationAssertion( "day") +AnnotationAssertion( "A time unit which is equal to 24 hours.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "day") +ClassAssertion( ) + +# Individual: (week) + +AnnotationAssertion( "week") +AnnotationAssertion( "A time unit which is equal to 7 days.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "week") +ClassAssertion( ) + +# Individual: (month) + +AnnotationAssertion( "month") +AnnotationAssertion( "A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "month") +ClassAssertion( ) + +# Individual: (year) + +AnnotationAssertion( "year") +AnnotationAssertion( "A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "year") +ClassAssertion( ) + +# Individual: (micromole) + +AnnotationAssertion( "micromole") +AnnotationAssertion( "A substance unit equal to a millionth of a mol or 10^[-6] mol.") +AnnotationAssertion( "umol") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "micromole") +ClassAssertion( ) + +# Individual: (nanomole) + +AnnotationAssertion( "nanomole") +AnnotationAssertion( "A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.") +AnnotationAssertion( "nmol") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nanomole") +ClassAssertion( ) + +# Individual: (picomole) + +AnnotationAssertion( "picomole") +AnnotationAssertion( "A substance unit equal to 10^[-12] mol.") +AnnotationAssertion( "pmol") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "picomole") +ClassAssertion( ) + +# Individual: (molar) + +AnnotationAssertion( "molar") +AnnotationAssertion( "A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).") +AnnotationAssertion( "M") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "molar") +ClassAssertion( ) + +# Individual: (millimolar) + +AnnotationAssertion( "millimolar") +AnnotationAssertion( "A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.") +AnnotationAssertion( "mM") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "millimolar") +ClassAssertion( ) + +# Individual: (micromolar) + +AnnotationAssertion( "micromolar") +AnnotationAssertion( "A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.") +AnnotationAssertion( "uM") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "micromolar") +ClassAssertion( ) + +# Individual: (nanomolar) + +AnnotationAssertion( "nanomolar") +AnnotationAssertion( "A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.") +AnnotationAssertion( "nM") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nanomolar") +ClassAssertion( ) + +# Individual: (picomolar) + +AnnotationAssertion( "picomolar") +AnnotationAssertion( "A unit of molarity which is equal to 10^[-12] M.") +AnnotationAssertion( "pM") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "picomolar") +ClassAssertion( ) + +# Individual: (cubic centimeter) + +AnnotationAssertion( "cubic centimeter") +AnnotationAssertion( "A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.") +AnnotationAssertion( "cc") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cubic centimeter") +ClassAssertion( ) + +# Individual: (milliliter) + +AnnotationAssertion( "milliliter") +AnnotationAssertion( "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.") +AnnotationAssertion( "ml") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "milliliter") +ClassAssertion( ) + +# Individual: (liter) + +AnnotationAssertion( "liter") +AnnotationAssertion( "A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.") +AnnotationAssertion( "L") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "liter") +ClassAssertion( ) + +# Individual: (cubic decimeter) + +AnnotationAssertion( "cubic decimeter") +AnnotationAssertion( "A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cubic decimeter") +ClassAssertion( ) + +# Individual: (microliter) + +AnnotationAssertion( "microliter") +AnnotationAssertion( "A volume unit which is equal to one millionth of a liter or 10^[-6] L.") +AnnotationAssertion( "ul") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "microliter") +ClassAssertion( ) + +# Individual: (nanoliter) + +AnnotationAssertion( "nanoliter") +AnnotationAssertion( "A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.") +AnnotationAssertion( "nl") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nanoliter") +ClassAssertion( ) + +# Individual: (picoliter) + +AnnotationAssertion( "picoliter") +AnnotationAssertion( "A volume unit which is equal to 10^[-12] L.") +AnnotationAssertion( "pl") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "picoliter") +ClassAssertion( ) + +# Individual: (hertz) + +AnnotationAssertion( "hertz") +AnnotationAssertion( "A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "hertz") +ClassAssertion( ) + +# Individual: (mass percentage) + +AnnotationAssertion( "mass percentage") +AnnotationAssertion( "A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.") +AnnotationAssertion( "% w/w") +AnnotationAssertion( "percent weight pr weight") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mass percentage") +ClassAssertion( ) + +# Individual: (mass volume percentage) + +AnnotationAssertion( "mass volume percentage") +AnnotationAssertion( "A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.") +AnnotationAssertion( "% w/v") +AnnotationAssertion( "percent vol per vol") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mass volume percentage") +ClassAssertion( ) + +# Individual: (volume percentage) + +AnnotationAssertion( "volume percentage") +AnnotationAssertion( "A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.") +AnnotationAssertion( "% v/v") +AnnotationAssertion( "percent vol per vol") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "volume percentage") +ClassAssertion( ) + +# Individual: (gram per liter) + +AnnotationAssertion( "gram per liter") +AnnotationAssertion( "A mass unit density which is equal to mass of an object in grams divided by the volume in liters.") +AnnotationAssertion( "g per L") +AnnotationAssertion( "g/L") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "gram per liter") +ClassAssertion( ) + +# Individual: (milligram per milliliter) + +AnnotationAssertion( "milligram per milliliter") +AnnotationAssertion( "A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.") +AnnotationAssertion( "mg per ml") +AnnotationAssertion( "mg/ml") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "milligram per milliliter") +ClassAssertion( ) + +# Individual: (degree Fahrenheit) + +AnnotationAssertion( "degree Fahrenheit") +AnnotationAssertion( "A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "degree Fahrenheit") +ClassAssertion( ) + +# Individual: (pH) + +AnnotationAssertion( "pH") +AnnotationAssertion( "A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "pH") +ClassAssertion( ) + +# Individual: (milliliter per liter) + +AnnotationAssertion( "milliliter per liter") +AnnotationAssertion( "A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.") +AnnotationAssertion( "ml per L") +AnnotationAssertion( "ml/l") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "milliliter per liter") +ClassAssertion( ) + +# Individual: (gram per deciliter) + +AnnotationAssertion( "gram per deciliter") +AnnotationAssertion( "A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.") +AnnotationAssertion( "g/dl") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "gram per deciliter") +ClassAssertion( ) + +# Individual: (colony forming unit per volume) + +AnnotationAssertion( "colony forming unit per volume") +AnnotationAssertion( "A concentration unit which a measure of viable bacterial numbers in a given volume.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "colony forming unit per volume") +ClassAssertion( ) + +# Individual: (microliters per minute) + +AnnotationAssertion( "microliters per minute") +AnnotationAssertion( "A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "microliters per minute") +ClassAssertion( ) + +# Individual: (count per nanomolar second) + +AnnotationAssertion( "count per nanomolar second") +AnnotationAssertion( "A rate unit which is equal to one over one nanomolar second.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "count per nanomolar second") +ClassAssertion( ) + +# Individual: (count per molar second) + +AnnotationAssertion( "count per molar second") +AnnotationAssertion( "A rate unit which is equal to one over one molar second.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "count per molar second") +ClassAssertion( ) + +# Individual: (count per nanomolar) + +AnnotationAssertion( "count per nanomolar") +AnnotationAssertion( "A rate unit which is equal to one over one nanomolar.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "count per nanomolar") +ClassAssertion( ) + +# Individual: (count per molar) + +AnnotationAssertion( "count per molar") +AnnotationAssertion( "A rate unit which is equal to one over one molar.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "count per molar") +ClassAssertion( ) + +# Individual: (microgram per liter) + +AnnotationAssertion( "microgram per liter") +AnnotationAssertion( "A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.") +AnnotationAssertion( "ng/ml") +AnnotationAssertion( "ug/L") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "microgram per liter") +ClassAssertion( ) + + +DifferentIndividuals( ) +DifferentIndividuals( ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +) \ No newline at end of file diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 1e0e4f9..61bc211 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -24,8 +24,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-02-06 + + 2024-10-23 @@ -69,7 +69,14 @@ - + + IAO:0000116 + uberon + editor_note + true + editor_note + editor note + @@ -3535,6 +3542,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -17715,6 +17728,32 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. + PATO:0002015 + composed of + compositionality + content + structure, composition + quality + PATO:0000025 + + + For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood). + composition + + + + + A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. + PATOC:GVG + + + + @@ -17785,6 +17824,34 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. + PATO:0001452 + conformation + relational structural quality + quality + PATO:0000141 + + structure + + + + + A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. + PATOC:GVG + + + + + conformation + VT:1000738 + + + + diff --git a/src/ontology/imports/pato_terms_combined.txt b/src/ontology/imports/pato_terms_combined.txt index 41ea132..e810796 100644 --- a/src/ontology/imports/pato_terms_combined.txt +++ b/src/ontology/imports/pato_terms_combined.txt @@ -1,4 +1,6 @@ -COB:0000800 +PATO:0001018 +PATO:0001739 +PATO:0001744 http://creativecommons.org/licenses/by/3.0/ http://purl.obolibrary.org/obo/BFO_0000003 http://purl.obolibrary.org/obo/BFO_0000004 @@ -6,6 +8,7 @@ http://purl.obolibrary.org/obo/BFO_0000015 http://purl.obolibrary.org/obo/BFO_0000016 http://purl.obolibrary.org/obo/BFO_0000017 http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/BFO_0000027 http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000182 @@ -23,7 +26,7 @@ http://purl.obolibrary.org/obo/CL_0017502 http://purl.obolibrary.org/obo/CL_0017503 http://purl.obolibrary.org/obo/CL_0017504 http://purl.obolibrary.org/obo/CL_0017505 -http://purl.obolibrary.org/obo/COB_0000082 +http://purl.obolibrary.org/obo/COB_0000800 http://purl.obolibrary.org/obo/DOID_4 http://purl.obolibrary.org/obo/ENVO_01000254 http://purl.obolibrary.org/obo/ENVO_01000637 @@ -44,13 +47,13 @@ http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.obolibrary.org/obo/IAO_0000116 http://purl.obolibrary.org/obo/IAO_0000117 http://purl.obolibrary.org/obo/IAO_0000118 http://purl.obolibrary.org/obo/IAO_0000119 http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/OBI_0000272 -http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/OBI_0000984 @@ -58,11 +61,14 @@ http://purl.obolibrary.org/obo/OBI_0001138 http://purl.obolibrary.org/obo/OBI_0001909 http://purl.obolibrary.org/obo/OBI_0002983 http://purl.obolibrary.org/obo/OBI_0302889 +http://purl.obolibrary.org/obo/PATO_0000025 http://purl.obolibrary.org/obo/PATO_0001018 http://purl.obolibrary.org/obo/PATO_0001236 http://purl.obolibrary.org/obo/PATO_0001241 +http://purl.obolibrary.org/obo/PATO_0001739 http://purl.obolibrary.org/obo/PATO_0002062 http://purl.obolibrary.org/obo/PO_0009012 +http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RBO_00000001 http://purl.obolibrary.org/obo/RBO_00000002 http://purl.obolibrary.org/obo/RBO_00000003 @@ -420,6 +426,16 @@ http://purl.obolibrary.org/obo/RBO_00015028 http://purl.obolibrary.org/obo/RBO_00015029 http://purl.obolibrary.org/obo/RBO_00015030 http://purl.obolibrary.org/obo/RBO_00015031 +http://purl.obolibrary.org/obo/RBO_00015032 +http://purl.obolibrary.org/obo/RBO_00015033 +http://purl.obolibrary.org/obo/RBO_00015034 +http://purl.obolibrary.org/obo/RBO_00015035 +http://purl.obolibrary.org/obo/RBO_00015036 +http://purl.obolibrary.org/obo/RBO_00015037 +http://purl.obolibrary.org/obo/RBO_00015038 +http://purl.obolibrary.org/obo/RBO_00015039 +http://purl.obolibrary.org/obo/RBO_00015040 +http://purl.obolibrary.org/obo/RBO_00015041 http://purl.obolibrary.org/obo/RBO_010000 http://purl.obolibrary.org/obo/RBO_010001 http://purl.obolibrary.org/obo/RBO_010002 @@ -441,7 +457,6 @@ http://purl.obolibrary.org/obo/RBO_010019 http://purl.obolibrary.org/obo/RBO_010020 http://purl.obolibrary.org/obo/RBO_2000 http://purl.obolibrary.org/obo/RBO_2001 -http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RO_0000086 http://purl.obolibrary.org/obo/RO_0002180 http://purl.obolibrary.org/obo/RO_0002233 @@ -451,12 +466,12 @@ http://purl.obolibrary.org/obo/RO_0002493 http://purl.obolibrary.org/obo/RO_0002608 http://purl.obolibrary.org/obo/SO_0000704 http://purl.obolibrary.org/obo/UBERON_0000000 -http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.obolibrary.org/obo/UO_0000127 http://purl.obolibrary.org/obo/UO_0000129 http://purl.obolibrary.org/obo/UO_0000160 http://purl.obolibrary.org/obo/UO_0000219 http://purl.obolibrary.org/obo/UO_1000135 +http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/description @@ -471,7 +486,4 @@ http://www.w3.org/2001/XMLSchema#nonNegativeInteger obo:PATO_0000025 obo:PATO_0000389 # acute obo:PATO_0001863 # chronic -PATO:0001018 -PATO:0001739 -PATO:0001744 term diff --git a/src/ontology/imports/pco_import.owl b/src/ontology/imports/pco_import.owl index 29c5dc2..277b969 100644 --- a/src/ontology/imports/pco_import.owl +++ b/src/ontology/imports/pco_import.owl @@ -1,108 +1,243 @@ - - - - - - 2024-02-06 - - - - - - - - - - - - - - - - - - - - - - - - - editor preferred label - editor preferred term - editor preferred label - editor preferred term - editor preferred term~editor preferred label - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - editor preferred label - editor preferred term - editor preferred label - editor preferred term - editor preferred term~editor preferred label - - - - - - - - example - example of usage - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - example of usage - - - - - - - - - - - - - - definition - definition - textual definition - - The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-10-23") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(rdfs:comment)) +Declaration(AnnotationProperty(rdfs:label)) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (editor preferred label) + +AnnotationAssertion( "editor preferred label"@en) +AnnotationAssertion( "editor preferred term"@en) +AnnotationAssertion( "editor preferred label") +AnnotationAssertion( "editor preferred term") +AnnotationAssertion( "editor preferred term~editor preferred label") +AnnotationAssertion( ) +AnnotationAssertion( "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "editor preferred label"@en) +AnnotationAssertion(rdfs:label "editor preferred term"@en) +AnnotationAssertion(rdfs:label "editor preferred label") +AnnotationAssertion(rdfs:label "editor preferred term") +AnnotationAssertion(rdfs:label "editor preferred term~editor preferred label") + +# Annotation Property: (example of usage) + +AnnotationAssertion( "example"@en) +AnnotationAssertion( "example of usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "example of usage"@en) + +# Annotation Property: (textual definition) + +AnnotationAssertion( "definition"@en) +AnnotationAssertion( "definition") +AnnotationAssertion( "textual definition") +AnnotationAssertion( ) +AnnotationAssertion( "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "2012-04-05: Barry Smith -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: @@ -110,1086 +245,626 @@ A statement of necessary and sufficient conditions explaining the meaning of an Alan Ruttenberg -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition - definition - textual definition - - +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") +AnnotationAssertion(rdfs:label "textual definition") +# Annotation Property: (editor note) - +AnnotationAssertion( "editor note"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "IAO:0000116") +AnnotationAssertion( "uberon") +AnnotationAssertion( "editor_note") +AnnotationAssertion( "true"^^xsd:boolean) +AnnotationAssertion( "editor_note") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "editor note"@en) +AnnotationAssertion(rdfs:label "editor note") - - +# Annotation Property: (term editor) +AnnotationAssertion( "term editor"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) +AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "term editor"@en) +AnnotationAssertion(rdfs:label "term editor") - +# Annotation Property: (alternative term) - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - term editor - term editor - - +AnnotationAssertion( "alternative term"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "alternative term"@en) +# Annotation Property: (definition source) - +AnnotationAssertion( "definition source"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) +AnnotationAssertion( "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition source"@en) +AnnotationAssertion(rdfs:label "definition source") - - alternative term - - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - alternative term - - +# Annotation Property: () +SubAnnotationPropertyOf( ) - +# Annotation Property: () - - definition source - - Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - - definition source - definition source - - +SubAnnotationPropertyOf( ) +# Annotation Property: () - +SubAnnotationPropertyOf( ) - - +# Annotation Property: () +SubAnnotationPropertyOf( ) - +# Annotation Property: () - - +SubAnnotationPropertyOf( ) +# Annotation Property: () - +SubAnnotationPropertyOf( ) - - +# Annotation Property: () +SubAnnotationPropertyOf( ) - +# Annotation Property: () - - +AnnotationAssertion(rdfs:isDefinedBy ) +# Annotation Property: () - +AnnotationAssertion(rdfs:isDefinedBy ) - - +# Annotation Property: () +AnnotationAssertion(rdfs:isDefinedBy ) - +# Annotation Property: (database_cross_reference) - - +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "database_cross_reference") +# Annotation Property: (has_exact_synonym) - +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "has_exact_synonym") - - +# Annotation Property: rdfs:comment (rdfs:comment) +AnnotationAssertion(rdfs:isDefinedBy rdfs:comment ) - +# Annotation Property: rdfs:label (label) - - +AnnotationAssertion( rdfs:label "label") +AnnotationAssertion(rdfs:isDefinedBy rdfs:label ) +AnnotationAssertion(rdfs:label rdfs:label "label") - +############################ +# Object Properties +############################ - - +# Object Property: (part of) +AnnotationAssertion( "is part of"@en) +AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) +AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a part and its whole"@en) +AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) +AnnotationAssertion( "part_of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") +InverseObjectProperties( ) +TransitiveObjectProperty() - - +# Object Property: (has part) +AnnotationAssertion( "has part"@en) +AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) +AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a whole and its part"@en) +AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) +AnnotationAssertion( "has_part"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part"@en) +TransitiveObjectProperty() - - +# Object Property: (preceded by) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - database_cross_reference - - - - - - - - - has_exact_synonym - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - label - - label - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - - - - - - - - - - - - preceded by - x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - - preceded by - - - - - - - - - - - - precedes - x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - - precedes - - - - - - - - - inheres in - this fragility inheres in this vase - this red color inheres in this apple - a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence - A dependent inheres in its bearer at all times for which the dependent exists. - inheres_in - - inheres in - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - bearer of - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - - participates in - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - - has participant - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - quality of - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - dos - 2017-09-17T13:52:24Z - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - - directly regulated by - - - - - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos - - - - - - - - - - David Osumi-Sutherland - - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - - ends after - - - - - - - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - - immediately preceded by - - - - - - - - - David Osumi-Sutherland - ends_at_start_of - meets - - - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - - immediately precedes - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - - - - - - overlaps - - - - - - - - - - - - - - - - - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit - Chris Mungall - David Hill - Tanya Berardini - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false - - - - - regulates - - - - - - - - - - - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. - Chris Mungall - - negatively regulates (process to process) - - - - - - negatively regulates - - - - - - - - - - - - - - - - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. - Chris Mungall - - positively regulates (process to process) - - - - - - positively regulates - - - - - - - - - - - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - - - capable of - - - - - - - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall - has function in - - capable of part of - - - - - - - - - - - - Chris Mungall - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - - temporally related to - - - - - - - - - - - - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall - consumes - - - - - - has input - - - - - - - - - - - - - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. - c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. - - - acts upstream of - - - - - - - - - - - - - - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. - c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. - affects - - - acts upstream of or within - - - - - - - - - - - - cjm - - - holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y - - causally upstream of, positive effect - - - - - - - - - - - cjm - holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y - - causally upstream of, negative effect - - - - - - - - A mereological relationship or a topological relationship - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - - - mereotopologically related to - - - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity - Chris Mungall - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. - - - enables - - - - - - - - A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall - This is a grouping relation that collects relations used for the purpose of connecting structure and function - - functionally related to - - - - - - - - - - inverse of enables - Chris Mungall - - - enabled by - - - - - - - - - - - - inverse of regulates - Chris Mungall - regulated by (processual) - - - regulated by - - - - - - - - - inverse of negatively regulates - Chris Mungall - - - negatively regulated by - - - - - - - - - inverse of positively regulates - Chris Mungall - - - positively regulated by - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - inverse of has input - Chris Mungall - - - - input of - - - - - - - - - - - - inverse of upstream of - Chris Mungall - - causally downstream of - - - - - - - - - - - - Chris Mungall - - immediately causally downstream of - - - - - - - - - This relation groups causal relations between material entities and causal relations between processes - This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. +AnnotationAssertion( "preceded by"@en) +AnnotationAssertion( "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) +AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) +AnnotationAssertion( "is preceded by"@en) +AnnotationAssertion( "preceded_by"@en) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (precedes) + +AnnotationAssertion( "precedes"@en) +AnnotationAssertion( "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "precedes"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (inheres in) + +AnnotationAssertion( "inheres in"@en) +AnnotationAssertion( "this fragility inheres in this vase"@en) +AnnotationAssertion( "this red color inheres in this apple"@en) +AnnotationAssertion( "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A dependent inheres in its bearer at all times for which the dependent exists."@en) +AnnotationAssertion( "inheres_in"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "inheres in"@en) +InverseObjectProperties( ) + +# Object Property: (bearer of) + +AnnotationAssertion( "bearer of"@en) +AnnotationAssertion( "this apple is bearer of this red color"@en) +AnnotationAssertion( "this vase is bearer of this fragility"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) +AnnotationAssertion( "bearer_of"@en) +AnnotationAssertion( "is bearer of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "bearer of"@en) +ObjectPropertyRange( ) + +# Object Property: (participates in) + +AnnotationAssertion( "participates in"@en) +AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) +AnnotationAssertion( "this input material (or this output material) participates in this process"@en) +AnnotationAssertion( "this investigator participates in this investigation"@en) +AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "participates_in"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "participates in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has participant) + +AnnotationAssertion( "has participant"@en) +AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) +AnnotationAssertion( "this investigation has participant this investigator"@en) +AnnotationAssertion( "this process has participant this input material (or this output material)"@en) +AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) +AnnotationAssertion( "has_participant"@en) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "has participant"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (quality of) + +AnnotationAssertion( "this red color is a quality of this apple"@en) +AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) +AnnotationAssertion( "is quality of"@en) +AnnotationAssertion( "quality_of"@en) +AnnotationAssertion(rdfs:label "quality of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has quality) + +AnnotationAssertion( "this apple has quality this red color"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) +AnnotationAssertion( "has_quality"@en) +AnnotationAssertion(rdfs:label "has quality"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (directly regulated by) + +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( "GOC:dos") rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "directly regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (ends after) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "ends after"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately preceded by) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( "starts_at_end_of") +AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "immediately preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately precedes) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( "ends_at_start_of") +AnnotationAssertion( "meets") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "immediately precedes"@en) +SubObjectPropertyOf( ) + +# Object Property: (overlaps) + +AnnotationAssertion( ) +AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") +AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "overlaps"@en) +SubObjectPropertyOf( ) + +# Object Property: (regulates) + +AnnotationAssertion( ) +AnnotationAssertion( "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.") +AnnotationAssertion( "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "David Hill") +AnnotationAssertion( "Tanya Berardini") +AnnotationAssertion( ) +AnnotationAssertion( "GO") +AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") +AnnotationAssertion( "regulates (processual)") +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "regulates"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulates) + +AnnotationAssertion( "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.") +AnnotationAssertion( "Chris Mungall"@en) +AnnotationAssertion( ) +AnnotationAssertion( "negatively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "negatively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (positively regulates) + +AnnotationAssertion( "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.") +AnnotationAssertion( "Chris Mungall"@en) +AnnotationAssertion( ) +AnnotationAssertion( "positively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "positively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (capable of) + +AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") +AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") +AnnotationAssertion( "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "has function realized in") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\".") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "capable of"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of part of) + +AnnotationAssertion( "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "has function in") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "capable of part of"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (temporally related to) + +AnnotationAssertion( ) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.") +AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "temporally related to"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has input) + +AnnotationAssertion( ) +AnnotationAssertion( "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "consumes") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "has input"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (acts upstream of) + +AnnotationAssertion( "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.") +AnnotationAssertion( "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "acts upstream of") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within) + +AnnotationAssertion( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") +AnnotationAssertion( "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.") +AnnotationAssertion( "affects") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "acts upstream of or within") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causally upstream of, positive effect") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion(rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causally upstream of, negative effect") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (mereotopologically related to) + +AnnotationAssertion( "A mereological relationship or a topological relationship") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "mereotopologically related to"@en) + +# Object Property: (enables) + +AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "catalyzes") +AnnotationAssertion( "executes") +AnnotationAssertion( "has") +AnnotationAssertion( "is catalyzing") +AnnotationAssertion( "is executing") +AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") +AnnotationAssertion( "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "enables"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (functionally related to) + +AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "functionally related to"@en) + +# Object Property: (enabled by) + +AnnotationAssertion( "inverse of enables") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "enabled by"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (regulated by) + +AnnotationAssertion( "inverse of regulates") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "regulated by (processual)") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "regulated by"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulated by) + +AnnotationAssertion( "inverse of negatively regulates") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "negatively regulated by"@en) +SubObjectPropertyOf( ) + +# Object Property: (positively regulated by) + +AnnotationAssertion( "inverse of positively regulates") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "positively regulated by"@en) +SubObjectPropertyOf( ) + +# Object Property: (member of) + +AnnotationAssertion( "An organism that is a member of a population of organisms") +AnnotationAssertion( "is member of is a mereological relation between a item and a collection.") +AnnotationAssertion( "is member of") +AnnotationAssertion( "member part of") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "member of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has member) + +AnnotationAssertion( "has member is a mereological relation between a collection and an item.") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has member"@en) +SubObjectPropertyOf( ) +IrreflexiveObjectProperty() + +# Object Property: (input of) + +AnnotationAssertion( "inverse of has input") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "input of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of upstream of") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causally downstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (causally related to) + +AnnotationAssertion( ) +AnnotationAssertion( "This relation groups causal relations between material entities and causal relations between processes") +AnnotationAssertion( "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: @@ -1197,2267 +872,1039 @@ To define causal relations in an activity-flow type network, we make use of 3 pr * Is the causal relation regulatory? * Is the influence positive or negative -The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. -Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causally related to - - - - - - - - - - - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain - Chris Mungall - - - - causally upstream of - - - - - - - - - - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. - Chris Mungall - - - immediately causally upstream of - - - - - - - - - - - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. - We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall - influences (processual) - affects - - causally upstream of or within - - - - - - - - - - inverse of causally upstream of or within - Chris Mungall - - - - causally downstream of or within - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall - - involved in regulation of - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall - - - involved in positive regulation of - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall - - - involved in negative regulation of - - - - - - - - - - - c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p - OWL does not allow defining object properties via a Union - Chris Mungall - involved in or reguates - - involved in or involved in regulation of - - - - - - - - - - - A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - Considering relabeling as 'pairwise interacts with' - This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. - in pairwise interaction with - - - interacts with - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - - - - - - - - An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall - binds - molecularly binds with - - molecularly interacts with - - http://purl.obolibrary.org/obo/MI_0915 - - - - - - - - - Axiomatization to GO to be added later - Chris Mungall - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. - - phosphorylates - - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - -A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré - molecularly controls - - directly regulates activity of - - - - - - - - Chris Mungall - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - - helper property (not for use in curation) - - - - - - - - - Chris Mungall - - is kinase activity - - - - - - - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - - - causal agent in process - - - - - - - - - - - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between processes - - - - - - - - - - - The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between entities - - - - - - - - - - Chris Mungall - - causally influenced by (entity-centric) - - causally influenced by - - - - - - - - - Chris Mungall - - interaction relation helper property - - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - - - - - - - Chris Mungall - - molecular interaction relation helper property - - - - - - - - - - - - - - - - - - - - - The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré - - causally influences (entity-centric) - - causally influences - - - - - - - - - - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - Chris Mungall - - directly regulates (processual) - - - - - - directly regulates - - - - - - - - - - - A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall - - - causal relation between material entity and a process - - - - - - - - - - - - - pyrethroid -> growth - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - - - capable of regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - - - capable of negatively regulating - - - - - - - - - - - - - renin -> arteriolar smooth muscle contraction - Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - - - capable of positively regulating - - - - - - - - - Inverse of 'causal agent in process' - - - process has causal agent - - - - - - - - - - - - - - cjm - 2018-01-26T23:49:30Z - - - acts upstream of or within, positive effect - - - - - - - - - - - - - - - cjm - 2018-01-26T23:49:51Z - - - acts upstream of or within, negative effect - - - - - - - - - - - - - - c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - - cjm - 2018-01-26T23:53:14Z - - - acts upstream of, positive effect - - - - - - - - - - - - - - - c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - - cjm - 2018-01-26T23:53:22Z - - - acts upstream of, negative effect - - - - - - - - - - - cjm - 2018-03-13T23:55:05Z - - causally upstream of or within, negative effect - - - - - - - - - - cjm - 2018-03-13T23:55:19Z - - causally upstream of or within, positive effect - - - - - - - - - - - The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré - - regulates activity of - - - - - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - https://orcid.org/0000-0001-8815-0078 - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - quality - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - Material anatomical entity that is a member of an individual species or is a viral or viroid particle. - organism or virus - Melissa Haendel - 9/18/11 - organism or virus or viroid - - - - - - - - - molecular process - - molecular_function - - - - - - - - - - catalytic activity - - - - - - - - - - - - true - - - - kinase activity - - - - - - - - - - transferase activity - - - - - - - - - - transferase activity, transferring phosphorus-containing groups - - - - - - - - - data item - Data items include counts of things, analyte concentrations, and statistical summaries. - - a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - JAR: datum -- well, this will be very tricky to define, but maybe some +Each of these 3 primitives can be composed to yield a cross-product of different relation types.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causally related to"@en) + +# Object Property: (causally upstream of) + +AnnotationAssertion( ) +AnnotationAssertion( "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causally upstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately causally upstream of) + +AnnotationAssertion( ) +AnnotationAssertion( "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within) + +AnnotationAssertion( "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.") +AnnotationAssertion( "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "influences (processual)") +AnnotationAssertion( "affects") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causally upstream of or within") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (causally downstream of or within) + +AnnotationAssertion( "inverse of causally upstream of or within") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causally downstream of or within") +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (involved in regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (involved in positive regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "involved in positive regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in negative regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "involved in negative regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in or involved in regulation of) + +AnnotationAssertion( "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p") +AnnotationAssertion( "OWL does not allow defining object properties via a Union") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "involved in or reguates") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "involved in or involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (interacts with) + +AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") +AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) +AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") +AnnotationAssertion( "in pairwise interaction with") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "interacts with") +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/oborel/obo-relations/wiki/InteractionRelations"^^xsd:anyURI) +SymmetricObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (molecularly interacts with) + +AnnotationAssertion( "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "binds") +AnnotationAssertion( "molecularly binds with") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "molecularly interacts with") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) +SubObjectPropertyOf( ) +SymmetricObjectProperty() + +# Object Property: (phosphorylates) + +AnnotationAssertion( "Axiomatization to GO to be added later") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "phosphorylates") +SubObjectPropertyOf( ) + +# Object Property: (directly regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Vasundra Touré") +AnnotationAssertion( "molecularly controls") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "directly regulates activity of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (helper property (not for use in curation)) + +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "helper property (not for use in curation)") + +# Object Property: (is kinase activity) + +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "is kinase activity") +SubObjectPropertyOf( ) + +# Object Property: (causal agent in process) + +AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causal agent in process") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (causal relation between processes) + +AnnotationAssertion( "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causal relation between processes") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (causal relation between entities) + +AnnotationAssertion( "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causal relation between entities") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (causally influenced by) + +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( "causally influenced by (entity-centric)") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causally influenced by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (interaction relation helper property) + +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "interaction relation helper property") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion( "https://github.com/oborel/obo-relations/wiki/InteractionRelations"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (molecular interaction relation helper property) + +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "molecular interaction relation helper property") +SubObjectPropertyOf( ) + +# Object Property: (causally influences) + +AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Vasundra Touré") +AnnotationAssertion( ) +AnnotationAssertion( "causally influences (entity-centric)") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causally influences") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly regulates) + +AnnotationAssertion( "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( "directly regulates (processual)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "directly regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causal relation between material entity and a process) + +AnnotationAssertion( "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.") +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causal relation between material entity and a process") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of regulating) + +AnnotationAssertion( "pyrethroid -> growth") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "capable of regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of negatively regulating) + +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "capable of negatively regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of positively regulating) + +AnnotationAssertion( "renin -> arteriolar smooth muscle contraction") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "capable of positively regulating") +SubObjectPropertyOf( ) + +# Object Property: (process has causal agent) + +AnnotationAssertion( "Inverse of 'causal agent in process'") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "process has causal agent") +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, positive effect) + +AnnotationAssertion( "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive") +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "acts upstream of, positive effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, negative effect) + +AnnotationAssertion( "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative") +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "acts upstream of, negative effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") +SubObjectPropertyOf( ) + +# Object Property: (regulates activity of) + +AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") +AnnotationAssertion( "Vasundra Touré") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + + +############################ +# Datatypes +############################ + +# Datatype: xsd:boolean (xsd:boolean) + +AnnotationAssertion(rdfs:isDefinedBy xsd:boolean ) + +# Datatype: xsd:string (xsd:string) + +AnnotationAssertion(rdfs:isDefinedBy xsd:string ) + + +############################ +# Classes +############################ + +# Class: (entity) + +AnnotationAssertion( "entity") +AnnotationAssertion( "Entity") +AnnotationAssertion( "Julius Caesar"@en) +AnnotationAssertion( "Verdi’s Requiem"@en) +AnnotationAssertion( "the Second World War"@en) +AnnotationAssertion( "your body mass index"@en) +AnnotationAssertion( "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") Annotation(rdfs:seeAlso ) "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"@en) +AnnotationAssertion(Annotation( ) "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "entity"@en) + +# Class: (continuant) + +AnnotationAssertion( "continuant") +AnnotationAssertion( "Continuant") +AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) +AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) +AnnotationAssertion(Annotation( ) "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en) +AnnotationAssertion(Annotation( ) "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ") +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (occurrent) + +AnnotationAssertion( "occurrent") +AnnotationAssertion( "Occurrent") +AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) +AnnotationAssertion( "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) +AnnotationAssertion( "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process."@en) +AnnotationAssertion(Annotation( ) "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.") +AnnotationAssertion(Annotation( ) "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])"@en) +AnnotationAssertion(Annotation( ) "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])"@en) +AnnotationAssertion(Annotation( ) "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (independent continuant) + +AnnotationAssertion( "ic") +AnnotationAssertion( "IndependentContinuant") +AnnotationAssertion( "a chair"@en) +AnnotationAssertion( "a heart"@en) +AnnotationAssertion( "a leg"@en) +AnnotationAssertion( "a molecule"@en) +AnnotationAssertion( "a spatial region"@en) +AnnotationAssertion( "an atom"@en) +AnnotationAssertion( "an orchestra."@en) +AnnotationAssertion( "an organism"@en) +AnnotationAssertion( "the bottom right portion of a human torso"@en) +AnnotationAssertion( "the interior of your mouth"@en) +AnnotationAssertion( "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) +AnnotationAssertion(Annotation( ) "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(Annotation( ) "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])"@en) +AnnotationAssertion(Annotation( ) "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") +AnnotationAssertion(Annotation( ) "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (process) + +AnnotationAssertion( "process") +AnnotationAssertion( "Process") +AnnotationAssertion( "a process of cell-division, \\ a beating of the heart"@en) +AnnotationAssertion( "a process of meiosis"@en) +AnnotationAssertion( "a process of sleeping"@en) +AnnotationAssertion( "the course of a disease"@en) +AnnotationAssertion( "the flight of a bird"@en) +AnnotationAssertion( "the life of an organism"@en) +AnnotationAssertion( "your process of aging."@en) +AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) +AnnotationAssertion(Annotation( ) "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) +AnnotationAssertion(Annotation( ) "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) + +# Class: (disposition) + +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (realizable entity) + +AnnotationAssertion( "realizable") +AnnotationAssertion( "RealizableEntity") +AnnotationAssertion( "the disposition of this piece of metal to conduct electricity."@en) +AnnotationAssertion( "the disposition of your blood to coagulate"@en) +AnnotationAssertion( "the function of your reproductive organs"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the role of this boundary to delineate where Utah and Colorado meet"@en) +AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion( "https://orcid.org/0000-0001-8815-0078") +AnnotationAssertion(Annotation( ) "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])"@en) +AnnotationAssertion(Annotation( ) "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (quality) + +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) + +# Class: (specifically dependent continuant) + +AnnotationAssertion( "sdc") +AnnotationAssertion( "SpecificallyDependentContinuant") +AnnotationAssertion( "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"@en) +AnnotationAssertion( "of one-sided specifically dependent continuants: the mass of this tomato"@en) +AnnotationAssertion( "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."@en) +AnnotationAssertion( "the disposition of this fish to decay"@en) +AnnotationAssertion( "the function of this heart: to pump blood"@en) +AnnotationAssertion( "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en) +AnnotationAssertion( "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en) +AnnotationAssertion( "the pink color of a medium rare piece of grilled filet mignon at its center"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the shape of this hole."@en) +AnnotationAssertion( "the smell of this portion of mozzarella"@en) +AnnotationAssertion( "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion(Annotation( ) "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."@en) +AnnotationAssertion(Annotation( ) "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (role) + +AnnotationAssertion( "role") +AnnotationAssertion( "Role") +AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) +AnnotationAssertion( "the priest role"@en) +AnnotationAssertion( "the role of a boundary to demarcate two neighboring administrative territories"@en) +AnnotationAssertion( "the role of a building in serving as a military target"@en) +AnnotationAssertion( "the role of a stone in marking a property boundary"@en) +AnnotationAssertion( "the role of subject in a clinical trial"@en) +AnnotationAssertion( "the student role"@en) +AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) +AnnotationAssertion( "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) +AnnotationAssertion(Annotation( ) "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (object aggregate) + +AnnotationAssertion( "object-aggregate") +AnnotationAssertion( "ObjectAggregate") +AnnotationAssertion( "a collection of cells in a blood biobank."@en) +AnnotationAssertion( "a swarm of bees is an aggregate of members who are linked together through natural bonds"@en) +AnnotationAssertion( "a symphony orchestra"@en) +AnnotationAssertion( "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)"@en) +AnnotationAssertion( "defined by fiat: the aggregate of members of an organization"@en) +AnnotationAssertion( "defined through physical attachment: the aggregate of atoms in a lump of granite"@en) +AnnotationAssertion( "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container"@en) +AnnotationAssertion( "defined via attributive delimitations such as: the patients in this hospital"@en) +AnnotationAssertion( "the aggregate of bearings in a constant velocity axle joint"@en) +AnnotationAssertion( "the aggregate of blood cells in your body"@en) +AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) +AnnotationAssertion( "the restaurants in Palo Alto"@en) +AnnotationAssertion( "your collection of Meissen ceramic plates."@en) +AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) +AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") +AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") +AnnotationAssertion(Annotation( ) "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.") +AnnotationAssertion(Annotation( ) "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "object aggregate"@en) +SubClassOf( ) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "gdc") +AnnotationAssertion( "GenericallyDependentContinuant") +AnnotationAssertion( "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) +AnnotationAssertion( "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) +AnnotationAssertion( "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) +AnnotationAssertion( "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) +AnnotationAssertion(Annotation( ) "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) +AnnotationAssertion(Annotation( ) "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "material") +AnnotationAssertion( "MaterialEntity") +AnnotationAssertion( "a flame"@en) +AnnotationAssertion( "a forest fire"@en) +AnnotationAssertion( "a human being"@en) +AnnotationAssertion( "a hurricane"@en) +AnnotationAssertion( "a photon"@en) +AnnotationAssertion( "a puff of smoke"@en) +AnnotationAssertion( "a sea wave"@en) +AnnotationAssertion( "a tornado"@en) +AnnotationAssertion( "an aggregate of human beings."@en) +AnnotationAssertion( "an energy wave"@en) +AnnotationAssertion( "an epidemic"@en) +AnnotationAssertion( "the undetached arm of a human being"@en) +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion( "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"@en) +AnnotationAssertion( "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."@en) +AnnotationAssertion( "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."@en) +AnnotationAssertion(Annotation( ) "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"@en) +AnnotationAssertion(Annotation( ) "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])"@en) +AnnotationAssertion(Annotation( ) "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) + +# Class: (organism or virus or viroid) + +AnnotationAssertion( "Material anatomical entity that is a member of an individual species or is a viral or viroid particle.") +AnnotationAssertion( "organism or virus"@en) +AnnotationAssertion( "Melissa Haendel") +AnnotationAssertion( "9/18/11") +AnnotationAssertion(rdfs:label "organism or virus or viroid") +SubClassOf( ) + +# Class: (molecular_function) + +AnnotationAssertion( "molecular process") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "molecular_function") +SubClassOf( ) + +# Class: (catalytic activity) + +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "catalytic activity") +SubClassOf( ) + +# Class: (kinase activity) + +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "kinase activity") +SubClassOf( ) +SubClassOf( ObjectHasSelf()) + +# Class: (transferase activity) + +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "transferase activity") +SubClassOf( ) + +# Class: (transferase activity, transferring phosphorus-containing groups) + +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "transferase activity, transferring phosphorus-containing groups") +SubClassOf( ) + +# Class: (data item) + +AnnotationAssertion( "data item"@en) +AnnotationAssertion( "Data items include counts of things, analyte concentrations, and statistical summaries."@en) +AnnotationAssertion( ) +AnnotationAssertion( "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) +AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) +AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) +AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith -JAR: A data item is an approximately justified approximately true approximate belief - 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Jonathan Rees - data - - data item - - - - - - - - - information content entity - information content entity - - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - - - - - - - measurement datum - Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - 2/2/2009 is_specified_output of some assay? - person:Chris Stoeckert - OBI_0000305 - group:OBI - - measurement datum - - - - - - - - - - - - - - - - - - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - - - - - - - - - - - - - - - - denotator type - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - - - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - quality (PATO) - PATO:0000072 - quality - PATO:0000001 - - quality - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATOC:GVG - - - - - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 - Wikipedia:Physical_property - relational physical quality - quality - PATO:0001018 - - - physical quality - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATOC:GVG - - - - - - - - - - A quality which inheres in an process. - PATO:0001239 - PATO:0001240 - quality of a process - quality of occurrent - quality of process - relational quality of occurrent - quality - PATO:0001236 - See comments of relational quality of a physical entity. - - process quality - - - - - A quality which inheres in an process. - PATOC:GVG - - - - - - - - - A quality which inheres in a continuant. - PATO:0001237 - PATO:0001238 - snap:Quality - monadic quality of a continuant - multiply inhering quality of a physical entity - quality of a continuant - quality of a single physical entity - quality of an object - quality of continuant - monadic quality of an object - monadic quality of continuant - quality - PATO:0001241 - Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. - - physical object quality - - - - - A quality which inheres in a continuant. - PATOC:GVG - - - - - - - - - george - 2009-06-05T09:16:46Z - quality - PATO:0002062 - - - physical quality of a process - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. - - A material entity that consists of two or more organisms, viruses, or viroids. - group of organism - organism collection - May be of the same or different species. - collection of organisms - - - - - - - - - - - - - - - - - - A material entity that is one or more organisms, viruses or viroids. - organismal entity - - - - - - - - - - - - - - 2 - - - - - - - A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. - pair of interacting organisms - - - - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - - failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - ready for release - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - - placeholder removed - placeholder removed - - - - - - - - - terms merged - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - - - - - - - term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - - - - - - - term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - - - - - - - universal - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - - - - - - - defined class - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - - - - - - - named class expression - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +JAR: A data item is an approximately justified approximately true approximate belief"@en) +AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Jonathan Rees"@en) +AnnotationAssertion( "data"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) + +# Class: (information content entity) + +AnnotationAssertion( "information content entity"@en) +AnnotationAssertion(rdfs:label "information content entity"@en) +SubClassOf( ) + +# Class: (curation status specification) + +AnnotationAssertion( "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "OBI_0000266"@en) +AnnotationAssertion(rdfs:label "curation status specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (data about an ontology part) + +AnnotationAssertion( "data about an ontology part"@en) +AnnotationAssertion( "Data about an ontology part is a data item about a part of an ontology, for example a term"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "data about an ontology part"@en) +SubClassOf( ) + +# Class: (measurement datum) + +AnnotationAssertion( "measurement datum"@en) +AnnotationAssertion( "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device."@en) +AnnotationAssertion( "2/2/2009 is_specified_output of some assay?"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000305"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "measurement datum"@en) +SubClassOf( ) + +# Class: (obsolescence reason specification) + +AnnotationAssertion( "obsolescence reason specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (denotator type) + +AnnotationAssertion( "denotator type"@en) +AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en) +AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Barry Smith, Werner Ceusters"@en) +AnnotationAssertion(rdfs:label "denotator type"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (quality) + +AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") +AnnotationAssertion( "quality (PATO)") +AnnotationAssertion( "PATO:0000072") +AnnotationAssertion( "quality") +AnnotationAssertion( "PATO:0000001") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "quality") +SubClassOf( ) + +# Class: (physical quality) + +AnnotationAssertion(Annotation( "PATOC:GVG") "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.") +AnnotationAssertion( "PATO:0002079") +AnnotationAssertion( "Wikipedia:Physical_property") +AnnotationAssertion( "relational physical quality") +AnnotationAssertion( "quality") +AnnotationAssertion( "PATO:0001018") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "physical quality") +SubClassOf( ) + +# Class: (process quality) + +AnnotationAssertion(Annotation( "PATOC:GVG") "A quality which inheres in an process.") +AnnotationAssertion( "PATO:0001239") +AnnotationAssertion( "PATO:0001240") +AnnotationAssertion( "quality of a process") +AnnotationAssertion( "quality of occurrent") +AnnotationAssertion( "quality of process") +AnnotationAssertion( "relational quality of occurrent") +AnnotationAssertion( "quality") +AnnotationAssertion( "PATO:0001236") +AnnotationAssertion(rdfs:comment "See comments of relational quality of a physical entity.") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "process quality") +SubClassOf( ) +DisjointClasses( ) + +# Class: (physical object quality) + +AnnotationAssertion(Annotation( "PATOC:GVG") "A quality which inheres in a continuant.") +AnnotationAssertion( "PATO:0001237") +AnnotationAssertion( "PATO:0001238") +AnnotationAssertion( "snap:Quality") +AnnotationAssertion( "monadic quality of a continuant") +AnnotationAssertion( "multiply inhering quality of a physical entity") +AnnotationAssertion( "quality of a continuant") +AnnotationAssertion( "quality of a single physical entity") +AnnotationAssertion( "quality of an object") +AnnotationAssertion( "quality of continuant") +AnnotationAssertion( "monadic quality of an object") +AnnotationAssertion( "monadic quality of continuant") +AnnotationAssertion( "quality") +AnnotationAssertion( "PATO:0001241") +AnnotationAssertion(rdfs:comment "Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "physical object quality") +SubClassOf( ) + +# Class: (physical quality of a process) + +AnnotationAssertion( "george") +AnnotationAssertion( "2009-06-05T09:16:46Z") +AnnotationAssertion( "quality") +AnnotationAssertion( "PATO:0002062") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "physical quality of a process") +SubClassOf( ) + +# Class: (collection of organisms) + +AnnotationAssertion( "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.") +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that consists of two or more organisms, viruses, or viroids."@en) +AnnotationAssertion( "group of organism") +AnnotationAssertion( "organism collection") +AnnotationAssertion(rdfs:comment "May be of the same or different species.") +AnnotationAssertion(rdfs:label "collection of organisms"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ) ObjectMinCardinality(2 ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (organismal entity) + +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is one or more organisms, viruses or viroids.") +AnnotationAssertion(rdfs:label "organismal entity"@en) +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (pair of interacting organisms) + +AnnotationAssertion( "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other."@en) +AnnotationAssertion(rdfs:label "pair of interacting organisms"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(2 ))) +SubClassOf( ) + +# Class: owl:Nothing (owl:Nothing) + +AnnotationAssertion(rdfs:isDefinedBy owl:Nothing ) + + +############################ +# Named Individuals +############################ + +# Individual: (example to be eventually removed) + +AnnotationAssertion( "example to be eventually removed"@en) +AnnotationAssertion(rdfs:label "example to be eventually removed"@en) +ClassAssertion( ) + +# Individual: (failed exploratory term) + +AnnotationAssertion( "failed exploratory term"@en) +AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "failed exploratory term"@en) +ClassAssertion( ) + +# Individual: (metadata complete) + +AnnotationAssertion( "metadata complete"@en) +AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) +AnnotationAssertion(rdfs:label "metadata complete"@en) +ClassAssertion( ) + +# Individual: (organizational term) + +AnnotationAssertion( "organizational term"@en) +AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion(rdfs:label "organizational term"@en) +ClassAssertion( ) + +# Individual: (ready for release) + +AnnotationAssertion( "ready for release"@en) +AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) +AnnotationAssertion(rdfs:label "ready for release"@en) +ClassAssertion( ) + +# Individual: (metadata incomplete) + +AnnotationAssertion( "metadata incomplete"@en) +AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) +AnnotationAssertion(rdfs:label "metadata incomplete"@en) +ClassAssertion( ) + +# Individual: (uncurated) + +AnnotationAssertion( "uncurated"@en) +AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) +AnnotationAssertion(rdfs:label "uncurated"@en) +ClassAssertion( ) + +# Individual: (pending final vetting) + +AnnotationAssertion( "pending final vetting"@en) +AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) +AnnotationAssertion(rdfs:label "pending final vetting"@en) +ClassAssertion( ) + +# Individual: (placeholder removed) + +AnnotationAssertion( "placeholder removed"@en) +AnnotationAssertion(rdfs:label "placeholder removed"@en) +ClassAssertion( ) + +# Individual: (terms merged) + +AnnotationAssertion( "terms merged"@en) +AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(rdfs:label "terms merged"@en) +ClassAssertion( ) + +# Individual: (term imported) + +AnnotationAssertion( "term imported"@en) +AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) +AnnotationAssertion(rdfs:label "term imported"@en) +ClassAssertion( ) + +# Individual: (term split) + +AnnotationAssertion( "term split"@en) +AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) +AnnotationAssertion(rdfs:label "term split"@en) +ClassAssertion( ) + +# Individual: (universal) + +AnnotationAssertion( "universal"@en) +AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en) +AnnotationAssertion(rdfs:label "universal"@en) +ClassAssertion( ) + +# Individual: (defined class) + +AnnotationAssertion( "defined class"@en) +AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en) +AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "defined class"@en) +ClassAssertion( ) + +# Individual: (named class expression) + +AnnotationAssertion( "named class expression"@en) +AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en) +AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "named class expression"@en) +ClassAssertion( ) + +# Individual: (to be replaced with external ontology term) + +AnnotationAssertion( "to be replaced with external ontology term"@en) +AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) +ClassAssertion( ) + +# Individual: (requires discussion) + +AnnotationAssertion( "requires discussion"@en) +AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "requires discussion"@en) +ClassAssertion( ) + + +SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) +DifferentIndividuals( ) +DifferentIndividuals( ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +) \ No newline at end of file diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 9caeca6..2ff3e40 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -1,84 +1,262 @@ - - - - - - 2024-02-06 - - - - - - - - - - - - - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - editor preferred term - - - - - - - - example of usage - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - example of usage - example of usage - - - - - - - - - - - - - - definition - - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-10-23") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(rdfs:comment)) +Declaration(AnnotationProperty(rdfs:label)) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (editor preferred term) + +AnnotationAssertion( "editor preferred term"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "editor preferred term"@en) + +# Annotation Property: (example of usage) + +AnnotationAssertion( "example of usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "example of usage"@en) +AnnotationAssertion(rdfs:label "example of usage") + +# Annotation Property: (definition) + +AnnotationAssertion( "definition"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "2012-04-05: Barry Smith -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: @@ -86,4622 +264,1913 @@ A statement of necessary and sufficient conditions explaining the meaning of an Alan Ruttenberg -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition - definition - - +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") +# Annotation Property: (editor note) - +AnnotationAssertion( "editor note"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "editor note"@en) - - +# Annotation Property: (term editor) +AnnotationAssertion( "term editor"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) +AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "term editor"@en) - +# Annotation Property: (alternative label) - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - term editor - - +AnnotationAssertion( "alternative label"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "OBO Operations committee") +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:comment "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") +AnnotationAssertion(rdfs:label "alternative label"@en) +# Annotation Property: (definition source) - +AnnotationAssertion( "definition source"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:label "definition source"@en) - - alternative label - - A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. - PERSON:Daniel Schober - OBO Operations committee - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - alternative label - - +# Annotation Property: () +SubAnnotationPropertyOf( ) - +# Annotation Property: (is a defining property chain axiom) - - definition source - - Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition source - - +AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL") +AnnotationAssertion(rdfs:label "is a defining property chain axiom") +# Annotation Property: (is a defining property chain axiom where second argument is reflexive) - +AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.") +AnnotationAssertion(rdfs:label "is a defining property chain axiom where second argument is reflexive") - - +# Annotation Property: () +SubAnnotationPropertyOf( ) - +# Annotation Property: () - - +SubAnnotationPropertyOf( ) +# Annotation Property: () - +SubAnnotationPropertyOf( ) - - +# Annotation Property: () +SubAnnotationPropertyOf( ) - +# Annotation Property: () - - +SubAnnotationPropertyOf( ) +# Annotation Property: () - +SubAnnotationPropertyOf( ) + +# Annotation Property: () - - +SubAnnotationPropertyOf( ) +# Annotation Property: (has_broad_synonym) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 - has broad synonym - has_broad_synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 - - - - - - - - database_cross_reference - - - - - - - - An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 - has exact synonym - has_exact_synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 - - - - - - - - - - - - - - - - - - - - - - - - - - +AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") +AnnotationAssertion(rdfs:label "has broad synonym"@en) +AnnotationAssertion(rdfs:label "has_broad_synonym") +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") + +# Annotation Property: (database_cross_reference) + +AnnotationAssertion(rdfs:label "database_cross_reference") + +# Annotation Property: (has exact synonym) + +AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") +AnnotationAssertion(rdfs:label "has exact synonym"@en) +AnnotationAssertion(rdfs:label "has_exact_synonym") +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") + + +############################ +# Object Properties +############################ + +# Object Property: (part of) + +AnnotationAssertion( "is part of"@en) +AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) +AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a part and its whole"@en) +AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) +AnnotationAssertion( "part_of"@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) +AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (has part) + +AnnotationAssertion( "has part"@en) +AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) +AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a whole and its part"@en) +AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) +AnnotationAssertion( "has_part"@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (preceded by) + +AnnotationAssertion( "preceded by"@en) +AnnotationAssertion( "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) +AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) +AnnotationAssertion( "is preceded by"@en) +AnnotationAssertion( "preceded_by"@en) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (precedes) + +AnnotationAssertion( "precedes"@en) +AnnotationAssertion( "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "precedes"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (characteristic of) + +AnnotationAssertion( "inheres in"@en) +AnnotationAssertion( "this fragility is a characteristic of this vase"@en) +AnnotationAssertion( "this red color is a characteristic of this apple"@en) +AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) +AnnotationAssertion( "inheres_in"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.") +AnnotationAssertion(rdfs:label "characteristic of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +FunctionalObjectProperty() + +# Object Property: (has characteristic) + +AnnotationAssertion( "bearer of"@en) +AnnotationAssertion( "this apple is bearer of this red color"@en) +AnnotationAssertion( "this vase is bearer of this fragility"@en) +AnnotationAssertion( "Inverse of characteristic_of"@en) +AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) +AnnotationAssertion( "bearer_of"@en) +AnnotationAssertion( "is bearer of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has characteristic"@en) +InverseFunctionalObjectProperty() +ObjectPropertyRange( ) + +# Object Property: (participates in) + +AnnotationAssertion( "participates in"@en) +AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) +AnnotationAssertion( "this input material (or this output material) participates in this process"@en) +AnnotationAssertion( "this investigator participates in this investigation"@en) +AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "participates_in"@en) +AnnotationAssertion(rdfs:label "participates in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has participant) + +AnnotationAssertion( "has participant"@en) +AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) +AnnotationAssertion( "this investigation has participant this investigator"@en) +AnnotationAssertion( "this process has participant this input material (or this output material)"@en) +AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) +AnnotationAssertion( "has_participant"@en) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion(rdfs:label "has participant"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (function of) + +AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) +AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "function_of"@en) +AnnotationAssertion( "is function of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "function of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (quality of) + +AnnotationAssertion( "this red color is a quality of this apple"@en) +AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) +AnnotationAssertion( "is quality of"@en) +AnnotationAssertion( "quality_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "quality of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (role of) + +AnnotationAssertion( "this investigator role is a role of this person"@en) +AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "is role of"@en) +AnnotationAssertion( "role_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "role of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has function) + +AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "has_function"@en) +AnnotationAssertion(rdfs:label "has function"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has quality) + +AnnotationAssertion( "this apple has quality this red color"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) +AnnotationAssertion( "has_quality"@en) +AnnotationAssertion(rdfs:label "has quality"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (has role) + +AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "has_role"@en) +AnnotationAssertion(rdfs:label "has role"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has disposition) + +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) +AnnotationAssertion(rdfs:label "has disposition"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (disposition of) + +AnnotationAssertion( "inverse of has disposition") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "disposition of"@en) +SubObjectPropertyOf( ) + +# Object Property: (has regulatory component activity) + +AnnotationAssertion( "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "has regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has negative regulatory component activity) + +AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") +AnnotationAssertion(rdfs:label "has negative regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has positive regulatory component activity) + +AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") +AnnotationAssertion(rdfs:label "has positive regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has component activity) + +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") +AnnotationAssertion(rdfs:label "has component activity") +SubObjectPropertyOf( ) + +# Object Property: (has component process) + +AnnotationAssertion( "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "has component process") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly regulated by) + +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( ) rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") +AnnotationAssertion(rdfs:label "directly regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (directly negatively regulated by) + +AnnotationAssertion(Annotation( ) "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "directly negatively regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (directly positively regulated by) + +AnnotationAssertion(Annotation( ) "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "directly positively regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has effector activity) + +AnnotationAssertion(Annotation( ) "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") +AnnotationAssertion(rdfs:label "has effector activity") +SubObjectPropertyOf( ) +FunctionalObjectProperty() + +# Object Property: (ends after) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) +AnnotationAssertion(rdfs:label "ends after"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately preceded by) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( "starts_at_end_of") +AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) +AnnotationAssertion(rdfs:label "immediately preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately precedes) + +AnnotationAssertion( ) +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( "ends_at_start_of") +AnnotationAssertion( "meets") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) +AnnotationAssertion(rdfs:label "immediately precedes"@en) +SubObjectPropertyOf( ) + +# Object Property: (overlaps) + +AnnotationAssertion( ) +AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") +AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "overlaps"@en) +SubObjectPropertyOf( ) +SymmetricObjectProperty() + +# Object Property: (has component) + +AnnotationAssertion( ) +AnnotationAssertion( "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") +AnnotationAssertion( "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.") +AnnotationAssertion( "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit."@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has component"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (develops from) + +AnnotationAssertion( ) +AnnotationAssertion( "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "This is the transitive form of the develops from relation") +AnnotationAssertion(rdfs:label "develops from"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (develops into) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of develops from") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "develops into"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (regulates) + +AnnotationAssertion( "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "GO") +AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") +AnnotationAssertion( "regulates (processual)") +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulates"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulates) + +AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "negatively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negatively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (positively regulates) + +AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "positively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (capable of) + +AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") +AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") +AnnotationAssertion( "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ") +AnnotationAssertion( ) +AnnotationAssertion( "has function realized in") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\".") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of part of) + +AnnotationAssertion( "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.") +AnnotationAssertion( ) +AnnotationAssertion( "has function in") +AnnotationAssertion(rdfs:label "capable of part of"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (temporally related to) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.") +AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") +AnnotationAssertion(rdfs:label "temporally related to"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has input) + +AnnotationAssertion( ) +AnnotationAssertion( "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.") +AnnotationAssertion( ) +AnnotationAssertion( "consumes") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has input"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (has output) + +AnnotationAssertion( ) +AnnotationAssertion( "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.") +AnnotationAssertion( ) +AnnotationAssertion( "produces") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has output"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_output"^^xsd:anyURI) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has developmental contribution from) + +AnnotationAssertion( "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]") +AnnotationAssertion( ) +AnnotationAssertion( "x has developmental contribution from y iff x has some part z such that z develops from y"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has developmental contribution from"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (developmentally contributes to) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of has developmental contribution from") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "developmentally contributes to"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (developmentally preceded by) + +AnnotationAssertion( ) +AnnotationAssertion( "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p") +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion( ) +AnnotationAssertion( "In general you should not use this relation to make assertions - use one of the more specific relations below this one") +AnnotationAssertion(rdfs:comment "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from") +AnnotationAssertion(rdfs:label "developmentally preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (acts upstream of) + +AnnotationAssertion( "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.") +AnnotationAssertion( "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within) + +AnnotationAssertion( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") +AnnotationAssertion( "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.") +AnnotationAssertion( "affects") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (developmentally succeeded by) + +AnnotationAssertion( ) +AnnotationAssertion( "Inverse of developmentally preceded by") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "developmentally succeeded by"@en) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, positive effect) + +AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y") +AnnotationAssertion(rdfs:label "causally upstream of, positive effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, negative effect) + +AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally upstream of, negative effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (characteristic of part of) + +AnnotationAssertion( "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.") +AnnotationAssertion( "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of") +AnnotationAssertion( ) +AnnotationAssertion( "inheres in part of") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "characteristic of part of"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (mereotopologically related to) + +AnnotationAssertion( "A mereological relationship or a topological relationship") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mereotopologically related to"@en) + +# Object Property: (developmentally related to) + +AnnotationAssertion( "A relationship that holds between entities participating in some developmental process (GO:0032502)") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development") +AnnotationAssertion(rdfs:label "developmentally related to"@en) + +# Object Property: (enables) + +AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") +AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") +AnnotationAssertion( ) +AnnotationAssertion( "catalyzes") +AnnotationAssertion( "executes") +AnnotationAssertion( "has") +AnnotationAssertion( "is catalyzing") +AnnotationAssertion( "is executing") +AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "enables"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (functionally related to) + +AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") +AnnotationAssertion( ) +AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") +AnnotationAssertion(rdfs:label "functionally related to"@en) + +# Object Property: (part of structure that is capable of) + +AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") +AnnotationAssertion( ) +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) +SubObjectPropertyOf( ) + +# Object Property: (involved in) + +AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") +AnnotationAssertion( ) +AnnotationAssertion( "actively involved in") +AnnotationAssertion( "enables part of") +AnnotationAssertion(rdfs:label "involved in"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (enabled by) + +AnnotationAssertion( "inverse of enables") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "enabled by"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (regulated by) + +AnnotationAssertion( "inverse of regulates") +AnnotationAssertion( ) +AnnotationAssertion( "regulated by (processual)") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulated by"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulated by) + +AnnotationAssertion( "inverse of negatively regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negatively regulated by"@en) +SubObjectPropertyOf( ) + +# Object Property: (positively regulated by) + +AnnotationAssertion( "inverse of positively regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively regulated by"@en) +SubObjectPropertyOf( ) + +# Object Property: (input of) + +AnnotationAssertion( "inverse of has input") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "input of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (output of) + +AnnotationAssertion( "inverse of has output") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "output of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has developmental potential involving) + +AnnotationAssertion( ) +AnnotationAssertion( "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has developmental potential involving"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has potential to developmentally contribute to) + +AnnotationAssertion( ) +AnnotationAssertion( "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has potential to developmentally contribute to"@en) +SubObjectPropertyOf( ) + +# Object Property: (has potential to develop into) + +AnnotationAssertion( ) +AnnotationAssertion( "x has the potential to develop into y iff x develops into y or if x is capable of developing into y"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has potential to develop into"@en) +SubObjectPropertyOf( ) + +# Object Property: (has potential to directly develop into) + +AnnotationAssertion( ) +AnnotationAssertion( "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has potential to directly develop into"@en) +SubObjectPropertyOf( ) + +# Object Property: (causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of upstream of") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally downstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (indirectly positively regulates) + +AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "indirectly activates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (indirectly negatively regulates) + +AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "indirectly inhibits") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (causally related to) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.") +AnnotationAssertion( "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. +To define causal relations in an activity-flow type network, we make use of 3 primitives: - + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative? - - +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. - +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. - - +Each of these 3 primitives can be composed to yield a cross-product of different relation types.") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causally related to"@en) + +# Object Property: (causally upstream of) + +AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally upstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately causally upstream of) + +AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within) + +AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") +AnnotationAssertion( "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2") +AnnotationAssertion( ) +AnnotationAssertion( "influences (processual)") +AnnotationAssertion( "affects") +AnnotationAssertion(rdfs:label "causally upstream of or within") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (causally downstream of or within) + +AnnotationAssertion( "inverse of causally upstream of or within") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally downstream of or within") +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (involved in regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (involved in positive regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in positive regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in negative regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in negative regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in or involved in regulation of) + +AnnotationAssertion( "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p") +AnnotationAssertion( "OWL does not allow defining object properties via a Union") +AnnotationAssertion( ) +AnnotationAssertion( "involved in or reguates") +AnnotationAssertion(rdfs:label "involved in or involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (interacts with) + +AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") +AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) +AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") +AnnotationAssertion( ) +AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") +AnnotationAssertion( "in pairwise interaction with") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "interacts with") +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) +AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) +SymmetricObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (molecularly interacts with) + +AnnotationAssertion( "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.") +AnnotationAssertion( ) +AnnotationAssertion( "binds") +AnnotationAssertion( "molecularly binds with") +AnnotationAssertion(rdfs:label "molecularly interacts with") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) +SubObjectPropertyOf( ) +SymmetricObjectProperty() + +# Object Property: (phosphorylates) + +AnnotationAssertion( "Axiomatization to GO to be added later") +AnnotationAssertion( ) +AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") +AnnotationAssertion(rdfs:label "phosphorylates") +SubObjectPropertyOf( ) + +# Object Property: (directly regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "molecularly controls") +AnnotationAssertion(rdfs:label "directly regulates activity of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly negatively regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly inhibits") +AnnotationAssertion( "molecularly decreases activity of") +AnnotationAssertion(rdfs:label "directly negatively regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly positively regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly activates") +AnnotationAssertion( "molecularly increases activity of") +AnnotationAssertion(rdfs:label "directly positively regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (helper property (not for use in curation)) + +AnnotationAssertion( ) +AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") +AnnotationAssertion(rdfs:label "helper property (not for use in curation)") + +# Object Property: (is kinase activity) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "is kinase activity") +SubObjectPropertyOf( ) + +# Object Property: (relation between physical entity and a process or stage) + +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.") +AnnotationAssertion(rdfs:label "relation between physical entity and a process or stage") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (existence overlaps) + +AnnotationAssertion( "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") +AnnotationAssertion(rdfs:label "existence overlaps") +SubObjectPropertyOf( ) + +# Object Property: (existence ends during) + +AnnotationAssertion( "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") +AnnotationAssertion(rdfs:label "existence ends during") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (existence ends with) + +AnnotationAssertion( "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") +AnnotationAssertion(rdfs:label "existence ends with") +SubObjectPropertyOf( ) + +# Object Property: (existence ends during or before) + +AnnotationAssertion( "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") +AnnotationAssertion(rdfs:label "existence ends during or before") +SubObjectPropertyOf( ) + +# Object Property: (causal agent in process) + +AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causal agent in process") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (causal relation between processes) + +AnnotationAssertion( "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causal relation between processes") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (depends on) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "depends on") +AnnotationAssertion(rdfs:seeAlso ) + +# Object Property: (causal relation between entities) + +AnnotationAssertion( "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causal relation between entities") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (causally influenced by) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "causally influenced by (entity-centric)") +AnnotationAssertion(rdfs:label "causally influenced by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (interaction relation helper property) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "interaction relation helper property") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (molecular interaction relation helper property) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "molecular interaction relation helper property") +SubObjectPropertyOf( ) + +# Object Property: (causally influences) + +AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "causally influences (entity-centric)") +AnnotationAssertion(rdfs:label "causally influences") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly regulates) + +AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly regulates (processual)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "directly regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has part structure that is capable of) + +AnnotationAssertion( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") +AnnotationAssertion( "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part structure that is capable of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causal relation between material entity and a process) + +AnnotationAssertion( "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.") +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causal relation between material entity and a process") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of regulating) + +AnnotationAssertion( "pyrethroid -> growth") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of negatively regulating) + +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of negatively regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of positively regulating) + +AnnotationAssertion( "renin -> arteriolar smooth muscle contraction") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of positively regulating") +SubObjectPropertyOf( ) + +# Object Property: (process has causal agent) + +AnnotationAssertion( "Inverse of 'causal agent in process'") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "process has causal agent") +SubObjectPropertyOf( ) + +# Object Property: (directly positively regulates) + +AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "directly positively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "directly positively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (directly negatively regulates) + +AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "directly negatively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "directly negatively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (realized in response to stimulus) + +AnnotationAssertion( "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-12-26T19:45:49Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "realized in response to stimulus") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (enables subfunction) + +AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "enables subfunction") +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, positive effect) + +AnnotationAssertion( "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of, positive effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, negative effect) + +AnnotationAssertion( "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (realized in response to) + +AnnotationAssertion( "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.") +AnnotationAssertion( "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)") +AnnotationAssertion( "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.") +AnnotationAssertion( "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "triggered by process") +AnnotationAssertion(rdfs:label "realized in response to"@en) +AnnotationAssertion(rdfs:seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"^^xsd:anyURI) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (regulates activity of) + +AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (indirectly causally upstream of) + +AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") +AnnotationAssertion( ) +AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) +SubObjectPropertyOf( ) + +# Object Property: (indirectly regulates) + +AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "indirectly regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (device utilizes material) + +AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") +AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") +AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) +AnnotationAssertion( "utilizes") +AnnotationAssertion(rdfs:label "device utilizes material"@en) + +# Object Property: (regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulates characteristic") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (positively regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively regulates characteristic") +SubObjectPropertyOf( ) + +# Object Property: (negatively regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negatively regulates characteristic") +SubObjectPropertyOf( ) - - - +############################ +# Classes +############################ +# Class: (continuant) + +AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) - +# Class: (occurrent) + +AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (independent continuant) + +AnnotationAssertion( "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(rdfs:comment "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ) - - +# Class: (process) +AnnotationAssertion( "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion(rdfs:comment "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) - +# Class: (disposition) - +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) +# Class: (realizable entity) - +AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) + +# Class: (quality) + +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) +# Class: (specifically dependent continuant) + +AnnotationAssertion( "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(rdfs:comment "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - - - - - - part of - - - https://wiki.geneontology.org/Part_of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - - - - has part - - - - - - - - - - - - - - - - - preceded by - x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - - - - - - - - precedes - x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - precedes - - - - - - - - - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple - a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. - characteristic of - - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - has characteristic - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - inverse of has disposition - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - disposition of - - - - - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - - 2017-05-24T09:30:46Z - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - has positive regulatory component activity - - - - - - - - - - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - has component activity - - - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - - 2017-05-24T09:49:21Z - has component process - - - - - - - - - - - 2017-09-17T13:52:24Z - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - directly regulated by - - - - - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - - - - - - - - - - - Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - - 2017-09-17T13:52:38Z - directly negatively regulated by - - - - - Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - - - - - - - - - - - Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - - 2017-09-17T13:52:47Z - directly positively regulated by - - - - - Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - - - - - - - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. - has effector activity - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - - - - - - - - - - - David Osumi-Sutherland - - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - ends after - - - - - - - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - immediately preceded by - - - - - - - - - - David Osumi-Sutherland - ends_at_start_of - meets - - - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - immediately precedes - - - - - - - - - - - - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - - - - - overlaps - - - - - - - - - true - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - has component - - - - - - - - - - - - - - - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - - - - - This is the transitive form of the develops from relation - develops from - - - - - - - - - - - - - inverse of develops from - - - - - develops into - - - - - - - - - - - - - - - - - - - - - p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - - - - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false - - - - regulates - - - - - - - - - - - p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - negatively regulates (process to process) - - - - - negatively regulates - - - - - - - - - - - - - - - - p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - positively regulates (process to process) - - - - - positively regulates - - - - - - - - - - - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - - capable of - - - - - - - - - - - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - - has function in - capable of part of - - - - - - - - - - true - - - - - - - - - - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporally related to - - - - - - - - - - - - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes - - - - - has input - https://wiki.geneontology.org/Has_input - - - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces - - - - - has output - https://wiki.geneontology.org/Has_output - - - - - - - - - - - - - - - - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - - x has developmental contribution from y iff x has some part z such that z develops from y - - has developmental contribution from - - - - - - - - - - - - - - - inverse of has developmental contribution from - - - developmentally contributes to - - - - - - - - - - - - - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p - false - - In general you should not use this relation to make assertions - use one of the more specific relations below this one - This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from - developmentally preceded by - - - - - - - - - - - - - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. - c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. - - acts upstream of - - - - - - - - - - - - - - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. - c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. - affects - - acts upstream of or within - https://wiki.geneontology.org/Acts_upstream_of_or_within - - - - - - - - - - Inverse of developmentally preceded by - - developmentally succeeded by - - - - - - - - - - p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - - - - - holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y - causally upstream of, positive effect - - - - - - - - - - - p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - - - - - causally upstream of, negative effect - - - - - - - - - - - - - - - - - - q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. - Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - - inheres in part of - - - characteristic of part of - - - - - - - - - - true - - - - - - - - A mereological relationship or a topological relationship - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - - mereotopologically related to - - - - - - - - A relationship that holds between entities participating in some developmental process (GO:0032502) - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development - developmentally related to - - - - - - - - - - - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity - c enables p iff c is capable of p and c acts to execute p. - - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. - - enables - https://wiki.geneontology.org/Enables - - - - - - - - A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - - This is a grouping relation that collects relations used for the purpose of connecting structure and function - functionally related to - - - - - - - - - - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - - false - part of structure that is capable of - - - - - - - - - true - - - - - - - - - - - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p - - actively involved in - enables part of - involved in - https://wiki.geneontology.org/Involved_in - - - - - - - - - - inverse of enables - - - enabled by - https://wiki.geneontology.org/Enabled_by - - - - - - - - - - - - inverse of regulates - - regulated by (processual) - - regulated by - - - - - - - - - inverse of negatively regulates - - - negatively regulated by - - - - - - - - - inverse of positively regulates - - - positively regulated by - - - - - - - - - - inverse of has input - - - - input of - - - - - - - - - - inverse of has output - - - - output of - - - - - - - - - - - - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - - has developmental potential involving - - - - - - - - - - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - has potential to developmentally contribute to - - - - - - - - - - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - has potential to develop into - - - - - - - - - - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - - has potential to directly develop into - - - - - - - - - - - - inverse of upstream of - - causally downstream of - - - - - - - - - - - - - immediately causally downstream of - - - - - - - - - - - - - - - - - - - - - - - - - - - p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - - indirectly activates - - indirectly positively regulates - https://wiki.geneontology.org/Indirectly_positively_regulates - - - - - - - - - - - - - - - - - - - - - - - p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - - indirectly inhibits - - indirectly negatively regulates - https://wiki.geneontology.org/Indirectly_negatively_regulates - - - - - - - - relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. - This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. +# Class: (role) + +AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (generically dependent continuant) -To define causal relations in an activity-flow type network, we make use of 3 primitives: +AnnotationAssertion( "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) +AnnotationAssertion(rdfs:comment "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) - * Temporal: how do the intervals of the two occurrents relate? - * Is the causal relation regulatory? - * Is the influence positive or negative? +# Class: (function) -The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. +AnnotationAssertion(rdfs:label "function"@en) +SubClassOf( ) -For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. +# Class: (material entity) -For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) -Each of these 3 primitives can be composed to yield a cross-product of different relation types. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causally related to - - - - - relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. - https://en.wikipedia.org/wiki/Causality - - - - - - - - - - - p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - - - - causally upstream of - - - - - - - - - - p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - - - immediately causally upstream of - - - - - - - - - - - p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. - We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - - influences (processual) - affects - causally upstream of or within - - - - - - - - - - inverse of causally upstream of or within - - - - causally downstream of or within - - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' regulates some p - - involved in regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - - involved in positive regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - - - involved in negative regulation of - - - - - - - - - - - c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p - OWL does not allow defining object properties via a Union - - involved in or reguates - involved in or involved in regulation of - - - - - - - - - - - A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - Considering relabeling as 'pairwise interacts with' - This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. - in pairwise interaction with - - interacts with - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - http://purl.obolibrary.org/obo/MI_0914 - - - - - - - - - - An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - - binds - molecularly binds with - molecularly interacts with - - http://purl.obolibrary.org/obo/MI_0915 - - - - - - - - - Axiomatization to GO to be added later - - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. - phosphorylates - - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - -A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - - - molecularly controls - directly regulates activity of - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - - - directly inhibits - molecularly decreases activity of - directly negatively regulates activity of - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - - - directly activates - molecularly increases activity of - directly positively regulates activity of - - - - - - - - - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property (not for use in curation) - - - - - - - - - - is kinase activity - - - - - - - - - - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. - relation between physical entity and a process or stage - - - - - - - - - x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence overlaps - - - - - - - - - - - - - - x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during - - - - - - - - - x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends with - - - - - - - - - - - - - - - - - - - - - - - - - x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during or before - - - - - - - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - - causal agent in process - - - - - - - - - - - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between processes - - - - - - - - - depends on - - - - - - - - - - - - The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between entities - - - - - - - - - - - - causally influenced by (entity-centric) - causally influenced by - - - - - - - - - - interaction relation helper property - - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - - - - - - - - - - molecular interaction relation helper property - - - - - - - - - - - - - - - - - - - - - The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - - - - causally influences (entity-centric) - causally influences - - - - - - - - - - p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - directly regulates (processual) - - - - - directly regulates - - - - - - - - - - - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' - s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - - has part structure that is capable of - - - - - - - - - - - A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - - causal relation between material entity and a process - - - - - - - - - - - - - pyrethroid -> growth - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - - capable of regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - - capable of negatively regulating - - - - - - - - - - - - - renin -> arteriolar smooth muscle contraction - Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - - capable of positively regulating - - - - - - - - - Inverse of 'causal agent in process' - - process has causal agent - - - - - - - - - - p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - - - - - directly positively regulates - https://wiki.geneontology.org/Directly_positively_regulates - - - - - - - - - - p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) - - - - - directly negatively regulates - https://wiki.geneontology.org/Directly_negatively_regulates - - - - - - - - - - - - - - - A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - - 2017-12-26T19:45:49Z - realized in response to stimulus - - - - - - - - - - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - - 2018-01-25T23:20:13Z - enables subfunction - - - - - - - - - - - - - - - 2018-01-26T23:49:30Z - - acts upstream of or within, positive effect - https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect - - - - - - - - - - - - - - - 2018-01-26T23:49:51Z - - acts upstream of or within, negative effect - https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect - - - - - - - - - - - - - - c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - - - 2018-01-26T23:53:14Z - - acts upstream of, positive effect - https://wiki.geneontology.org/Acts_upstream_of,_positive_effect - - - - - - - - - - - - - - c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - - - 2018-01-26T23:53:22Z - - acts upstream of, negative effect - https://wiki.geneontology.org/Acts_upstream_of,_negative_effect - - - - - - - - - - - 2018-03-13T23:55:05Z - causally upstream of or within, negative effect - https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect - - - - - - - - - - - 2018-03-13T23:55:19Z - causally upstream of or within, positive effect - - - - - - - - - - - - A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. - An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) - Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. - r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - - - - - triggered by process - realized in response to - https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit - - - - - triggered by process - - - - - - - - - - - - The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - - regulates activity of - - - - - - - - - p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - - 2022-09-26T06:07:17Z - indirectly causally upstream of - - - - - - - - - - p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - - 2022-09-26T06:08:01Z - indirectly regulates - - - - - - - - - - - - A diagnostic testing device utilizes a specimen. - X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. - See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z - utilizes - device utilizes material - - - - - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. - - regulates characteristic - - - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. - - positively regulates characteristic - - - - - - - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. - - negatively regulates characteristic - - - - - - - - - - - - - - - - - - - - - - - - - - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - continuant - - - - - - - - - - - - - - - - - - - - An entity that has temporal parts and that happens, unfolds or develops through time. - occurrent - - - - - - - - - - - - - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - independent continuant - - - - - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - process - - - - - - - - - - disposition - - - - - - - - - - - - - - - - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - realizable entity - - - - - - - - - - - - - - - quality - - - - - - - - - - - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - specifically dependent continuant - - - - - - - - - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - role - - - - - - - - - - - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - generically dependent continuant - - - - - - - - - function - - - - - - - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity - - - - - - - - - - - - - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - CALOHA:TS-2035 - FBbt:00007002 - FMA:68646 - GO:0005623 - KUPO:0000002 - MESH:D002477 - VHOG:0001533 - WBbt:0004017 - XAO:0003012 - The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). - cell - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - CARO:mah - - - - - - - - - A system which has the disposition to environ one or more material entities. - 2013-09-23T16:04:08Z - EcoLexicon:environment - environment - In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. - environmental system - - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - - - - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - molecular function - GO:0003674 - Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. - molecular_function - - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - GOC:pdt - - - - - - - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - jl - 2012-09-19T15:05:24Z - Wikipedia:Biological_process - biological process - physiological process - single organism process - single-organism process - GO:0008150 - Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. - biological_process - - - - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - GOC:pdt - - - - - - - - - - - - true - - - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - Reactome:R-HSA-6788855 - Reactome:R-HSA-6788867 - phosphokinase activity - GO:0016301 - Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. - kinase activity - - - - - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - ISBN:0198506732 - - - - - Reactome:R-HSA-6788855 - FN3KRP phosphorylates PsiAm, RibAm - - - - - Reactome:R-HSA-6788867 - FN3K phosphorylates ketosamines - - - - - - - - - information content entity - information content entity - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000001 - quality - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATOC:GVG - - - - - - - - - A material entity consisting of multiple components that are causally integrated. - May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 - - http://www.jbiomedsem.com/content/4/1/43 - system - - - - - - - - - Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. - - - AAO:0010825 - AEO:0000003 - BILA:0000003 - CARO:0000003 - EHDAA2:0003003 - EMAPA:0 - FBbt:00007001 - FMA:305751 - FMA:67135 - GAID:781 - HAO:0000003 - MA:0003000 - MESH:D000825 - SCTID:362889002 - TAO:0000037 - TGMA:0001823 - VHOG:0001759 - XAO:0003000 - ZFA:0000037 - http://dbpedia.org/ontology/AnatomicalStructure - biological structure - connected biological structure - UBERON:0000061 - - - anatomical structure - - - - - Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. - CARO:0000003 - - - - - connected biological structure - CARO:0000003 - - - - - - - - - - Anatomical entity that has mass. - - - AAO:0010264 - AEO:0000006 - BILA:0000006 - CARO:0000006 - EHDAA2:0003006 - FBbt:00007016 - FMA:67165 - HAO:0000006 - TAO:0001836 - TGMA:0001826 - VHOG:0001721 - UBERON:0000465 - - - material anatomical entity - - - - - Anatomical entity that has mass. - http://orcid.org/0000-0001-9114-8737 - - - - - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - - AAO:0010841 - AEO:0000000 - BILA:0000000 - BIRNLEX:6 - CARO:0000000 - EHDAA2:0002229 - FBbt:10000000 - FMA:62955 - HAO:0000000 - MA:0000001 - NCIT:C12219 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - WBbt:0000100 - XAO:0000000 - ZFA:0100000 - UBERON:0001062 - - - anatomical entity - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - FMA:62955 - http://orcid.org/0000-0001-9114-8737 - - - - - UMLS:C1515976 - ncithesaurus:Anatomic_Structure_System_or_Substance - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - ready for release - - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# Class: () +SubClassOf( ) + +# Class: (cell) + +AnnotationAssertion(Annotation( "CARO:mah") "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.") +AnnotationAssertion( "CALOHA:TS-2035") +AnnotationAssertion( "FBbt:00007002") +AnnotationAssertion( "FMA:68646") +AnnotationAssertion( "GO:0005623") +AnnotationAssertion( "KUPO:0000002") +AnnotationAssertion( "MESH:D002477") +AnnotationAssertion( "VHOG:0001533") +AnnotationAssertion( "WBbt:0004017") +AnnotationAssertion( "XAO:0003012") +AnnotationAssertion(rdfs:comment "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).") +AnnotationAssertion(rdfs:label "cell") +SubClassOf( ) + +# Class: (environmental system) + +AnnotationAssertion(Annotation( "DOI:10.1186/2041-1480-4-43") "A system which has the disposition to environ one or more material entities.") +AnnotationAssertion( "2013-09-23T16:04:08Z") +AnnotationAssertion( "EcoLexicon:environment") +AnnotationAssertion( "environment") +AnnotationAssertion(rdfs:comment "In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class \"system\". The relation \"environed_by\" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.") +AnnotationAssertion(rdfs:label "environmental system") +SubClassOf( ) + +# Class: (molecular_function) + +AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") +AnnotationAssertion( "molecular function") +AnnotationAssertion( "GO:0003674") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") +AnnotationAssertion(rdfs:label "molecular_function") + +# Class: (biological_process) + +AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-09-19T15:05:24Z") +AnnotationAssertion( "Wikipedia:Biological_process") +AnnotationAssertion( "biological process") +AnnotationAssertion( "physiological process") +AnnotationAssertion( "single organism process") +AnnotationAssertion( "single-organism process") +AnnotationAssertion( "GO:0008150") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:label "biological_process") + +# Class: (kinase activity) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") +AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") +AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") +AnnotationAssertion( "phosphokinase activity") +AnnotationAssertion( "GO:0016301") +AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") +AnnotationAssertion(rdfs:label "kinase activity") +SubClassOf( ) +SubClassOf( ObjectHasSelf()) + +# Class: (information content entity) + +AnnotationAssertion( "information content entity"@en) +AnnotationAssertion(rdfs:label "information content entity"@en) +SubClassOf( ) + +# Class: (curation status specification) + +AnnotationAssertion( "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "OBI_0000266"@en) +AnnotationAssertion(rdfs:label "curation status specification"@en) +EquivalentClasses( ObjectOneOf( )) + +# Class: (quality) + +AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") +AnnotationAssertion( "PATO:0000001") +AnnotationAssertion(rdfs:label "quality") +SubClassOf( ) + +# Class: (system) + +AnnotationAssertion( "A material entity consisting of multiple components that are causally integrated.") +AnnotationAssertion( "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43") +AnnotationAssertion( ) +AnnotationAssertion( "http://www.jbiomedsem.com/content/4/1/43") +AnnotationAssertion(rdfs:label "system") +SubClassOf( ) + +# Class: (anatomical structure) + +AnnotationAssertion(Annotation( "CARO:0000003") "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "AAO:0010825") +AnnotationAssertion( "AEO:0000003") +AnnotationAssertion( "BILA:0000003") +AnnotationAssertion( "CARO:0000003") +AnnotationAssertion( "EHDAA2:0003003") +AnnotationAssertion( "EMAPA:0") +AnnotationAssertion( "FBbt:00007001") +AnnotationAssertion( "FMA:305751") +AnnotationAssertion( "FMA:67135") +AnnotationAssertion( "GAID:781") +AnnotationAssertion( "HAO:0000003") +AnnotationAssertion( "MA:0003000") +AnnotationAssertion( "MESH:D000825") +AnnotationAssertion( "SCTID:362889002") +AnnotationAssertion( "TAO:0000037") +AnnotationAssertion( "TGMA:0001823") +AnnotationAssertion( "VHOG:0001759") +AnnotationAssertion( "XAO:0003000") +AnnotationAssertion( "ZFA:0000037") +AnnotationAssertion( "http://dbpedia.org/ontology/AnatomicalStructure") +AnnotationAssertion( "biological structure") +AnnotationAssertion(Annotation( "CARO:0000003") "connected biological structure") +AnnotationAssertion( "UBERON:0000061") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "anatomical structure") +SubClassOf( ) + +# Class: (material anatomical entity) + +AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-9114-8737") "Anatomical entity that has mass.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "AAO:0010264") +AnnotationAssertion( "AEO:0000006") +AnnotationAssertion( "BILA:0000006") +AnnotationAssertion( "CARO:0000006") +AnnotationAssertion( "EHDAA2:0003006") +AnnotationAssertion( "FBbt:00007016") +AnnotationAssertion( "FMA:67165") +AnnotationAssertion( "HAO:0000006") +AnnotationAssertion( "TAO:0001836") +AnnotationAssertion( "TGMA:0001826") +AnnotationAssertion( "VHOG:0001721") +AnnotationAssertion( "UBERON:0000465") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "material anatomical entity") +SubClassOf( ) +SubClassOf( ) + +# Class: (anatomical entity) + +AnnotationAssertion(Annotation( "FMA:62955") Annotation( "http://orcid.org/0000-0001-9114-8737") "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "AAO:0010841") +AnnotationAssertion( "AEO:0000000") +AnnotationAssertion( "BILA:0000000") +AnnotationAssertion( "BIRNLEX:6") +AnnotationAssertion( "CARO:0000000") +AnnotationAssertion( "EHDAA2:0002229") +AnnotationAssertion( "FBbt:10000000") +AnnotationAssertion( "FMA:62955") +AnnotationAssertion( "HAO:0000000") +AnnotationAssertion( "MA:0000001") +AnnotationAssertion( "NCIT:C12219") +AnnotationAssertion( "TAO:0100000") +AnnotationAssertion( "TGMA:0001822") +AnnotationAssertion(Annotation( "ncithesaurus:Anatomic_Structure_System_or_Substance") "UMLS:C1515976") +AnnotationAssertion( "WBbt:0000100") +AnnotationAssertion( "XAO:0000000") +AnnotationAssertion( "ZFA:0100000") +AnnotationAssertion( "UBERON:0001062") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "anatomical entity") +SubClassOf( ) + + +############################ +# Named Individuals +############################ + +# Individual: (example to be eventually removed) + +AnnotationAssertion( "example to be eventually removed"@en) +AnnotationAssertion(rdfs:label "example to be eventually removed"@en) + +# Individual: (metadata complete) + +AnnotationAssertion( "metadata complete"@en) +AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) +AnnotationAssertion(rdfs:label "metadata complete"@en) + +# Individual: (organizational term) + +AnnotationAssertion( "organizational term"@en) +AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion(rdfs:label "organizational term"@en) + +# Individual: (ready for release) + +AnnotationAssertion( "ready for release"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) +AnnotationAssertion(rdfs:label "ready for release"@en) + +# Individual: (metadata incomplete) + +AnnotationAssertion( "metadata incomplete"@en) +AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) +AnnotationAssertion(rdfs:label "metadata incomplete"@en) + +# Individual: (uncurated) + +AnnotationAssertion( "uncurated"@en) +AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) +AnnotationAssertion(rdfs:label "uncurated"@en) + +# Individual: (pending final vetting) + +AnnotationAssertion( "pending final vetting"@en) +AnnotationAssertion( ) +AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) +AnnotationAssertion(rdfs:label "pending final vetting"@en) +ClassAssertion( ) + +# Individual: (to be replaced with external ontology term) + +AnnotationAssertion( "to be replaced with external ontology term"@en) +AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) + +# Individual: (requires discussion) + +AnnotationAssertion( "requires discussion"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "requires discussion"@en) +ClassAssertion( ) + + +SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) +DifferentIndividuals( ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +) \ No newline at end of file diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl index 1fdba70..04304d1 100644 --- a/src/ontology/imports/uberon_import.owl +++ b/src/ontology/imports/uberon_import.owl @@ -32,8 +32,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-02-06 + + 2024-10-23 diff --git a/src/ontology/imports/uberon_terms_combined.txt b/src/ontology/imports/uberon_terms_combined.txt index 1caa3e4..96d5be2 100644 --- a/src/ontology/imports/uberon_terms_combined.txt +++ b/src/ontology/imports/uberon_terms_combined.txt @@ -1,4 +1,3 @@ -COB:0000800 http://creativecommons.org/licenses/by/3.0/ http://purl.obolibrary.org/obo/BFO_0000003 http://purl.obolibrary.org/obo/BFO_0000004 @@ -6,6 +5,7 @@ http://purl.obolibrary.org/obo/BFO_0000015 http://purl.obolibrary.org/obo/BFO_0000016 http://purl.obolibrary.org/obo/BFO_0000017 http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/BFO_0000027 http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000182 @@ -23,7 +23,7 @@ http://purl.obolibrary.org/obo/CL_0017502 http://purl.obolibrary.org/obo/CL_0017503 http://purl.obolibrary.org/obo/CL_0017504 http://purl.obolibrary.org/obo/CL_0017505 -http://purl.obolibrary.org/obo/COB_0000082 +http://purl.obolibrary.org/obo/COB_0000800 http://purl.obolibrary.org/obo/DOID_4 http://purl.obolibrary.org/obo/ENVO_01000254 http://purl.obolibrary.org/obo/ENVO_01000637 @@ -44,13 +44,13 @@ http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.obolibrary.org/obo/IAO_0000116 http://purl.obolibrary.org/obo/IAO_0000117 http://purl.obolibrary.org/obo/IAO_0000118 http://purl.obolibrary.org/obo/IAO_0000119 http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/OBI_0000272 -http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/OBI_0000984 @@ -58,11 +58,14 @@ http://purl.obolibrary.org/obo/OBI_0001138 http://purl.obolibrary.org/obo/OBI_0001909 http://purl.obolibrary.org/obo/OBI_0002983 http://purl.obolibrary.org/obo/OBI_0302889 +http://purl.obolibrary.org/obo/PATO_0000025 http://purl.obolibrary.org/obo/PATO_0001018 http://purl.obolibrary.org/obo/PATO_0001236 http://purl.obolibrary.org/obo/PATO_0001241 +http://purl.obolibrary.org/obo/PATO_0001739 http://purl.obolibrary.org/obo/PATO_0002062 http://purl.obolibrary.org/obo/PO_0009012 +http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RBO_00000001 http://purl.obolibrary.org/obo/RBO_00000002 http://purl.obolibrary.org/obo/RBO_00000003 @@ -418,6 +421,18 @@ http://purl.obolibrary.org/obo/RBO_00015026 http://purl.obolibrary.org/obo/RBO_00015027 http://purl.obolibrary.org/obo/RBO_00015028 http://purl.obolibrary.org/obo/RBO_00015029 +http://purl.obolibrary.org/obo/RBO_00015030 +http://purl.obolibrary.org/obo/RBO_00015031 +http://purl.obolibrary.org/obo/RBO_00015032 +http://purl.obolibrary.org/obo/RBO_00015033 +http://purl.obolibrary.org/obo/RBO_00015034 +http://purl.obolibrary.org/obo/RBO_00015035 +http://purl.obolibrary.org/obo/RBO_00015036 +http://purl.obolibrary.org/obo/RBO_00015037 +http://purl.obolibrary.org/obo/RBO_00015038 +http://purl.obolibrary.org/obo/RBO_00015039 +http://purl.obolibrary.org/obo/RBO_00015040 +http://purl.obolibrary.org/obo/RBO_00015041 http://purl.obolibrary.org/obo/RBO_010000 http://purl.obolibrary.org/obo/RBO_010001 http://purl.obolibrary.org/obo/RBO_010002 @@ -439,7 +454,6 @@ http://purl.obolibrary.org/obo/RBO_010019 http://purl.obolibrary.org/obo/RBO_010020 http://purl.obolibrary.org/obo/RBO_2000 http://purl.obolibrary.org/obo/RBO_2001 -http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RO_0000086 http://purl.obolibrary.org/obo/RO_0002180 http://purl.obolibrary.org/obo/RO_0002233 @@ -450,12 +464,12 @@ http://purl.obolibrary.org/obo/RO_0002608 http://purl.obolibrary.org/obo/SO_0000704 http://purl.obolibrary.org/obo/UBERON_0000000 http://purl.obolibrary.org/obo/UBERON_0002371 -http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.obolibrary.org/obo/UO_0000127 http://purl.obolibrary.org/obo/UO_0000129 http://purl.obolibrary.org/obo/UO_0000160 http://purl.obolibrary.org/obo/UO_0000219 http://purl.obolibrary.org/obo/UO_1000135 +http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/description diff --git a/src/ontology/imports/uo_import.owl b/src/ontology/imports/uo_import.owl index 2ce1d84..48dc575 100644 --- a/src/ontology/imports/uo_import.owl +++ b/src/ontology/imports/uo_import.owl @@ -8,8 +8,8 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2024-02-06 + + 2024-10-23 diff --git a/src/ontology/imports/uo_terms_combined.txt b/src/ontology/imports/uo_terms_combined.txt index 405ff42..bf4cb17 100644 --- a/src/ontology/imports/uo_terms_combined.txt +++ b/src/ontology/imports/uo_terms_combined.txt @@ -1,4 +1,4 @@ -COB:0000800 +UO:0000127 # radiation unit http://creativecommons.org/licenses/by/3.0/ http://purl.obolibrary.org/obo/BFO_0000003 http://purl.obolibrary.org/obo/BFO_0000004 @@ -6,6 +6,7 @@ http://purl.obolibrary.org/obo/BFO_0000015 http://purl.obolibrary.org/obo/BFO_0000016 http://purl.obolibrary.org/obo/BFO_0000017 http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/BFO_0000027 http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000182 @@ -22,7 +23,7 @@ http://purl.obolibrary.org/obo/CL_0000000 http://purl.obolibrary.org/obo/CL_0017502 http://purl.obolibrary.org/obo/CL_0017503 http://purl.obolibrary.org/obo/CL_0017504 -http://purl.obolibrary.org/obo/COB_0000082 +http://purl.obolibrary.org/obo/COB_0000800 http://purl.obolibrary.org/obo/DOID_4 http://purl.obolibrary.org/obo/ENVO_01000254 http://purl.obolibrary.org/obo/ENVO_01000637 @@ -43,13 +44,13 @@ http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.obolibrary.org/obo/IAO_0000116 http://purl.obolibrary.org/obo/IAO_0000117 http://purl.obolibrary.org/obo/IAO_0000118 http://purl.obolibrary.org/obo/IAO_0000119 http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/OBI_0000272 -http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/OBI_0000984 @@ -57,11 +58,14 @@ http://purl.obolibrary.org/obo/OBI_0001138 http://purl.obolibrary.org/obo/OBI_0001909 http://purl.obolibrary.org/obo/OBI_0002983 http://purl.obolibrary.org/obo/OBI_0302889 +http://purl.obolibrary.org/obo/PATO_0000025 http://purl.obolibrary.org/obo/PATO_0001018 http://purl.obolibrary.org/obo/PATO_0001236 http://purl.obolibrary.org/obo/PATO_0001241 +http://purl.obolibrary.org/obo/PATO_0001739 http://purl.obolibrary.org/obo/PATO_0002062 http://purl.obolibrary.org/obo/PO_0009012 +http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RBO_00000001 http://purl.obolibrary.org/obo/RBO_00000002 http://purl.obolibrary.org/obo/RBO_00000003 @@ -417,6 +421,18 @@ http://purl.obolibrary.org/obo/RBO_00015026 http://purl.obolibrary.org/obo/RBO_00015027 http://purl.obolibrary.org/obo/RBO_00015028 http://purl.obolibrary.org/obo/RBO_00015029 +http://purl.obolibrary.org/obo/RBO_00015030 +http://purl.obolibrary.org/obo/RBO_00015031 +http://purl.obolibrary.org/obo/RBO_00015032 +http://purl.obolibrary.org/obo/RBO_00015033 +http://purl.obolibrary.org/obo/RBO_00015034 +http://purl.obolibrary.org/obo/RBO_00015035 +http://purl.obolibrary.org/obo/RBO_00015036 +http://purl.obolibrary.org/obo/RBO_00015037 +http://purl.obolibrary.org/obo/RBO_00015038 +http://purl.obolibrary.org/obo/RBO_00015039 +http://purl.obolibrary.org/obo/RBO_00015040 +http://purl.obolibrary.org/obo/RBO_00015041 http://purl.obolibrary.org/obo/RBO_010000 http://purl.obolibrary.org/obo/RBO_010001 http://purl.obolibrary.org/obo/RBO_010002 @@ -438,7 +454,6 @@ http://purl.obolibrary.org/obo/RBO_010019 http://purl.obolibrary.org/obo/RBO_010020 http://purl.obolibrary.org/obo/RBO_2000 http://purl.obolibrary.org/obo/RBO_2001 -http://purl.obolibrary.org/obo/RBO.owl http://purl.obolibrary.org/obo/RO_0000086 http://purl.obolibrary.org/obo/RO_0002180 http://purl.obolibrary.org/obo/RO_0002233 @@ -448,12 +463,12 @@ http://purl.obolibrary.org/obo/RO_0002493 http://purl.obolibrary.org/obo/RO_0002608 http://purl.obolibrary.org/obo/SO_0000704 http://purl.obolibrary.org/obo/UBERON_0000000 -http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.obolibrary.org/obo/UO_0000127 http://purl.obolibrary.org/obo/UO_0000129 http://purl.obolibrary.org/obo/UO_0000160 http://purl.obolibrary.org/obo/UO_0000219 http://purl.obolibrary.org/obo/UO_1000135 +http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/description @@ -466,4 +481,3 @@ http://www.geneontology.org/formats/oboInOwl#hasDbXref http://www.geneontology.org/formats/oboInOwl#hasExactSynonym http://www.w3.org/2001/XMLSchema#nonNegativeInteger term -UO:0000127 # radiation unit diff --git a/src/ontology/rbo-edit.owl b/src/ontology/rbo-edit.owl index 878c393..7b79592 100644 --- a/src/ontology/rbo-edit.owl +++ b/src/ontology/rbo-edit.owl @@ -24,7 +24,7 @@ Import() Import() Import() Import() -Import() +#Import() Import() Import() Import() @@ -126,8 +126,8 @@ SubClassOf(obo:PO_0009012 obo:BFO_0000015) # Class: obo:RBO_00002118 (Radioactive decay) -SubClassOf(obo:RBO_00002118 ObjectSomeValuesFrom(obo:OBI_0000299 obo:RBO_00015000)) -SubClassOf(obo:RBO_00002118 ObjectMinCardinality(1 obo:OBI_0000293 obo:CHEBI_33252)) +SubClassOf(obo:RBO_00002118 ObjectSomeValuesFrom(obo:RO_0002234 obo:RBO_00015000)) +#SubClassOf(obo:RBO_00002118 ObjectMinCardinality(1 obo:RO_0002233 obo:CHEBI_33252)) # Class: obo:RBO_00002122 (Environmental radiation monitoring) diff --git a/src/ontology/rbo-odk.yaml b/src/ontology/rbo-odk.yaml index 65a9ae9..7bde640 100644 --- a/src/ontology/rbo-odk.yaml +++ b/src/ontology/rbo-odk.yaml @@ -40,8 +40,9 @@ import_group: - id: efo mirror_from: https://www.ebi.ac.uk/efo/efo.owl module_type: custom - - id: ncbitaxon - module_type: custom +# - id: ncbitaxon +# module_type: custom +# is_large: TRUE obo_format_options: '' primary_release: full reasoner: ELK diff --git a/src/ontology/rbo.Makefile b/src/ontology/rbo.Makefile index 5913c20..92a4294 100644 --- a/src/ontology/rbo.Makefile +++ b/src/ontology/rbo.Makefile @@ -28,6 +28,7 @@ imports/pato_import.owl: mirror/pato.owl imports/pato_terms_combined.txt if [ $(IMP) = true ]; then $(ROBOT) extract -i $< -T imports/pato_terms_combined.txt --force true --method BOT \ remove -t "http://purl.obolibrary.org/obo/BFO_0000023" -t "http://purl.obolibrary.org/obo/CHEBI_50906" --axioms subclass --trim false --signature true \ remove -t "http://purl.obolibrary.org/obo/BFO_0000023" -t "http://purl.obolibrary.org/obo/CHEBI_50906" --axioms equivalent --trim false --signature true \ + remove -t "http://purl.obolibrary.org/obo/PATO_0001291" --trim false --signature true \ query --update ../sparql/inject-subset-declaration.ru \ annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi diff --git a/src/ontology/reports/rbo-edit.owl-obo-report.tsv b/src/ontology/reports/rbo-edit.owl-obo-report.tsv index 98e4b91..d551d85 100644 --- a/src/ontology/reports/rbo-edit.owl-obo-report.tsv +++ b/src/ontology/reports/rbo-edit.owl-obo-report.tsv @@ -1,4 +1,23 @@ Level Rule Name Subject Property Value +ERROR deprecated_boolean_datatype environmental study owl:deprecated A owl:deprecated +ERROR deprecated_boolean_datatype therapeutics study owl:deprecated A owl:deprecated +ERROR deprecated_boolean_datatype nuclear accident study owl:deprecated A owl:deprecated +ERROR deprecated_boolean_datatype biological process owl:deprecated owl:deprecated +ERROR deprecated_boolean_datatype cellular process owl:deprecated owl:deprecated +ERROR deprecated_boolean_datatype unplanned naturally occurring radiation exposure owl:deprecated TRUE +ERROR deprecated_boolean_datatype irradiation owl:deprecated TRUE +ERROR deprecated_boolean_datatype miligray per second owl:deprecated TRUE +ERROR deprecated_boolean_datatype radiation quality owl:deprecated TRUE +ERROR duplicate_label unplanned naturally occurring radiation exposure rdfs:label unplanned naturally occurring radiation exposure +ERROR duplicate_label unplanned naturally occurring radiation exposure rdfs:label unplanned naturally occurring radiation exposure +ERROR duplicate_label therapeutics study rdfs:label therapeutics study +ERROR duplicate_label therapeutics study rdfs:label therapeutics study +ERROR duplicate_label space flight rdfs:label space flight +ERROR duplicate_label space flight rdfs:label space flight +ERROR duplicate_label nuclear accident study rdfs:label nuclear accident study +ERROR duplicate_label nuclear accident study rdfs:label nuclear accident study +ERROR duplicate_label environmental study rdfs:label environmental study +ERROR duplicate_label environmental study rdfs:label environmental study ERROR missing_label BFO:0000023 rdfs:label ERROR missing_label CHEBI:33252 rdfs:label ERROR missing_label CHEBI:36080 rdfs:label @@ -17,16 +36,6 @@ ERROR missing_label SO:0000704 rdfs:label ERROR missing_label UBERON:0000000 rdfs:label ERROR missing_label UO:0000127 rdfs:label ERROR missing_label UO:0000160 rdfs:label -ERROR duplicate_label unplanned naturally occurring radiation exposure rdfs:label unplanned naturally occurring radiation exposure -ERROR duplicate_label unplanned naturally occurring radiation exposure rdfs:label unplanned naturally occurring radiation exposure -ERROR duplicate_label therapeutics study rdfs:label therapeutics study -ERROR duplicate_label therapeutics study rdfs:label therapeutics study -ERROR duplicate_label space flight rdfs:label space flight -ERROR duplicate_label space flight rdfs:label space flight -ERROR duplicate_label nuclear accident study rdfs:label nuclear accident study -ERROR duplicate_label nuclear accident study rdfs:label nuclear accident study -ERROR duplicate_label environmental study rdfs:label environmental study -ERROR duplicate_label environmental study rdfs:label environmental study WARN annotation_whitespace radiation response modifier IAO:0000115 Radiation response modifiers are agents that alter tumor or normal tissue response to radiation, such as radiation sensitizers and radiation protectors. WARN annotation_whitespace Iron-56 nucleus IAO:0000115 An atomic nucleus with 26 protons and 30 neutrons WARN annotation_whitespace Iron-56 nucleus IAO:0000118 Fe-56 ion;Fe-56 nucleus;Fe-56 @@ -59,7 +68,19 @@ WARN annotation_whitespace Titanium-48 nucleus IAO:0000118 Ti-48 ion;Ti-48 nuc WARN annotation_whitespace Krypton-84 nucleus IAO:0000115 An atomic nucleus with 36 protons and 48 neutrons WARN annotation_whitespace Krypton-84 nucleus IAO:0000118 Kr-84 ion;Kr-84 nucleus;Kr-84 WARN annotation_whitespace external radiation exposure IAO:0000112 Mice exposed to external radiation from a Sr source. -WARN missing_definition has atomic number IAO:0000115 +WARN duplicate_label_synonym charged particle IAO:0000118 charged particle +WARN duplicate_scoped_synonym ionizing radiation IAO:0000118 ionising radiation +WARN duplicate_scoped_synonym ionizing radiation oboInOwl:hasExactSynonym ionising radiation +WARN duplicate_scoped_synonym as low as reasonably achievable IAO:0000118 ALARA +WARN duplicate_scoped_synonym as low as reasonably achievable oboInOwl:hasExactSynonym ALARA +WARN duplicate_scoped_synonym delta ray IAO:0000118 delta electron +WARN duplicate_scoped_synonym delta ray oboInOwl:hasExactSynonym delta electron +WARN duplicate_scoped_synonym linear energy transfer IAO:0000118 LET +WARN duplicate_scoped_synonym linear energy transfer oboInOwl:hasExactSynonym LET +WARN duplicate_scoped_synonym relative biological effectiveness IAO:0000118 RBE +WARN duplicate_scoped_synonym relative biological effectiveness oboInOwl:hasExactSynonym RBE +WARN equivalent_class_axiom_no_genus particle track RO:0000086 particle track structure +WARN equivalent_class_axiom_no_genus track formation OBI:0000299 particle track WARN missing_definition BFO:0000023 IAO:0000115 WARN missing_definition CHEBI:33252 IAO:0000115 WARN missing_definition CHEBI:36080 IAO:0000115 @@ -68,6 +89,7 @@ WARN missing_definition CL:0000000 IAO:0000115 WARN missing_definition CL:0017502 IAO:0000115 WARN missing_definition CL:0017503 IAO:0000115 WARN missing_definition CL:0017504 IAO:0000115 +WARN missing_definition has atomic number IAO:0000115 WARN missing_definition DOID:4 IAO:0000115 WARN missing_definition GO:0005575 IAO:0000115 WARN missing_definition GO:0009314 IAO:0000115 @@ -89,22 +111,13 @@ WARN missing_definition SO:0000704 IAO:0000115 WARN missing_definition UBERON:0000000 IAO:0000115 WARN missing_definition UO:0000127 IAO:0000115 WARN missing_definition UO:0000160 IAO:0000115 -WARN duplicate_scoped_synonym ionizing radiation IAO:0000118 ionising radiation -WARN duplicate_scoped_synonym ionizing radiation oboInOwl:hasExactSynonym ionising radiation -WARN duplicate_scoped_synonym as low as reasonably achievable IAO:0000118 ALARA -WARN duplicate_scoped_synonym as low as reasonably achievable oboInOwl:hasExactSynonym ALARA -WARN duplicate_scoped_synonym delta ray IAO:0000118 delta electron -WARN duplicate_scoped_synonym delta ray oboInOwl:hasExactSynonym delta electron -WARN duplicate_scoped_synonym linear energy transfer IAO:0000118 LET -WARN duplicate_scoped_synonym linear energy transfer oboInOwl:hasExactSynonym LET -WARN duplicate_scoped_synonym relative biological effectiveness IAO:0000118 RBE -WARN duplicate_scoped_synonym relative biological effectiveness oboInOwl:hasExactSynonym RBE INFO lowercase_definition spacecraft module IAO:0000115 a self-contained unit of a spacecraft INFO lowercase_definition gamma radiation IAO:0000115 electromagnetic radiation with photon energies greater than approximately 100 keV -INFO lowercase_definition Gammacell 40 IAO:0000115 -INFO lowercase_definition RARAF 5.5 MV microbeam IAO:0000115 -INFO lowercase_definition Swift HALE IAO:0000115 -INFO lowercase_definition ER-2 IAO:0000115 -INFO lowercase_definition WB-57 IAO:0000115 -INFO lowercase_definition Faxitron CP160 IAO:0000115 -INFO lowercase_definition X-Rad320 IAO:0000115 +INFO lowercase_definition Gammacell 40 IAO:0000115 http://www.theratronics.ca/PDFs/GC40_BTMB_8008GC40E_2_v112013_webSECURE.pdf +INFO lowercase_definition RARAF 5.5 MV microbeam IAO:0000115 https://www.crr.columbia.edu/services/ion-beam-and-neutron-core-facility +INFO lowercase_definition Swift HALE IAO:0000115 https://www.nasa.gov/feature/ames/nasa-small-business-partnership-prepares-drone-for-30-day-science-flights +INFO lowercase_definition ER-2 IAO:0000115 https://www.nasa.gov/centers/armstrong/aircraft/ER-2/index.html +INFO lowercase_definition WB-57 IAO:0000115 https://airbornescience.nasa.gov/aircraft/WB-57_-_JSC +INFO lowercase_definition Faxitron CP160 IAO:0000115 doi: 10.2349/biij.2.1.e1 +INFO lowercase_definition X-Rad320 IAO:0000115 https://precisionxray.com/x-rad/xrad-320/ +INFO lowercase_definition epithermal neutron IAO:0000115 a neutron with energy greater than a thermal neutron, but less than a fast neutron. The approximate energy range is 0.025-0.4 eV. diff --git a/src/ontology/reports/rbo.owl-obo-report.tsv b/src/ontology/reports/rbo.owl-obo-report.tsv index 3a047b5..4639538 100644 --- a/src/ontology/reports/rbo.owl-obo-report.tsv +++ b/src/ontology/reports/rbo.owl-obo-report.tsv @@ -1,55 +1,22 @@ Level Rule Name Subject Property Value -ERROR multiple_equivalent_classes response to light stimulus owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid13334 -ERROR multiple_equivalent_classes response to light stimulus owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid13338 -ERROR multiple_equivalent_classes response to organic substance owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid13599 -ERROR multiple_equivalent_classes response to organic substance owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid13603 -ERROR multiple_equivalent_classes response to inorganic substance owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid13616 -ERROR multiple_equivalent_classes response to inorganic substance owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid13620 -ERROR multiple_equivalent_classes response to organonitrogen compound owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid13655 -ERROR multiple_equivalent_classes response to organonitrogen compound owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid13659 -ERROR multiple_equivalent_classes response to organic cyclic compound owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid14485 -ERROR multiple_equivalent_classes response to organic cyclic compound owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid14489 -ERROR multiple_equivalent_classes RNA biosynthetic process owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid17046 -ERROR multiple_equivalent_classes RNA biosynthetic process owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid17050 -ERROR multiple_equivalent_classes response to chemical owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid18364 -ERROR multiple_equivalent_classes response to chemical owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid18368 -ERROR multiple_equivalent_classes response to amino acid owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid18719 -ERROR multiple_equivalent_classes response to amino acid owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid18723 -ERROR multiple_equivalent_classes membrane biogenesis owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid19090 -ERROR multiple_equivalent_classes membrane biogenesis owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid19094 -ERROR multiple_equivalent_classes response to carbamate owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid20101 -ERROR multiple_equivalent_classes response to carbamate owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid20105 -ERROR multiple_equivalent_classes response to ammonium ion owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid22793 -ERROR multiple_equivalent_classes response to ammonium ion owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid22797 -ERROR multiple_equivalent_classes nuclear membrane biogenesis owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid26264 -ERROR multiple_equivalent_classes nuclear membrane biogenesis owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid26268 -ERROR multiple_equivalent_classes catalytic activity, acting on a protein owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid26558 -ERROR multiple_equivalent_classes catalytic activity, acting on a protein owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid26562 -ERROR multiple_equivalent_classes catalytic activity, acting on RNA owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid26575 -ERROR multiple_equivalent_classes catalytic activity, acting on RNA owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid26579 -ERROR multiple_equivalent_classes catalytic activity, acting on a nucleic acid owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid26757 -ERROR multiple_equivalent_classes catalytic activity, acting on a nucleic acid owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid26761 -ERROR multiple_equivalent_classes response to peptide owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid27868 -ERROR multiple_equivalent_classes response to peptide owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid27872 -ERROR multiple_equivalent_classes response to nitrogen compound owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid27917 -ERROR multiple_equivalent_classes response to nitrogen compound owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid27921 -ERROR multiple_equivalent_classes response to oxygen-containing compound owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid27928 -ERROR multiple_equivalent_classes response to oxygen-containing compound owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid27932 -ERROR multiple_equivalent_classes obsolescence reason specification owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid34926 -ERROR multiple_equivalent_classes obsolescence reason specification owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid34932 -ERROR multiple_equivalent_classes epithelium owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid37648 -ERROR multiple_equivalent_classes epithelium owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid37652 -ERROR multiple_equivalent_classes trunk or cervical vertebra owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid46380 -ERROR multiple_equivalent_classes trunk or cervical vertebra owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid46384 -ERROR multiple_equivalent_classes cervical vertebra endochondral element owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid53679 -ERROR multiple_equivalent_classes cervical vertebra endochondral element owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid53683 -ERROR multiple_equivalent_classes thoracic vertebra endochondral element owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid53691 -ERROR multiple_equivalent_classes thoracic vertebra endochondral element owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid53695 -ERROR multiple_equivalent_classes caudal vertebra endochondral element owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid54090 -ERROR multiple_equivalent_classes caudal vertebra endochondral element owl:equivalentClass b655b656-432c-411a-9886-7f3d22091f2bgenid54094 -ERROR missing_label http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled label -ERROR missing_label xsd:boolean label -ERROR missing_label xsd:string label +ERROR deprecated_boolean_datatype environmental study owl:deprecated A owl:deprecated +ERROR deprecated_boolean_datatype therapeutics study owl:deprecated A owl:deprecated +ERROR deprecated_boolean_datatype nuclear accident study owl:deprecated A owl:deprecated +ERROR deprecated_boolean_datatype biological process owl:deprecated owl:deprecated +ERROR deprecated_boolean_datatype cellular process owl:deprecated owl:deprecated +ERROR deprecated_boolean_datatype unplanned naturally occurring radiation exposure owl:deprecated TRUE +ERROR deprecated_boolean_datatype irradiation owl:deprecated TRUE +ERROR deprecated_boolean_datatype miligray per second owl:deprecated TRUE +ERROR deprecated_boolean_datatype radiation quality owl:deprecated TRUE +ERROR deprecated_class_reference device rdfs:subClassOf portion of material +ERROR deprecated_class_reference device rdfs:subClassOf sensor +ERROR deprecated_class_reference device rdfs:subClassOf manufactured product +ERROR deprecated_class_reference device rdfs:subClassOf processed material entity +ERROR deprecated_class_reference device rdfs:subClassOf X-ray source +ERROR deprecated_class_reference device rdfs:subClassOf spacecraft +ERROR deprecated_class_reference device rdfs:subClassOf radiation dosimeter device +ERROR deprecated_class_reference device rdfs:subClassOf particle accelerator +ERROR deprecated_class_reference device rdfs:subClassOf nuclear reactor ERROR duplicate_label unplanned naturally occurring radiation exposure label unplanned naturally occurring radiation exposure ERROR duplicate_label unplanned naturally occurring radiation exposure label unplanned naturally occurring radiation exposure ERROR duplicate_label thorium label thorium @@ -88,29 +55,32 @@ ERROR duplicate_label environmental study label environmental study ERROR duplicate_label environmental study label environmental study ERROR duplicate_label cellular process label cellular process ERROR duplicate_label cellular process label cellular process +ERROR missing_label http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled label +ERROR missing_label xsd:boolean label +ERROR missing_label xsd:string label ERROR multiple_definitions independent continuant textual definition A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.@en -ERROR multiple_definitions independent continuant textual definition -ERROR multiple_definitions independent continuant textual definition +ERROR multiple_definitions independent continuant textual definition b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) +ERROR multiple_definitions independent continuant textual definition b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])@en ERROR multiple_definitions process textual definition A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs. ERROR multiple_definitions process textual definition An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.@en -ERROR multiple_definitions process textual definition

+ERROR multiple_definitions process textual definition p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])@en ERROR multiple_definitions specifically dependent continuant textual definition A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.@en ERROR multiple_definitions specifically dependent continuant textual definition An experimental factor which is a property or characteristic of some other entity. For example, the mouse has the colour white. -ERROR multiple_definitions specifically dependent continuant textual definition -ERROR multiple_definitions specifically dependent continuant textual definition +ERROR multiple_definitions specifically dependent continuant textual definition b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])@en +ERROR multiple_definitions specifically dependent continuant textual definition b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])@en ERROR multiple_definitions role textual definition A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.@en ERROR multiple_definitions role textual definition A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease. ERROR multiple_definitions generically dependent continuant textual definition A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.@en -ERROR multiple_definitions generically dependent continuant textual definition +ERROR multiple_definitions generically dependent continuant textual definition b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])@en ERROR multiple_definitions material entity textual definition A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. ERROR multiple_definitions material entity textual definition An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.@en -ERROR multiple_definitions part_of textual definition +ERROR multiple_definitions part_of textual definition For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) ERROR multiple_definitions part_of textual definition a core relation that holds between a part and its whole@en ERROR multiple_definitions cell textual definition A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. ERROR multiple_definitions cell textual definition A material entity that has a plasma membrane and results from cellular division. -ERROR multiple_definitions cellular_component textual definition -ERROR multiple_definitions cellular_component textual definition -ERROR multiple_definitions cellular_component textual definition +ERROR multiple_definitions cellular_component textual definition A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). +ERROR multiple_definitions cellular_component textual definition A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). +ERROR multiple_definitions cellular_component textual definition A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). ERROR multiple_definitions biological_process textual definition A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. ERROR multiple_definitions biological_process textual definition A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. ERROR multiple_definitions gene expression textual definition The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. @@ -123,15 +93,19 @@ ERROR multiple_definitions plan specification textual definition A directive inf ERROR multiple_definitions plan specification textual definition A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.@en ERROR multiple_definitions textual definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.@en ERROR multiple_definitions textual definition textual definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.@en -ERROR multiple_definitions alternative term textual definition +ERROR multiple_definitions alternative term textual definition A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.@en ERROR multiple_definitions alternative term textual definition An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)@en -ERROR multiple_definitions definition source textual definition -ERROR multiple_definitions definition source textual definition +ERROR multiple_definitions definition source textual definition Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007@en +ERROR multiple_definitions definition source textual definition formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007@en +ERROR multiple_definitions processed material entity textual definition A material entity processed by human activity with an intent to produce +ERROR multiple_definitions processed material entity textual definition Is a material entity that is created or changed during material processing.@en ERROR multiple_definitions population textual definition A population is a group of material entities consisting of individuals which share a particular characteristic such as inhabiting a particular region or area or ability to interbreed. ERROR multiple_definitions population textual definition a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area@en ERROR multiple_definitions protocol textual definition A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.@en ERROR multiple_definitions protocol textual definition A protocol is an information entity which is a set of instructions that describe an how an experiment is done. ERROR multiple_definitions protocol textual definition a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process. +ERROR multiple_definitions X-ray source textual definition A device that is used to generate X-rays. +ERROR multiple_definitions X-ray source textual definition A device that is used to generate X-rays.@en ERROR multiple_definitions organism textual definition A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. ERROR multiple_definitions organism textual definition A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.@en ERROR multiple_definitions organism textual definition A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. E.g Drosophila melanogaster @@ -146,10 +120,10 @@ ERROR multiple_definitions has participant textual definition a relation between ERROR multiple_definitions overlaps textual definition x overlaps y if and only if there exists some z such that x has part z and z part of y ERROR multiple_definitions overlaps textual definition x overlaps y iff they have some part in common. ERROR multiple_definitions regulates (processual) textual definition p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. -ERROR multiple_definitions regulates (processual) textual definition -ERROR multiple_definitions negatively regulates textual definition +ERROR multiple_definitions regulates (processual) textual definition process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. +ERROR multiple_definitions negatively regulates textual definition Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. ERROR multiple_definitions negatively regulates textual definition p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. -ERROR multiple_definitions positively regulates textual definition +ERROR multiple_definitions positively regulates textual definition Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. ERROR multiple_definitions positively regulates textual definition p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. ERROR multiple_definitions inheres in part of textual definition q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. ERROR multiple_definitions inheres in part of textual definition q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. @@ -162,10 +136,10 @@ ERROR multiple_definitions immediately causally upstream of textual definition p ERROR multiple_definitions causally upstream of or within textual definition p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. ERROR multiple_definitions causally upstream of or within textual definition p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. ERROR multiple_definitions existence ends during textual definition Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. -ERROR multiple_definitions existence ends during textual definition = α(y).> +ERROR multiple_definitions existence ends during textual definition x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). ERROR multiple_definitions causal relation between processes textual definition p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. ERROR multiple_definitions causal relation between processes textual definition p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. -ERROR multiple_definitions directly regulates textual definition +ERROR multiple_definitions directly regulates textual definition Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. ERROR multiple_definitions directly regulates textual definition p directly regulates q iff p is immediately causally upstream of q and p regulates q. ERROR multiple_definitions anatomical cluster textual definition Anatomical group that has its parts adjacent to one another. ERROR multiple_definitions anatomical cluster textual definition Anatomical group whose component anatomical structures lie in close proximity to each other. @@ -175,6 +149,24 @@ ERROR multiple_definitions absorbed dose unit textual definition A derived unit ERROR multiple_definitions absorbed dose unit textual definition A unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue. ERROR multiple_definitions has exact synonym textual definition An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. ERROR multiple_definitions has exact synonym textual definition An alternative label for a given entity such as a commonly used abbreviation or synonym. +ERROR multiple_equivalent_class_definitions response to light stimulus owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions response to organic substance owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions response to inorganic substance owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions response to organonitrogen compound owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions response to organic cyclic compound owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions RNA biosynthetic process owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions response to chemical owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions response to amino acid owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions membrane biogenesis owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions response to carbamate owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions response to ammonium ion owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions nuclear membrane biogenesis owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions catalytic activity, acting on a protein owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions catalytic activity, acting on RNA owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions catalytic activity, acting on a nucleic acid owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions response to peptide owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions response to nitrogen compound owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions response to oxygen-containing compound owl:equivalentClass blank node ERROR multiple_labels continuant label continuant ERROR multiple_labels continuant label continuant@en ERROR multiple_labels independent continuant label independent continuant @@ -220,6 +212,8 @@ ERROR multiple_labels subatomic particle label subatomic particle ERROR multiple_labels subatomic particle label subatomic particle@en ERROR multiple_labels cell label cell ERROR multiple_labels cell label cell@en +ERROR multiple_labels has atomic number label has atomic number +ERROR multiple_labels has atomic number label has atomic number@en ERROR multiple_labels results in distribution of label results in distribution of ERROR multiple_labels results in distribution of label results_in_distribution_of ERROR multiple_labels results in fission of label results in fission of @@ -253,28 +247,23 @@ ERROR multiple_labels alternative term label alternative term ERROR multiple_labels alternative term label alternative term@en ERROR multiple_labels definition source label definition source ERROR multiple_labels definition source label definition source@en +ERROR multiple_labels is about label is about +ERROR multiple_labels is about label is about@en ERROR multiple_labels Mus label Mus ERROR multiple_labels Mus label Mus ERROR multiple_labels planned process label completely executed planned process@en ERROR multiple_labels planned process label planned process ERROR multiple_labels planned process label planned process@en +ERROR multiple_labels processed material entity label processed material@en +ERROR multiple_labels processed material entity label processed material entity@en ERROR multiple_labels population label population ERROR multiple_labels population label population@en ERROR multiple_labels protocol label protocol ERROR multiple_labels protocol label protocol@en -ERROR multiple_labels has_input label has specified input@en -ERROR multiple_labels has_input label has_input -ERROR multiple_labels has_input label has_specified_input -ERROR multiple_labels has_input label has_specified_input@en -ERROR multiple_labels is specified input of label is specified input of@en -ERROR multiple_labels is specified input of label is_input_of -ERROR multiple_labels is specified input of label is_specified_input_of@en ERROR multiple_labels has_output label has specified output@en ERROR multiple_labels has_output label has_output ERROR multiple_labels has_output label has_specified_output ERROR multiple_labels has_output label has_specified_output@en -ERROR multiple_labels is_specified_output_of label is specified output of@en -ERROR multiple_labels is_specified_output_of label is_specified_output_of@en ERROR multiple_labels organism label organism ERROR multiple_labels organism label organism@en ERROR multiple_labels inheres in label characteristic of@en @@ -435,52 +424,73 @@ ERROR multiple_labels Date label Date@en-us ERROR multiple_labels Description label Description ERROR multiple_labels Description label Description@en-us ERROR multiple_labels Description label description -ERROR multiple_labels title label Title -ERROR multiple_labels title label Title@en-us -ERROR multiple_labels title label title +ERROR multiple_labels Title label Title +ERROR multiple_labels Title label Title@en-us +ERROR multiple_labels Title label title ERROR multiple_labels created_by label created by ERROR multiple_labels created_by label created_by ERROR multiple_labels has_broad_synonym label has broad synonym@en ERROR multiple_labels has_broad_synonym label has_broad_synonym ERROR multiple_labels has exact synonym label has exact synonym@en ERROR multiple_labels has exact synonym label has_exact_synonym -WARN annotation_whitespace continuant IAO:0000602 <(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] > -WARN annotation_whitespace continuant IAO:0000602 <(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] > -WARN annotation_whitespace continuant IAO:0000602 <(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] > -WARN annotation_whitespace continuant IAO:0000602 <(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] > -WARN annotation_whitespace occurrent IAO:0000602 <(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] > -WARN annotation_whitespace occurrent IAO:0000602 <(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] > -WARN annotation_whitespace independent continuant IAO:0000602 <(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] > -WARN annotation_whitespace independent continuant IAO:0000602 <(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] > -WARN annotation_whitespace independent continuant IAO:0000602 <(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] > -WARN annotation_whitespace spatial region IAO:0000602 <(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] > -WARN annotation_whitespace spatial region IAO:0000602 <(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] > -WARN annotation_whitespace process IAO:0000602 <(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] > -WARN annotation_whitespace disposition IAO:0000602 <(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] > -WARN annotation_whitespace disposition IAO:0000602 <(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] > -WARN annotation_whitespace realizable entity IAO:0000602 <(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] > -WARN annotation_whitespace realizable entity IAO:0000602 <(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] > -WARN annotation_whitespace quality IAO:0000602 <(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] > -WARN annotation_whitespace quality IAO:0000602 <(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] > -WARN annotation_whitespace specifically dependent continuant IAO:0000602 <(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] > -WARN annotation_whitespace specifically dependent continuant IAO:0000602 <(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] > -WARN annotation_whitespace role IAO:0000602 <(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] > +WARN annotation_whitespace continuant IAO:0000602 (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] +WARN annotation_whitespace continuant IAO:0000602 (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] +WARN annotation_whitespace continuant IAO:0000602 (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] +WARN annotation_whitespace continuant IAO:0000602 (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] +WARN annotation_whitespace occurrent IAO:0000602 (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] +WARN annotation_whitespace occurrent IAO:0000602 (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] +WARN annotation_whitespace independent continuant IAO:0000602 (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] +WARN annotation_whitespace independent continuant IAO:0000602 (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] +WARN annotation_whitespace independent continuant IAO:0000602 (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] +WARN annotation_whitespace spatial region IAO:0000602 (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] +WARN annotation_whitespace spatial region IAO:0000602 (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] +WARN annotation_whitespace process IAO:0000602 (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] +WARN annotation_whitespace disposition IAO:0000602 (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] +WARN annotation_whitespace disposition IAO:0000602 (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] +WARN annotation_whitespace realizable entity IAO:0000602 (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] +WARN annotation_whitespace realizable entity IAO:0000602 (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] +WARN annotation_whitespace quality IAO:0000602 (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] +WARN annotation_whitespace quality IAO:0000602 (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] +WARN annotation_whitespace specifically dependent continuant IAO:0000602 (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] +WARN annotation_whitespace role IAO:0000602 (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] WARN annotation_whitespace object aggregate editor note An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects -WARN annotation_whitespace object aggregate IAO:0000602 <(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] > -WARN annotation_whitespace generically dependent continuant IAO:0000602 <(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] > -WARN annotation_whitespace function IAO:0000602 <(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] > -WARN annotation_whitespace material entity IAO:0000602 <(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] > -WARN annotation_whitespace material entity IAO:0000602 <(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] > -WARN annotation_whitespace material entity IAO:0000602 <(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] > -WARN annotation_whitespace cell database_cross_reference -WARN annotation_whitespace cell database_cross_reference -WARN annotation_whitespace cell database_cross_reference -WARN annotation_whitespace cell database_cross_reference -WARN annotation_whitespace cell database_cross_reference -WARN annotation_whitespace cell database_cross_reference -WARN annotation_whitespace cell database_cross_reference -WARN annotation_whitespace datum label IAO:0000232 <9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. > -WARN annotation_whitespace textual definition editor note <2012-04-05: Barry SmithThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.Can you fix to something like:A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.Alan RuttenbergYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition:We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. @en> +WARN annotation_whitespace object aggregate IAO:0000602 (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] +WARN annotation_whitespace generically dependent continuant IAO:0000602 (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] +WARN annotation_whitespace function IAO:0000602 (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] +WARN annotation_whitespace material entity IAO:0000602 (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] +WARN annotation_whitespace material entity IAO:0000602 (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] +WARN annotation_whitespace material entity IAO:0000602 (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] +WARN annotation_whitespace cell database_cross_reference "CALOHA:TS-2035 +" +WARN annotation_whitespace cell database_cross_reference FMA:68646 +WARN annotation_whitespace cell database_cross_reference GO:0005623 +WARN annotation_whitespace cell database_cross_reference "KUPO:0000002 + +" +WARN annotation_whitespace cell database_cross_reference VHOG:0001533 +WARN annotation_whitespace cell database_cross_reference WBbt:0004017 +WARN annotation_whitespace cell database_cross_reference XAO:0003012 +WARN annotation_whitespace textual definition editor note "2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. @en" +WARN annotation_whitespace domain entity does not exist editor note This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). @en WARN annotation_whitespace radiation response modifier textual definition Radiation response modifiers are agents that alter tumor or normal tissue response to radiation, such as radiation sensitizers and radiation protectors. WARN annotation_whitespace Iron-56 nucleus textual definition An atomic nucleus with 26 protons and 30 neutrons WARN annotation_whitespace Iron-56 nucleus alternative term Fe-56 ion;Fe-56 nucleus;Fe-56 @@ -514,23 +524,35 @@ WARN annotation_whitespace Krypton-84 nucleus textual definition An atomic nucle WARN annotation_whitespace Krypton-84 nucleus alternative term Kr-84 ion;Kr-84 nucleus;Kr-84 WARN annotation_whitespace external radiation exposure example of usage Mice exposed to external radiation from a Sr source. WARN annotation_whitespace internal experimental radiation exposure rdfs:comment Research subjects participating in a clinical trial using an internally implanted radiation source have an internal experimental radiation exposure -WARN annotation_whitespace contained in editor note -WARN annotation_whitespace ends during rdfs:comment +WARN annotation_whitespace contained in editor note "Intended meaning: +domain: material entity +range: spatial region or site (immaterial continuant) + @en" +WARN annotation_whitespace ends during rdfs:comment X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). @en WARN annotation_whitespace synapsed by textual definition Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. @en WARN annotation_whitespace synapsed to textual definition " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. @en" WARN annotation_whitespace spatially disjoint from editor note There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. @en WARN annotation_whitespace capable of textual definition A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. WARN annotation_whitespace developmentally induced by definition source Developmental Biology, Gilbert, 8th edition, figure 6.5(F) -WARN annotation_whitespace results in maturation of example of usage < an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process> +WARN annotation_whitespace results in maturation of example of usage an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process WARN annotation_whitespace results in transport along textual definition Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l WARN annotation_whitespace siemens has exact synonym mho WARN annotation_whitespace electric field strength unit has exact synonym E-field strength -WARN annotation_whitespace title Description " +WARN annotation_whitespace Title Description " Typically, a Title will be a name by which the resource is formally known. @en-us" -WARN annotation_whitespace BALB/c rdfs:comment BALB/c>CD1>129X1/SvJ. Variations were also found in the timeline of response and cell types most impacted.BALB/c mice immunized with PLP180-199 develop an atypical form of experimental autoimmune encephalomyelitis (EAE) in which susceptibility is determined by location. In the spinal cord 60-70% mice develop pathological lesions and in the brain and cerebellum 100% of mice develop sever lesions.Dorso-ventral vaginal septa is observed in some BALB/cJ females, and may contribute to non-productive females in this strain. (Cunliffe-Beamer T, Lab Anim Sci, 1976)> +WARN annotation_whitespace BALB/c rdfs:comment "Description from https://www.jax.org/strain/000651: + +BALB/c mice are particularly well known for the production of plasmacytomas following injection with mineral oil forming the basis for the production of monoclonal antibodies. Although not all BALB/c substrains have been examined for plasmacytoma induction, substrains derived from the Andervont (An) lineage (which includes BALB/cByJ) typically are susceptible, while those descended from BALB/cJ are resistant (see: Potter M, 1985). Mammary tumor incidence is normally low but infection with mammary tumor virus by fostering to MMTV+ C3H mice dramatically increases tumor number and age of onset. BALB/c mice develop other cancers later in life including reticular neoplasms, primary lung tumors, and renal tumors. Rare spontaneous myoepitheliomas arising from myoepithelial cells of various exocrine glands have been observed in both BALB/cJ and BALB/cByJ substrains. + +White et al. reported a variation in thioglycolate medium-induced peritoneal leukocyte recruitment in 4 analyzed strains. The response of total leukocyte recruitment, from greatest to least, was C57BL/6J>BALB/c>CD1>129X1/SvJ. Variations were also found in the timeline of response and cell types most impacted. + +BALB/c mice immunized with PLP180-199 develop an atypical form of experimental autoimmune encephalomyelitis (EAE) in which susceptibility is determined by location. In the spinal cord 60-70% mice develop pathological lesions and in the brain and cerebellum 100% of mice develop sever lesions. + +Dorso-ventral vaginal septa is observed in some BALB/cJ females, and may contribute to non-productive females in this strain. (Cunliffe-Beamer T, Lab Anim Sci, 1976) +" WARN annotation_whitespace CAST/EiJ textual definition " Both CAST/EiJ and CASA/RkJ (Stock No. 000735) were derived from wild mice trapped in Thailand. CAST is often combined with the common laboratory strains to generate F1 hybrids with high levels of heterozygosity for use in genetic mapping. Unlike the wild-derived strain SPRET, male F1 mice from a CAST cross are fertile. @@ -562,8 +584,8 @@ WARN duplicate_exact_synonym Stage IIB (AJCC 7th) alternative term Stage IIB WARN duplicate_exact_synonym Stage IIB (FIGO) alternative term Stage IIB WARN duplicate_exact_synonym Stage IIA (AJCC 7th) alternative term Stage IIA WARN duplicate_exact_synonym Stage IIA (FIGO) alternative term Stage IIA -WARN duplicate_exact_synonym pathologic lymph node stage for colon and rectum according to AJCC 7th edition alternative term -WARN duplicate_exact_synonym pathologic lymph node stage for lung according to AJCC 7th edition alternative term +WARN duplicate_exact_synonym pathologic lymph node stage for colon and rectum according to AJCC 7th edition alternative term pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) +WARN duplicate_exact_synonym pathologic lymph node stage for lung according to AJCC 7th edition alternative term pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) WARN duplicate_exact_synonym picometer has exact synonym pm WARN duplicate_exact_synonym picomolal has exact synonym pm WARN duplicate_exact_synonym mass volume percentage alternative term percent vol per vol @@ -578,10 +600,6 @@ WARN duplicate_exact_synonym Mus has exact synonym Mus WARN duplicate_exact_synonym Mus has exact synonym Mus WARN duplicate_exact_synonym Mus has exact synonym mouse WARN duplicate_exact_synonym Mus musculus has exact synonym mouse -WARN duplicate_exact_synonym Platyrrhini has exact synonym monkeys -WARN duplicate_exact_synonym Cercopithecidae has exact synonym monkeys -WARN duplicate_exact_synonym Platyrrhini has exact synonym monkey -WARN duplicate_exact_synonym Cercopithecidae has exact synonym monkey WARN duplicate_exact_synonym millimeter has exact synonym mm WARN duplicate_exact_synonym millimolal has exact synonym mm WARN duplicate_exact_synonym meter has exact synonym m @@ -629,8 +647,6 @@ WARN duplicate_exact_synonym parts per quadrillion has exact synonym 10^[-15] WARN duplicate_exact_synonym femto has exact synonym 10^[-15] WARN duplicate_exact_synonym parts per trillion has exact synonym 10^[-12] WARN duplicate_exact_synonym pico has exact synonym 10^[-12] -WARN equivalent_pair role owl:equivalentClass -WARN equivalent_pair protein owl:equivalentClass WARN duplicate_label_synonym specifically dependent continuant has exact synonym specifically dependent continuant WARN duplicate_label_synonym part_of has exact synonym part of WARN duplicate_label_synonym electron has exact synonym electron @@ -666,6 +682,7 @@ WARN duplicate_label_synonym metabolite has exact synonym metabolite WARN duplicate_label_synonym molecule has exact synonym molecule WARN duplicate_label_synonym oxide has exact synonym oxide WARN duplicate_label_synonym oxygen molecular entity has exact synonym oxygen molecular entity +WARN duplicate_label_synonym phosphate has exact synonym phosphate WARN duplicate_label_synonym phosphoric acid has exact synonym phosphoric acid WARN duplicate_label_synonym sulfates has exact synonym sulfates WARN duplicate_label_synonym sulfur molecular entity has exact synonym sulfur molecular entity @@ -686,6 +703,7 @@ WARN duplicate_label_synonym photon has exact synonym photon WARN duplicate_label_synonym alpha-particle has exact synonym alpha-particle WARN duplicate_label_synonym neutron has exact synonym neutron WARN duplicate_label_synonym thallium has exact synonym thallium +WARN duplicate_label_synonym amide has exact synonym amide WARN duplicate_label_synonym organyl group has exact synonym organyl group WARN duplicate_label_synonym atom has exact synonym atom WARN duplicate_label_synonym nucleon has exact synonym nucleon @@ -729,6 +747,7 @@ WARN duplicate_label_synonym macromolecule has exact synonym macromolecule WARN duplicate_label_synonym phenols has exact synonym phenols WARN duplicate_label_synonym reagent has exact synonym reagent WARN duplicate_label_synonym aldohexose has exact synonym aldohexose +WARN duplicate_label_synonym azane has exact synonym azane WARN duplicate_label_synonym inhibitor has exact synonym inhibitor WARN duplicate_label_synonym catalyst has exact synonym catalyst WARN duplicate_label_synonym amino acid zwitterion has exact synonym amino acid zwitterion @@ -778,33 +797,43 @@ WARN duplicate_label_synonym tungsten-183 has exact synonym tungsten-183 WARN duplicate_label_synonym cadmium-111 has exact synonym cadmium-111 WARN duplicate_label_synonym cadmium-113 has exact synonym cadmium-113 WARN duplicate_label_synonym molybdenum-95 has exact synonym molybdenum-95 -WARN duplicate_label_synonym glucagon has_related_synonym glucagon -WARN duplicate_label_synonym somatostatin has_related_synonym somatostatin -WARN duplicate_label_synonym mesenchymal stem cell has_related_synonym mesenchymal stem cell -WARN duplicate_label_synonym ice field has_related_synonym ice field +WARN duplicate_label_synonym dosimeter has exact synonym dosimeter +WARN duplicate_label_synonym nucleus has exact synonym nucleus +WARN duplicate_label_synonym behavior has exact synonym behavior +WARN duplicate_label_synonym mastication has exact synonym mastication WARN duplicate_label_synonym information content entity has exact synonym information content entity +WARN duplicate_label_synonym plan specification has exact synonym plan specification +WARN duplicate_label_synonym chewing has exact synonym chewing WARN duplicate_label_synonym Mus has exact synonym Mus +WARN duplicate_label_synonym actinium has exact synonym actinium +WARN duplicate_label_synonym americium has exact synonym americium +WARN duplicate_label_synonym californium has exact synonym californium +WARN duplicate_label_synonym neptunium has exact synonym neptunium +WARN duplicate_label_synonym plutonium has exact synonym plutonium +WARN duplicate_label_synonym thorium has exact synonym thorium +WARN duplicate_label_synonym uranium has exact synonym uranium +WARN duplicate_label_synonym biological process has exact synonym biological process +WARN duplicate_label_synonym charged particle alternative term charged particle +WARN duplicate_label_synonym overlaps alternative term overlaps +WARN duplicate_label_synonym connected to alternative term connected to WARN duplicate_label_synonym inheres in part of alternative term inheres in part of +WARN duplicate_label_synonym produces alternative term produces +WARN duplicate_label_synonym executes alternative term executes WARN duplicate_label_synonym sympathetic nervous system has exact synonym sympathetic nervous system WARN duplicate_label_synonym endocrine pancreas has exact synonym endocrine pancreas WARN duplicate_label_synonym exocrine pancreas has exact synonym exocrine pancreas -WARN duplicate_label_synonym lung bud has_related_synonym lung bud +WARN duplicate_label_synonym life cycle stage has exact synonym life cycle stage WARN duplicate_label_synonym anal canal has exact synonym anal canal WARN duplicate_label_synonym colonic mucosa has exact synonym colonic mucosa WARN duplicate_label_synonym organism substance has exact synonym organism substance WARN duplicate_label_synonym simple columnar epithelium has exact synonym simple columnar epithelium WARN duplicate_label_synonym endocrine system has exact synonym endocrine system -WARN duplicate_label_synonym pleura has_related_synonym pleura WARN duplicate_label_synonym respiratory system has exact synonym respiratory system WARN duplicate_label_synonym musculature has exact synonym musculature WARN duplicate_label_synonym posterior vena cava has exact synonym posterior vena cava -WARN duplicate_label_synonym caudal vertebra has_broad_synonym caudal vertebra -WARN duplicate_label_synonym sigmoid colon has_related_synonym sigmoid colon -WARN duplicate_label_synonym sphincter pupillae has_related_synonym sphincter pupillae WARN duplicate_label_synonym orbit of skull has exact synonym orbit of skull WARN duplicate_label_synonym cranial ganglion has exact synonym cranial ganglion WARN duplicate_label_synonym uvea has exact synonym uvea -WARN duplicate_label_synonym optic choroid has_related_synonym optic choroid WARN duplicate_label_synonym rhombomere has exact synonym rhombomere WARN duplicate_label_synonym submucosa of esophagus has exact synonym submucosa of esophagus WARN duplicate_label_synonym gray matter has exact synonym gray matter @@ -816,14 +845,12 @@ WARN duplicate_label_synonym artery smooth muscle tissue has exact synonym arter WARN duplicate_label_synonym gray matter of spinal cord has exact synonym gray matter of spinal cord WARN duplicate_label_synonym sinoatrial node has exact synonym sinoatrial node WARN duplicate_label_synonym cardiac Purkinje fiber has exact synonym cardiac Purkinje fiber -WARN duplicate_label_synonym cranial muscle has_related_synonym cranial muscle WARN duplicate_label_synonym cartilage tissue has exact synonym cartilage tissue WARN duplicate_label_synonym esophagus mucosa has exact synonym esophagus mucosa WARN duplicate_label_synonym iris epithelium has exact synonym iris epithelium WARN duplicate_label_synonym cervical spinal cord has exact synonym cervical spinal cord WARN duplicate_label_synonym trigeminal nucleus has exact synonym trigeminal nucleus WARN duplicate_label_synonym thoracic spinal cord has exact synonym thoracic spinal cord -WARN duplicate_label_synonym periderm has_related_synonym periderm WARN duplicate_label_synonym skeletal muscle tissue of eye has exact synonym skeletal muscle tissue of eye WARN duplicate_label_synonym cardiac muscle tissue of interventricular septum has exact synonym cardiac muscle tissue of interventricular septum WARN duplicate_label_synonym skeletal muscle tissue of pharynx has exact synonym skeletal muscle tissue of pharynx @@ -835,14 +862,12 @@ WARN duplicate_label_synonym skeletal muscle tissue of trunk has exact synonym s WARN duplicate_label_synonym reproductive gland has exact synonym reproductive gland WARN duplicate_label_synonym germinal neuroepithelium has exact synonym germinal neuroepithelium WARN duplicate_label_synonym biliary ductule has exact synonym biliary ductule -WARN duplicate_label_synonym biliary ductule has_related_synonym biliary ductule WARN duplicate_label_synonym primary heart field has exact synonym primary heart field WARN duplicate_label_synonym cardiac vein has exact synonym cardiac vein WARN duplicate_label_synonym internal genitalia has exact synonym internal genitalia WARN duplicate_label_synonym external genitalia has exact synonym external genitalia WARN duplicate_label_synonym paired limb/fin bud has exact synonym paired limb/fin bud WARN duplicate_label_synonym pharyngeal arch artery has exact synonym pharyngeal arch artery -WARN duplicate_label_synonym pharyngeal arch artery has_related_synonym pharyngeal arch artery WARN duplicate_label_synonym anterior limiting lamina of cornea has exact synonym anterior limiting lamina of cornea WARN duplicate_label_synonym raphe nuclei has exact synonym raphe nuclei WARN duplicate_label_synonym pelvic appendage has exact synonym pelvic appendage @@ -852,18 +877,13 @@ WARN duplicate_label_synonym parenchyma of central nervous system has exact syno WARN duplicate_label_synonym cervical region has exact synonym cervical region WARN duplicate_label_synonym primitive heart tube has exact synonym primitive heart tube WARN duplicate_label_synonym paired limb/fin field has exact synonym paired limb/fin field -WARN duplicate_label_synonym muscular coat has_related_synonym muscular coat -WARN duplicate_label_synonym vertebral canal has_related_synonym vertebral canal WARN duplicate_label_synonym head mesenchyme from mesoderm has exact synonym head mesenchyme from mesoderm WARN duplicate_label_synonym lumen of digestive tract has exact synonym lumen of digestive tract WARN duplicate_label_synonym ovary stroma has exact synonym ovary stroma WARN duplicate_label_synonym pancreatic lobule has exact synonym pancreatic lobule WARN duplicate_label_synonym anatomical junction has exact synonym anatomical junction WARN duplicate_label_synonym pelvic girdle skeleton has exact synonym pelvic girdle skeleton -WARN duplicate_label_synonym perichordal bone has_related_synonym perichordal bone -WARN duplicate_label_synonym tail vasculature has_related_synonym tail vasculature WARN duplicate_label_synonym ciliary processes has exact synonym ciliary processes -WARN duplicate_label_synonym palatoquadrate arch has_related_synonym palatoquadrate arch WARN duplicate_label_synonym facial skeleton has exact synonym facial skeleton WARN duplicate_label_synonym hematopoietic tissue has exact synonym hematopoietic tissue WARN duplicate_label_synonym foramen of skull has exact synonym foramen of skull @@ -879,1452 +899,10 @@ WARN duplicate_label_synonym left crus of diaphragm has exact synonym left crus WARN duplicate_label_synonym anal canal epithelium has exact synonym anal canal epithelium WARN duplicate_label_synonym abdominal viscera has exact synonym abdominal viscera WARN duplicate_label_synonym lung field has exact synonym lung field -WARN missing_definition has atomic number textual definition -WARN missing_definition fiat object part textual definition -WARN missing_definition site textual definition -WARN missing_definition object textual definition -WARN missing_definition has participant textual definition -WARN missing_definition immaterial entity textual definition -WARN missing_definition carbamate textual definition -WARN missing_definition electron donor textual definition -WARN missing_definition water textual definition -WARN missing_definition dioxygen textual definition -WARN missing_definition carbon dioxide textual definition -WARN missing_definition noradrenaline(1+) textual definition -WARN missing_definition dinitrogen textual definition -WARN missing_definition manganese atom textual definition -WARN missing_definition 5beta-cholane textual definition -WARN missing_definition alkaline earth metal atom textual definition -WARN missing_definition alkali metal atom textual definition -WARN missing_definition aminoglycan textual definition -WARN missing_definition benzopyrrole textual definition -WARN missing_definition bromine atom textual definition -WARN missing_definition cadmium atom textual definition -WARN missing_definition calcium atom textual definition -WARN missing_definition carbon oxide textual definition -WARN missing_definition carbonyl group textual definition -WARN missing_definition chloride salt textual definition -WARN missing_definition chlorine atom textual definition -WARN missing_definition chlorine molecular entity textual definition -WARN missing_definition cyclic peptide textual definition -WARN missing_definition monoatomic cation textual definition -WARN missing_definition fluorine atom textual definition -WARN missing_definition glycogens textual definition -WARN missing_definition halogen molecular entity textual definition -WARN missing_definition halogen textual definition -WARN missing_definition inorganic anion textual definition -WARN missing_definition inorganic oxide textual definition -WARN missing_definition inorganic salt textual definition -WARN missing_definition monoatomic ion textual definition -WARN missing_definition organic salt textual definition -WARN missing_definition iron molecular entity textual definition -WARN missing_definition lead atom textual definition -WARN missing_definition linear tetrapyrrole textual definition -WARN missing_definition magnesium atom textual definition -WARN missing_definition mercury atom textual definition -WARN missing_definition metal cation textual definition -WARN missing_definition monoatomic monocation textual definition -WARN missing_definition nitrogen atom textual definition -WARN missing_definition nonmetal atom textual definition -WARN missing_definition organic ion textual definition -WARN missing_definition organic oxide textual definition -WARN missing_definition oxygen atom textual definition -WARN missing_definition oxygen molecular entity textual definition -WARN missing_definition phosphoric acid derivative textual definition -WARN missing_definition phosphorus molecular entity textual definition -WARN missing_definition potassium atom textual definition -WARN missing_definition sodium atom textual definition -WARN missing_definition sodium chloride textual definition -WARN missing_definition sodium molecular entity textual definition -WARN missing_definition sulfur atom textual definition -WARN missing_definition sulfur molecular entity textual definition -WARN missing_definition tin atom textual definition -WARN missing_definition organic heterobicyclic compound textual definition -WARN missing_definition uranium atom textual definition -WARN missing_definition zinc atom textual definition -WARN missing_definition boron atom textual definition -WARN missing_definition arsenic atom textual definition -WARN missing_definition selenium atom textual definition -WARN missing_definition silicon atom textual definition -WARN missing_definition carbon atom textual definition -WARN missing_definition vanadium atom textual definition -WARN missing_definition tungsten textual definition -WARN missing_definition phosphorus atom textual definition -WARN missing_definition molybdenum atom textual definition -WARN missing_definition copper atom textual definition -WARN missing_definition carbonic acid textual definition -WARN missing_definition aluminium atom textual definition -WARN missing_definition gold atom textual definition -WARN missing_definition azanide textual definition -WARN missing_definition hydridodioxygen(1+) textual definition -WARN missing_definition lithium atom textual definition -WARN missing_definition helium atom textual definition -WARN missing_definition monoatomic dication textual definition -WARN missing_definition astatine atom textual definition -WARN missing_definition germanium atom textual definition -WARN missing_definition tellurium atom textual definition -WARN missing_definition silver atom textual definition -WARN missing_definition antimony atom textual definition -WARN missing_definition caesium atom textual definition -WARN missing_definition ruthenium atom textual definition -WARN missing_definition osmium atom textual definition -WARN missing_definition barium atom textual definition -WARN missing_definition europium atom textual definition -WARN missing_definition oxoacid derivative textual definition -WARN missing_definition inorganic hydride textual definition -WARN missing_definition monoatomic hydrogen textual definition -WARN missing_definition elemental hydrogen textual definition -WARN missing_definition elemental oxygen textual definition -WARN missing_definition diatomic oxygen textual definition -WARN missing_definition diatomic nitrogen textual definition -WARN missing_definition elemental nitrogen textual definition -WARN missing_definition molecular messenger textual definition -WARN missing_definition fuel textual definition -WARN missing_definition bismuth atom textual definition -WARN missing_definition carbon group element atom textual definition -WARN missing_definition noble gas atom textual definition -WARN missing_definition neon atom textual definition -WARN missing_definition radon atom textual definition -WARN missing_definition monoatomic helium textual definition -WARN missing_definition helium(2+) textual definition -WARN missing_definition boron group element atom textual definition -WARN missing_definition lanthanoid atom textual definition -WARN missing_definition actinoid atom textual definition -WARN missing_definition rare earth metal atom textual definition -WARN missing_definition rubidium atom textual definition -WARN missing_definition francium atom textual definition -WARN missing_definition strontium atom textual definition -WARN missing_definition radium atom textual definition -WARN missing_definition scandium atom textual definition -WARN missing_definition yttrium atom textual definition -WARN missing_definition scandium group element atom textual definition -WARN missing_definition lanthanum atom textual definition -WARN missing_definition actinium atom textual definition -WARN missing_definition zinc group element atom textual definition -WARN missing_definition titanium atom textual definition -WARN missing_definition zirconium atom textual definition -WARN missing_definition hafnium atom textual definition -WARN missing_definition niobium atom textual definition -WARN missing_definition titanium group element atom textual definition -WARN missing_definition rutherfordium atom textual definition -WARN missing_definition vanadium group element atom textual definition -WARN missing_definition tantalum atom textual definition -WARN missing_definition dubnium atom textual definition -WARN missing_definition chromium group element atom textual definition -WARN missing_definition seaborgium atom textual definition -WARN missing_definition manganese group element atom textual definition -WARN missing_definition technetium atom textual definition -WARN missing_definition bohrium atom textual definition -WARN missing_definition iron group element atom textual definition -WARN missing_definition hassium atom textual definition -WARN missing_definition cobalt group element atom textual definition -WARN missing_definition meitnerium atom textual definition -WARN missing_definition nickel group element atom textual definition -WARN missing_definition platinum textual definition -WARN missing_definition platinum group metal atom textual definition -WARN missing_definition copper group element atom textual definition -WARN missing_definition darmstadtium textual definition -WARN missing_definition cerium textual definition -WARN missing_definition technetium-99 textual definition -WARN missing_definition neodymium atom textual definition -WARN missing_definition promethium atom textual definition -WARN missing_definition samarium atom textual definition -WARN missing_definition gadolinium atom textual definition -WARN missing_definition terbium atom textual definition -WARN missing_definition dysprosium atom textual definition -WARN missing_definition erbium textual definition -WARN missing_definition thulium atom textual definition -WARN missing_definition ytterbium textual definition -WARN missing_definition lutetium atom textual definition -WARN missing_definition thorium textual definition -WARN missing_definition protactinium atom textual definition -WARN missing_definition neptunium atom textual definition -WARN missing_definition plutonium atom textual definition -WARN missing_definition americium atom textual definition -WARN missing_definition curium atom textual definition -WARN missing_definition berkelium atom textual definition -WARN missing_definition californium atom textual definition -WARN missing_definition einsteinium atom textual definition -WARN missing_definition fermium textual definition -WARN missing_definition mendelevium atom textual definition -WARN missing_definition nobelium textual definition -WARN missing_definition lawrencium atom textual definition -WARN missing_definition sulfur oxoacid textual definition -WARN missing_definition pnictogen oxoacid textual definition -WARN missing_definition sulfur oxoacid derivative textual definition -WARN missing_definition pnictogen oxoanion textual definition -WARN missing_definition phosphorus oxoanion textual definition -WARN missing_definition elemental pnictogen textual definition -WARN missing_definition sulfur oxoanion textual definition -WARN missing_definition chalcogen oxoacid textual definition -WARN missing_definition chalcogen oxoanion textual definition -WARN missing_definition radon-220 atom textual definition -WARN missing_definition radon-222 atom textual definition -WARN missing_definition radon-219 atom textual definition -WARN missing_definition actinoid molecular entity textual definition -WARN missing_definition uranium molecular entity textual definition -WARN missing_definition alkali metal cation textual definition -WARN missing_definition s-block element atom textual definition -WARN missing_definition d-block element atom textual definition -WARN missing_definition f-block element atom textual definition -WARN missing_definition benzenediols textual definition -WARN missing_definition carbon group molecular entity textual definition -WARN missing_definition hydrogen molecular entity textual definition -WARN missing_definition polycyclic compound textual definition -WARN missing_definition organic aromatic compound textual definition -WARN missing_definition f-block molecular entity textual definition -WARN missing_definition helium molecular entity textual definition -WARN missing_definition elemental helium textual definition -WARN missing_definition oxygen hydride textual definition -WARN missing_definition information biomacromolecule textual definition -WARN missing_definition proteinogenic amino-acid residue textual definition -WARN missing_definition carbohydrate acid textual definition -WARN missing_definition carbohydrate acid anion textual definition -WARN missing_definition iron group molecular entity textual definition -WARN missing_definition copper group molecular entity textual definition -WARN missing_definition nickel group molecular entity textual definition -WARN missing_definition platinum molecular entity textual definition -WARN missing_definition canonical nucleoside residue textual definition -WARN missing_definition canonical ribonucleoside residue textual definition -WARN missing_definition canonical deoxyribonucleoside residue textual definition -WARN missing_definition halide salt textual definition -WARN missing_definition gold molecular entity textual definition -WARN missing_definition nitrogen hydride textual definition -WARN missing_definition fossil fuel textual definition -WARN missing_definition hydroxy steroid textual definition -WARN missing_definition alkali metal salt textual definition -WARN missing_definition natural product fundamental parent textual definition -WARN missing_definition steroid fundamental parent textual definition -WARN missing_definition cholane textual definition -WARN missing_definition carbon oxoacid textual definition -WARN missing_definition dicarboxylic acid anion textual definition -WARN missing_definition sulfated glycosaminoglycan textual definition -WARN missing_definition carbohydrate sulfate textual definition -WARN missing_definition pnictogen hydride textual definition -WARN missing_definition cholanoid textual definition -WARN missing_definition inorganic chloride textual definition -WARN missing_definition bile acid anion textual definition -WARN missing_definition 5beta-cholanic acid textual definition -WARN missing_definition cholanic acids textual definition -WARN missing_definition phosphorus oxoacid derivative textual definition -WARN missing_definition phosphorus oxoacids and derivatives textual definition -WARN missing_definition chalcogen hydride textual definition -WARN missing_definition argon molecular entity textual definition -WARN missing_definition inorganic ion textual definition -WARN missing_definition inorganic cation textual definition -WARN missing_definition carbon-14 atom textual definition -WARN missing_definition carbon-13 atom textual definition -WARN missing_definition carbon-11 atom textual definition -WARN missing_definition carbon-10 atom textual definition -WARN missing_definition carbon-12 atom textual definition -WARN missing_definition oxygen-19 atom textual definition -WARN missing_definition nitrogen-16 atom textual definition -WARN missing_definition nitrogen-17 atom textual definition -WARN missing_definition chalcocarbonic acid textual definition -WARN missing_definition amino-acid anion textual definition -WARN missing_definition organic hydride textual definition -WARN missing_definition mononuclear parent hydride textual definition -WARN missing_definition elemental sodium textual definition -WARN missing_definition polonium-190 atom textual definition -WARN missing_definition polonium-191 atom textual definition -WARN missing_definition polonium-192 atom textual definition -WARN missing_definition polonium-193 atom textual definition -WARN missing_definition polonium-194 atom textual definition -WARN missing_definition polonium-195 atom textual definition -WARN missing_definition polonium-196 atom textual definition -WARN missing_definition polonium-197 atom textual definition -WARN missing_definition polonium-198 atom textual definition -WARN missing_definition polonium-199 atom textual definition -WARN missing_definition polonium-200 atom textual definition -WARN missing_definition polonium-201 atom textual definition -WARN missing_definition polonium-202 atom textual definition -WARN missing_definition polonium-204 atom textual definition -WARN missing_definition halide textual definition -WARN missing_definition sulfuric acid derivative textual definition -WARN missing_definition organic heteropolycyclic compound textual definition -WARN missing_definition polycyclic heteroarene textual definition -WARN missing_definition aminoalkylindole textual definition -WARN missing_definition organic sodium salt textual definition -WARN missing_definition inorganic sodium salt textual definition -WARN missing_definition carbonate textual definition -WARN missing_definition hydroxy group textual definition -WARN missing_definition hydrogensulfate textual definition -WARN missing_definition oxo group textual definition -WARN missing_definition carboxy group textual definition -WARN missing_definition sulfur oxide textual definition -WARN missing_definition argon atom textual definition -WARN missing_definition hydrogen atom textual definition -WARN missing_definition holmium atom textual definition -WARN missing_definition iridium atom textual definition -WARN missing_definition krypton atom textual definition -WARN missing_definition praseodymium atom textual definition -WARN missing_definition rhenium atom textual definition -WARN missing_definition xenon atom textual definition -WARN missing_definition canonical nucleotide residue textual definition -WARN missing_definition canonical deoxyribonucleotide residue textual definition -WARN missing_definition canonical ribonucleotide residue textual definition -WARN missing_definition onium compound textual definition -WARN missing_definition nucleotide residue textual definition -WARN missing_definition nucleoside residue textual definition -WARN missing_definition nitrogen molecular entity textual definition -WARN missing_definition organic divalent group textual definition -WARN missing_definition organic univalent group textual definition -WARN missing_definition organic polycyclic compound textual definition -WARN missing_definition physiological role textual definition -WARN missing_definition inorganic hydroxy compound textual definition -WARN missing_definition greenhouse gas textual definition -WARN missing_definition environmental contaminant textual definition -WARN missing_definition neuronal receptor cell textual definition -WARN missing_definition neural crest derived neuron textual definition -WARN missing_definition branched duct epithelial cell textual definition -WARN missing_definition squamous epithelial cell textual definition -WARN missing_definition neuron associated cell textual definition -WARN missing_definition CNS neuron (sensu Vertebrata) textual definition -WARN missing_definition visual pigment cell textual definition -WARN missing_definition protein secreting cell textual definition -WARN missing_definition seromucus secreting cell textual definition -WARN missing_definition peptide hormone secreting cell textual definition -WARN missing_definition insulin secreting cell textual definition -WARN missing_definition somatostatin secreting cell textual definition -WARN missing_definition steroid hormone secreting cell textual definition -WARN missing_definition binucleate cell textual definition -WARN missing_definition eukaryotic cell textual definition -WARN missing_definition Eumycetozoan cell textual definition -WARN missing_definition eye photoreceptor cell textual definition -WARN missing_definition crystallin accumulating cell textual definition -WARN missing_definition mucus secreting cell textual definition -WARN missing_definition extracellular matrix secreting cell textual definition -WARN missing_definition oxygen accumulating cell textual definition -WARN missing_definition extraembryonic cell textual definition -WARN missing_definition ganglion interneuron textual definition -WARN missing_definition endopolyploid cell textual definition -WARN missing_definition carbohydrate secreting cell textual definition -WARN missing_definition biogenic amine secreting cell textual definition -WARN missing_definition fungal cell textual definition -WARN missing_definition fibroblast of dermis textual definition -WARN missing_definition epithelial cell of lower respiratory tract textual definition -WARN missing_definition visual system neuron textual definition -WARN missing_definition microcirculation associated smooth muscle cell textual definition -WARN missing_definition cardiac blood vessel endothelial cell textual definition -WARN missing_definition His-Purkinje system cell textual definition -WARN missing_definition cardiac endothelial cell textual definition -WARN missing_definition camera-type eye photoreceptor cell textual definition -WARN missing_definition cardiac glial cell textual definition -WARN missing_definition cardiac myoblast textual definition -WARN missing_definition stomach neuroendocrine cell textual definition -WARN missing_definition lung ciliated cell textual definition -WARN missing_definition lung secretory cell textual definition -WARN missing_definition trophectodermal cell textual definition -WARN missing_definition lung endothelial cell textual definition -WARN missing_definition pulmonary artery endothelial cell textual definition -WARN missing_definition lacks_part textual definition -WARN missing_definition lacks_plasma_membrane_part textual definition -WARN missing_definition action specification textual definition -WARN missing_definition concretizes textual definition -WARN missing_definition intended to realize textual definition -WARN missing_definition realizes textual definition -WARN missing_definition information representation textual definition -WARN missing_definition physical information carrier textual definition -WARN missing_definition has number of atomic nuclei textual definition -WARN missing_definition atherosclerosis textual definition -WARN missing_definition iris disease textual definition -WARN missing_definition liver disease textual definition -WARN missing_definition bone marrow disease textual definition -WARN missing_definition cornea cancer textual definition -WARN missing_definition grain of desert sand textual definition -WARN missing_definition wood textual definition -WARN missing_definition platinum mine textual definition -WARN missing_definition gold mine textual definition -WARN missing_definition coal mine textual definition -WARN missing_definition contaminated water textual definition -WARN missing_definition coal mine waste material textual definition -WARN missing_definition temperate grassland biome textual definition -WARN missing_definition litter layer textual definition -WARN missing_definition human house textual definition -WARN missing_definition swamp forest textual definition -WARN missing_definition needleleaf forest textual definition -WARN missing_definition sclerophyllous forest textual definition -WARN missing_definition montane forest textual definition -WARN missing_definition ceiling textual definition -WARN missing_definition atmospheric wind textual definition -WARN missing_definition water raindrop textual definition -WARN missing_definition algal material textual definition -WARN missing_definition forest canopy textual definition -WARN missing_definition gill tissue material textual definition -WARN missing_definition aquatic ecosystem textual definition -WARN missing_definition marine ecosystem textual definition -WARN missing_definition terrestrial ecosystem textual definition -WARN missing_definition temperate grassland textual definition -WARN missing_definition iron mine textual definition -WARN missing_definition uranium mine textual definition -WARN missing_definition iron ore textual definition -WARN missing_definition gold ore textual definition -WARN missing_definition platinum ore textual definition -WARN missing_definition cement dust textual definition -WARN missing_definition dust from plant parts textual definition -WARN missing_definition forest process textual definition -WARN missing_definition forest area expansion textual definition -WARN missing_definition generation of energy from coal textual definition -WARN missing_definition stellar radiation energy textual definition -WARN missing_definition coal power plant textual definition -WARN missing_definition solar power station textual definition -WARN missing_definition ocean thermal power station textual definition -WARN missing_definition tidal power plant textual definition -WARN missing_definition integumental system environment textual definition -WARN missing_definition results in distribution of textual definition -WARN missing_definition results in fission of textual definition -WARN missing_definition hasAncestryStatus textual definition -WARN missing_definition has measurement value textual definition -WARN missing_definition has measurement unit label textual definition -WARN missing_definition jaw movement textual definition -WARN missing_definition root textual definition -WARN missing_definition Cricetinae textual definition -WARN missing_definition Mesocricetus textual definition -WARN missing_definition Muridae textual definition -WARN missing_definition Mus caroli textual definition -WARN missing_definition Mus musculus textual definition -WARN missing_definition Mus spretus textual definition -WARN missing_definition Rattus textual definition -WARN missing_definition Viruses textual definition -WARN missing_definition Obtectomera textual definition -WARN missing_definition Lumbricinae textual definition -WARN missing_definition Lumbricus terrestris complex textual definition -WARN missing_definition Lumbricus rubellus complex textual definition -WARN missing_definition Sedentaria textual definition -WARN missing_definition Canalipalpata textual definition -WARN missing_definition Xenoturbellida textual definition -WARN missing_definition Xenoturbella textual definition -WARN missing_definition Sarsostraca textual definition -WARN missing_definition Phyllopoda textual definition -WARN missing_definition Anomopoda textual definition -WARN missing_definition Eubrachyura textual definition -WARN missing_definition Heterotremata textual definition -WARN missing_definition Myxini textual definition -WARN missing_definition Teleostomi textual definition -WARN missing_definition Euteleostomi textual definition -WARN missing_definition Chromadorea textual definition -WARN missing_definition Ecdysozoa textual definition -WARN missing_definition Lophotrochozoa textual definition -WARN missing_definition Neoteleostei textual definition -WARN missing_definition Eurypterygia textual definition -WARN missing_definition Ctenosquamata textual definition -WARN missing_definition Acanthomorphata textual definition -WARN missing_definition Euacanthomorphacea textual definition -WARN missing_definition Acipenserinae textual definition -WARN missing_definition Acipenserini textual definition -WARN missing_definition Zygnemophyceae textual definition -WARN missing_definition Streptophytina textual definition -WARN missing_definition Xenacoelomorpha textual definition -WARN missing_definition cellular organisms textual definition -WARN missing_definition Archelosauria textual definition -WARN missing_definition Dipnotetrapodomorpha textual definition -WARN missing_definition Eumycetozoa textual definition -WARN missing_definition Boreoeutheria textual definition -WARN missing_definition Acrogymnospermae textual definition -WARN missing_definition Mesangiospermae textual definition -WARN missing_definition Petrosaviidae textual definition -WARN missing_definition Gnetidae textual definition -WARN missing_definition Pinales textual definition -WARN missing_definition Acoelomorpha textual definition -WARN missing_definition Saccharomycotina textual definition -WARN missing_definition Schizosaccharomycetes textual definition -WARN missing_definition Cyclostomata textual definition -WARN missing_definition Osteoglossocephalai textual definition -WARN missing_definition Euteleosteomorpha textual definition -WARN missing_definition Percomorphaceae textual definition -WARN missing_definition Carangaria textual definition -WARN missing_definition Eupercaria textual definition -WARN missing_definition Xenoturbellidae textual definition -WARN missing_definition Galloanserae textual definition -WARN missing_definition Eisenia andrei textual definition -WARN missing_definition Acipenseroidei textual definition -WARN missing_definition Actinopteri textual definition -WARN missing_definition Clupeocephala textual definition -WARN missing_definition Otophysi textual definition -WARN missing_definition Cypriniphysae textual definition -WARN missing_definition Otomorpha textual definition -WARN missing_definition Myomorpha textual definition -WARN missing_definition Enchytraeida textual definition -WARN missing_definition Pancrustacea textual definition -WARN missing_definition Mandibulata textual definition -WARN missing_definition Bacteria textual definition -WARN missing_definition Dictyosteliaceae textual definition -WARN missing_definition Dictyosteliales textual definition -WARN missing_definition Homininae textual definition -WARN missing_definition Archaea textual definition -WARN missing_definition Multicrustacea textual definition -WARN missing_definition Hirudinida textual definition -WARN missing_definition Rhabditina textual definition -WARN missing_definition Rhabditomorpha textual definition -WARN missing_definition Evosea textual definition -WARN missing_definition Discoba textual definition -WARN missing_definition Xenopus textual definition -WARN missing_definition Zygnematophycidae textual definition -WARN missing_definition Ochrophyta textual definition -WARN missing_definition Spiralia textual definition -WARN missing_definition Sar textual definition -WARN missing_definition Danionidae textual definition -WARN missing_definition Danioninae textual definition -WARN missing_definition Eukaryota textual definition -WARN missing_definition Bovinae textual definition -WARN missing_definition Crassiclitellata textual definition -WARN missing_definition Conifers I textual definition -WARN missing_definition Phaeophyceae textual definition -WARN missing_definition Oryzomys textual definition -WARN missing_definition Cancroidea textual definition -WARN missing_definition Pipoidea textual definition -WARN missing_definition Ranoidea textual definition -WARN missing_definition Anthophila textual definition -WARN missing_definition Cyprinoidei textual definition -WARN missing_definition Pleuronectoidei textual definition -WARN missing_definition Tetraodontiformes textual definition -WARN missing_definition Tetraodontoidei textual definition -WARN missing_definition Tetraodontidae textual definition -WARN missing_definition Takifugu textual definition -WARN missing_definition Takifugu rubripes textual definition -WARN missing_definition Laurasiatheria textual definition -WARN missing_definition Euarchontoglires textual definition -WARN missing_definition Glires textual definition -WARN missing_definition Simiiformes textual definition -WARN missing_definition Cercopithecoidea textual definition -WARN missing_definition Hominoidea textual definition -WARN missing_definition Zygnematales textual definition -WARN missing_definition Embryophyta textual definition -WARN missing_definition Bryophyta textual definition -WARN missing_definition Sophophora textual definition -WARN missing_definition melanogaster group textual definition -WARN missing_definition melanogaster subgroup textual definition -WARN missing_definition Chondrostei textual definition -WARN missing_definition Teleostei textual definition -WARN missing_definition Tetradontoidea textual definition -WARN missing_definition Ostariophysi textual definition -WARN missing_definition Tetrapoda textual definition -WARN missing_definition Amniota textual definition -WARN missing_definition Theria textual definition -WARN missing_definition Sauria textual definition -WARN missing_definition Dictyostelia textual definition -WARN missing_definition Viridiplantae textual definition -WARN missing_definition Coniferophyta textual definition -WARN missing_definition Pinidae textual definition -WARN missing_definition Opisthokonta textual definition -WARN missing_definition Pinaceae textual definition -WARN missing_definition Metazoa textual definition -WARN missing_definition Bilateria textual definition -WARN missing_definition Protostomia textual definition -WARN missing_definition Neoptera textual definition -WARN missing_definition Endopterygota textual definition -WARN missing_definition Deuterostomia textual definition -WARN missing_definition Carnivora textual definition -WARN missing_definition Alveolata textual definition -WARN missing_definition Stramenopiles textual definition -WARN missing_definition Euglenozoa textual definition -WARN missing_definition Gnetopsida textual definition -WARN missing_definition Cricetidae textual definition -WARN missing_definition Muroidea textual definition -WARN missing_definition Gnetales textual definition -WARN missing_definition Felinae textual definition -WARN missing_definition Magnoliopsida textual definition -WARN missing_definition Schizosaccharomycetales textual definition -WARN missing_definition Apoidea textual definition -WARN missing_definition Streptophyta textual definition -WARN missing_definition Suina textual definition -WARN missing_definition Pecora textual definition -WARN missing_definition Ditrysia textual definition -WARN missing_definition Papilionoidea textual definition -WARN missing_definition Haplorrhini textual definition -WARN missing_definition Feliformia textual definition -WARN missing_definition Caniformia textual definition -WARN missing_definition Artemiidae textual definition -WARN missing_definition Glaucocystophyceae textual definition -WARN missing_definition Poales textual definition -WARN missing_definition Murinae textual definition -WARN missing_definition Sigmodontinae textual definition -WARN missing_definition Mammalia textual definition -WARN missing_definition Glossata textual definition -WARN missing_definition Neolepidoptera textual definition -WARN missing_definition Heteroneura textual definition -WARN missing_definition Siboglinidae textual definition -WARN missing_definition Neopterygii textual definition -WARN missing_definition Batrachia textual definition -WARN missing_definition Protacanthopterygii textual definition -WARN missing_definition Clitellata textual definition -WARN missing_definition Dinosauria textual definition -WARN missing_definition Saurischia textual definition -WARN missing_definition Theropoda textual definition -WARN missing_definition Coelurosauria textual definition -WARN missing_definition Muscomorpha textual definition -WARN missing_definition Schizophora textual definition -WARN missing_definition Acalyptratae textual definition -WARN missing_definition Ephydroidea textual definition -WARN missing_definition Drosophilinae textual definition -WARN missing_definition Liliopsida textual definition -WARN missing_definition Poaceae textual definition -WARN missing_definition Dikarya textual definition -WARN missing_definition Taphrinomycotina textual definition -WARN missing_definition Drosophilini textual definition -WARN missing_definition commelinids textual definition -WARN missing_definition Fungi textual definition -WARN missing_definition Cyclorrhapha textual definition -WARN missing_definition Eremoneura textual definition -WARN missing_definition Ascomycota textual definition -WARN missing_definition Saccharomycetes textual definition -WARN missing_definition Saccharomycetales textual definition -WARN missing_definition Saccharomycetaceae textual definition -WARN missing_definition Schizosaccharomycetaceae textual definition -WARN missing_definition Schizosaccharomyces textual definition -WARN missing_definition Schizosaccharomyces pombe textual definition -WARN missing_definition Saccharomyces textual definition -WARN missing_definition Saccharomyces cerevisiae textual definition -WARN missing_definition Salmoninae textual definition -WARN missing_definition Insecta textual definition -WARN missing_definition Amoebozoa textual definition -WARN missing_definition Hirudinea textual definition -WARN missing_definition Rhabditoidea textual definition -WARN missing_definition Peloderinae textual definition -WARN missing_definition PX clade textual definition -WARN missing_definition Dictyostelium textual definition -WARN missing_definition Pinopsida textual definition -WARN missing_definition Tracheophyta textual definition -WARN missing_definition Spermatophyta textual definition -WARN missing_definition Porifera textual definition -WARN missing_definition Eumetazoa textual definition -WARN missing_definition Cnidaria textual definition -WARN missing_definition Platyhelminthes textual definition -WARN missing_definition Nematoda textual definition -WARN missing_definition Rhabditida textual definition -WARN missing_definition Caenorhabditis textual definition -WARN missing_definition Caenorhabditis elegans textual definition -WARN missing_definition Rhabditidae textual definition -WARN missing_definition Annelida textual definition -WARN missing_definition Polychaeta textual definition -WARN missing_definition Sabellida textual definition -WARN missing_definition Oligochaeta textual definition -WARN missing_definition Enchytraeidae textual definition -WARN missing_definition Enchytraeus textual definition -WARN missing_definition Lumbricina textual definition -WARN missing_definition Lumbricidae textual definition -WARN missing_definition Eisenia textual definition -WARN missing_definition Eisenia fetida textual definition -WARN missing_definition Lumbricus textual definition -WARN missing_definition Lumbricus terrestris textual definition -WARN missing_definition Hirudiniformes textual definition -WARN missing_definition Hirudinidae textual definition -WARN missing_definition Mollusca textual definition -WARN missing_definition Arthropoda textual definition -WARN missing_definition Crustacea textual definition -WARN missing_definition Branchiopoda textual definition -WARN missing_definition Anostraca textual definition -WARN missing_definition Artemia textual definition -WARN missing_definition Cladocera textual definition -WARN missing_definition Daphnia textual definition -WARN missing_definition Malacostraca textual definition -WARN missing_definition Eucarida textual definition -WARN missing_definition Decapoda textual definition -WARN missing_definition Pleocyemata textual definition -WARN missing_definition Brachyura textual definition -WARN missing_definition Cancridae textual definition -WARN missing_definition Hexapoda textual definition -WARN missing_definition Lepidoptera textual definition -WARN missing_definition Diptera textual definition -WARN missing_definition saccharomyceta textual definition -WARN missing_definition Brachycera textual definition -WARN missing_definition Eumalacostraca textual definition -WARN missing_definition Drosophilidae textual definition -WARN missing_definition Drosophila textual definition -WARN missing_definition Drosophila melanogaster textual definition -WARN missing_definition Hymenoptera textual definition -WARN missing_definition Apocrita textual definition -WARN missing_definition Aculeata textual definition -WARN missing_definition Apidae textual definition -WARN missing_definition Pterygota textual definition -WARN missing_definition Chordata textual definition -WARN missing_definition Tunicata textual definition -WARN missing_definition Vertebrata textual definition -WARN missing_definition Myxiniformes textual definition -WARN missing_definition Myxinidae textual definition -WARN missing_definition Daphniidae textual definition -WARN missing_definition Gnathostomata textual definition -WARN missing_definition Chondrichthyes textual definition -WARN missing_definition Euphyllophyta textual definition -WARN missing_definition Holocephali textual definition -WARN missing_definition Chimaeriformes textual definition -WARN missing_definition Dipnomorpha textual definition -WARN missing_definition Actinopterygii textual definition -WARN missing_definition Acipenseriformes textual definition -WARN missing_definition Acipenseridae textual definition -WARN missing_definition Acipenser textual definition -WARN missing_definition Cypriniformes textual definition -WARN missing_definition Danio textual definition -WARN missing_definition Danio rerio textual definition -WARN missing_definition Salmoniformes textual definition -WARN missing_definition Salmonidae textual definition -WARN missing_definition Oncorhynchus textual definition -WARN missing_definition Salmo textual definition -WARN missing_definition Pleuronectiformes textual definition -WARN missing_definition Pleuronectidae textual definition -WARN missing_definition Sarcopterygii textual definition -WARN missing_definition Amphibia textual definition -WARN missing_definition Anura textual definition -WARN missing_definition Pipidae textual definition -WARN missing_definition Xenopus textual definition -WARN missing_definition Xenopus laevis textual definition -WARN missing_definition Xenopodinae textual definition -WARN missing_definition Ranidae textual definition -WARN missing_definition Neobatrachia textual definition -WARN missing_definition Diplostraca textual definition -WARN missing_definition Sauropsida textual definition -WARN missing_definition Archosauria textual definition -WARN missing_definition Dicondylia textual definition -WARN missing_definition Artemia salina textual definition -WARN missing_definition Amphiesmenoptera textual definition -WARN missing_definition Mus textual definition -WARN missing_definition Aves textual definition -WARN missing_definition Palaeognathae textual definition -WARN missing_definition Struthioniformes textual definition -WARN missing_definition Struthionidae textual definition -WARN missing_definition Struthio textual definition -WARN missing_definition Struthio camelus textual definition -WARN missing_definition Neognathae textual definition -WARN missing_definition Anseriformes textual definition -WARN missing_definition Anatidae textual definition -WARN missing_definition Panarthropoda textual definition -WARN missing_definition Columbiformes textual definition -WARN missing_definition Columbidae textual definition -WARN missing_definition Craniata textual definition -WARN missing_definition Galliformes textual definition -WARN missing_definition Phasianidae textual definition -WARN missing_definition Gallus textual definition -WARN missing_definition Gallus gallus textual definition -WARN missing_definition Phasianinae textual definition -WARN missing_definition Enchytraeus crypticus textual definition -WARN missing_definition Artiodactyla textual definition -WARN missing_definition Prototheria textual definition -WARN missing_definition Monotremata textual definition -WARN missing_definition Tachyglossidae textual definition -WARN missing_definition Eutheria textual definition -WARN missing_definition Primates textual definition -WARN missing_definition Platyrrhini textual definition -WARN missing_definition Catarrhini textual definition -WARN missing_definition Cercopithecidae textual definition -WARN missing_definition Cercopithecinae textual definition -WARN missing_definition Macaca textual definition -WARN missing_definition Macaca mulatta textual definition -WARN missing_definition Hominidae textual definition -WARN missing_definition Homo textual definition -WARN missing_definition Homo sapiens textual definition -WARN missing_definition Canidae textual definition -WARN missing_definition Canis textual definition -WARN missing_definition Vulpes textual definition -WARN missing_definition Felidae textual definition -WARN missing_definition Felis textual definition -WARN missing_definition Felis catus textual definition -WARN missing_definition Suidae textual definition -WARN missing_definition Sus textual definition -WARN missing_definition Ruminantia textual definition -WARN missing_definition Cervidae textual definition -WARN missing_definition Rangifer textual definition -WARN missing_definition Odocoileinae textual definition -WARN missing_definition Bovidae textual definition -WARN missing_definition Bos textual definition -WARN missing_definition Bos taurus textual definition -WARN missing_definition Ovis textual definition -WARN missing_definition Ovis aries textual definition -WARN missing_definition Caprinae textual definition -WARN missing_definition Lagomorpha textual definition -WARN missing_definition Rodentia textual definition -WARN missing_definition plan textual definition -WARN missing_definition qualitative textual definition -WARN missing_definition physical quality of a process textual definition -WARN missing_definition sloped downward textual definition -WARN missing_definition astronaut textual definition -WARN missing_definition military textual definition -WARN missing_definition medical professional textual definition -WARN missing_definition dentist textual definition -WARN missing_definition radiologist textual definition -WARN missing_definition risk estimate textual definition -WARN missing_definition lifetime risk estimate textual definition -WARN missing_definition biological process textual definition -WARN missing_definition cellular process textual definition -WARN missing_definition track formation textual definition -WARN missing_definition mass number textual definition -WARN missing_definition contained in textual definition -WARN missing_definition contains textual definition -WARN missing_definition innervated_by textual definition -WARN missing_definition has component activity textual definition -WARN missing_definition directly regulated by textual definition -WARN missing_definition before or simultaneous with textual definition -WARN missing_definition during which ends textual definition -WARN missing_definition ends after textual definition -WARN missing_definition immediately preceded by textual definition -WARN missing_definition immediately precedes textual definition -WARN missing_definition ends during textual definition -WARN missing_definition temporally related to textual definition -WARN missing_definition part of developmental precursor of textual definition -WARN missing_definition results in formation of textual definition -WARN missing_definition results in growth of textual definition -WARN missing_definition results in transport to from or in textual definition -WARN missing_definition formed as result of textual definition -WARN missing_definition immediately causally downstream of textual definition -WARN missing_definition phosphorylates textual definition -WARN missing_definition helper property (not for use in curation) textual definition -WARN missing_definition is kinase activity textual definition -WARN missing_definition receives input from textual definition -WARN missing_definition sends output to textual definition -WARN missing_definition relation between physical entity and a process or stage textual definition -WARN missing_definition depends on textual definition -WARN missing_definition causal relation between entities textual definition -WARN missing_definition causally influenced by textual definition -WARN missing_definition interaction relation helper property textual definition -WARN missing_definition molecular interaction relation helper property textual definition -WARN missing_definition results in assembly of textual definition -WARN missing_definition results in disassembly of textual definition -WARN missing_definition acts upstream of or within, positive effect textual definition -WARN missing_definition acts upstream of or within, negative effect textual definition -WARN missing_definition causally upstream of or within, negative effect textual definition -WARN missing_definition causally upstream of or within, positive effect textual definition -WARN missing_definition results in fusion of textual definition -WARN missing_definition agent role textual definition -WARN missing_definition chemosensory organ textual definition -WARN missing_definition anterior region of body textual definition -WARN missing_definition posterior region of body textual definition -WARN missing_definition membranous layer textual definition -WARN missing_definition vertebral foramen of atlas textual definition -WARN missing_definition head sensillum textual definition -WARN missing_definition subdivision of head textual definition -WARN missing_definition muscle of iris textual definition -WARN missing_definition gastric juice textual definition -WARN missing_definition parenchyma of pancreas textual definition -WARN missing_definition organ cavity textual definition -WARN missing_definition posterior neural tube textual definition -WARN missing_definition anterior neural tube textual definition -WARN missing_definition set of muscles of vertebral column textual definition -WARN missing_definition biliary bud textual definition -WARN missing_definition right horn of sinus venosus textual definition -WARN missing_definition basal plate metencephalon textual definition -WARN missing_definition outflow tract pulmonary component textual definition -WARN missing_definition developing anatomical structure textual definition -WARN missing_definition cervical region textual definition -WARN missing_definition non-neural ectoderm textual definition -WARN missing_definition extrahepatic part of hepatic duct textual definition -WARN missing_definition left dorsal aorta textual definition -WARN missing_definition right dorsal aorta textual definition -WARN missing_definition chemosensory system textual definition -WARN missing_definition extraembryonic mesoderm textual definition -WARN missing_definition spinal cord segment textual definition -WARN missing_definition pre-muscle condensation textual definition -WARN missing_definition zone of bone organ textual definition -WARN missing_definition neurocranial trabecula textual definition -WARN missing_definition posterior surface of head textual definition -WARN missing_definition common atrial chamber textual definition -WARN missing_definition ethmoid bone primordium textual definition -WARN missing_definition tetrapod frontal bone primordium textual definition -WARN missing_definition future spinal cord textual definition -WARN missing_definition future trigeminal ganglion textual definition -WARN missing_definition presumptive blood textual definition -WARN missing_definition glandular cuboidal epithelium textual definition -WARN missing_definition presumptive gut textual definition -WARN missing_definition mechanosensory system textual definition -WARN missing_definition 1st arch mandibular component textual definition -WARN missing_definition 1st arch maxillary component textual definition -WARN missing_definition early pharyngeal endoderm textual definition -WARN missing_definition microvascular endothelium textual definition -WARN missing_definition liver bud textual definition -WARN missing_definition respiratory primordium textual definition -WARN missing_definition pharyngeal region of foregut textual definition -WARN missing_definition indifferent external genitalia textual definition -WARN missing_definition embryonic nasal process textual definition -WARN missing_definition subdivision of trunk textual definition -WARN missing_definition midbrain mantle layer textual definition -WARN missing_definition spinal cord mantle layer textual definition -WARN missing_definition midbrain hindbrain boundary neural plate textual definition -WARN missing_definition trunk paraxial mesoderm textual definition -WARN missing_definition artery of lip textual definition -WARN missing_definition gut mesentery textual definition -WARN missing_definition dorsal pancreas textual definition -WARN missing_definition ventral pancreas textual definition -WARN missing_definition entire pharyngeal arch endoderm textual definition -WARN missing_definition sac textual definition -WARN missing_definition anterior lateral plate mesoderm textual definition -WARN missing_definition lobule textual definition -WARN missing_definition optic neural crest textual definition -WARN missing_definition aortic system textual definition -WARN missing_definition layer of sclera textual definition -WARN missing_definition germ layer / neural crest textual definition -WARN missing_definition pancreas dorsal primordium textual definition -WARN missing_definition pancreas ventral primordium textual definition -WARN missing_definition pneumatic cavity of bone textual definition -WARN missing_definition primary subdivision of cranial skeletal system textual definition -WARN missing_definition intra-ocular muscle textual definition -WARN missing_definition fibrous membrane of synovial tendon sheath textual definition -WARN missing_definition embryonic skin basal layer textual definition -WARN missing_definition lumen of gastrointestinal system textual definition -WARN missing_definition future upper lip textual definition -WARN missing_definition future lower lip textual definition -WARN missing_definition jaw muscle textual definition -WARN missing_definition fibrous connective tissue textual definition -WARN missing_definition collection of collagen fibrils textual definition -WARN missing_definition palatal part of dermatocranium textual definition -WARN missing_definition internal anal region textual definition -WARN missing_definition respiratory system arterial smooth muscle textual definition -WARN missing_definition extraembryonic cavity textual definition -WARN missing_definition external anal region textual definition -WARN missing_definition cloacal villus textual definition -WARN missing_definition subdivision of tube textual definition -WARN missing_definition subepicardial layer of epicardium textual definition -WARN missing_definition heart plus pericardium textual definition -WARN missing_definition heterogeneous tissue textual definition -WARN missing_definition spinal cord column textual definition -WARN missing_definition lamina of gray matter of spinal cord textual definition -WARN missing_definition fibrocollagenous connective tissue textual definition -WARN missing_definition skeletal musculature textual definition -WARN missing_definition cardiac muscle tissue of ventricle textual definition -WARN missing_definition dorsal side of post-anal tail textual definition -WARN missing_definition reproductive system mucosa textual definition -WARN missing_definition carotid artery endothelium textual definition -WARN missing_definition mucous gland of lung textual definition -WARN missing_definition gray matter of hindbrain textual definition -WARN missing_definition gray matter of midbrain textual definition -WARN missing_definition sensory organ epithelium textual definition -WARN missing_definition surface of eyeball textual definition -WARN missing_definition splenic arteriole textual definition -WARN missing_definition hindbrain marginal layer textual definition -WARN missing_definition spinal cord ventricular layer textual definition -WARN missing_definition sympathetic nerve textual definition -WARN missing_definition lymphomyeloid tissue textual definition -WARN missing_definition gland lumen textual definition -WARN missing_definition zone of organ textual definition -WARN missing_definition epithelial layer of duct textual definition -WARN missing_definition jaw epithelium textual definition -WARN missing_definition rectal artery textual definition -WARN missing_definition excretory duct textual definition -WARN missing_definition branch of external carotid artery textual definition -WARN missing_definition uveal vein textual definition -WARN missing_definition colic artery textual definition -WARN missing_definition cavity of cardiac chamber textual definition -WARN missing_definition serous cavity textual definition -WARN missing_definition wall of blood vessel textual definition -WARN missing_definition respiratory primordium epithelium textual definition -WARN missing_definition respiratory primordium mesenchyme textual definition -WARN missing_definition fibroelastic connective tissue textual definition -WARN missing_definition orifice of skull textual definition -WARN missing_definition pelvic vein textual definition -WARN missing_definition anterior wall of left ventricle textual definition -WARN missing_definition myocardium of anterior wall of left ventricle textual definition -WARN missing_definition myocardium of anterior wall of right ventricle textual definition -WARN missing_definition vasculature of spleen textual definition -WARN missing_definition vasculature of central nervous system plus retina textual definition -WARN missing_definition vasculature of central nervous system textual definition -WARN missing_definition wall of gallbladder textual definition -WARN missing_definition wall of brachiocephalic artery textual definition -WARN missing_definition wall of subclavian artery textual definition -WARN missing_definition wall of anal canal textual definition -WARN missing_definition wall of pulmonary artery textual definition -WARN missing_definition wall of synovial tendon sheath textual definition -WARN missing_definition wall of eyeball textual definition -WARN missing_definition wall of orbit textual definition -WARN missing_definition wall of common carotid artery textual definition -WARN missing_definition sigmoid vein textual definition -WARN missing_definition pancreatic artery textual definition -WARN missing_definition axial vasculature textual definition -WARN missing_definition panarthropod head textual definition -WARN missing_definition electric current unit textual definition -WARN missing_definition temperature unit textual definition -WARN missing_definition substance unit textual definition -WARN missing_definition luminous intensity unit textual definition -WARN missing_definition ampere textual definition -WARN missing_definition kelvin textual definition -WARN missing_definition mole textual definition -WARN missing_definition candela textual definition -WARN missing_definition picometer textual definition -WARN missing_definition femtogram textual definition -WARN missing_definition millisecond textual definition -WARN missing_definition microsecond textual definition -WARN missing_definition picosecond textual definition -WARN missing_definition milliampere textual definition -WARN missing_definition microampere textual definition -WARN missing_definition millimole textual definition -WARN missing_definition femtomole textual definition -WARN missing_definition attomole textual definition -WARN missing_definition base unit textual definition -WARN missing_definition area unit textual definition -WARN missing_definition acceleration unit textual definition -WARN missing_definition angular velocity unit textual definition -WARN missing_definition angular acceleration unit textual definition -WARN missing_definition concentration unit textual definition -WARN missing_definition mass density unit textual definition -WARN missing_definition luminance unit textual definition -WARN missing_definition area density unit textual definition -WARN missing_definition molar mass unit textual definition -WARN missing_definition molar volume unit textual definition -WARN missing_definition momentum unit textual definition -WARN missing_definition rotational frequency unit textual definition -WARN missing_definition specific volume unit textual definition -WARN missing_definition speed/velocity unit textual definition -WARN missing_definition unit of molarity textual definition -WARN missing_definition unit of molality textual definition -WARN missing_definition molal textual definition -WARN missing_definition millimolal textual definition -WARN missing_definition micromolal textual definition -WARN missing_definition nanomolal textual definition -WARN missing_definition picomolal textual definition -WARN missing_definition femtomolar textual definition -WARN missing_definition unit of normality textual definition -WARN missing_definition normal textual definition -WARN missing_definition mole fraction textual definition -WARN missing_definition meter per second per second textual definition -WARN missing_definition radian per second per second textual definition -WARN missing_definition radian per second textual definition -WARN missing_definition square meter textual definition -WARN missing_definition square centimeter textual definition -WARN missing_definition square millimeter textual definition -WARN missing_definition kilogram per cubic meter textual definition -WARN missing_definition gram per cubic centimeter textual definition -WARN missing_definition candela per square meter textual definition -WARN missing_definition kilogram per square meter textual definition -WARN missing_definition kilogram per mole textual definition -WARN missing_definition gram per mole textual definition -WARN missing_definition cubic meter per mole textual definition -WARN missing_definition cubic centimeter per mole textual definition -WARN missing_definition kilogram meter per second textual definition -WARN missing_definition turns per second textual definition -WARN missing_definition cubic meter per kilogram textual definition -WARN missing_definition meter per second textual definition -WARN missing_definition volume unit textual definition -WARN missing_definition cubic meter textual definition -WARN missing_definition femtoliter textual definition -WARN missing_definition frequency unit textual definition -WARN missing_definition force unit textual definition -WARN missing_definition newton textual definition -WARN missing_definition pressure unit textual definition -WARN missing_definition pascal textual definition -WARN missing_definition energy unit textual definition -WARN missing_definition joule textual definition -WARN missing_definition power unit textual definition -WARN missing_definition watt textual definition -WARN missing_definition illuminance unit textual definition -WARN missing_definition lux textual definition -WARN missing_definition luminous flux unit textual definition -WARN missing_definition lumen textual definition -WARN missing_definition catalytic activity unit textual definition -WARN missing_definition katal textual definition -WARN missing_definition angle unit textual definition -WARN missing_definition plane angle unit textual definition -WARN missing_definition radian textual definition -WARN missing_definition solid angle unit textual definition -WARN missing_definition steradian textual definition -WARN missing_definition radiation unit textual definition -WARN missing_definition activity (of a radionuclide) unit textual definition -WARN missing_definition dose equivalent unit textual definition -WARN missing_definition exposure unit textual definition -WARN missing_definition becquerel textual definition -WARN missing_definition curie textual definition -WARN missing_definition gray textual definition -WARN missing_definition rad textual definition -WARN missing_definition roentgen textual definition -WARN missing_definition sievert textual definition -WARN missing_definition millisievert textual definition -WARN missing_definition microsievert textual definition -WARN missing_definition Roentgen equivalent man textual definition -WARN missing_definition microgray textual definition -WARN missing_definition milligray textual definition -WARN missing_definition nanogray textual definition -WARN missing_definition nanosievert textual definition -WARN missing_definition millicurie textual definition -WARN missing_definition microcurie textual definition -WARN missing_definition disintegrations per minute textual definition -WARN missing_definition counts per minute textual definition -WARN missing_definition nanosecond textual definition -WARN missing_definition century textual definition -WARN missing_definition half life textual definition -WARN missing_definition foot candle textual definition -WARN missing_definition irradiance unit textual definition -WARN missing_definition watt per square meter textual definition -WARN missing_definition einstein per square meter per second textual definition -WARN missing_definition light unit textual definition -WARN missing_definition watt per steradian per square meter textual definition -WARN missing_definition radiant intensity unit textual definition -WARN missing_definition microeinstein per square meter per second textual definition -WARN missing_definition radiance unit textual definition -WARN missing_definition watt per steradian textual definition -WARN missing_definition parts per notation unit textual definition -WARN missing_definition parts per hundred textual definition -WARN missing_definition parts per thousand textual definition -WARN missing_definition parts per million textual definition -WARN missing_definition parts per billion textual definition -WARN missing_definition parts per trillion textual definition -WARN missing_definition parts per quadrillion textual definition -WARN missing_definition gram per milliliter textual definition -WARN missing_definition kilogram per liter textual definition -WARN missing_definition unit per volume unit textual definition -WARN missing_definition unit per milliliter textual definition -WARN missing_definition unit per liter textual definition -WARN missing_definition mass per unit volume textual definition -WARN missing_definition enzyme unit textual definition -WARN missing_definition density unit textual definition -WARN missing_definition linear density unit textual definition -WARN missing_definition kilogram per meter textual definition -WARN missing_definition degree textual definition -WARN missing_definition dimensionless unit textual definition -WARN missing_definition percent textual definition -WARN missing_definition pi textual definition -WARN missing_definition count unit textual definition -WARN missing_definition ratio unit textual definition -WARN missing_definition fraction textual definition -WARN missing_definition molecule count textual definition -WARN missing_definition purity percentage textual definition -WARN missing_definition confluence percentage textual definition -WARN missing_definition liter per kilogram textual definition -WARN missing_definition milliliter per kilogram textual definition -WARN missing_definition microliter per kilogram textual definition -WARN missing_definition cell concentration unit textual definition -WARN missing_definition cells per milliliter textual definition -WARN missing_definition catalytic (activity) concentration unit textual definition -WARN missing_definition katal per cubic meter textual definition -WARN missing_definition katal per liter textual definition -WARN missing_definition volume per unit volume textual definition -WARN missing_definition milliliter per cubic meter textual definition -WARN missing_definition deciliter textual definition -WARN missing_definition colony forming unit textual definition -WARN missing_definition plaque forming unit textual definition -WARN missing_definition colony forming unit per milliliter textual definition -WARN missing_definition plaque forming unit per volume textual definition -WARN missing_definition plaque forming unit per milliliter textual definition -WARN missing_definition disintegrations per second textual definition -WARN missing_definition electric potential difference unit textual definition -WARN missing_definition volt textual definition -WARN missing_definition electric charge textual definition -WARN missing_definition coulomb textual definition -WARN missing_definition dalton textual definition -WARN missing_definition kilodalton textual definition -WARN missing_definition watt-hour textual definition -WARN missing_definition kilowatt-hour textual definition -WARN missing_definition magnetic flux unit textual definition -WARN missing_definition weber textual definition -WARN missing_definition magnetic flux density unit textual definition -WARN missing_definition tesla textual definition -WARN missing_definition volt-hour textual definition -WARN missing_definition kilovolt-hour textual definition -WARN missing_definition information unit textual definition -WARN missing_definition bit textual definition -WARN missing_definition byte textual definition -WARN missing_definition kilobyte textual definition -WARN missing_definition megabyte textual definition -WARN missing_definition image resolution unit textual definition -WARN missing_definition chroma sampling unit textual definition -WARN missing_definition dynamic range unit textual definition -WARN missing_definition spatial resolution unit textual definition -WARN missing_definition dots per inch textual definition -WARN missing_definition micron pixel textual definition -WARN missing_definition pixels per inch textual definition -WARN missing_definition pixels per millimeter textual definition -WARN missing_definition base pair textual definition -WARN missing_definition kibibyte textual definition -WARN missing_definition mebibyte textual definition -WARN missing_definition millivolt textual definition -WARN missing_definition kilovolt textual definition -WARN missing_definition microvolt textual definition -WARN missing_definition nanovolt textual definition -WARN missing_definition picovolt textual definition -WARN missing_definition megavolt textual definition -WARN missing_definition surface tension unit textual definition -WARN missing_definition newton per meter textual definition -WARN missing_definition dyne per cm textual definition -WARN missing_definition viscosity unit textual definition -WARN missing_definition pascal second textual definition -WARN missing_definition poise textual definition -WARN missing_definition decibel textual definition -WARN missing_definition effective dose unit textual definition -WARN missing_definition conduction unit textual definition -WARN missing_definition electrical conduction unit textual definition -WARN missing_definition heat conduction unit textual definition -WARN missing_definition siemens textual definition -WARN missing_definition watt per meter kelvin textual definition -WARN missing_definition electronvolt textual definition -WARN missing_definition electric field strength unit textual definition -WARN missing_definition volt per meter textual definition -WARN missing_definition absorbance unit textual definition -WARN missing_definition volumetric flow rate unit textual definition -WARN missing_definition millimetres of mercury textual definition -WARN missing_definition milligram per liter textual definition -WARN missing_definition microgram per milliliter textual definition -WARN missing_definition nanogram per milliliter textual definition -WARN missing_definition milliunits per milliliter textual definition -WARN missing_definition rate unit textual definition -WARN missing_definition kilogram per hectare textual definition -WARN missing_definition giga textual definition -WARN missing_definition mega textual definition -WARN missing_definition kilo textual definition -WARN missing_definition deci textual definition -WARN missing_definition milli textual definition -WARN missing_definition centi textual definition -WARN missing_definition micro textual definition -WARN missing_definition nano textual definition -WARN missing_definition pico textual definition -WARN missing_definition femto textual definition -WARN missing_definition atto textual definition -WARN missing_definition dose unit textual definition -WARN missing_definition milligram per kilogram textual definition -WARN missing_definition milligram per square meter textual definition -WARN missing_definition dosage unit textual definition -WARN missing_definition milligram per kilogram per day textual definition -WARN missing_definition relative light unit textual definition -WARN missing_definition relative luminescence unit textual definition -WARN missing_definition relative fluorescence unit textual definition -WARN missing_definition megaHertz textual definition -WARN missing_definition centiMorgan textual definition -WARN missing_definition centiRay textual definition -WARN missing_definition mega base pair textual definition -WARN missing_definition giga base pair textual definition -WARN missing_definition square micrometer textual definition -WARN missing_definition millisiemens textual definition -WARN missing_definition micromole per litre textual definition -WARN missing_definition micromole per kilogram textual definition -WARN missing_definition millimeters per day textual definition -WARN missing_definition kilometer per hour textual definition -WARN missing_definition milli textual definition -WARN missing_definition hectare textual definition -WARN missing_definition inch textual definition -WARN missing_definition thou textual definition -WARN missing_definition foot textual definition -WARN missing_definition yard textual definition -WARN missing_definition chain textual definition -WARN missing_definition furlong textual definition -WARN missing_definition mile textual definition -WARN missing_definition league textual definition -WARN missing_definition maritime length unit textual definition -WARN missing_definition fathom textual definition -WARN missing_definition cable textual definition -WARN missing_definition nautical mile textual definition -WARN missing_definition perch textual definition -WARN missing_definition rood textual definition -WARN missing_definition acre textual definition -WARN missing_definition fluid ounce textual definition -WARN missing_definition gill textual definition -WARN missing_definition pint textual definition -WARN missing_definition quart textual definition -WARN missing_definition gallon textual definition -WARN missing_definition grain textual definition -WARN missing_definition drachm textual definition -WARN missing_definition ounce textual definition -WARN missing_definition pound textual definition -WARN missing_definition stone textual definition -WARN missing_definition quarter textual definition -WARN missing_definition hundredweight textual definition -WARN missing_definition ton textual definition -WARN missing_definition slug textual definition -WARN missing_definition teaspoon textual definition -WARN missing_definition micromole textual definition -WARN missing_definition gram per square meter textual definition -WARN missing_definition nanogram per microliter textual definition -WARN missing_definition large calorie textual definition -WARN missing_definition micrograms per wheaton bottle textual definition -WARN missing_definition picoampere textual definition -WARN missing_definition centigray textual definition -WARN missing_definition gigaelectronvolt textual definition -WARN missing_definition gigaelectronvolt per nucleon textual definition -WARN missing_definition megaelectronvolt per nucleon textual definition -WARN missing_definition kiloelectronvolt per micron textual definition -WARN missing_definition gray per minute textual definition -WARN missing_definition centigray per minute textual definition -WARN missing_definition milligray per minute textual definition -WARN missing_definition milligray per day textual definition -WARN missing_definition milligray per hour textual definition -WARN missing_definition milligray per second textual definition -WARN missing_definition kilometer textual definition -WARN missing_definition milligram per deciliter textual definition -WARN missing_definition microgram per deciliter textual definition -WARN missing_definition meter based unit textual definition -WARN missing_definition second based unit textual definition -WARN missing_definition ampere based unit textual definition -WARN missing_definition kelvin based unit textual definition -WARN missing_definition mole based unit textual definition -WARN missing_definition candela based unit textual definition -WARN missing_definition angstrom based unit textual definition -WARN missing_definition gram based unit textual definition -WARN missing_definition degree Celsius based unit textual definition -WARN missing_definition minute based unit textual definition -WARN missing_definition hour based unit textual definition -WARN missing_definition day based unit textual definition -WARN missing_definition week based unit textual definition -WARN missing_definition month based unit textual definition -WARN missing_definition year based unit textual definition -WARN missing_definition molar based unit textual definition -WARN missing_definition molal based unit textual definition -WARN missing_definition normal based unit textual definition -WARN missing_definition mole fraction based unit textual definition -WARN missing_definition meter per second per second based unit textual definition -WARN missing_definition radian per second per second based unit textual definition -WARN missing_definition radian per second based unit textual definition -WARN missing_definition square meter based unit textual definition -WARN missing_definition square centimeter based unit textual definition -WARN missing_definition square millimeter based unit textual definition -WARN missing_definition gram per cubic centimeter based unit textual definition -WARN missing_definition candela per square meter based unit textual definition -WARN missing_definition gram per mole based unit textual definition -WARN missing_definition cubic meter per mole based unit textual definition -WARN missing_definition cubic centimeter per mole based unit textual definition -WARN missing_definition turns per second based unit textual definition -WARN missing_definition cubic meter per kilogram based unit textual definition -WARN missing_definition meter per second based unit textual definition -WARN missing_definition cubic meter based unit textual definition -WARN missing_definition cubic centimeter based unit textual definition -WARN missing_definition liter based unit textual definition -WARN missing_definition cubic decimeter based unit textual definition -WARN missing_definition hertz based unit textual definition -WARN missing_definition newton based unit textual definition -WARN missing_definition pascal based unit textual definition -WARN missing_definition joule based unit textual definition -WARN missing_definition watt based unit textual definition -WARN missing_definition lux based unit textual definition -WARN missing_definition lumen based unit textual definition -WARN missing_definition katal based unit textual definition -WARN missing_definition radian based unit textual definition -WARN missing_definition steradian based unit textual definition -WARN missing_definition becquerel based unit textual definition -WARN missing_definition curie based unit textual definition -WARN missing_definition gray based unit textual definition -WARN missing_definition rad based unit textual definition -WARN missing_definition roentgen based unit textual definition -WARN missing_definition sievert based unit textual definition -WARN missing_definition Roentgen equivalent man based unit textual definition -WARN missing_definition disintegrations per minute based unit textual definition -WARN missing_definition counts per minute based unit textual definition -WARN missing_definition century based unit textual definition -WARN missing_definition half life based unit textual definition -WARN missing_definition foot candle based unit textual definition -WARN missing_definition watt per square meter based unit textual definition -WARN missing_definition einstein per square meter per second based unit textual definition -WARN missing_definition watt per steradian per square meter based unit textual definition -WARN missing_definition watt per steradian based unit textual definition -WARN missing_definition mass percentage based unit textual definition -WARN missing_definition mass volume percentage based unit textual definition -WARN missing_definition volume percentage based unit textual definition -WARN missing_definition parts per hundred based unit textual definition -WARN missing_definition parts per thousand based unit textual definition -WARN missing_definition parts per million based unit textual definition -WARN missing_definition parts per billion based unit textual definition -WARN missing_definition parts per trillion based unit textual definition -WARN missing_definition parts per quadrillion based unit textual definition -WARN missing_definition gram per milliliter based unit textual definition -WARN missing_definition gram per liter based unit textual definition -WARN missing_definition unit per milliliter based unit textual definition -WARN missing_definition unit per liter based unit textual definition -WARN missing_definition mass per unit volume based unit textual definition -WARN missing_definition enzyme unit based unit textual definition -WARN missing_definition degree based unit textual definition -WARN missing_definition pi based unit textual definition -WARN missing_definition molecule count based unit textual definition -WARN missing_definition purity percentage based unit textual definition -WARN missing_definition confluence percentage based unit textual definition -WARN missing_definition degree Fahrenheit based unit textual definition -WARN missing_definition pH based unit textual definition -WARN missing_definition liter per kilogram based unit textual definition -WARN missing_definition cells per milliliter based unit textual definition -WARN missing_definition katal per cubic meter based unit textual definition -WARN missing_definition katal per liter based unit textual definition -WARN missing_definition gram per deciliter based unit textual definition -WARN missing_definition colony forming unit based unit textual definition -WARN missing_definition plaque forming unit based unit textual definition -WARN missing_definition colony forming unit per milliliter based unit textual definition -WARN missing_definition plaque forming unit per milliliter based unit textual definition -WARN missing_definition disintegrations per second based unit textual definition -WARN missing_definition volt based unit textual definition -WARN missing_definition coulomb based unit textual definition -WARN missing_definition dalton based unit textual definition -WARN missing_definition watt-hour based unit textual definition -WARN missing_definition weber based unit textual definition -WARN missing_definition tesla based unit textual definition -WARN missing_definition volt-hour based unit textual definition -WARN missing_definition bit based unit textual definition -WARN missing_definition byte based unit textual definition -WARN missing_definition chroma sampling unit based unit textual definition -WARN missing_definition dynamic range unit based unit textual definition -WARN missing_definition dots per inch based unit textual definition -WARN missing_definition pixels per inch based unit textual definition -WARN missing_definition pixels per millimeter based unit textual definition -WARN missing_definition base pair based unit textual definition -WARN missing_definition kibibyte based unit textual definition -WARN missing_definition mebibyte based unit textual definition -WARN missing_definition newton per meter based unit textual definition -WARN missing_definition dyne per cm based unit textual definition -WARN missing_definition pascal second based unit textual definition -WARN missing_definition poise based unit textual definition -WARN missing_definition effective dose unit based unit textual definition -WARN missing_definition siemens based unit textual definition -WARN missing_definition watt per meter kelvin based unit textual definition -WARN missing_definition electronvolt based unit textual definition -WARN missing_definition volt per meter based unit textual definition -WARN missing_definition absorbance unit based unit textual definition -WARN missing_definition count per nanomolar second based unit textual definition -WARN missing_definition count per molar second based unit textual definition -WARN missing_definition count per nanomolar based unit textual definition -WARN missing_definition count per molar based unit textual definition -WARN missing_definition dosage unit based unit textual definition -WARN missing_definition relative light unit based unit textual definition -WARN missing_definition relative luminescence unit based unit textual definition -WARN missing_definition relative fluorescence unit based unit textual definition -WARN missing_definition square micrometer based unit textual definition -WARN missing_definition hectare based unit textual definition -WARN missing_definition inch based unit textual definition -WARN missing_definition thou based unit textual definition -WARN missing_definition foot based unit textual definition -WARN missing_definition yard based unit textual definition -WARN missing_definition chain based unit textual definition -WARN missing_definition furlong based unit textual definition -WARN missing_definition mile based unit textual definition -WARN missing_definition league based unit textual definition -WARN missing_definition maritime length unit based unit textual definition -WARN missing_definition fathom based unit textual definition -WARN missing_definition cable based unit textual definition -WARN missing_definition nautical mile based unit textual definition -WARN missing_definition perch based unit textual definition -WARN missing_definition rood based unit textual definition -WARN missing_definition acre based unit textual definition -WARN missing_definition fluid ounce based unit textual definition -WARN missing_definition gill based unit textual definition -WARN missing_definition pint based unit textual definition -WARN missing_definition quart based unit textual definition -WARN missing_definition gallon based unit textual definition -WARN missing_definition grain based unit textual definition -WARN missing_definition drachm based unit textual definition -WARN missing_definition ounce based unit textual definition -WARN missing_definition pound based unit textual definition -WARN missing_definition stone based unit textual definition -WARN missing_definition quarter based unit textual definition -WARN missing_definition hundredweight based unit textual definition -WARN missing_definition ton based unit textual definition -WARN missing_definition slug based unit textual definition -WARN missing_definition teaspoon based unit textual definition -WARN missing_definition gram per square meter based unit textual definition -WARN missing_definition large calorie based unit textual definition -WARN missing_definition gray per minute based unit textual definition -WARN missing_definition has parent hydride textual definition -WARN missing_definition is conjugate acid of textual definition -WARN missing_definition is conjugate base of textual definition -WARN missing_definition is substituent group from textual definition -WARN missing_definition is tautomer of textual definition -WARN missing_definition channel for textual definition -WARN missing_definition channels_from textual definition -WARN missing_definition channels_into textual definition -WARN missing_definition layer part of textual definition -WARN missing_definition protects textual definition -WARN missing_definition subdivision of textual definition -WARN missing_definition Creator textual definition -WARN missing_definition Date textual definition -WARN missing_definition Description textual definition -WARN missing_definition title textual definition -WARN missing_definition license textual definition -WARN missing_definition http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled textual definition -WARN missing_definition Mus musculus subspecies textual definition -WARN missing_definition created_by textual definition -WARN missing_definition creation date textual definition -WARN missing_definition has_alternative_id textual definition -WARN missing_definition database_cross_reference textual definition -WARN missing_definition has_obo_namespace textual definition -WARN missing_definition has_related_synonym textual definition -WARN missing_definition in_subset textual definition -WARN missing_definition xsd:boolean textual definition -WARN missing_definition xsd:string textual definition +WARN duplicate_label_synonym rad has exact synonym rad +WARN duplicate_label_synonym mass per unit volume has exact synonym mass per unit volume +WARN duplicate_label_synonym fraction alternative term fraction +WARN duplicate_label_synonym pH has exact synonym pH WARN duplicate_scoped_synonym deoxyribonucleic acid has exact synonym deoxyribonucleic acids WARN duplicate_scoped_synonym deoxyribonucleic acid has_related_synonym deoxyribonucleic acids WARN duplicate_scoped_synonym ketone has exact synonym ketones @@ -2752,12 +1330,8 @@ WARN duplicate_scoped_synonym Eukaryota has exact synonym eukaryotes WARN duplicate_scoped_synonym Eukaryota has_related_synonym Eucaryotae WARN duplicate_scoped_synonym Eukaryota has_related_synonym Eukarya WARN duplicate_scoped_synonym Eukaryota has_related_synonym eukaryotes -WARN duplicate_scoped_synonym Phaeophyceae has exact synonym brown algae -WARN duplicate_scoped_synonym Phaeophyceae has_related_synonym brown algae WARN duplicate_scoped_synonym Embryophyta has exact synonym land plants WARN duplicate_scoped_synonym Embryophyta has_related_synonym land plants -WARN duplicate_scoped_synonym Bryophyta has exact synonym mosses -WARN duplicate_scoped_synonym Bryophyta has_related_synonym mosses WARN duplicate_scoped_synonym Tetrapoda alternative term tetrapods WARN duplicate_scoped_synonym Tetrapoda has exact synonym tetrapods WARN duplicate_scoped_synonym Amniota alternative term amniotes @@ -2768,19 +1342,11 @@ WARN duplicate_scoped_synonym Metazoa alternative term metazoans WARN duplicate_scoped_synonym Metazoa alternative term multicellular animals WARN duplicate_scoped_synonym Metazoa has exact synonym metazoans WARN duplicate_scoped_synonym Metazoa has exact synonym multicellular animals -WARN duplicate_scoped_synonym Carnivora has exact synonym carnivores -WARN duplicate_scoped_synonym Carnivora has_related_synonym carnivores WARN duplicate_scoped_synonym Magnoliopsida has exact synonym flowering plants WARN duplicate_scoped_synonym Magnoliopsida has_related_synonym flowering plants -WARN duplicate_scoped_synonym Apoidea has exact synonym bees -WARN duplicate_scoped_synonym Apoidea has_related_synonym bees -WARN duplicate_scoped_synonym Papilionoidea has exact synonym butterflies -WARN duplicate_scoped_synonym Papilionoidea has_related_synonym butterflies WARN duplicate_scoped_synonym Mammalia alternative term mammals WARN duplicate_scoped_synonym Mammalia has exact synonym mammals WARN duplicate_scoped_synonym Mammalia has_related_synonym mammals -WARN duplicate_scoped_synonym Liliopsida has exact synonym monocots -WARN duplicate_scoped_synonym Liliopsida has_related_synonym monocots WARN duplicate_scoped_synonym Tracheophyta has exact synonym vascular plants WARN duplicate_scoped_synonym Tracheophyta has_related_synonym vascular plants WARN duplicate_scoped_synonym Spermatophyta has exact synonym seed plants @@ -2793,20 +1359,10 @@ WARN duplicate_scoped_synonym Platyhelminthes has exact synonym flatworms WARN duplicate_scoped_synonym Platyhelminthes has_related_synonym flatworms WARN duplicate_scoped_synonym Nematoda has exact synonym nematodes WARN duplicate_scoped_synonym Nematoda has_related_synonym nematodes -WARN duplicate_scoped_synonym Mollusca has exact synonym molluscs -WARN duplicate_scoped_synonym Mollusca has_related_synonym molluscs WARN duplicate_scoped_synonym Arthropoda has exact synonym arthropods WARN duplicate_scoped_synonym Arthropoda has_related_synonym arthropods -WARN duplicate_scoped_synonym Crustacea has exact synonym crustaceans -WARN duplicate_scoped_synonym Crustacea has_related_synonym crustaceans -WARN duplicate_scoped_synonym Lepidoptera has exact synonym moths -WARN duplicate_scoped_synonym Lepidoptera has_related_synonym moths WARN duplicate_scoped_synonym Diptera has exact synonym flies WARN duplicate_scoped_synonym Diptera has_related_synonym flies -WARN duplicate_scoped_synonym Hymenoptera has exact synonym hymenopterans -WARN duplicate_scoped_synonym Hymenoptera has_related_synonym hymenopterans -WARN duplicate_scoped_synonym Apocrita has exact synonym wasps, ants & bees -WARN duplicate_scoped_synonym Apocrita has_related_synonym wasps, ants & bees WARN duplicate_scoped_synonym Chordata has exact synonym chordates WARN duplicate_scoped_synonym Chordata has_related_synonym chordates WARN duplicate_scoped_synonym Tunicata has exact synonym tunicates @@ -2982,8 +1538,8 @@ WARN duplicate_scoped_synonym nanomolar alternative term nM WARN duplicate_scoped_synonym nanomolar has exact synonym nM WARN duplicate_scoped_synonym picomolar alternative term pM WARN duplicate_scoped_synonym picomolar has exact synonym pM -WARN duplicate_scoped_synonym cubic centimeter alternative term -WARN duplicate_scoped_synonym cubic centimeter has exact synonym +WARN duplicate_scoped_synonym cubic centimeter alternative term cc: +WARN duplicate_scoped_synonym cubic centimeter has exact synonym cc: WARN duplicate_scoped_synonym milliliter alternative term ml WARN duplicate_scoped_synonym milliliter has exact synonym ml WARN duplicate_scoped_synonym liter alternative term L @@ -3004,29 +1560,1440 @@ WARN duplicate_scoped_synonym gram per deciliter alternative term g/dl WARN duplicate_scoped_synonym gram per deciliter has exact synonym g/dl WARN duplicate_scoped_synonym microgram per liter alternative term ug/L WARN duplicate_scoped_synonym microgram per liter has exact synonym ug/L -WARN invalid_xref cell database_cross_reference -WARN invalid_xref cell database_cross_reference -WARN invalid_xref cell database_cross_reference -WARN invalid_xref cell database_cross_reference -INFO lowercase_definition independent continuant textual definition -INFO lowercase_definition independent continuant textual definition -INFO lowercase_definition process textual definition

-INFO lowercase_definition disposition IAO:0000600 -INFO lowercase_definition quality IAO:0000600 -INFO lowercase_definition specifically dependent continuant textual definition -INFO lowercase_definition specifically dependent continuant textual definition -INFO lowercase_definition role IAO:0000600 -INFO lowercase_definition object aggregate IAO:0000600 -INFO lowercase_definition generically dependent continuant textual definition +WARN equivalent_class_axiom_no_genus information representation concretizes information content entity +WARN equivalent_class_axiom_no_genus regulation of behavior regulates (processual) behavior process +WARN equivalent_class_axiom_no_genus classified data set is specified output of class prediction data transformation +WARN equivalent_class_axiom_no_genus material processing achieves_planned_objective material transformation objective +WARN equivalent_class_axiom_no_genus manufacturing achieves_planned_objective manufacturing objective +WARN equivalent_class_axiom_no_genus clustered data set is specified output of class discovery data transformation +WARN equivalent_class_axiom_no_genus decision tree building data transformation achieves_planned_objective decision tree induction objective +WARN equivalent_class_axiom_no_genus statistical model validation achieves_planned_objective cross validation objective +WARN equivalent_class_axiom_no_genus data transformation achieves_planned_objective data transformation objective +WARN equivalent_class_axiom_no_genus partitioning data transformation achieves_planned_objective partitioning objective +WARN equivalent_class_axiom_no_genus particle track has quality particle track structure +WARN equivalent_class_axiom_no_genus track formation has_output particle track +WARN equivalent_pair role owl:equivalentClass role +WARN equivalent_pair protein owl:equivalentClass protein +WARN invalid_xref cell database_cross_reference FMA:68646 +WARN invalid_xref cell database_cross_reference "KUPO:0000002 + +" +WARN invalid_xref cell database_cross_reference VHOG:0001533 +WARN invalid_xref cell database_cross_reference XAO:0003012 +WARN missing_definition fiat object part textual definition +WARN missing_definition site textual definition +WARN missing_definition object textual definition +WARN missing_definition has participant textual definition +WARN missing_definition immaterial entity textual definition +WARN missing_definition carbamate textual definition +WARN missing_definition electron donor textual definition +WARN missing_definition water textual definition +WARN missing_definition dioxygen textual definition +WARN missing_definition carbon dioxide textual definition +WARN missing_definition noradrenaline(1+) textual definition +WARN missing_definition dinitrogen textual definition +WARN missing_definition manganese atom textual definition +WARN missing_definition 5beta-cholane textual definition +WARN missing_definition alkaline earth metal atom textual definition +WARN missing_definition alkali metal atom textual definition +WARN missing_definition aminoglycan textual definition +WARN missing_definition benzopyrrole textual definition +WARN missing_definition bromine atom textual definition +WARN missing_definition cadmium atom textual definition +WARN missing_definition calcium atom textual definition +WARN missing_definition carbon oxide textual definition +WARN missing_definition carbonyl group textual definition +WARN missing_definition chloride salt textual definition +WARN missing_definition chlorine atom textual definition +WARN missing_definition chlorine molecular entity textual definition +WARN missing_definition cyclic peptide textual definition +WARN missing_definition monoatomic cation textual definition +WARN missing_definition fluorine atom textual definition +WARN missing_definition glycogens textual definition +WARN missing_definition halogen molecular entity textual definition +WARN missing_definition halogen textual definition +WARN missing_definition inorganic anion textual definition +WARN missing_definition inorganic oxide textual definition +WARN missing_definition inorganic salt textual definition +WARN missing_definition monoatomic ion textual definition +WARN missing_definition organic salt textual definition +WARN missing_definition iron molecular entity textual definition +WARN missing_definition lead atom textual definition +WARN missing_definition linear tetrapyrrole textual definition +WARN missing_definition magnesium atom textual definition +WARN missing_definition mercury atom textual definition +WARN missing_definition metal cation textual definition +WARN missing_definition monoatomic monocation textual definition +WARN missing_definition nitrogen atom textual definition +WARN missing_definition nonmetal atom textual definition +WARN missing_definition organic ion textual definition +WARN missing_definition organic oxide textual definition +WARN missing_definition oxygen atom textual definition +WARN missing_definition oxygen molecular entity textual definition +WARN missing_definition phosphoric acid derivative textual definition +WARN missing_definition phosphorus molecular entity textual definition +WARN missing_definition potassium atom textual definition +WARN missing_definition sodium atom textual definition +WARN missing_definition sodium chloride textual definition +WARN missing_definition sodium molecular entity textual definition +WARN missing_definition sulfur atom textual definition +WARN missing_definition sulfur molecular entity textual definition +WARN missing_definition tin atom textual definition +WARN missing_definition organic heterobicyclic compound textual definition +WARN missing_definition uranium atom textual definition +WARN missing_definition zinc atom textual definition +WARN missing_definition boron atom textual definition +WARN missing_definition arsenic atom textual definition +WARN missing_definition selenium atom textual definition +WARN missing_definition silicon atom textual definition +WARN missing_definition carbon atom textual definition +WARN missing_definition vanadium atom textual definition +WARN missing_definition tungsten textual definition +WARN missing_definition phosphorus atom textual definition +WARN missing_definition molybdenum atom textual definition +WARN missing_definition copper atom textual definition +WARN missing_definition carbonic acid textual definition +WARN missing_definition aluminium atom textual definition +WARN missing_definition gold atom textual definition +WARN missing_definition azanide textual definition +WARN missing_definition hydridodioxygen(1+) textual definition +WARN missing_definition lithium atom textual definition +WARN missing_definition helium atom textual definition +WARN missing_definition monoatomic dication textual definition +WARN missing_definition astatine atom textual definition +WARN missing_definition germanium atom textual definition +WARN missing_definition tellurium atom textual definition +WARN missing_definition silver atom textual definition +WARN missing_definition antimony atom textual definition +WARN missing_definition caesium atom textual definition +WARN missing_definition ruthenium atom textual definition +WARN missing_definition osmium atom textual definition +WARN missing_definition barium atom textual definition +WARN missing_definition europium atom textual definition +WARN missing_definition oxoacid derivative textual definition +WARN missing_definition inorganic hydride textual definition +WARN missing_definition monoatomic hydrogen textual definition +WARN missing_definition elemental hydrogen textual definition +WARN missing_definition elemental oxygen textual definition +WARN missing_definition diatomic oxygen textual definition +WARN missing_definition diatomic nitrogen textual definition +WARN missing_definition elemental nitrogen textual definition +WARN missing_definition molecular messenger textual definition +WARN missing_definition fuel textual definition +WARN missing_definition bismuth atom textual definition +WARN missing_definition carbon group element atom textual definition +WARN missing_definition noble gas atom textual definition +WARN missing_definition neon atom textual definition +WARN missing_definition radon atom textual definition +WARN missing_definition monoatomic helium textual definition +WARN missing_definition helium(2+) textual definition +WARN missing_definition boron group element atom textual definition +WARN missing_definition lanthanoid atom textual definition +WARN missing_definition actinoid atom textual definition +WARN missing_definition rare earth metal atom textual definition +WARN missing_definition rubidium atom textual definition +WARN missing_definition francium atom textual definition +WARN missing_definition strontium atom textual definition +WARN missing_definition radium atom textual definition +WARN missing_definition scandium atom textual definition +WARN missing_definition yttrium atom textual definition +WARN missing_definition scandium group element atom textual definition +WARN missing_definition lanthanum atom textual definition +WARN missing_definition actinium atom textual definition +WARN missing_definition zinc group element atom textual definition +WARN missing_definition titanium atom textual definition +WARN missing_definition zirconium atom textual definition +WARN missing_definition hafnium atom textual definition +WARN missing_definition niobium atom textual definition +WARN missing_definition titanium group element atom textual definition +WARN missing_definition rutherfordium atom textual definition +WARN missing_definition vanadium group element atom textual definition +WARN missing_definition tantalum atom textual definition +WARN missing_definition dubnium atom textual definition +WARN missing_definition chromium group element atom textual definition +WARN missing_definition seaborgium atom textual definition +WARN missing_definition manganese group element atom textual definition +WARN missing_definition technetium atom textual definition +WARN missing_definition bohrium atom textual definition +WARN missing_definition iron group element atom textual definition +WARN missing_definition hassium atom textual definition +WARN missing_definition cobalt group element atom textual definition +WARN missing_definition meitnerium atom textual definition +WARN missing_definition nickel group element atom textual definition +WARN missing_definition platinum textual definition +WARN missing_definition platinum group metal atom textual definition +WARN missing_definition copper group element atom textual definition +WARN missing_definition darmstadtium textual definition +WARN missing_definition cerium textual definition +WARN missing_definition technetium-99 textual definition +WARN missing_definition neodymium atom textual definition +WARN missing_definition promethium atom textual definition +WARN missing_definition samarium atom textual definition +WARN missing_definition gadolinium atom textual definition +WARN missing_definition terbium atom textual definition +WARN missing_definition dysprosium atom textual definition +WARN missing_definition erbium textual definition +WARN missing_definition thulium atom textual definition +WARN missing_definition ytterbium textual definition +WARN missing_definition lutetium atom textual definition +WARN missing_definition thorium textual definition +WARN missing_definition protactinium atom textual definition +WARN missing_definition neptunium atom textual definition +WARN missing_definition plutonium atom textual definition +WARN missing_definition americium atom textual definition +WARN missing_definition curium atom textual definition +WARN missing_definition berkelium atom textual definition +WARN missing_definition californium atom textual definition +WARN missing_definition einsteinium atom textual definition +WARN missing_definition fermium textual definition +WARN missing_definition mendelevium atom textual definition +WARN missing_definition nobelium textual definition +WARN missing_definition lawrencium atom textual definition +WARN missing_definition sulfur oxoacid textual definition +WARN missing_definition pnictogen oxoacid textual definition +WARN missing_definition sulfur oxoacid derivative textual definition +WARN missing_definition pnictogen oxoanion textual definition +WARN missing_definition phosphorus oxoanion textual definition +WARN missing_definition elemental pnictogen textual definition +WARN missing_definition sulfur oxoanion textual definition +WARN missing_definition chalcogen oxoacid textual definition +WARN missing_definition chalcogen oxoanion textual definition +WARN missing_definition radon-220 atom textual definition +WARN missing_definition radon-222 atom textual definition +WARN missing_definition radon-219 atom textual definition +WARN missing_definition actinoid molecular entity textual definition +WARN missing_definition uranium molecular entity textual definition +WARN missing_definition alkali metal cation textual definition +WARN missing_definition s-block element atom textual definition +WARN missing_definition d-block element atom textual definition +WARN missing_definition f-block element atom textual definition +WARN missing_definition benzenediols textual definition +WARN missing_definition carbon group molecular entity textual definition +WARN missing_definition hydrogen molecular entity textual definition +WARN missing_definition polycyclic compound textual definition +WARN missing_definition organic aromatic compound textual definition +WARN missing_definition f-block molecular entity textual definition +WARN missing_definition helium molecular entity textual definition +WARN missing_definition elemental helium textual definition +WARN missing_definition oxygen hydride textual definition +WARN missing_definition information biomacromolecule textual definition +WARN missing_definition proteinogenic amino-acid residue textual definition +WARN missing_definition carbohydrate acid textual definition +WARN missing_definition carbohydrate acid anion textual definition +WARN missing_definition iron group molecular entity textual definition +WARN missing_definition copper group molecular entity textual definition +WARN missing_definition nickel group molecular entity textual definition +WARN missing_definition platinum molecular entity textual definition +WARN missing_definition canonical nucleoside residue textual definition +WARN missing_definition canonical ribonucleoside residue textual definition +WARN missing_definition canonical deoxyribonucleoside residue textual definition +WARN missing_definition halide salt textual definition +WARN missing_definition gold molecular entity textual definition +WARN missing_definition nitrogen hydride textual definition +WARN missing_definition fossil fuel textual definition +WARN missing_definition hydroxy steroid textual definition +WARN missing_definition alkali metal salt textual definition +WARN missing_definition natural product fundamental parent textual definition +WARN missing_definition steroid fundamental parent textual definition +WARN missing_definition cholane textual definition +WARN missing_definition carbon oxoacid textual definition +WARN missing_definition dicarboxylic acid anion textual definition +WARN missing_definition sulfated glycosaminoglycan textual definition +WARN missing_definition carbohydrate sulfate textual definition +WARN missing_definition pnictogen hydride textual definition +WARN missing_definition cholanoid textual definition +WARN missing_definition inorganic chloride textual definition +WARN missing_definition bile acid anion textual definition +WARN missing_definition 5beta-cholanic acid textual definition +WARN missing_definition cholanic acids textual definition +WARN missing_definition phosphorus oxoacid derivative textual definition +WARN missing_definition phosphorus oxoacids and derivatives textual definition +WARN missing_definition chalcogen hydride textual definition +WARN missing_definition argon molecular entity textual definition +WARN missing_definition inorganic ion textual definition +WARN missing_definition inorganic cation textual definition +WARN missing_definition carbon-14 atom textual definition +WARN missing_definition carbon-13 atom textual definition +WARN missing_definition carbon-11 atom textual definition +WARN missing_definition carbon-10 atom textual definition +WARN missing_definition carbon-12 atom textual definition +WARN missing_definition oxygen-19 atom textual definition +WARN missing_definition nitrogen-16 atom textual definition +WARN missing_definition nitrogen-17 atom textual definition +WARN missing_definition chalcocarbonic acid textual definition +WARN missing_definition amino-acid anion textual definition +WARN missing_definition organic hydride textual definition +WARN missing_definition mononuclear parent hydride textual definition +WARN missing_definition elemental sodium textual definition +WARN missing_definition polonium-190 atom textual definition +WARN missing_definition polonium-191 atom textual definition +WARN missing_definition polonium-192 atom textual definition +WARN missing_definition polonium-193 atom textual definition +WARN missing_definition polonium-194 atom textual definition +WARN missing_definition polonium-195 atom textual definition +WARN missing_definition polonium-196 atom textual definition +WARN missing_definition polonium-197 atom textual definition +WARN missing_definition polonium-198 atom textual definition +WARN missing_definition polonium-199 atom textual definition +WARN missing_definition polonium-200 atom textual definition +WARN missing_definition polonium-201 atom textual definition +WARN missing_definition polonium-202 atom textual definition +WARN missing_definition polonium-204 atom textual definition +WARN missing_definition halide textual definition +WARN missing_definition sulfuric acid derivative textual definition +WARN missing_definition organic heteropolycyclic compound textual definition +WARN missing_definition polycyclic heteroarene textual definition +WARN missing_definition aminoalkylindole textual definition +WARN missing_definition organic sodium salt textual definition +WARN missing_definition inorganic sodium salt textual definition +WARN missing_definition carbonate textual definition +WARN missing_definition hydroxy group textual definition +WARN missing_definition hydrogensulfate textual definition +WARN missing_definition oxo group textual definition +WARN missing_definition carboxy group textual definition +WARN missing_definition sulfur oxide textual definition +WARN missing_definition argon atom textual definition +WARN missing_definition hydrogen atom textual definition +WARN missing_definition holmium atom textual definition +WARN missing_definition iridium atom textual definition +WARN missing_definition krypton atom textual definition +WARN missing_definition praseodymium atom textual definition +WARN missing_definition rhenium atom textual definition +WARN missing_definition xenon atom textual definition +WARN missing_definition canonical nucleotide residue textual definition +WARN missing_definition canonical deoxyribonucleotide residue textual definition +WARN missing_definition canonical ribonucleotide residue textual definition +WARN missing_definition onium compound textual definition +WARN missing_definition nucleotide residue textual definition +WARN missing_definition nucleoside residue textual definition +WARN missing_definition nitrogen molecular entity textual definition +WARN missing_definition organic divalent group textual definition +WARN missing_definition organic univalent group textual definition +WARN missing_definition organic polycyclic compound textual definition +WARN missing_definition physiological role textual definition +WARN missing_definition inorganic hydroxy compound textual definition +WARN missing_definition greenhouse gas textual definition +WARN missing_definition environmental contaminant textual definition +WARN missing_definition neuronal receptor cell textual definition +WARN missing_definition neural crest derived neuron textual definition +WARN missing_definition branched duct epithelial cell textual definition +WARN missing_definition squamous epithelial cell textual definition +WARN missing_definition neuron associated cell textual definition +WARN missing_definition CNS neuron (sensu Vertebrata) textual definition +WARN missing_definition visual pigment cell textual definition +WARN missing_definition protein secreting cell textual definition +WARN missing_definition seromucus secreting cell textual definition +WARN missing_definition peptide hormone secreting cell textual definition +WARN missing_definition insulin secreting cell textual definition +WARN missing_definition somatostatin secreting cell textual definition +WARN missing_definition steroid hormone secreting cell textual definition +WARN missing_definition binucleate cell textual definition +WARN missing_definition eukaryotic cell textual definition +WARN missing_definition Eumycetozoan cell textual definition +WARN missing_definition eye photoreceptor cell textual definition +WARN missing_definition crystallin accumulating cell textual definition +WARN missing_definition mucus secreting cell textual definition +WARN missing_definition extracellular matrix secreting cell textual definition +WARN missing_definition oxygen accumulating cell textual definition +WARN missing_definition extraembryonic cell textual definition +WARN missing_definition ganglion interneuron textual definition +WARN missing_definition endopolyploid cell textual definition +WARN missing_definition carbohydrate secreting cell textual definition +WARN missing_definition biogenic amine secreting cell textual definition +WARN missing_definition fungal cell textual definition +WARN missing_definition fibroblast of dermis textual definition +WARN missing_definition epithelial cell of lower respiratory tract textual definition +WARN missing_definition visual system neuron textual definition +WARN missing_definition microcirculation associated smooth muscle cell textual definition +WARN missing_definition cardiac blood vessel endothelial cell textual definition +WARN missing_definition His-Purkinje system cell textual definition +WARN missing_definition cardiac endothelial cell textual definition +WARN missing_definition camera-type eye photoreceptor cell textual definition +WARN missing_definition cardiac glial cell textual definition +WARN missing_definition cardiac myoblast textual definition +WARN missing_definition stomach neuroendocrine cell textual definition +WARN missing_definition lung ciliated cell textual definition +WARN missing_definition lung secretory cell textual definition +WARN missing_definition trophectodermal cell textual definition +WARN missing_definition lung endothelial cell textual definition +WARN missing_definition pulmonary artery endothelial cell textual definition +WARN missing_definition lacks_part textual definition +WARN missing_definition lacks_plasma_membrane_part textual definition +WARN missing_definition executed by textual definition +WARN missing_definition action specification textual definition +WARN missing_definition concretizes textual definition +WARN missing_definition intended to realize textual definition +WARN missing_definition realizes textual definition +WARN missing_definition information representation textual definition +WARN missing_definition measurement datum textual definition +WARN missing_definition physical information carrier textual definition +WARN missing_definition has number of atomic nuclei textual definition +WARN missing_definition atherosclerosis textual definition +WARN missing_definition iris disease textual definition +WARN missing_definition liver disease textual definition +WARN missing_definition bone marrow disease textual definition +WARN missing_definition cornea cancer textual definition +WARN missing_definition grain of desert sand textual definition +WARN missing_definition wood textual definition +WARN missing_definition platinum mine textual definition +WARN missing_definition gold mine textual definition +WARN missing_definition coal mine textual definition +WARN missing_definition contaminated water textual definition +WARN missing_definition coal mine waste material textual definition +WARN missing_definition temperate grassland biome textual definition +WARN missing_definition litter layer textual definition +WARN missing_definition human house textual definition +WARN missing_definition swamp forest textual definition +WARN missing_definition needleleaf forest textual definition +WARN missing_definition sclerophyllous forest textual definition +WARN missing_definition montane forest textual definition +WARN missing_definition ceiling textual definition +WARN missing_definition atmospheric wind textual definition +WARN missing_definition water raindrop textual definition +WARN missing_definition algal material textual definition +WARN missing_definition forest canopy textual definition +WARN missing_definition gill tissue material textual definition +WARN missing_definition aquatic ecosystem textual definition +WARN missing_definition marine ecosystem textual definition +WARN missing_definition terrestrial ecosystem textual definition +WARN missing_definition temperate grassland textual definition +WARN missing_definition iron mine textual definition +WARN missing_definition uranium mine textual definition +WARN missing_definition iron ore textual definition +WARN missing_definition gold ore textual definition +WARN missing_definition platinum ore textual definition +WARN missing_definition cement dust textual definition +WARN missing_definition dust from plant parts textual definition +WARN missing_definition forest process textual definition +WARN missing_definition forest area expansion textual definition +WARN missing_definition generation of energy from coal textual definition +WARN missing_definition stellar radiation energy textual definition +WARN missing_definition coal power plant textual definition +WARN missing_definition solar power station textual definition +WARN missing_definition ocean thermal power station textual definition +WARN missing_definition tidal power plant textual definition +WARN missing_definition integumental system environment textual definition +WARN missing_definition results in distribution of textual definition +WARN missing_definition results in fission of textual definition +WARN missing_definition hasAncestryStatus textual definition +WARN missing_definition has measurement unit label textual definition +WARN missing_definition jaw movement textual definition +WARN missing_definition root textual definition +WARN missing_definition Muridae textual definition +WARN missing_definition Mus caroli textual definition +WARN missing_definition Mus musculus textual definition +WARN missing_definition Mus spretus textual definition +WARN missing_definition Rattus textual definition +WARN missing_definition Viruses textual definition +WARN missing_definition Sedentaria textual definition +WARN missing_definition Canalipalpata textual definition +WARN missing_definition Xenoturbellida textual definition +WARN missing_definition Xenoturbella textual definition +WARN missing_definition Myxini textual definition +WARN missing_definition Teleostomi textual definition +WARN missing_definition Euteleostomi textual definition +WARN missing_definition Chromadorea textual definition +WARN missing_definition Ecdysozoa textual definition +WARN missing_definition Lophotrochozoa textual definition +WARN missing_definition Neoteleostei textual definition +WARN missing_definition Eurypterygia textual definition +WARN missing_definition Ctenosquamata textual definition +WARN missing_definition Acanthomorphata textual definition +WARN missing_definition Euacanthomorphacea textual definition +WARN missing_definition Acipenserinae textual definition +WARN missing_definition Acipenserini textual definition +WARN missing_definition Zygnemophyceae textual definition +WARN missing_definition Streptophytina textual definition +WARN missing_definition Xenacoelomorpha textual definition +WARN missing_definition cellular organisms textual definition +WARN missing_definition Archelosauria textual definition +WARN missing_definition Dipnotetrapodomorpha textual definition +WARN missing_definition Eumycetozoa textual definition +WARN missing_definition Boreoeutheria textual definition +WARN missing_definition Acrogymnospermae textual definition +WARN missing_definition Gnetidae textual definition +WARN missing_definition Acoelomorpha textual definition +WARN missing_definition Saccharomycotina textual definition +WARN missing_definition Schizosaccharomycetes textual definition +WARN missing_definition Cyclostomata textual definition +WARN missing_definition Osteoglossocephalai textual definition +WARN missing_definition Euteleosteomorpha textual definition +WARN missing_definition Percomorphaceae textual definition +WARN missing_definition Eupercaria textual definition +WARN missing_definition Xenoturbellidae textual definition +WARN missing_definition Acipenseroidei textual definition +WARN missing_definition Actinopteri textual definition +WARN missing_definition Clupeocephala textual definition +WARN missing_definition Otophysi textual definition +WARN missing_definition Cypriniphysae textual definition +WARN missing_definition Otomorpha textual definition +WARN missing_definition Myomorpha textual definition +WARN missing_definition Pancrustacea textual definition +WARN missing_definition Mandibulata textual definition +WARN missing_definition Bacteria textual definition +WARN missing_definition Dictyosteliaceae textual definition +WARN missing_definition Dictyosteliales textual definition +WARN missing_definition Homininae textual definition +WARN missing_definition Archaea textual definition +WARN missing_definition Rhabditina textual definition +WARN missing_definition Rhabditomorpha textual definition +WARN missing_definition Evosea textual definition +WARN missing_definition Discoba textual definition +WARN missing_definition Xenopus textual definition +WARN missing_definition Zygnematophycidae textual definition +WARN missing_definition Spiralia textual definition +WARN missing_definition Sar textual definition +WARN missing_definition Danionidae textual definition +WARN missing_definition Danioninae textual definition +WARN missing_definition Eukaryota textual definition +WARN missing_definition Pipoidea textual definition +WARN missing_definition Cyprinoidei textual definition +WARN missing_definition Tetraodontiformes textual definition +WARN missing_definition Tetraodontoidei textual definition +WARN missing_definition Tetraodontidae textual definition +WARN missing_definition Takifugu textual definition +WARN missing_definition Takifugu rubripes textual definition +WARN missing_definition Euarchontoglires textual definition +WARN missing_definition Glires textual definition +WARN missing_definition Simiiformes textual definition +WARN missing_definition Hominoidea textual definition +WARN missing_definition Zygnematales textual definition +WARN missing_definition Embryophyta textual definition +WARN missing_definition Sophophora textual definition +WARN missing_definition melanogaster group textual definition +WARN missing_definition melanogaster subgroup textual definition +WARN missing_definition Chondrostei textual definition +WARN missing_definition Teleostei textual definition +WARN missing_definition Tetradontoidea textual definition +WARN missing_definition Ostariophysi textual definition +WARN missing_definition Tetrapoda textual definition +WARN missing_definition Amniota textual definition +WARN missing_definition Theria textual definition +WARN missing_definition Sauria textual definition +WARN missing_definition Dictyostelia textual definition +WARN missing_definition Viridiplantae textual definition +WARN missing_definition Coniferophyta textual definition +WARN missing_definition Opisthokonta textual definition +WARN missing_definition Metazoa textual definition +WARN missing_definition Bilateria textual definition +WARN missing_definition Protostomia textual definition +WARN missing_definition Neoptera textual definition +WARN missing_definition Endopterygota textual definition +WARN missing_definition Deuterostomia textual definition +WARN missing_definition Alveolata textual definition +WARN missing_definition Euglenozoa textual definition +WARN missing_definition Gnetopsida textual definition +WARN missing_definition Muroidea textual definition +WARN missing_definition Gnetales textual definition +WARN missing_definition Magnoliopsida textual definition +WARN missing_definition Schizosaccharomycetales textual definition +WARN missing_definition Streptophyta textual definition +WARN missing_definition Haplorrhini textual definition +WARN missing_definition Glaucocystophyceae textual definition +WARN missing_definition Murinae textual definition +WARN missing_definition Mammalia textual definition +WARN missing_definition Siboglinidae textual definition +WARN missing_definition Neopterygii textual definition +WARN missing_definition Batrachia textual definition +WARN missing_definition Dinosauria textual definition +WARN missing_definition Saurischia textual definition +WARN missing_definition Theropoda textual definition +WARN missing_definition Coelurosauria textual definition +WARN missing_definition Muscomorpha textual definition +WARN missing_definition Schizophora textual definition +WARN missing_definition Acalyptratae textual definition +WARN missing_definition Ephydroidea textual definition +WARN missing_definition Drosophilinae textual definition +WARN missing_definition Dikarya textual definition +WARN missing_definition Taphrinomycotina textual definition +WARN missing_definition Drosophilini textual definition +WARN missing_definition Fungi textual definition +WARN missing_definition Cyclorrhapha textual definition +WARN missing_definition Eremoneura textual definition +WARN missing_definition Ascomycota textual definition +WARN missing_definition Saccharomycetes textual definition +WARN missing_definition Saccharomycetales textual definition +WARN missing_definition Saccharomycetaceae textual definition +WARN missing_definition Schizosaccharomycetaceae textual definition +WARN missing_definition Schizosaccharomyces textual definition +WARN missing_definition Schizosaccharomyces pombe textual definition +WARN missing_definition Saccharomyces textual definition +WARN missing_definition Saccharomyces cerevisiae textual definition +WARN missing_definition Insecta textual definition +WARN missing_definition Amoebozoa textual definition +WARN missing_definition Rhabditoidea textual definition +WARN missing_definition Peloderinae textual definition +WARN missing_definition Dictyostelium textual definition +WARN missing_definition Tracheophyta textual definition +WARN missing_definition Spermatophyta textual definition +WARN missing_definition Porifera textual definition +WARN missing_definition Eumetazoa textual definition +WARN missing_definition Cnidaria textual definition +WARN missing_definition Platyhelminthes textual definition +WARN missing_definition Nematoda textual definition +WARN missing_definition Rhabditida textual definition +WARN missing_definition Caenorhabditis textual definition +WARN missing_definition Caenorhabditis elegans textual definition +WARN missing_definition Rhabditidae textual definition +WARN missing_definition Annelida textual definition +WARN missing_definition Polychaeta textual definition +WARN missing_definition Sabellida textual definition +WARN missing_definition Arthropoda textual definition +WARN missing_definition Hexapoda textual definition +WARN missing_definition Diptera textual definition +WARN missing_definition saccharomyceta textual definition +WARN missing_definition Brachycera textual definition +WARN missing_definition Drosophilidae textual definition +WARN missing_definition Drosophila textual definition +WARN missing_definition Drosophila melanogaster textual definition +WARN missing_definition Pterygota textual definition +WARN missing_definition Chordata textual definition +WARN missing_definition Tunicata textual definition +WARN missing_definition Vertebrata textual definition +WARN missing_definition Myxiniformes textual definition +WARN missing_definition Myxinidae textual definition +WARN missing_definition Gnathostomata textual definition +WARN missing_definition Chondrichthyes textual definition +WARN missing_definition Euphyllophyta textual definition +WARN missing_definition Holocephali textual definition +WARN missing_definition Chimaeriformes textual definition +WARN missing_definition Dipnomorpha textual definition +WARN missing_definition Actinopterygii textual definition +WARN missing_definition Acipenseriformes textual definition +WARN missing_definition Acipenseridae textual definition +WARN missing_definition Acipenser textual definition +WARN missing_definition Cypriniformes textual definition +WARN missing_definition Danio textual definition +WARN missing_definition Danio rerio textual definition +WARN missing_definition Sarcopterygii textual definition +WARN missing_definition Amphibia textual definition +WARN missing_definition Anura textual definition +WARN missing_definition Pipidae textual definition +WARN missing_definition Xenopus textual definition +WARN missing_definition Xenopus laevis textual definition +WARN missing_definition Xenopodinae textual definition +WARN missing_definition Sauropsida textual definition +WARN missing_definition Archosauria textual definition +WARN missing_definition Dicondylia textual definition +WARN missing_definition Mus textual definition +WARN missing_definition Aves textual definition +WARN missing_definition Palaeognathae textual definition +WARN missing_definition Struthioniformes textual definition +WARN missing_definition Struthionidae textual definition +WARN missing_definition Struthio textual definition +WARN missing_definition Struthio camelus textual definition +WARN missing_definition Neognathae textual definition +WARN missing_definition Panarthropoda textual definition +WARN missing_definition Columbiformes textual definition +WARN missing_definition Columbidae textual definition +WARN missing_definition Craniata textual definition +WARN missing_definition Prototheria textual definition +WARN missing_definition Monotremata textual definition +WARN missing_definition Tachyglossidae textual definition +WARN missing_definition Eutheria textual definition +WARN missing_definition Primates textual definition +WARN missing_definition Catarrhini textual definition +WARN missing_definition Hominidae textual definition +WARN missing_definition Homo textual definition +WARN missing_definition Homo sapiens textual definition +WARN missing_definition Rodentia textual definition +WARN missing_definition qualitative textual definition +WARN missing_definition physical quality of a process textual definition +WARN missing_definition sloped downward textual definition +WARN missing_definition astronaut textual definition +WARN missing_definition military textual definition +WARN missing_definition medical professional textual definition +WARN missing_definition dentist textual definition +WARN missing_definition radiologist textual definition +WARN missing_definition risk estimate textual definition +WARN missing_definition lifetime risk estimate textual definition +WARN missing_definition biological process textual definition +WARN missing_definition cellular process textual definition +WARN missing_definition track formation textual definition +WARN missing_definition mass number textual definition +WARN missing_definition is concretized as textual definition +WARN missing_definition contained in textual definition +WARN missing_definition contains textual definition +WARN missing_definition innervated_by textual definition +WARN missing_definition has component activity textual definition +WARN missing_definition directly regulated by textual definition +WARN missing_definition before or simultaneous with textual definition +WARN missing_definition during which ends textual definition +WARN missing_definition ends after textual definition +WARN missing_definition immediately preceded by textual definition +WARN missing_definition immediately precedes textual definition +WARN missing_definition ends during textual definition +WARN missing_definition temporally related to textual definition +WARN missing_definition part of developmental precursor of textual definition +WARN missing_definition results in formation of textual definition +WARN missing_definition results in growth of textual definition +WARN missing_definition results in transport to from or in textual definition +WARN missing_definition formed as result of textual definition +WARN missing_definition immediately causally downstream of textual definition +WARN missing_definition phosphorylates textual definition +WARN missing_definition helper property (not for use in curation) textual definition +WARN missing_definition is kinase activity textual definition +WARN missing_definition receives input from textual definition +WARN missing_definition sends output to textual definition +WARN missing_definition relation between physical entity and a process or stage textual definition +WARN missing_definition depends on textual definition +WARN missing_definition causal relation between entities textual definition +WARN missing_definition causally influenced by textual definition +WARN missing_definition interaction relation helper property textual definition +WARN missing_definition molecular interaction relation helper property textual definition +WARN missing_definition results in assembly of textual definition +WARN missing_definition results in disassembly of textual definition +WARN missing_definition acts upstream of or within, positive effect textual definition +WARN missing_definition acts upstream of or within, negative effect textual definition +WARN missing_definition causally upstream of or within, negative effect textual definition +WARN missing_definition causally upstream of or within, positive effect textual definition +WARN missing_definition results in fusion of textual definition +WARN missing_definition agent role textual definition +WARN missing_definition executes textual definition +WARN missing_definition chemosensory organ textual definition +WARN missing_definition anterior region of body textual definition +WARN missing_definition posterior region of body textual definition +WARN missing_definition membranous layer textual definition +WARN missing_definition vertebral foramen of atlas textual definition +WARN missing_definition head sensillum textual definition +WARN missing_definition subdivision of head textual definition +WARN missing_definition muscle of iris textual definition +WARN missing_definition gastric juice textual definition +WARN missing_definition parenchyma of pancreas textual definition +WARN missing_definition organ cavity textual definition +WARN missing_definition posterior neural tube textual definition +WARN missing_definition anterior neural tube textual definition +WARN missing_definition set of muscles of vertebral column textual definition +WARN missing_definition biliary bud textual definition +WARN missing_definition right horn of sinus venosus textual definition +WARN missing_definition basal plate metencephalon textual definition +WARN missing_definition outflow tract pulmonary component textual definition +WARN missing_definition developing anatomical structure textual definition +WARN missing_definition cervical region textual definition +WARN missing_definition non-neural ectoderm textual definition +WARN missing_definition extrahepatic part of hepatic duct textual definition +WARN missing_definition left dorsal aorta textual definition +WARN missing_definition right dorsal aorta textual definition +WARN missing_definition chemosensory system textual definition +WARN missing_definition extraembryonic mesoderm textual definition +WARN missing_definition spinal cord segment textual definition +WARN missing_definition pre-muscle condensation textual definition +WARN missing_definition zone of bone organ textual definition +WARN missing_definition neurocranial trabecula textual definition +WARN missing_definition posterior surface of head textual definition +WARN missing_definition common atrial chamber textual definition +WARN missing_definition ethmoid bone primordium textual definition +WARN missing_definition tetrapod frontal bone primordium textual definition +WARN missing_definition future spinal cord textual definition +WARN missing_definition future trigeminal ganglion textual definition +WARN missing_definition presumptive blood textual definition +WARN missing_definition glandular cuboidal epithelium textual definition +WARN missing_definition presumptive gut textual definition +WARN missing_definition mechanosensory system textual definition +WARN missing_definition 1st arch mandibular component textual definition +WARN missing_definition 1st arch maxillary component textual definition +WARN missing_definition early pharyngeal endoderm textual definition +WARN missing_definition microvascular endothelium textual definition +WARN missing_definition liver bud textual definition +WARN missing_definition respiratory primordium textual definition +WARN missing_definition pharyngeal region of foregut textual definition +WARN missing_definition indifferent external genitalia textual definition +WARN missing_definition embryonic nasal process textual definition +WARN missing_definition subdivision of trunk textual definition +WARN missing_definition midbrain mantle layer textual definition +WARN missing_definition spinal cord mantle layer textual definition +WARN missing_definition midbrain hindbrain boundary neural plate textual definition +WARN missing_definition trunk paraxial mesoderm textual definition +WARN missing_definition artery of lip textual definition +WARN missing_definition gut mesentery textual definition +WARN missing_definition dorsal pancreas textual definition +WARN missing_definition ventral pancreas textual definition +WARN missing_definition entire pharyngeal arch endoderm textual definition +WARN missing_definition sac textual definition +WARN missing_definition anterior lateral plate mesoderm textual definition +WARN missing_definition lobule textual definition +WARN missing_definition optic neural crest textual definition +WARN missing_definition aortic system textual definition +WARN missing_definition layer of sclera textual definition +WARN missing_definition germ layer / neural crest textual definition +WARN missing_definition pancreas dorsal primordium textual definition +WARN missing_definition pancreas ventral primordium textual definition +WARN missing_definition pneumatic cavity of bone textual definition +WARN missing_definition primary subdivision of cranial skeletal system textual definition +WARN missing_definition intra-ocular muscle textual definition +WARN missing_definition fibrous membrane of synovial tendon sheath textual definition +WARN missing_definition embryonic skin basal layer textual definition +WARN missing_definition lumen of gastrointestinal system textual definition +WARN missing_definition future upper lip textual definition +WARN missing_definition future lower lip textual definition +WARN missing_definition jaw muscle textual definition +WARN missing_definition fibrous connective tissue textual definition +WARN missing_definition collection of collagen fibrils textual definition +WARN missing_definition palatal part of dermatocranium textual definition +WARN missing_definition internal anal region textual definition +WARN missing_definition respiratory system arterial smooth muscle textual definition +WARN missing_definition extraembryonic cavity textual definition +WARN missing_definition external anal region textual definition +WARN missing_definition cloacal villus textual definition +WARN missing_definition subdivision of tube textual definition +WARN missing_definition subepicardial layer of epicardium textual definition +WARN missing_definition heart plus pericardium textual definition +WARN missing_definition heterogeneous tissue textual definition +WARN missing_definition spinal cord column textual definition +WARN missing_definition lamina of gray matter of spinal cord textual definition +WARN missing_definition fibrocollagenous connective tissue textual definition +WARN missing_definition skeletal musculature textual definition +WARN missing_definition cardiac muscle tissue of ventricle textual definition +WARN missing_definition dorsal side of post-anal tail textual definition +WARN missing_definition reproductive system mucosa textual definition +WARN missing_definition carotid artery endothelium textual definition +WARN missing_definition mucous gland of lung textual definition +WARN missing_definition gray matter of hindbrain textual definition +WARN missing_definition gray matter of midbrain textual definition +WARN missing_definition sensory organ epithelium textual definition +WARN missing_definition surface of eyeball textual definition +WARN missing_definition splenic arteriole textual definition +WARN missing_definition hindbrain marginal layer textual definition +WARN missing_definition spinal cord ventricular layer textual definition +WARN missing_definition sympathetic nerve textual definition +WARN missing_definition lymphomyeloid tissue textual definition +WARN missing_definition gland lumen textual definition +WARN missing_definition zone of organ textual definition +WARN missing_definition epithelial layer of duct textual definition +WARN missing_definition jaw epithelium textual definition +WARN missing_definition rectal artery textual definition +WARN missing_definition excretory duct textual definition +WARN missing_definition branch of external carotid artery textual definition +WARN missing_definition uveal vein textual definition +WARN missing_definition colic artery textual definition +WARN missing_definition cavity of cardiac chamber textual definition +WARN missing_definition serous cavity textual definition +WARN missing_definition wall of blood vessel textual definition +WARN missing_definition respiratory primordium epithelium textual definition +WARN missing_definition respiratory primordium mesenchyme textual definition +WARN missing_definition fibroelastic connective tissue textual definition +WARN missing_definition orifice of skull textual definition +WARN missing_definition pelvic vein textual definition +WARN missing_definition anterior wall of left ventricle textual definition +WARN missing_definition myocardium of anterior wall of left ventricle textual definition +WARN missing_definition myocardium of anterior wall of right ventricle textual definition +WARN missing_definition vasculature of spleen textual definition +WARN missing_definition vasculature of central nervous system plus retina textual definition +WARN missing_definition vasculature of central nervous system textual definition +WARN missing_definition wall of gallbladder textual definition +WARN missing_definition wall of brachiocephalic artery textual definition +WARN missing_definition wall of subclavian artery textual definition +WARN missing_definition wall of anal canal textual definition +WARN missing_definition wall of pulmonary artery textual definition +WARN missing_definition wall of synovial tendon sheath textual definition +WARN missing_definition wall of eyeball textual definition +WARN missing_definition wall of orbit textual definition +WARN missing_definition wall of common carotid artery textual definition +WARN missing_definition sigmoid vein textual definition +WARN missing_definition pancreatic artery textual definition +WARN missing_definition axial vasculature textual definition +WARN missing_definition panarthropod head textual definition +WARN missing_definition length unit textual definition +WARN missing_definition mass unit textual definition +WARN missing_definition time unit textual definition +WARN missing_definition electric current unit textual definition +WARN missing_definition temperature unit textual definition +WARN missing_definition substance unit textual definition +WARN missing_definition luminous intensity unit textual definition +WARN missing_definition ampere textual definition +WARN missing_definition kelvin textual definition +WARN missing_definition mole textual definition +WARN missing_definition candela textual definition +WARN missing_definition picometer textual definition +WARN missing_definition femtogram textual definition +WARN missing_definition millisecond textual definition +WARN missing_definition microsecond textual definition +WARN missing_definition picosecond textual definition +WARN missing_definition milliampere textual definition +WARN missing_definition microampere textual definition +WARN missing_definition millimole textual definition +WARN missing_definition femtomole textual definition +WARN missing_definition attomole textual definition +WARN missing_definition base unit textual definition +WARN missing_definition area unit textual definition +WARN missing_definition acceleration unit textual definition +WARN missing_definition angular velocity unit textual definition +WARN missing_definition angular acceleration unit textual definition +WARN missing_definition concentration unit textual definition +WARN missing_definition mass density unit textual definition +WARN missing_definition luminance unit textual definition +WARN missing_definition area density unit textual definition +WARN missing_definition molar mass unit textual definition +WARN missing_definition molar volume unit textual definition +WARN missing_definition momentum unit textual definition +WARN missing_definition rotational frequency unit textual definition +WARN missing_definition specific volume unit textual definition +WARN missing_definition speed/velocity unit textual definition +WARN missing_definition unit of molarity textual definition +WARN missing_definition unit of molality textual definition +WARN missing_definition molal textual definition +WARN missing_definition millimolal textual definition +WARN missing_definition micromolal textual definition +WARN missing_definition nanomolal textual definition +WARN missing_definition picomolal textual definition +WARN missing_definition femtomolar textual definition +WARN missing_definition unit of normality textual definition +WARN missing_definition normal textual definition +WARN missing_definition mole fraction textual definition +WARN missing_definition meter per second per second textual definition +WARN missing_definition radian per second per second textual definition +WARN missing_definition radian per second textual definition +WARN missing_definition square meter textual definition +WARN missing_definition square centimeter textual definition +WARN missing_definition square millimeter textual definition +WARN missing_definition kilogram per cubic meter textual definition +WARN missing_definition gram per cubic centimeter textual definition +WARN missing_definition candela per square meter textual definition +WARN missing_definition kilogram per square meter textual definition +WARN missing_definition kilogram per mole textual definition +WARN missing_definition gram per mole textual definition +WARN missing_definition cubic meter per mole textual definition +WARN missing_definition cubic centimeter per mole textual definition +WARN missing_definition kilogram meter per second textual definition +WARN missing_definition turns per second textual definition +WARN missing_definition cubic meter per kilogram textual definition +WARN missing_definition meter per second textual definition +WARN missing_definition volume unit textual definition +WARN missing_definition cubic meter textual definition +WARN missing_definition femtoliter textual definition +WARN missing_definition frequency unit textual definition +WARN missing_definition force unit textual definition +WARN missing_definition newton textual definition +WARN missing_definition pressure unit textual definition +WARN missing_definition pascal textual definition +WARN missing_definition energy unit textual definition +WARN missing_definition joule textual definition +WARN missing_definition power unit textual definition +WARN missing_definition watt textual definition +WARN missing_definition illuminance unit textual definition +WARN missing_definition lux textual definition +WARN missing_definition luminous flux unit textual definition +WARN missing_definition lumen textual definition +WARN missing_definition catalytic activity unit textual definition +WARN missing_definition katal textual definition +WARN missing_definition angle unit textual definition +WARN missing_definition plane angle unit textual definition +WARN missing_definition radian textual definition +WARN missing_definition solid angle unit textual definition +WARN missing_definition steradian textual definition +WARN missing_definition radiation unit textual definition +WARN missing_definition activity (of a radionuclide) unit textual definition +WARN missing_definition dose equivalent unit textual definition +WARN missing_definition exposure unit textual definition +WARN missing_definition becquerel textual definition +WARN missing_definition curie textual definition +WARN missing_definition gray textual definition +WARN missing_definition rad textual definition +WARN missing_definition roentgen textual definition +WARN missing_definition sievert textual definition +WARN missing_definition millisievert textual definition +WARN missing_definition microsievert textual definition +WARN missing_definition Roentgen equivalent man textual definition +WARN missing_definition microgray textual definition +WARN missing_definition milligray textual definition +WARN missing_definition nanogray textual definition +WARN missing_definition nanosievert textual definition +WARN missing_definition millicurie textual definition +WARN missing_definition microcurie textual definition +WARN missing_definition disintegrations per minute textual definition +WARN missing_definition counts per minute textual definition +WARN missing_definition nanosecond textual definition +WARN missing_definition century textual definition +WARN missing_definition half life textual definition +WARN missing_definition foot candle textual definition +WARN missing_definition irradiance unit textual definition +WARN missing_definition watt per square meter textual definition +WARN missing_definition einstein per square meter per second textual definition +WARN missing_definition light unit textual definition +WARN missing_definition watt per steradian per square meter textual definition +WARN missing_definition radiant intensity unit textual definition +WARN missing_definition microeinstein per square meter per second textual definition +WARN missing_definition radiance unit textual definition +WARN missing_definition watt per steradian textual definition +WARN missing_definition parts per notation unit textual definition +WARN missing_definition parts per hundred textual definition +WARN missing_definition parts per thousand textual definition +WARN missing_definition parts per million textual definition +WARN missing_definition parts per billion textual definition +WARN missing_definition parts per trillion textual definition +WARN missing_definition parts per quadrillion textual definition +WARN missing_definition gram per milliliter textual definition +WARN missing_definition kilogram per liter textual definition +WARN missing_definition unit per volume unit textual definition +WARN missing_definition unit per milliliter textual definition +WARN missing_definition unit per liter textual definition +WARN missing_definition mass per unit volume textual definition +WARN missing_definition enzyme unit textual definition +WARN missing_definition density unit textual definition +WARN missing_definition linear density unit textual definition +WARN missing_definition kilogram per meter textual definition +WARN missing_definition degree textual definition +WARN missing_definition dimensionless unit textual definition +WARN missing_definition percent textual definition +WARN missing_definition pi textual definition +WARN missing_definition count unit textual definition +WARN missing_definition ratio unit textual definition +WARN missing_definition fraction textual definition +WARN missing_definition molecule count textual definition +WARN missing_definition purity percentage textual definition +WARN missing_definition confluence percentage textual definition +WARN missing_definition liter per kilogram textual definition +WARN missing_definition milliliter per kilogram textual definition +WARN missing_definition microliter per kilogram textual definition +WARN missing_definition cell concentration unit textual definition +WARN missing_definition cells per milliliter textual definition +WARN missing_definition catalytic (activity) concentration unit textual definition +WARN missing_definition katal per cubic meter textual definition +WARN missing_definition katal per liter textual definition +WARN missing_definition volume per unit volume textual definition +WARN missing_definition milliliter per cubic meter textual definition +WARN missing_definition deciliter textual definition +WARN missing_definition colony forming unit textual definition +WARN missing_definition plaque forming unit textual definition +WARN missing_definition colony forming unit per milliliter textual definition +WARN missing_definition plaque forming unit per volume textual definition +WARN missing_definition plaque forming unit per milliliter textual definition +WARN missing_definition disintegrations per second textual definition +WARN missing_definition electric potential difference unit textual definition +WARN missing_definition volt textual definition +WARN missing_definition electric charge textual definition +WARN missing_definition coulomb textual definition +WARN missing_definition dalton textual definition +WARN missing_definition kilodalton textual definition +WARN missing_definition watt-hour textual definition +WARN missing_definition kilowatt-hour textual definition +WARN missing_definition magnetic flux unit textual definition +WARN missing_definition weber textual definition +WARN missing_definition magnetic flux density unit textual definition +WARN missing_definition tesla textual definition +WARN missing_definition volt-hour textual definition +WARN missing_definition kilovolt-hour textual definition +WARN missing_definition information unit textual definition +WARN missing_definition bit textual definition +WARN missing_definition byte textual definition +WARN missing_definition kilobyte textual definition +WARN missing_definition megabyte textual definition +WARN missing_definition image resolution unit textual definition +WARN missing_definition chroma sampling unit textual definition +WARN missing_definition dynamic range unit textual definition +WARN missing_definition spatial resolution unit textual definition +WARN missing_definition dots per inch textual definition +WARN missing_definition micron pixel textual definition +WARN missing_definition pixels per inch textual definition +WARN missing_definition pixels per millimeter textual definition +WARN missing_definition base pair textual definition +WARN missing_definition kibibyte textual definition +WARN missing_definition mebibyte textual definition +WARN missing_definition millivolt textual definition +WARN missing_definition kilovolt textual definition +WARN missing_definition microvolt textual definition +WARN missing_definition nanovolt textual definition +WARN missing_definition picovolt textual definition +WARN missing_definition megavolt textual definition +WARN missing_definition surface tension unit textual definition +WARN missing_definition newton per meter textual definition +WARN missing_definition dyne per cm textual definition +WARN missing_definition viscosity unit textual definition +WARN missing_definition pascal second textual definition +WARN missing_definition poise textual definition +WARN missing_definition decibel textual definition +WARN missing_definition effective dose unit textual definition +WARN missing_definition conduction unit textual definition +WARN missing_definition electrical conduction unit textual definition +WARN missing_definition heat conduction unit textual definition +WARN missing_definition siemens textual definition +WARN missing_definition watt per meter kelvin textual definition +WARN missing_definition electronvolt textual definition +WARN missing_definition electric field strength unit textual definition +WARN missing_definition volt per meter textual definition +WARN missing_definition absorbance unit textual definition +WARN missing_definition volumetric flow rate unit textual definition +WARN missing_definition millimetres of mercury textual definition +WARN missing_definition milligram per liter textual definition +WARN missing_definition microgram per milliliter textual definition +WARN missing_definition nanogram per milliliter textual definition +WARN missing_definition milliunits per milliliter textual definition +WARN missing_definition rate unit textual definition +WARN missing_definition kilogram per hectare textual definition +WARN missing_definition giga textual definition +WARN missing_definition mega textual definition +WARN missing_definition kilo textual definition +WARN missing_definition deci textual definition +WARN missing_definition milli textual definition +WARN missing_definition centi textual definition +WARN missing_definition micro textual definition +WARN missing_definition nano textual definition +WARN missing_definition pico textual definition +WARN missing_definition femto textual definition +WARN missing_definition atto textual definition +WARN missing_definition dose unit textual definition +WARN missing_definition milligram per kilogram textual definition +WARN missing_definition milligram per square meter textual definition +WARN missing_definition dosage unit textual definition +WARN missing_definition milligram per kilogram per day textual definition +WARN missing_definition relative light unit textual definition +WARN missing_definition relative luminescence unit textual definition +WARN missing_definition relative fluorescence unit textual definition +WARN missing_definition megaHertz textual definition +WARN missing_definition centiMorgan textual definition +WARN missing_definition centiRay textual definition +WARN missing_definition mega base pair textual definition +WARN missing_definition giga base pair textual definition +WARN missing_definition square micrometer textual definition +WARN missing_definition millisiemens textual definition +WARN missing_definition micromole per litre textual definition +WARN missing_definition micromole per kilogram textual definition +WARN missing_definition millimeters per day textual definition +WARN missing_definition kilometer per hour textual definition +WARN missing_definition milli textual definition +WARN missing_definition hectare textual definition +WARN missing_definition inch textual definition +WARN missing_definition thou textual definition +WARN missing_definition foot textual definition +WARN missing_definition yard textual definition +WARN missing_definition chain textual definition +WARN missing_definition furlong textual definition +WARN missing_definition mile textual definition +WARN missing_definition league textual definition +WARN missing_definition maritime length unit textual definition +WARN missing_definition fathom textual definition +WARN missing_definition cable textual definition +WARN missing_definition nautical mile textual definition +WARN missing_definition perch textual definition +WARN missing_definition rood textual definition +WARN missing_definition acre textual definition +WARN missing_definition fluid ounce textual definition +WARN missing_definition gill textual definition +WARN missing_definition pint textual definition +WARN missing_definition quart textual definition +WARN missing_definition gallon textual definition +WARN missing_definition grain textual definition +WARN missing_definition drachm textual definition +WARN missing_definition ounce textual definition +WARN missing_definition pound textual definition +WARN missing_definition stone textual definition +WARN missing_definition quarter textual definition +WARN missing_definition hundredweight textual definition +WARN missing_definition ton textual definition +WARN missing_definition slug textual definition +WARN missing_definition teaspoon textual definition +WARN missing_definition micromole textual definition +WARN missing_definition gram per square meter textual definition +WARN missing_definition nanogram per microliter textual definition +WARN missing_definition large calorie textual definition +WARN missing_definition micrograms per wheaton bottle textual definition +WARN missing_definition picoampere textual definition +WARN missing_definition centigray textual definition +WARN missing_definition gigaelectronvolt textual definition +WARN missing_definition gigaelectronvolt per nucleon textual definition +WARN missing_definition megaelectronvolt per nucleon textual definition +WARN missing_definition kiloelectronvolt per micron textual definition +WARN missing_definition gray per minute textual definition +WARN missing_definition centigray per minute textual definition +WARN missing_definition milligray per minute textual definition +WARN missing_definition milligray per day textual definition +WARN missing_definition milligray per hour textual definition +WARN missing_definition milligray per second textual definition +WARN missing_definition kilometer textual definition +WARN missing_definition milligram per deciliter textual definition +WARN missing_definition microgram per deciliter textual definition +WARN missing_definition meter based unit textual definition +WARN missing_definition second based unit textual definition +WARN missing_definition ampere based unit textual definition +WARN missing_definition kelvin based unit textual definition +WARN missing_definition mole based unit textual definition +WARN missing_definition candela based unit textual definition +WARN missing_definition angstrom based unit textual definition +WARN missing_definition gram based unit textual definition +WARN missing_definition degree Celsius based unit textual definition +WARN missing_definition minute based unit textual definition +WARN missing_definition hour based unit textual definition +WARN missing_definition day based unit textual definition +WARN missing_definition week based unit textual definition +WARN missing_definition month based unit textual definition +WARN missing_definition year based unit textual definition +WARN missing_definition molar based unit textual definition +WARN missing_definition molal based unit textual definition +WARN missing_definition normal based unit textual definition +WARN missing_definition mole fraction based unit textual definition +WARN missing_definition meter per second per second based unit textual definition +WARN missing_definition radian per second per second based unit textual definition +WARN missing_definition radian per second based unit textual definition +WARN missing_definition square meter based unit textual definition +WARN missing_definition square centimeter based unit textual definition +WARN missing_definition square millimeter based unit textual definition +WARN missing_definition gram per cubic centimeter based unit textual definition +WARN missing_definition candela per square meter based unit textual definition +WARN missing_definition gram per mole based unit textual definition +WARN missing_definition cubic meter per mole based unit textual definition +WARN missing_definition cubic centimeter per mole based unit textual definition +WARN missing_definition turns per second based unit textual definition +WARN missing_definition cubic meter per kilogram based unit textual definition +WARN missing_definition meter per second based unit textual definition +WARN missing_definition cubic meter based unit textual definition +WARN missing_definition cubic centimeter based unit textual definition +WARN missing_definition liter based unit textual definition +WARN missing_definition cubic decimeter based unit textual definition +WARN missing_definition hertz based unit textual definition +WARN missing_definition newton based unit textual definition +WARN missing_definition pascal based unit textual definition +WARN missing_definition joule based unit textual definition +WARN missing_definition watt based unit textual definition +WARN missing_definition lux based unit textual definition +WARN missing_definition lumen based unit textual definition +WARN missing_definition katal based unit textual definition +WARN missing_definition radian based unit textual definition +WARN missing_definition steradian based unit textual definition +WARN missing_definition becquerel based unit textual definition +WARN missing_definition curie based unit textual definition +WARN missing_definition gray based unit textual definition +WARN missing_definition rad based unit textual definition +WARN missing_definition roentgen based unit textual definition +WARN missing_definition sievert based unit textual definition +WARN missing_definition Roentgen equivalent man based unit textual definition +WARN missing_definition disintegrations per minute based unit textual definition +WARN missing_definition counts per minute based unit textual definition +WARN missing_definition century based unit textual definition +WARN missing_definition half life based unit textual definition +WARN missing_definition foot candle based unit textual definition +WARN missing_definition watt per square meter based unit textual definition +WARN missing_definition einstein per square meter per second based unit textual definition +WARN missing_definition watt per steradian per square meter based unit textual definition +WARN missing_definition watt per steradian based unit textual definition +WARN missing_definition mass percentage based unit textual definition +WARN missing_definition mass volume percentage based unit textual definition +WARN missing_definition volume percentage based unit textual definition +WARN missing_definition parts per hundred based unit textual definition +WARN missing_definition parts per thousand based unit textual definition +WARN missing_definition parts per million based unit textual definition +WARN missing_definition parts per billion based unit textual definition +WARN missing_definition parts per trillion based unit textual definition +WARN missing_definition parts per quadrillion based unit textual definition +WARN missing_definition gram per milliliter based unit textual definition +WARN missing_definition gram per liter based unit textual definition +WARN missing_definition unit per milliliter based unit textual definition +WARN missing_definition unit per liter based unit textual definition +WARN missing_definition mass per unit volume based unit textual definition +WARN missing_definition enzyme unit based unit textual definition +WARN missing_definition degree based unit textual definition +WARN missing_definition pi based unit textual definition +WARN missing_definition molecule count based unit textual definition +WARN missing_definition purity percentage based unit textual definition +WARN missing_definition confluence percentage based unit textual definition +WARN missing_definition degree Fahrenheit based unit textual definition +WARN missing_definition pH based unit textual definition +WARN missing_definition liter per kilogram based unit textual definition +WARN missing_definition cells per milliliter based unit textual definition +WARN missing_definition katal per cubic meter based unit textual definition +WARN missing_definition katal per liter based unit textual definition +WARN missing_definition gram per deciliter based unit textual definition +WARN missing_definition colony forming unit based unit textual definition +WARN missing_definition plaque forming unit based unit textual definition +WARN missing_definition colony forming unit per milliliter based unit textual definition +WARN missing_definition plaque forming unit per milliliter based unit textual definition +WARN missing_definition disintegrations per second based unit textual definition +WARN missing_definition volt based unit textual definition +WARN missing_definition coulomb based unit textual definition +WARN missing_definition dalton based unit textual definition +WARN missing_definition watt-hour based unit textual definition +WARN missing_definition weber based unit textual definition +WARN missing_definition tesla based unit textual definition +WARN missing_definition volt-hour based unit textual definition +WARN missing_definition bit based unit textual definition +WARN missing_definition byte based unit textual definition +WARN missing_definition chroma sampling unit based unit textual definition +WARN missing_definition dynamic range unit based unit textual definition +WARN missing_definition dots per inch based unit textual definition +WARN missing_definition pixels per inch based unit textual definition +WARN missing_definition pixels per millimeter based unit textual definition +WARN missing_definition base pair based unit textual definition +WARN missing_definition kibibyte based unit textual definition +WARN missing_definition mebibyte based unit textual definition +WARN missing_definition newton per meter based unit textual definition +WARN missing_definition dyne per cm based unit textual definition +WARN missing_definition pascal second based unit textual definition +WARN missing_definition poise based unit textual definition +WARN missing_definition effective dose unit based unit textual definition +WARN missing_definition siemens based unit textual definition +WARN missing_definition watt per meter kelvin based unit textual definition +WARN missing_definition electronvolt based unit textual definition +WARN missing_definition volt per meter based unit textual definition +WARN missing_definition absorbance unit based unit textual definition +WARN missing_definition count per nanomolar second based unit textual definition +WARN missing_definition count per molar second based unit textual definition +WARN missing_definition count per nanomolar based unit textual definition +WARN missing_definition count per molar based unit textual definition +WARN missing_definition dosage unit based unit textual definition +WARN missing_definition relative light unit based unit textual definition +WARN missing_definition relative luminescence unit based unit textual definition +WARN missing_definition relative fluorescence unit based unit textual definition +WARN missing_definition square micrometer based unit textual definition +WARN missing_definition hectare based unit textual definition +WARN missing_definition inch based unit textual definition +WARN missing_definition thou based unit textual definition +WARN missing_definition foot based unit textual definition +WARN missing_definition yard based unit textual definition +WARN missing_definition chain based unit textual definition +WARN missing_definition furlong based unit textual definition +WARN missing_definition mile based unit textual definition +WARN missing_definition league based unit textual definition +WARN missing_definition maritime length unit based unit textual definition +WARN missing_definition fathom based unit textual definition +WARN missing_definition cable based unit textual definition +WARN missing_definition nautical mile based unit textual definition +WARN missing_definition perch based unit textual definition +WARN missing_definition rood based unit textual definition +WARN missing_definition acre based unit textual definition +WARN missing_definition fluid ounce based unit textual definition +WARN missing_definition gill based unit textual definition +WARN missing_definition pint based unit textual definition +WARN missing_definition quart based unit textual definition +WARN missing_definition gallon based unit textual definition +WARN missing_definition grain based unit textual definition +WARN missing_definition drachm based unit textual definition +WARN missing_definition ounce based unit textual definition +WARN missing_definition pound based unit textual definition +WARN missing_definition stone based unit textual definition +WARN missing_definition quarter based unit textual definition +WARN missing_definition hundredweight based unit textual definition +WARN missing_definition ton based unit textual definition +WARN missing_definition slug based unit textual definition +WARN missing_definition teaspoon based unit textual definition +WARN missing_definition gram per square meter based unit textual definition +WARN missing_definition large calorie based unit textual definition +WARN missing_definition gray per minute based unit textual definition +WARN missing_definition has parent hydride textual definition +WARN missing_definition is conjugate acid of textual definition +WARN missing_definition is conjugate base of textual definition +WARN missing_definition is substituent group from textual definition +WARN missing_definition is tautomer of textual definition +WARN missing_definition channel for textual definition +WARN missing_definition channels_from textual definition +WARN missing_definition channels_into textual definition +WARN missing_definition layer part of textual definition +WARN missing_definition protects textual definition +WARN missing_definition subdivision of textual definition +WARN missing_definition Creator textual definition +WARN missing_definition Date textual definition +WARN missing_definition Description textual definition +WARN missing_definition Title textual definition +WARN missing_definition license textual definition +WARN missing_definition http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled textual definition +WARN missing_definition Mus musculus subspecies textual definition +WARN missing_definition Obsolete Class textual definition +WARN missing_definition created_by textual definition +WARN missing_definition creation date textual definition +WARN missing_definition has_alternative_id textual definition +WARN missing_definition database_cross_reference textual definition +WARN missing_definition has_obo_namespace textual definition +WARN missing_definition has_related_synonym textual definition +WARN missing_definition in_subset textual definition +WARN missing_definition xsd:boolean textual definition +WARN missing_definition xsd:string textual definition +WARN missing_obsolete_label device label device +WARN missing_subset_declaration obo:doid#DO_AGR_slim rdfs:subPropertyOf +WARN missing_subset_declaration obo:doid#DO_CFDE_slim rdfs:subPropertyOf +WARN missing_subset_declaration obo:doid#DO_FlyBase_slim rdfs:subPropertyOf +WARN missing_subset_declaration obo:doid#DO_GXD_slim rdfs:subPropertyOf +WARN missing_subset_declaration obo:doid#DO_MGI_slim rdfs:subPropertyOf +WARN missing_subset_declaration obo:doid#DO_RAD_slim rdfs:subPropertyOf +WARN missing_subset_declaration obo:doid#DO_cancer_slim rdfs:subPropertyOf +WARN missing_subset_declaration obo:doid#DO_rare_slim rdfs:subPropertyOf +WARN missing_subset_declaration obo:doid#NCIthesaurus rdfs:subPropertyOf +WARN missing_subset_declaration obo:doid#TopNodes_DOcancerslim rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_subset_declaration blank node rdfs:subPropertyOf +WARN missing_synonymtype_declaration OMO:0003000 rdfs:subPropertyOf +WARN missing_synonymtype_declaration OMO:0003002 rdfs:subPropertyOf +WARN missing_synonymtype_declaration OMO:0003003 rdfs:subPropertyOf +WARN missing_synonymtype_declaration OMO:0003004 rdfs:subPropertyOf +WARN missing_synonymtype_declaration OMO:0003011 rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:bspo#vertebrate rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:chebi#INN rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:chebi#IUPAC_NAME rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:go#syngo_official_label rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:go#systematic_synonym rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon#blast_name rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon#common_name rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon#equivalent_name rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon#genbank_common_name rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon#in_part rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon#misnomer rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon#misspelling rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon#scientific_name rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon#synonym rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon/subsets/taxslim#blast_name rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon/subsets/taxslim#common_name rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon/subsets/taxslim#genbank_common_name rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:ncbitaxon/subsets/taxslim#synonym rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:po#Japanese rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:po#Plural rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:po#Spanish rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:pr#Gene-based rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:pr#PRO-short-label rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:uberon/core#DEPRECATED rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:uberon/core#HUMAN_PREFERRED rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:uberon/core#INCONSISTENT rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:uberon/core#PENDING_REVIEW rdfs:subPropertyOf +WARN missing_synonymtype_declaration obo:uberon/core#SENSU rdfs:subPropertyOf +WARN multiple_equivalent_classes response to light stimulus owl:equivalentClass blank node +WARN multiple_equivalent_classes response to organic substance owl:equivalentClass blank node +WARN multiple_equivalent_classes response to inorganic substance owl:equivalentClass blank node +WARN multiple_equivalent_classes response to organonitrogen compound owl:equivalentClass blank node +WARN multiple_equivalent_classes response to organic cyclic compound owl:equivalentClass blank node +WARN multiple_equivalent_classes RNA biosynthetic process owl:equivalentClass blank node +WARN multiple_equivalent_classes response to chemical owl:equivalentClass blank node +WARN multiple_equivalent_classes response to amino acid owl:equivalentClass blank node +WARN multiple_equivalent_classes membrane biogenesis owl:equivalentClass blank node +WARN multiple_equivalent_classes response to carbamate owl:equivalentClass blank node +WARN multiple_equivalent_classes response to ammonium ion owl:equivalentClass blank node +WARN multiple_equivalent_classes nuclear membrane biogenesis owl:equivalentClass blank node +WARN multiple_equivalent_classes catalytic activity, acting on a protein owl:equivalentClass blank node +WARN multiple_equivalent_classes catalytic activity, acting on RNA owl:equivalentClass blank node +WARN multiple_equivalent_classes catalytic activity, acting on a nucleic acid owl:equivalentClass blank node +WARN multiple_equivalent_classes response to peptide owl:equivalentClass blank node +WARN multiple_equivalent_classes response to nitrogen compound owl:equivalentClass blank node +WARN multiple_equivalent_classes response to oxygen-containing compound owl:equivalentClass blank node +WARN multiple_equivalent_classes obsolescence reason specification owl:equivalentClass blank node +INFO lowercase_definition independent continuant textual definition b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) +INFO lowercase_definition independent continuant textual definition b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])@en +INFO lowercase_definition process textual definition p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])@en +INFO lowercase_definition disposition IAO:0000600 b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])@en +INFO lowercase_definition quality IAO:0000600 a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])@en +INFO lowercase_definition specifically dependent continuant textual definition b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])@en +INFO lowercase_definition specifically dependent continuant textual definition b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])@en +INFO lowercase_definition role IAO:0000600 b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])@en +INFO lowercase_definition object aggregate IAO:0000600 b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])@en +INFO lowercase_definition generically dependent continuant textual definition b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])@en INFO lowercase_definition part_of textual definition a core relation that holds between a part and its whole@en INFO lowercase_definition has_part textual definition a core relation that holds between a whole and its part@en -INFO lowercase_definition realized in IAO:0000600 <[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])@en> -INFO lowercase_definition realizes IAO:0000600 -INFO lowercase_definition preceded by textual definition -INFO lowercase_definition precedes textual definition +INFO lowercase_definition realized in IAO:0000600 [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])@en +INFO lowercase_definition realizes IAO:0000600 to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])@en +INFO lowercase_definition preceded by textual definition x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.@en +INFO lowercase_definition precedes textual definition x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.@en INFO lowercase_definition occurs in textual definition b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t@en INFO lowercase_definition contains process textual definition [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t@en -INFO lowercase_definition continuant fiat boundary textual definition +INFO lowercase_definition continuant fiat boundary textual definition b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])@en INFO lowercase_definition anterior to textual definition x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. INFO lowercase_definition dorsal to textual definition x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). INFO lowercase_definition posterior to textual definition x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. @@ -3036,39 +3003,37 @@ INFO lowercase_definition in distal side of textual definition x in distal side INFO lowercase_definition immediately deep to textual definition x immediately deep to y iff x deep_to y and x is contiguous with y. INFO lowercase_definition immediately superficial to textual definition x immediately superficial to y iff x superficial to y and x is contiguous with y. INFO lowercase_definition lipid textual definition 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. -INFO lowercase_definition catecholamine textual definition 4-(2-Aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution. INFO lowercase_definition partially_surrounded_by textual definition x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x INFO lowercase_definition ore textual definition a type of rock that contains sufficient minerals with important elements including metals that can be economically extracted from the rock. INFO lowercase_definition nuclear energy textual definition potential energy that binds nucleons to form the atomic nucleus (and nuclear reactions). INFO lowercase_definition data item textual definition a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.@en -INFO lowercase_definition definition source textual definition -INFO lowercase_definition is quality measurement of textual definition m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q@en -INFO lowercase_definition is quality measured as textual definition inverse of the relation of is quality measurement of@en -INFO lowercase_definition behavior process textual definition "<\""The action, reaction, or performance of an organism in response to external or internal stimuli.\"" [GO:GO\:0007610]>" +INFO lowercase_definition definition source textual definition formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007@en +INFO lowercase_definition behavior process textual definition "\""The action, reaction, or performance of an organism in response to external or internal stimuli.\"" [GO:GO\:0007610]" INFO lowercase_definition kinesthetic behavior textual definition "\""Movement behavior of the body or its parts.\""" -INFO lowercase_definition regulation of behavior textual definition "<\""Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli.\"" [GO:0050795]>" +INFO lowercase_definition regulation of behavior textual definition "\""Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli.\"" [GO:0050795]" INFO lowercase_definition regulator role textual definition a regulatory role involved with making and/or enforcing relevant legislation and governmental orders@en INFO lowercase_definition regulatory role textual definition a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.@en INFO lowercase_definition material supplier role textual definition a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.@en INFO lowercase_definition specimen role textual definition a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation@en INFO lowercase_definition population textual definition a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area@en INFO lowercase_definition protocol textual definition a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process. -INFO lowercase_definition zip textual definition -INFO lowercase_definition tar textual definition +INFO lowercase_definition zip textual definition zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)@en +INFO lowercase_definition tar textual definition tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)@en INFO lowercase_definition material transformation objective textual definition an objective specifiction that creates an specific output object from input materials.@en INFO lowercase_definition manufacturing objective textual definition is the objective to manufacture a material of a certain function (device)@en -INFO lowercase_definition GenePattern software textual definition a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. -INFO lowercase_definition service provider role textual definition is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person -INFO lowercase_definition leave one out cross validation method textual definition +INFO lowercase_definition GenePattern software textual definition a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.@en +INFO lowercase_definition service provider role textual definition is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person@en +INFO lowercase_definition leave one out cross validation method textual definition is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data@en INFO lowercase_definition spacecraft module textual definition a self-contained unit of a spacecraft INFO lowercase_definition gamma radiation textual definition electromagnetic radiation with photon energies greater than approximately 100 keV -INFO lowercase_definition Gammacell 40 textual definition -INFO lowercase_definition RARAF 5.5 MV microbeam textual definition -INFO lowercase_definition Swift HALE textual definition -INFO lowercase_definition ER-2 textual definition -INFO lowercase_definition WB-57 textual definition -INFO lowercase_definition Faxitron CP160 textual definition -INFO lowercase_definition X-Rad320 textual definition +INFO lowercase_definition Gammacell 40 textual definition http://www.theratronics.ca/PDFs/GC40_BTMB_8008GC40E_2_v112013_webSECURE.pdf +INFO lowercase_definition RARAF 5.5 MV microbeam textual definition https://www.crr.columbia.edu/services/ion-beam-and-neutron-core-facility +INFO lowercase_definition Swift HALE textual definition https://www.nasa.gov/feature/ames/nasa-small-business-partnership-prepares-drone-for-30-day-science-flights +INFO lowercase_definition ER-2 textual definition https://www.nasa.gov/centers/armstrong/aircraft/ER-2/index.html +INFO lowercase_definition WB-57 textual definition https://airbornescience.nasa.gov/aircraft/WB-57_-_JSC +INFO lowercase_definition Faxitron CP160 textual definition doi: 10.2349/biij.2.1.e1 +INFO lowercase_definition X-Rad320 textual definition https://precisionxray.com/x-rad/xrad-320/ +INFO lowercase_definition epithermal neutron textual definition a neutron with energy greater than a thermal neutron, but less than a fast neutron. The approximate energy range is 0.025-0.4 eV. INFO lowercase_definition inheres in textual definition a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.@en INFO lowercase_definition inheres in textual definition a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence@en INFO lowercase_definition bearer of textual definition a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence@en @@ -3095,7 +3060,7 @@ INFO lowercase_definition synapsed to textual definition " Relation between a ne INFO lowercase_definition overlaps textual definition x overlaps y if and only if there exists some z such that x has part z and z part of y INFO lowercase_definition overlaps textual definition x overlaps y iff they have some part in common. INFO lowercase_definition only in taxon textual definition x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. -INFO lowercase_definition in taxon textual definition +INFO lowercase_definition in taxon textual definition x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. INFO lowercase_definition connected to textual definition a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b INFO lowercase_definition connects textual definition c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. INFO lowercase_definition attached to part of textual definition a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. @@ -3104,7 +3069,7 @@ INFO lowercase_definition develops from textual definition x develops from y if INFO lowercase_definition develops into textual definition inverse of develops from INFO lowercase_definition directly develops into textual definition inverse of directly develops from INFO lowercase_definition regulates (processual) textual definition p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. -INFO lowercase_definition regulates (processual) textual definition +INFO lowercase_definition regulates (processual) textual definition process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. INFO lowercase_definition negatively regulates textual definition p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. INFO lowercase_definition positively regulates textual definition p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. INFO lowercase_definition capable of part of textual definition c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. @@ -3112,26 +3077,26 @@ INFO lowercase_definition surrounded by textual definition x surrounded_by y if INFO lowercase_definition adjacent to textual definition x adjacent to y if and only if x and y share a boundary. INFO lowercase_definition surrounds textual definition inverse of surrounded by INFO lowercase_definition starts textual definition inverse of starts with -INFO lowercase_definition starts with textual definition +INFO lowercase_definition starts with textual definition x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. INFO lowercase_definition develops from part of textual definition x develops from part of y if and only if there exists some z such that x develops from z and z is part of y INFO lowercase_definition develops in textual definition x develops_in y if x is located in y whilst x is developing INFO lowercase_definition ends textual definition inverse of ends with -INFO lowercase_definition ends with textual definition α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.> +INFO lowercase_definition ends with textual definition x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. INFO lowercase_definition has start location textual definition x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y INFO lowercase_definition has end location textual definition x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y -INFO lowercase_definition has input textual definition

+INFO lowercase_definition has input textual definition p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. INFO lowercase_definition has output textual definition p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. INFO lowercase_definition connecting branch of textual definition b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. INFO lowercase_definition has connecting branch textual definition inverse of connecting branch of INFO lowercase_definition has developmental contribution from textual definition x has developmental contribution from y iff x has some part z such that z develops from y@en INFO lowercase_definition developmentally contributes to textual definition inverse of has developmental contribution from -INFO lowercase_definition developmentally induced by textual definition +INFO lowercase_definition developmentally induced by textual definition t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T INFO lowercase_definition acts upstream of textual definition c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. INFO lowercase_definition acts upstream of or within textual definition c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. INFO lowercase_definition developmentally replaces textual definition x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else INFO lowercase_definition results in developmental progression of textual definition p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). INFO lowercase_definition results in development of textual definition p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. -INFO lowercase_definition has habitat textual definition +INFO lowercase_definition has habitat textual definition x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. INFO lowercase_definition causally upstream of, positive effect textual definition p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. INFO lowercase_definition causally upstream of, negative effect textual definition p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. INFO lowercase_definition inheres in part of textual definition q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. @@ -3174,18 +3139,18 @@ INFO lowercase_definition involved in positive regulation of textual definition INFO lowercase_definition involved in negative regulation of textual definition c involved in regulation of p if c is involved in some p' and p' negatively regulates some p INFO lowercase_definition involved in or involved in regulation of textual definition c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p INFO lowercase_definition is active in textual definition c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. -INFO lowercase_definition contributes to morphology of textual definition

+INFO lowercase_definition contributes to morphology of textual definition p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. INFO lowercase_definition composed primarily of textual definition x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. INFO lowercase_definition has part that occurs in textual definition p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. -INFO lowercase_definition existence starts during textual definition = α(y) & α(x) <= ω(y).> -INFO lowercase_definition existence starts with textual definition -INFO lowercase_definition existence overlaps textual definition = α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))> -INFO lowercase_definition existence starts and ends during textual definition = α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)> -INFO lowercase_definition existence ends during textual definition = α(y).> -INFO lowercase_definition existence ends with textual definition +INFO lowercase_definition existence starts during textual definition x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). +INFO lowercase_definition existence starts with textual definition x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). +INFO lowercase_definition existence overlaps textual definition x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) +INFO lowercase_definition existence starts and ends during textual definition x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) +INFO lowercase_definition existence ends during textual definition x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). +INFO lowercase_definition existence ends with textual definition x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). INFO lowercase_definition transformation of textual definition x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships INFO lowercase_definition immediate transformation of textual definition x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t -INFO lowercase_definition existence starts during or after textual definition = α (y).> +INFO lowercase_definition existence starts during or after textual definition x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). INFO lowercase_definition existence ends during or before textual definition x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. INFO lowercase_definition causal relation between processes textual definition p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. INFO lowercase_definition causal relation between processes textual definition p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. @@ -3202,7 +3167,7 @@ INFO lowercase_definition results in breakdown of textual definition p results i INFO lowercase_definition results in organization of textual definition p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c INFO lowercase_definition directly positively regulates textual definition p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. INFO lowercase_definition directly negatively regulates textual definition p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. -INFO lowercase_definition produces textual definition +INFO lowercase_definition produces textual definition a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. INFO lowercase_definition produced by textual definition a produced_by b iff some process that occurs_in b has_output a. INFO lowercase_definition has primary input or output textual definition p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. INFO lowercase_definition has primary output textual definition p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. @@ -3215,7 +3180,7 @@ INFO lowercase_definition indirectly causally upstream of textual definition p i INFO lowercase_definition indirectly regulates textual definition p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. INFO lowercase_definition different in magnitude relative to textual definition q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. INFO lowercase_definition increased in magnitude relative to textual definition q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. -INFO lowercase_definition has cross section textual definition +INFO lowercase_definition has cross section textual definition s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. INFO lowercase_definition results in changes to anatomical or cellular structure textual definition p has anatomical participant c iff p has participant c, and c is an anatomical entity INFO lowercase_definition anteriorly connected to textual definition x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. INFO lowercase_definition distally connected to textual definition x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. @@ -3223,7 +3188,6 @@ INFO lowercase_definition indirectly_supplies textual definition a indirectly_su INFO lowercase_definition posteriorly connected to textual definition x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. INFO lowercase_definition proximally connected to textual definition x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. INFO lowercase_definition site_of textual definition c site_of p if c is the bearer of a disposition that is realized by a process that has p as part. -INFO lowercase_definition 129 mouse strain textual definition <129 is a mouse strain as described in Jackson Laboratory http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml> INFO lowercase_definition CAST/EiJ textual definition " Both CAST/EiJ and CASA/RkJ (Stock No. 000735) were derived from wild mice trapped in Thailand. CAST is often combined with the common laboratory strains to generate F1 hybrids with high levels of heterozygosity for use in genetic mapping. Unlike the wild-derived strain SPRET, male F1 mice from a CAST cross are fertile. @@ -3235,3 +3199,4 @@ Wild-derived mice are genetically distinct from common laboratory mice for a num INFO lowercase_definition Earth textual definition third planet from the Sun in the Solar System INFO missing_superclass entity rdfs:subClassOf INFO missing_superclass cellular response to toxic substance rdfs:subClassOf +INFO missing_superclass Obsolete Class rdfs:subClassOf diff --git a/src/ontology/run.sh b/src/ontology/run.sh index 4203e42..67f3028 100755 --- a/src/ontology/run.sh +++ b/src/ontology/run.sh @@ -8,10 +8,36 @@ # The assumption is that you are working in the src/ontology folder; # we therefore map the whole repo (../..) to a docker volume. # +# To use singularity instead of docker, please issue +# export USE_SINGULARITY= +# before running this script. +# # See README-editors.md for more details. -IMAGE=${IMAGE:-odkfull} +if [ -f run.sh.conf ]; then + . ./run.sh.conf +fi +# Look for a GitHub token +if [ -n "$GH_TOKEN" ]; then + : +elif [ -f ../../.github/token.txt ]; then + GH_TOKEN=$(cat ../../.github/token.txt) +elif [ -f $XDG_CONFIG_HOME/ontology-development-kit/github/token ]; then + GH_TOKEN=$(cat $XDG_CONFIG_HOME/ontology-development-kit/github/token) +elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/token" ]; then + GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token") +fi + +ODK_IMAGE=${ODK_IMAGE:-odkfull} +TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }') +if [ -n "$TAG_IN_IMAGE" ]; then + # Override ODK_TAG env var if IMAGE already includes a tag + ODK_TAG=$TAG_IN_IMAGE + ODK_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $1 }') +fi +ODK_TAG=${ODK_TAG:-latest} +ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx16G} ODK_DEBUG=${ODK_DEBUG:-no} TIMECMD= @@ -19,7 +45,33 @@ if [ x$ODK_DEBUG = xyes ]; then # If you wish to change the format string, take care of using # non-breaking spaces (U+00A0) instead of normal spaces, to # prevent the shell from tokenizing the format string. + echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps." TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb" fi -docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx8G' -e JAVA_OPTS='-Xmx8G' --rm -i obolibrary/$IMAGE $TIMECMD "$@" +VOLUME_BIND=$PWD/../../:/work +WORK_DIR=/work/src/ontology + +if [ -n "$ODK_BINDS" ]; then + VOLUME_BIND="$VOLUME_BIND,$ODK_BINDS" +fi + +if [ -n "$USE_SINGULARITY" ]; then + + singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \ + --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \ + --bind $VOLUME_BIND \ + -W $WORK_DIR \ + docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" +else + BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')" + docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \ + -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \ + --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" +fi + +case "$@" in +*update_repo*|*release*) + echo "Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/." + ;; +esac \ No newline at end of file diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh index 358330f..946c703 100644 --- a/src/scripts/update_repo.sh +++ b/src/scripts/update_repo.sh @@ -24,5 +24,7 @@ mkdir -p $ROOTDIR/.github/workflows cp -n target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml + echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)" -echo "Update successfully completed." \ No newline at end of file +echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml." +echo "Ontology repository update successfully completed." \ No newline at end of file diff --git a/src/sparql/edges.sparql b/src/sparql/edges.sparql index 5fec04e..edf658b 100644 --- a/src/sparql/edges.sparql +++ b/src/sparql/edges.sparql @@ -1,4 +1,3 @@ -prefix obo: prefix owl: prefix rdfs: prefix rdf: diff --git a/src/sparql/illegal-date-violation.sparql b/src/sparql/illegal-date-violation.sparql new file mode 100644 index 0000000..25ec660 --- /dev/null +++ b/src/sparql/illegal-date-violation.sparql @@ -0,0 +1,10 @@ +PREFIX dct: +PREFIX xsd: + +SELECT DISTINCT ?term ?property ?value WHERE +{ + VALUES ?property {dct:date dct:issued dct:created} + ?term ?property ?value . + FILTER (datatype(?value) != xsd:date || !regex(str(?value), '^\\d{4}-\\d\\d-\\d\\d$')) +} + diff --git a/src/sparql/inject-subset-declaration.ru b/src/sparql/inject-subset-declaration.ru index 18a8430..788313b 100644 --- a/src/sparql/inject-subset-declaration.ru +++ b/src/sparql/inject-subset-declaration.ru @@ -7,5 +7,5 @@ INSERT { ?y rdfs:subPropertyOf ?y . FILTER(isIRI(?y)) - FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)")) + FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://purl.obolibrary.org/obo)")) } \ No newline at end of file diff --git a/src/sparql/inject-synonymtype-declaration.ru b/src/sparql/inject-synonymtype-declaration.ru new file mode 100644 index 0000000..cad57ed --- /dev/null +++ b/src/sparql/inject-synonymtype-declaration.ru @@ -0,0 +1,11 @@ +PREFIX : +PREFIX rdf: +PREFIX rdfs: + +INSERT { ?y rdfs:subPropertyOf . } + +WHERE { + ?x ?y . + FILTER(isIRI(?y)) + FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://purl.obolibrary.org/obo)")) +} \ No newline at end of file diff --git a/src/sparql/multiple-replaced_by-violation.sparql b/src/sparql/multiple-replaced_by-violation.sparql new file mode 100644 index 0000000..65bb8de --- /dev/null +++ b/src/sparql/multiple-replaced_by-violation.sparql @@ -0,0 +1,12 @@ +PREFIX replaced_by: + +SELECT DISTINCT ?entity ?property ?value WHERE { + VALUES ?property { + replaced_by: + } + ?entity ?property ?value1 . + ?entity ?property ?value2 . + FILTER(?value1!=?value2) + BIND(CONCAT(str(?value1), CONCAT("|", str(?value2))) as ?value) +} + diff --git a/src/sparql/simple-seed.sparql b/src/sparql/simple-seed.sparql index a96d263..247fbde 100644 --- a/src/sparql/simple-seed.sparql +++ b/src/sparql/simple-seed.sparql @@ -1,5 +1,4 @@ prefix owl: -prefix obo: SELECT DISTINCT ?cls WHERE { diff --git a/src/sparql/subsets-labeled.sparql b/src/sparql/subsets-labeled.sparql index 7bc992f..5ca7e31 100644 --- a/src/sparql/subsets-labeled.sparql +++ b/src/sparql/subsets-labeled.sparql @@ -1,5 +1,4 @@ prefix oio: -prefix def: prefix owl: prefix inSubset: prefix rdfs: diff --git a/src/sparql/term-tracker-uri-violation.sparql b/src/sparql/term-tracker-uri-violation.sparql new file mode 100644 index 0000000..6fbd993 --- /dev/null +++ b/src/sparql/term-tracker-uri-violation.sparql @@ -0,0 +1,9 @@ +PREFIX xsd: +PREFIX term_tracker_item: + +SELECT ?term ?term_tracker ?term_tracker_type WHERE { + ?term term_tracker_item: ?term_tracker . + FILTER(DATATYPE(?term_tracker) != xsd:anyURI) + BIND(DATATYPE(?term_tracker) as ?term_tracker_type) +} + diff --git a/src/templates/RBO_classes.owl b/src/templates/RBO_classes.owl index fdd154b..599a416 100644 --- a/src/templates/RBO_classes.owl +++ b/src/templates/RBO_classes.owl @@ -41,6 +41,12 @@ + + + + + + @@ -384,9 +390,9 @@ - + The amount of ionizing radiation to which a member of the population on Earth is exposed from natural sources, such as terrestrial radiation from naturally-occurring radionuclides in the soil, cosmic radiation originating in outer space, and naturally-occurring ra - background ionizing radiation + ionizing background radiation @@ -2777,7 +2783,16 @@ - Atomic nuclei, with atomic number 2 or greater and kinetic energy imparted by natural or artificial means + A type of ionizing radiation consisting of charged particles that are relatively massive compared to other types of radiation, such as alpha, beta, and gamma radiation. Heavy ion radiation is composed of atomic nuclei that have been stripped of their electrons, resulting in positively charged particles. + Heavy ion radiation has several notable characteristics and contexts: + +High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. + +Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation. + +Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. + +In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, "heavy" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10. heavy ion radiation @@ -3658,7 +3673,7 @@ https://orcid.org/0000-0001-9227-0670 ambient radiation background radiation - anthropogenic background radiation + anthropogenic ionizing background radiation @@ -3670,7 +3685,7 @@ Radiation originating in the terrestrial or extra-terrestrial environment. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 - natural background radiation + natural ionizing background radiation @@ -3734,6 +3749,81 @@ + + + + + thermal neutron + A neutron that has (by collision with other particles) reached an energy state equal to that of its surroundings, typically on the order of 0.025 eV. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + https://www.nrc.gov/reading-rm/basic-ref/glossary/neutron-thermal.html + thermal neutron + + + + + + + + + epithermal neutron + a neutron with energy greater than a thermal neutron, but less than a fast neutron. The approximate energy range is 0.025-0.4 eV. + http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670 + https://ns.ph.liv.ac.uk/~ajb/radiometrics/glossary/epithermal_neutron.html + epithermal neutron + + + + + + + + + background radiation + The ambient radiation in a defined environment emanating from natural or anthropogenic sources. + For uses involving experimentation or radiation therapy, use "anthropogenic background radiation" instead. Use this concept to indicate source is a mixture of anthropogenic and naturally occurring (ambient), or unknown or if the discrimination is not sought. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + background radiation + + + + + + + + + non-ionizing background radiation + Background radiation that does not result in ionization of target material + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + non-ionizing background radiation + + + + + + + + + anthropogenic non-ionizing background radiation + Non-ionizing background radiation that is the result of a human planned process. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + anthropogenic non-ionizing background radiation + + + + + + + + + natural non-ionizing background radiation + Non-ionizing background radiation that is not the result of a human planned process. + http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670 + natural non-ionizing background radiation + + + + diff --git a/src/templates/RBO_classes.tsv b/src/templates/RBO_classes.tsv index 61f943e..c8c0ad3 100644 --- a/src/templates/RBO_classes.tsv +++ b/src/templates/RBO_classes.tsv @@ -3,13 +3,13 @@ ID LABEL A editor preferred term AI has curation status A alternative term SPLIT obo:RBO_00000001 ionizing radiation categorized by source Ionizing radiation classified by the material entity which generates or emits it. obo:RBO_00000116 obo:RBO_00000002 space radiation Radiation originating outside the Earth's atmosphere. http://purl.obolibrary.org/obo/RBO_00000001 obo:RBO_00000003 ground radiation Radiation produced on Earth or on another planetary body by natural or artificial means. One of the principal sources of ground radiation is radon gas. http://purl.obolibrary.org/obo/RBO_00000001 -obo:RBO_00000004 tissue equivalent material Material presenting, when irradiated, interaction properties similar to those of soft tissue. ICRP glossary (http://icrpaedia.org/Tissue_equivalent_material) BFO:0000040 -obo:RBO_00000010 light ion An atomic nucleus, fully stripped of its orbital electrons, and containing 2, 3, 4, 5, or 6 protons. charged particle|atomic nucleus -obo:RBO_00000011 active dosimeter A radiation measuring device which records dose at the time of detection, with data available in real time Ionization chambers and silicon solid state detectors can be used as active dosimeters. obo:RBO_00000115 +obo:RBO_00000004 tissue equivalent material "Material presenting, when irradiated, interaction properties similar to those of soft tissue." ICRP glossary (http://icrpaedia.org/Tissue_equivalent_material) BFO:0000040 +obo:RBO_00000010 light ion "An atomic nucleus, fully stripped of its orbital electrons, and containing 2, 3, 4, 5, or 6 protons." charged particle|atomic nucleus +obo:RBO_00000011 active dosimeter "A radiation measuring device which records dose at the time of detection, with data available in real time" Ionization chambers and silicon solid state detectors can be used as active dosimeters. obo:RBO_00000115 obo:RBO_00000012 passive dosimeter A radiation measuring device which integrates the amount of radiation to which it is exposed. Passive detectors are interrogated at a later time to determine the dose. Thermoluminescent dosimeters and plastic nuclear track detectors are passive detectors. obo:RBO_00000115 -obo:RBO_00000013 background ionizing radiation The amount of ionizing radiation to which a member of the population on Earth is exposed from natural sources, such as terrestrial radiation from naturally-occurring radionuclides in the soil, cosmic radiation originating in outer space, and naturally-occurring ra obo:RBO_00015000 -obo:RBO_00000014 effective dose The sum of the equivalent doses to all organs in the body, each adjusted to account for the sensitivity of the organ to radiation. Effective dose is calculated for the whole body. Effective dose is expressed in millisieverts (mSv). The effective dose was calculated to be 300 mSv. radiation dose -obo:RBO_00000015 mixed radiation The process of exposing the same sample to more than one type and/or energy of radiation, in sequence or simultaneously. The samples were exposed to a mixed radiation field consisting of several ions at different energies. particle accelerator radiation mixed field|mixed radiation field +obo:RBO_00000013 ionizing background radiation "The amount of ionizing radiation to which a member of the population on Earth is exposed from natural sources, such as terrestrial radiation from naturally-occurring radionuclides in the soil, cosmic radiation originating in outer space, and naturally-occurring ra" obo:RBO_00015038 +obo:RBO_00000014 effective dose "The sum of the equivalent doses to all organs in the body, each adjusted to account for the sensitivity of the organ to radiation. Effective dose is calculated for the whole body. Effective dose is expressed in millisieverts (mSv)." The effective dose was calculated to be 300 mSv. radiation dose +obo:RBO_00000015 mixed radiation "The process of exposing the same sample to more than one type and/or energy of radiation, in sequence or simultaneously." The samples were exposed to a mixed radiation field consisting of several ions at different energies. particle accelerator radiation mixed field|mixed radiation field obo:RBO_00000016 radiation environment Radiation classified by where the exposure to the radiation is occurring. ENVO:01000254 obo:RBO_00000017 earth surface That part of the Earth exposed to the Earth atmosphere. radiation environment obo:RBO_00000018 earth atmosphere The region between the Earth's surface and an altitude of approximately 100 km radiation environment @@ -19,64 +19,64 @@ obo:RBO_00000021 fractionated radiation exposure fractionated A radiation dose obo:RBO_00000022 millirad A unit of absorbed dose equal to 1/1000 of a rad UO:1000135 mrad obo:RBO_00000023 equivalent dose The product of the mean absorbed dose in an organ or tissue and the radiation weighting factor (w_R )of the radiation type of interest The equivalent dose was calculated to be 300 mSv. radiation dose obo:RBO_00000024 dose fraction The absorbed radiation dose administered in a single one of a series comprising a fractionated radiation exposure The total dose was administered in five dose fractions. radiation dose -obo:RBO_00000026 cosmic radiation Penetrating ionizing radiation, both particulate and electromagnetic, that originates in outer space space radiation +obo:RBO_00000026 cosmic radiation "Penetrating ionizing radiation, both particulate and electromagnetic, that originates in outer space" space radiation obo:RBO_00000027 galactic cosmic radiation Galactic cosmic radiation consists of high-energy charged particles originating from outside the solar system Galactic cosmic radiation is one of the principal sources of radiation dose outside low-earth orbit cosmic radiation obo:RBO_00000028 solar cosmic radiation Solar cosmic radiation is high-energy charged particles that originate from the sun. Solar cosmic radiation contributes to the radiation dose to humans in space. cosmic radiation obo:RBO_00000029 dose rate The measurement datum representing a dose to an organism or object per unit time. The dose rate was 0.5 mGy/min. IAO:0000109 -obo:RBO_00000033 spacecraft Vehicles, crewed or uncrewed, which are designed to orbit about the Earth or another celestial body or be placed into a trajectory to another celestial body or location in space. NASA Thesaurus, 1988 The Apollo spacecraft took 24 astronauts to the Moon between 1968 and 1972. OBI:0000968 CHEBI:33250 +obo:RBO_00000033 spacecraft "Vehicles, crewed or uncrewed, which are designed to orbit about the Earth or another celestial body or be placed into a trajectory to another celestial body or location in space." "NASA Thesaurus, 1988" The Apollo spacecraft took 24 astronauts to the Moon between 1968 and 1972. OBI:0000968 CHEBI:33250 obo:RBO_00000044 spacecraft module a self-contained unit of a spacecraft spacecraft obo:RBO_00000045 international space station module ISS module A self-contained unit of the International Space Station. The experiment was conducted in the International Space Station module Columbus|The experiment was conducted on the Russian module of the ISS. spacecraft module -obo:RBO_00000046 space station A spacecraft capable of supporting a human crew in orbit for an extended period of time. It lacks major propulsion or landing systems. Stations must have docking ports to allow other spacecraft to dock to transfer crew and supplies. Wikipedia Mir was a space station that operated in low Earth orbit from 1986 to 2001, operated by the Soviet Union and later by Russia. spacecraft -obo:RBO_00000047 particle accelerator beamline The path leading from a particle accelerator to an experimental station used in experiments in particle physics, materials science, chemistry, and molecular biology, or in irradiation tests or to produce isotopes. Wikipedia The HIMAC accelerator has a beamline dedicated for radiation biology experiments. obo:RBO_00000121 +obo:RBO_00000046 space station A spacecraft capable of supporting a human crew in orbit for an extended period of time. It lacks major propulsion or landing systems. Stations must have docking ports to allow other spacecraft to dock to transfer crew and supplies. Wikipedia "Mir was a space station that operated in low Earth orbit from 1986 to 2001, operated by the Soviet Union and later by Russia." spacecraft +obo:RBO_00000047 particle accelerator beamline "The path leading from a particle accelerator to an experimental station used in experiments in particle physics, materials science, chemistry, and molecular biology, or in irradiation tests or to produce isotopes." Wikipedia The HIMAC accelerator has a beamline dedicated for radiation biology experiments. obo:RBO_00000121 obo:RBO_00000049 particle accelerator radiation Radiation produced by a particle accelerator. ground radiation obo:RBO_00000050 nuclear reactor radiation Radiation produced by a nuclear reactor. ground radiation obo:RBO_00000051 cesium-137 gamma radiation Cs-137 gamma High energy photons emitted during nuclear decay of the Cesium-137 isotope. obo:RBO_00000120 Cs-137 obo:RBO_00000052 cobalt-60 gamma radiation Co-60 gamma High energy photons emitted during nuclear decay of the Cobalt-60 isotope. obo:RBO_00000120 Co-60 obo:RBO_00000058 cobalt-57 gamma radiation Co-57 gamma High energy photons emitted during nuclear decay of the Cobalt-57 isotope. obo:RBO_00000120 Co-57 obo:RBO_00000060 -obo:RBO_00000060 radionuclide Isotopes that exhibit radioactivity and undergo radioactive decay. (From Grant & Hackh's Chemical Dictionary, 5th ed & McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) http://purl.bioontology.org/ontology/MESH/D011868 CHEBI:33250 -obo:RBO_00000061 actinide A series of radioactive elements from ACTINIUM, atomic number 89, to and including LAWRENCIUM, atomic number 103 http://purl.bioontology.org/ontology/MESH/D008671 radionuclide -obo:RBO_00000062 actinium A trivalent radioactive element and the prototypical member of the actinide family. It has the atomic symbol Ac, and atomic number 89. Its principal isotope is 227 and it decays primarily by beta-emission. http://purl.bioontology.org/ontology/MESH/D000186 actinide -obo:RBO_00000063 americium A completely man-made radioactive actinide with atomic symbol Am, and atomic number 95. Its valence can range from +3 to +6. Because of its nonmagnetic ground state, it is an excellent superconductor. It is also used in bone mineral analysis and as a radiation source for radiotherapy http://purl.bioontology.org/ontology/MESH/D000576 actinide -obo:RBO_00000064 californium A man-made radioactive actinide with atomic symbol Cf, atomic number 98, and atomic weight 251. Its valence can be +2 or +3. Californium has medical use as a radiation source for radiotherapy http://purl.bioontology.org/ontology/MESH/D002142 actinide -obo:RBO_00000065 neptunium A radioactive element of the actinide metals family. It has the atomic symbol Np, and atomic number 93. http://purl.bioontology.org/ontology/MESH/D009405 actinide -obo:RBO_00000066 plutonium A naturally radioactive element of the actinide metals series. It has the atomic symbol Pu, and atomic number 94. Plutonium is used as a nuclear fuel, to produce radioisotopes for research, in radionuclide batteries for pacemakers, and as the agent of fission in nuclear weapons. http://purl.bioontology.org/ontology/MESH/D011005 actinide -obo:RBO_00000067 thorium A radioactive element of the actinide series of metals. It has an atomic symbol Th, atomic number 90, and atomic weight 232.04. It is used as fuel in nuclear reactors to produce fissionable uranium isotopes. Because of its radioopacity, various thorium compounds are used to facilitate visualization in roentgenography. http://purl.bioontology.org/ontology/MESH/D013910 actinide -obo:RBO_00000068 uranium A radioactive element of the actinide series of metals. It has an atomic symbol U, atomic number 92, and atomic weight 238.03. U-235 is used as the fissionable fuel in nuclear weapons and as fuel in nuclear power reactors. http://purl.bioontology.org/ontology/MESH/D014501 actinide +obo:RBO_00000060 radionuclide "Isotopes that exhibit radioactivity and undergo radioactive decay. (From Grant & Hackh's Chemical Dictionary, 5th ed & McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)" http://purl.bioontology.org/ontology/MESH/D011868 CHEBI:33250 +obo:RBO_00000061 actinide "A series of radioactive elements from ACTINIUM, atomic number 89, to and including LAWRENCIUM, atomic number 103" http://purl.bioontology.org/ontology/MESH/D008671 radionuclide +obo:RBO_00000062 actinium "A trivalent radioactive element and the prototypical member of the actinide family. It has the atomic symbol Ac, and atomic number 89. Its principal isotope is 227 and it decays primarily by beta-emission." http://purl.bioontology.org/ontology/MESH/D000186 actinide +obo:RBO_00000063 americium "A completely man-made radioactive actinide with atomic symbol Am, and atomic number 95. Its valence can range from +3 to +6. Because of its nonmagnetic ground state, it is an excellent superconductor. It is also used in bone mineral analysis and as a radiation source for radiotherapy" http://purl.bioontology.org/ontology/MESH/D000576 actinide +obo:RBO_00000064 californium "A man-made radioactive actinide with atomic symbol Cf, atomic number 98, and atomic weight 251. Its valence can be +2 or +3. Californium has medical use as a radiation source for radiotherapy" http://purl.bioontology.org/ontology/MESH/D002142 actinide +obo:RBO_00000065 neptunium "A radioactive element of the actinide metals family. It has the atomic symbol Np, and atomic number 93." http://purl.bioontology.org/ontology/MESH/D009405 actinide +obo:RBO_00000066 plutonium "A naturally radioactive element of the actinide metals series. It has the atomic symbol Pu, and atomic number 94. Plutonium is used as a nuclear fuel, to produce radioisotopes for research, in radionuclide batteries for pacemakers, and as the agent of fission in nuclear weapons." http://purl.bioontology.org/ontology/MESH/D011005 actinide +obo:RBO_00000067 thorium "A radioactive element of the actinide series of metals. It has an atomic symbol Th, atomic number 90, and atomic weight 232.04. It is used as fuel in nuclear reactors to produce fissionable uranium isotopes. Because of its radioopacity, various thorium compounds are used to facilitate visualization in roentgenography." http://purl.bioontology.org/ontology/MESH/D013910 actinide +obo:RBO_00000068 uranium "A radioactive element of the actinide series of metals. It has an atomic symbol U, atomic number 92, and atomic weight 238.03. U-235 is used as the fissionable fuel in nuclear weapons and as fuel in nuclear power reactors." http://purl.bioontology.org/ontology/MESH/D014501 actinide obo:RBO_00000069 ultraviolet radiation UV UV radiation Electromagnetic radiation with photon energies approximately 3-120 eV. High energy UV radiation can be ioinizing. http://son.nasa.gov/tass/content/electrospectrum.htm obo:RBO_00000114 -obo:RBO_00000070 radioprotectant radioprotector A substance present at the time of irradiation that mitigates or prevents the biological effects of irradiation. Richard T. Hoppe, Theodore Locke Phillips, Mack Roach, Leibel and Phillips Textbook of Radiation Oncology (Third Edition), W.B. Saunders, (2010), ISBN 9781416058977, https://doi.org/10.1016/B978-1-4160-5897-7.00093-7. E.G. amifostine. CHEBI:24432 +obo:RBO_00000070 radioprotectant radioprotector A substance present at the time of irradiation that mitigates or prevents the biological effects of irradiation. "Richard T. Hoppe, Theodore Locke Phillips, Mack Roach, Leibel and Phillips Textbook of Radiation Oncology (Third Edition), W.B. Saunders, (2010), ISBN 9781416058977, https://doi.org/10.1016/B978-1-4160-5897-7.00093-7." E.G. amifostine. CHEBI:24432 obo:RBO_00000071 radionuclide chelator Radionuclide chelators are small organic molecules or in some cases larger peptides that chemically sequester the radionuclide ion by forming a complex that determines the thermodynamic stability and kinetic inertness of the radionuclide. CHEBI:24432 obo:RBO_00000072 co-carcinogen A co-carcinogen is generally a chemical that promotes the effects of a carcinogen in the production of cancer. In some circumstances exposure to radiation or physical trauma is considered to be co-carcinogenic. CHEBI:24432 -obo:RBO_00000073 radiation response modifier Radiation response modifiers are agents that alter tumor or normal tissue response to radiation, such as radiation sensitizers and radiation protectors. Citrin DE, Mitchell JB. Altering the response to radiation: sensitizers and protectors. Semin Oncol. 2014 Dec;41(6):848-59. doi: 10.1053/j.seminoncol.2014.09.013. Epub 2014 Oct 7. PMID: 25499642; PMCID: PMC4270009. CHEBI:24432 -obo:RBO_00000074 peptide radiation response modifier Radiation response modifiers that are peptides. Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 radiation response modifier +obo:RBO_00000073 radiation response modifier "Radiation response modifiers are agents that alter tumor or normal tissue response to radiation, such as radiation sensitizers and radiation protectors. " "Citrin DE, Mitchell JB. Altering the response to radiation: sensitizers and protectors. Semin Oncol. 2014 Dec;41(6):848-59. doi: 10.1053/j.seminoncol.2014.09.013. Epub 2014 Oct 7. PMID: 25499642; PMCID: PMC4270009." CHEBI:24432 +obo:RBO_00000074 peptide radiation response modifier Radiation response modifiers that are peptides. "Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577" radiation response modifier obo:RBO_00000075 small molecule radiation response modifier Radiation response modifiers that are small molecules. radiation response modifier -obo:RBO_00000076 nuclear industry worker A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers. Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 occupational role +obo:RBO_00000076 nuclear industry worker "A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers." "Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1" occupational role obo:RBO_00000077 astronaut occupational role obo:RBO_00000078 military occupational role obo:RBO_00000079 medical professional occupational role obo:RBO_00000080 dentist medical professional obo:RBO_00000081 radiologist medical professional -obo:RBO_00000082 radiobiology study type radiobiology investigation The theme or modality of an experimental, theoretical, critical or summative study involving radiation, radioactive materials including their impacts on orgnisms and society. OBI:0000011 -obo:RBO_00000083 epidemiological study An epidemiological study is the study (scientific, systematic, and data-driven) of the distribution (frequency, pattern) and determinants (causes, risk factors) of health-related states and events (not just diseases) in specified populations (neighborhood, school, city, state, country, global) https://www.cdc.gov/csels/dsepd/ss1978/lesson1/section1.html radiobiology study type +obo:RBO_00000082 radiobiology study type radiobiology investigation "The theme or modality of an experimental, theoretical, critical or summative study involving radiation, radioactive materials including their impacts on orgnisms and society." OBI:0000011 +obo:RBO_00000083 epidemiological study "An epidemiological study is the study (scientific, systematic, and data-driven) of the distribution (frequency, pattern) and determinants (causes, risk factors) of health-related states and events (not just diseases) in specified populations (neighborhood, school, city, state, country, global)" https://www.cdc.gov/csels/dsepd/ss1978/lesson1/section1.html radiobiology study type obo:RBO_00000084 environmental study A study of the impact of radiation on the composition of or processes within the natural or anthropogenic environment. radiobiology study type A owl:deprecated obo:RBO_00000085 lifespan study A study who endpoint is the lifespan of the organism under investifgation. radiobiology study type -obo:RBO_00000086 carcinogenesis study A study of the effect of agents including radiation, seperately or together, on the incidence or type of neoplasia or pre-neoplasia. radiobiology study type +obo:RBO_00000086 carcinogenesis study "A study of the effect of agents including radiation, seperately or together, on the incidence or type of neoplasia or pre-neoplasia." radiobiology study type obo:RBO_00000087 tissue damage study A study in which the structural or processual damage to normal tissue caused by radiation is assessed. Often by histopathology or molecular profiling. radiobiology study type obo:RBO_00000088 dna damage and repair study A study of the mechanism or effects of radiation on dna damage and its repair. radiobiology study type obo:RBO_00000089 physiological study A study of the effects of internal or external radiation on cellular or organismal physiology. radiobiology study type -obo:RBO_00000090 anatomical study A study of the effects of radiation on the integrity, composition and quality of adult, fetal or embryonic anatomical structures. radiobiology study type +obo:RBO_00000090 anatomical study "A study of the effects of radiation on the integrity, composition and quality of adult, fetal or embryonic anatomical structures." radiobiology study type obo:RBO_00000091 external exposure study A study of the effects of external irradiation on an organism. radiobiology study type -obo:RBO_00000092 internal contamination study A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. radiobiology study type +obo:RBO_00000092 internal contamination study "A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems." radiobiology study type obo:RBO_00000093 mixed exposure route study A study of the effects of radiation exposure where the exposoure has an internal and external mode of application. radiobiology study type obo:RBO_00000094 acute external exposure study A study of the effects of external irradiation on an organism where the most of the dose is given in a single or small number of fractions closely in time. external exposure study obo:RBO_00000095 chronic external exposure study A study of the effects of external irradiation on an organism where the dose is given over a protracted time period either continuously or in many fractions. Often these are lose dose studies. external exposure study -obo:RBO_00000096 chronic internal contamination study A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. The dose is delivered over a long period of time, often continuously and generlly at low dose. For example long term Radon exposure by inhalation. internal contamination study -obo:RBO_00000097 acute internal contamination study A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. Most of the dose is given over a short period of time and is generally unfractionated, such as in brachytherapy. internal contamination study +obo:RBO_00000096 chronic internal contamination study "A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. The dose is delivered over a long period of time, often continuously and generlly at low dose. For example long term Radon exposure by inhalation." internal contamination study +obo:RBO_00000097 acute internal contamination study "A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. Most of the dose is given over a short period of time and is generally unfractionated, such as in brachytherapy." internal contamination study obo:RBO_00000098 acute mixed exposure route study A study of the effects of radiation exposure where the exposoure has an internal and external mode of application. Acute exposure involves usually a single exposure over a short period of time with no fractionation. mixed exposure route study obo:RBO_00000099 chronic mixed exposure route study A study of the effects of radiation exposure where the exposoure has an internal and external mode of application. Chronic exposure involves usually a continuous or highly fractionated exposure over a long period of time. mixed exposure route study obo:RBO_00000100 gene expression study A study of the effects of radiation on gene expression. radiobiology study type obo:RBO_00000101 proteomics study A study of the effects of radiation on the proteome or individual proteins. radiobiology study type -obo:RBO_00000102 marker discovery study A study that aims at the discovery of protein, RNA or other molecular entities or modifcations that can act as reliable surrogates for the prediction or measurement of the effects of radiation or the response of the organism to radiation. radiobiology study type -obo:RBO_00000103 therapeutics study A study that aims at the discovery, development or assessment of efficacy of therapeutic agents or processes designed to mitigate or cure the effects of radiation exposure. radiobiology study type A owl:deprecated +obo:RBO_00000102 marker discovery study "A study that aims at the discovery of protein, RNA or other molecular entities or modifcations that can act as reliable surrogates for the prediction or measurement of the effects of radiation or the response of the organism to radiation." radiobiology study type +obo:RBO_00000103 therapeutics study "A study that aims at the discovery, development or assessment of efficacy of therapeutic agents or processes designed to mitigate or cure the effects of radiation exposure." radiobiology study type A owl:deprecated obo:RBO_00000104 survival study "A study that uses survival as an endpoint. Generally applicable to animal studies rather than human studies which would use the ""lifespan"" measure (RBO:00000085)" radiobiology study type obo:RBO_00000105 metabolomics study A study of the effects of radiation on the metabolome or individual metabolites. radiobiology study type obo:RBO_00000106 nuclear accident study A study of the contributing factors consequences and prevention of nuclear accidents radiobiology study type A owl:deprecated @@ -84,8 +84,8 @@ obo:RBO_00000107 toxicity study A study of the toxicity of chemical or biolog obo:RBO_00000108 endocrine study A study of the effects of radiation on the endocrine system or of endocrine hormones on the effects of radiation. obo:RBO_00000089 obo:RBO_00000109 offspring study transgenerational study A study of the effects of radiation on the offspring of an irradiated animal or plant. radiobiology study type obo:RBO_00000110 biokinetics study pharmacokinetics A study of the distribution and metabolism orf drugs or biologicals used for therapeutic purposes. radiobiology study type -obo:RBO_00000111 occupational role A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. BFO:0000023 -obo:RBO_00000112 high linear energy transfer radiation Neutrons or charged particles, such as protons or alpha particles that produce ionizing events densely spaced on a molecular scale (e.g., >10 keV-micron^[-1]. NCRP https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf obo:RBO_00000116 NCIT:C17052 +obo:RBO_00000111 occupational role "A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society." BFO:0000023 +obo:RBO_00000112 high linear energy transfer radiation "Neutrons or charged particles, such as protons or alpha particles that produce ionizing events densely spaced on a molecular scale (e.g., >10 keV-micron^[-1]." NCRP https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf obo:RBO_00000116 NCIT:C17052 obo:RBO_00000113 low linear energy transfer radiation X and gamma rays or light charged particles such as electrons that produce sparse ionizing events far apart on a molecular scale. NCRP https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf obo:RBO_00000116 low LET|low-LET NCIT:C17052 obo:RBO_00000114 ionizing electromagnetic radiation Electromagnetic radiation having sufficient energy to remove one or more electrons from an atom obo:RBO_00000116 obo:RBO_00000115 radiation dosimeter device radiation dosimeter radiation dosimeter A device that is used to measure the amount of ionizing radiation exposure or absorption. NCIT OBI:0000968 dosimeter NCIT:C150121 @@ -98,185 +98,193 @@ obo:RBO_00000121 particle accelerator A device used to impart kinetic energy obo:RBO_00000122 nuclear reactor A device in which nuclear fission may be initiated and controlled in a self-sustaining chain reaction to generate energy or produce useful radiation. OBI:0000968|obo:RBO_00005014 MESH:D009688 obo:RBO_00000123 biological process BFO:0000015 GO:0008150 owl:deprecated obo:RBO_00000124 cellular process obo:RBO_00000123 GO:0009987 owl:deprecated -obo:RBO_00005001 heavy ion radiation Atomic nuclei, with atomic number 2 or greater and kinetic energy imparted by natural or artificial means obo:RBO_00000117 -obo:RBO_00005002 light ion radiation Atomic nuclei, variously defined as having atomic number 2, 3, 4, 5 or 6 and kinetic energy imparted by natural or artificial means obo:RBO_00000117 +obo:RBO_00005001 heavy ion radiation "A type of ionizing radiation consisting of charged particles that are relatively massive compared to other types of radiation, such as alpha, beta, and gamma radiation. Heavy ion radiation is composed of atomic nuclei that have been stripped of their electrons, resulting in positively charged particles." "Heavy ion radiation has several notable characteristics and contexts: + +High Linear Energy Transfer (LET): Heavy ion radiation has a high linear energy transfer, which means it deposits a significant amount of energy per unit path length as it travels through tissue. This characteristic can lead to more localized and potentially more damaging effects on cells and tissues. + +Enhanced Biological Effectiveness: Due to its high LET, heavy ion radiation in many cases has enhanced biological effectiveness, meaning it can cause more severe biological damage per unit of absorbed dose compared to other types of radiation. + +Space Radiation: Heavy ions are a component of the galactic cosmic radiation present in space. + +In common use, the distinction between heavy ions and light ions is somewhat flexible and context dependent. For example, ""heavy"" is sometimes used to refer to any ion heavier than a helium nucleus or even a proton; in practice the dividing line between light and heavy lies around atomic numbers 6-10." obo:RBO_00000117 +obo:RBO_00005002 light ion radiation "Atomic nuclei, variously defined as having atomic number 2, 3, 4, 5 or 6 and kinetic energy imparted by natural or artificial means" obo:RBO_00000117 obo:RBO_00005003 charged particle A particle with a positive or negative electric charge BFO:0000040 obo:RBO_00005009 space flight space flight spaceflight Activity carried out by crewed or robotic vehicles outside the Earth's atmmosphere. ENVO:03000010 Space flight -obo:RBO_010000 as low as reasonably achievable ALARA ALARA A principle of radiation protection philosophy that requires that exposures to ionizing radiation be kept as low as reasonably achievable, economic and social factors being taken into account. The protection from radiation exposure is ALARA when the expen NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) One of the measures to ensure ALARA is to minimize the time spent working around radioactive materials. Jack Miller obo:IAO_0000104 ALARA -obo:RBO_010001 radiation attenuation The reduction of radiation intensity upon passage of radiation through matter NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Attenuation in concrete or leadshielding is a common method of radiation protection on Earth, but is impractical in space due to mass constraints. Jack Miller BFO:0000182 -obo:RBO_010002 biodosimetry Use of a biological response as an indicator of a dose of an effective agent (e.g., the extent of decline in peripheral blood lymphocytes of humans exposed to ionizing radiation can be used as an indicator of the absorbed dose to the whole body from that NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Biodosimetry was used to measure the exposure of some victims of the Chernobyl nuclear accident. Jack Miller CHMO:0002796 -obo:RBO_010003 bystander effect The term used to describe the effects on cells in proximity to irradiated cells, but through which radiation has not passed. In experimental radiation biology, the bystander effect can be investigated by targeting individual cells, or by using doses low enough that the probability for a given cell to be hit by a particle is less than one. NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) The bystander effect can be studied by identifying cells that were traversed by a charged particle. Jack Miller obo:RBO_00005074 -obo:RBO_010006 delta ray delta electron Highly energetic electrons produced during inelastic collisions between ionizing radiation and atomic electrons. In a small proportion of collisions, the ejected electron receives a considerable amount of energy (i.e., >1,000 eV), allowing it to travel a NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Delta ray energies increase with the velocity of the incident particle. Jack Miller charged particle radiation delta electron -obo:RBO_010007 dose equivalent The product of the absorbed dose (D) at a point and the quality factor (Q) at that point for the radiation type (i.e., H = DQ). The unit of H is J-kg^[-1] with the special name sievert (Sv) NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) The average annual dose equivalent for crew members on the ISS is approximately 300 mSv. Jack Miller radiation dose +obo:RBO_010000 as low as reasonably achievable ALARA ALARA "A principle of radiation protection philosophy that requires that exposures to ionizing radiation be kept as low as reasonably achievable, economic and social factors being taken into account. The protection from radiation exposure is ALARA when the expen" NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) One of the measures to ensure ALARA is to minimize the time spent working around radioactive materials. Jack Miller obo:IAO_0000104 ALARA +obo:RBO_010001 radiation attenuation The reduction of radiation intensity upon passage of radiation through matter NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) "Attenuation in concrete or leadshielding is a common method of radiation protection on Earth, but is impractical in space due to mass constraints." Jack Miller BFO:0000182 +obo:RBO_010002 biodosimetry "Use of a biological response as an indicator of a dose of an effective agent (e.g., the extent of decline in peripheral blood lymphocytes of humans exposed to ionizing radiation can be used as an indicator of the absorbed dose to the whole body from that" NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Biodosimetry was used to measure the exposure of some victims of the Chernobyl nuclear accident. Jack Miller CHMO:0002796 +obo:RBO_010003 bystander effect "The term used to describe the effects on cells in proximity to irradiated cells, but through which radiation has not passed. In experimental radiation biology, the bystander effect can be investigated by targeting individual cells, or by using doses low enough that the probability for a given cell to be hit by a particle is less than one." NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) The bystander effect can be studied by identifying cells that were traversed by a charged particle. Jack Miller obo:RBO_00005074 +obo:RBO_010006 delta ray delta electron "Highly energetic electrons produced during inelastic collisions between ionizing radiation and atomic electrons. In a small proportion of collisions, the ejected electron receives a considerable amount of energy (i.e., >1,000 eV), allowing it to travel a" NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Delta ray energies increase with the velocity of the incident particle. Jack Miller charged particle radiation delta electron +obo:RBO_010007 dose equivalent "The product of the absorbed dose (D) at a point and the quality factor (Q) at that point for the radiation type (i.e., H = DQ). The unit of H is J-kg^[-1] with the special name sievert (Sv)" NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) The average annual dose equivalent for crew members on the ISS is approximately 300 mSv. Jack Miller radiation dose obo:RBO_010008 excess lifetime risk of cancer The increased risk from induced cancer due to exposure when the effects over an entire lifetime are accounted for. Individuals who would have died of cancer anyway but die early because of exposure are not included NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Jack Miller obo:RBO_00000119 obo:RBO_010009 fast neutron Neutrons of energies above a few hundred kiloelectron volts (keV) NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) The sample was irradiated with fast neutrons. Jack Miller obo:RBO_00015001 -obo:RBO_010010 fluence The number of particles or photons per unit of cross-sectional area perpendicular to the direction of the particle (units of m^2 or cm^2) (i.e., particles-m^[-2] or particles-cm^[-2]). NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) The value of the fluence was approximately 1 particle per cm2. Jack Miller IAO:0000109 -obo:RBO_010011 flux The quotient of dN by dt, where dN is the increment of the particle number in the time interval dt. The unit for flux is reciprocal second (s^[-1].) NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) The flux of cosmic ray muons per cm2 at the surface of the Earth is approximately 1.0. Jack Miller IAO:0000109 -obo:RBO_010012 heavy ion An atomic nucleus, fully stripped of its orbital electrons, containing 2 or more protons. Nuclei containing between 2 protons (helium) and 6 protons (carbon) are sometimes referred to as light ions. In RBO--needs def from NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Jack Miller CHEBI:33252|obo:RBO_00005003 +obo:RBO_010010 fluence "The number of particles or photons per unit of cross-sectional area perpendicular to the direction of the particle (units of m^2 or cm^2) (i.e., particles-m^[-2] or particles-cm^[-2])." NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) The value of the fluence was approximately 1 particle per cm2. Jack Miller IAO:0000109 +obo:RBO_010011 flux "The quotient of dN by dt, where dN is the increment of the particle number in the time interval dt. The unit for flux is reciprocal second (s^[-1].)" NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) The flux of cosmic ray muons per cm2 at the surface of the Earth is approximately 1.0. Jack Miller IAO:0000109 +obo:RBO_010012 heavy ion "An atomic nucleus, fully stripped of its orbital electrons, containing 2 or more protons. Nuclei containing between 2 protons (helium) and 6 protons (carbon) are sometimes referred to as light ions." In RBO--needs def from NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Jack Miller CHEBI:33252|obo:RBO_00005003 obo:RBO_010013 linear energy transfer LET The energy deposited by an ionizing charged particle or photon in any medium per unit path length. NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Biological effects are a function of LET. Jack Miller IAO:0000109 LET obo:RBO_010014 organ dose The mean absorbed radiation dose in a specified tissue or organ of the human body. NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Radiation protection standards take into account organ dose as well as whole body dose. Jack Miller radiation dose obo:RBO_010015 quality factor Dimensionless factor developed for purposes of radiation protection and assessing health risks in general terms that accounts for the relative biological effectiveness of different radiations in producing stochastic effects and is used to relate absorbed NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Neutrons have a high quality factor compared to photons. Jack Miller OBI:0001909 obo:RBO_010016 radiation dose "A measurement datum of the quantity of radiation absorbed by a substance or organism. The term ""radiation dose"" may for example refer to absorbed dose, organ dose, dose equivalent or equivalent dose, depending upon context and weighting factor(s)." "The samples received a dose of 1 Gy. (The use of the gray unit implies that ""dose"" refers to a measured quantity, typically absorbed dose or organ dose.)|The samples received a dose of 1 Sv. (The use of the sievert unit implies that ""dose"" refers to a der" Jack Miller OBI:0000984 -obo:RBO_010017 radiation quality Is a quality of radiation that reflects the fluence spectrum of charged and neutral particles within the material or medium where dose is being deposited. NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) and see https://melodi-online.eu/wp-content/uploads/2021/04/02-What-is-radiation-quality-Goodhead.pdf Radiation quality is often expressed in terms of the linear energy transfer of the ionising particles that deliver the absorbed dose. Rossi, Harald H. Specification of Radiation Quality. Radiation Research, vol. 10, no. 5, Radiation Research Society, 1959, pp. 522 31, https://doi.org/10.2307/3570787. But this is an over simplification. Jack Miller PATO:0001018 TRUE +obo:RBO_010017 radiation quality Is a quality of radiation that reflects the fluence spectrum of charged and neutral particles within the material or medium where dose is being deposited. NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) and see https://melodi-online.eu/wp-content/uploads/2021/04/02-What-is-radiation-quality-Goodhead.pdf "Radiation quality is often expressed in terms of the linear energy transfer of the ionising particles that deliver the absorbed dose. Rossi, Harald H. Specification of Radiation Quality. Radiation Research, vol. 10, no. 5, Radiation Research Society, 1959, pp. 522 31, https://doi.org/10.2307/3570787. But this is an over simplification." Jack Miller PATO:0001018 TRUE obo:RBO_010018 radiation weighting factor A factor used to allow for differences in the biological effectiveness between different radiations when calculating equivalent dose (H_T) (see equivalent dose). These factors are independent of the tissue or organ irradiated. NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Radiation weighting factors may change as more data on biological effects are obtained. Jack Miller OBI:0001909 -obo:RBO_010019 relative biological effectiveness RBE Factor used to compare the biological effectiveness of absorbed doses from different types of ionizing radiation, determined experimentally. RBE is the ratio of the absorbed dose of a reference radiation to the absorbed dose of the radiation in question r NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Neutrons have been found to have a higher RBE than electrons. Jack Miller IAO:0000109 RBE +obo:RBO_010019 relative biological effectiveness RBE "Factor used to compare the biological effectiveness of absorbed doses from different types of ionizing radiation, determined experimentally. RBE is the ratio of the absorbed dose of a reference radiation to the absorbed dose of the radiation in question r" NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Neutrons have been found to have a higher RBE than electrons. Jack Miller IAO:0000109 RBE obo:RBO_010020 tissue equivalence Denotes a substance with absorbing and scattering properties for a given radiation that sufficiently match those of a particular biological tissue. NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) Tissue equivalent materials can be used to study radiation effects at depth in the human body. Jack Miller PATO:0001018 obo:RBO_00005010 absorbed radiation dose The amount of energy from any type of ionizing radiation deposited in a specified mass of any medium. Jack Miller obo:RBO_010016 obo:RBO_00005011 absorbed radiation dose rate The amount of energy from any type of ionizing radiation deposited in a specified mass of any medium per unit time. Jack Miller obo:RBO_00000029 obo:RBO_00005012 ionizing radiation energy The kinetic energy carried by a particle or photon of ionizing radiation. Jack Miller obo:RBO_00000116 obo:RBO_00005013 x-ray radiation x-ray x-ray Electromagnetic radiation with photon energies approximately between 0.1 and 120 keV. The upper end of the x-ray spectrum overlaps with the lower end of the gamma ray spectrum. http://son.nasa.gov/tass/content/electrospectrum.htm Jack Miller obo:RBO_00000114 obo:RBO_00005014 radiation source A material entity which emits radiation Jack Miller material entity -obo:RBO_00005015 sham irradiation sham irradiation sham Sham irradiation refers to a procedure in which participants or subjects in an experiment are exposed to simulated radiation, mimicking precisely the conditions of actual irradiation. The purpose of using sham irradiation is to create a control group that experiences the non-specific effects of the experimental setup, while excluding the specific effects associated with radiation exposure. Jack Miller obo:OBI_0000272 +obo:RBO_00005015 sham irradiation sham irradiation sham "Sham irradiation refers to a procedure in which participants or subjects in an experiment are exposed to simulated radiation, mimicking precisely the conditions of actual irradiation. The purpose of using sham irradiation is to create a control group that experiences the non-specific effects of the experimental setup, while excluding the specific effects associated with radiation exposure." Jack Miller obo:OBI_0000272 obo:RBO_00005016 radiation fractionation protocol fractionation protocol fractionation protocol A protocol for administering a total radiation dose in two or more increments separated by a specified time interval Jack Miller obo:IAO_0000104 obo:RBO_00005017 cis-lunar space cis-lunar space The region of space between the Earth and the Moon Jack Miller obo:RBO_00000016 -obo:RBO_00005018 lunar orbit lunar orbit A region of space defined by a regular, repeating path of a specified object about Earth's moon Jack Miller obo:RBO_00000016 +obo:RBO_00005018 lunar orbit lunar orbit "A region of space defined by a regular, repeating path of a specified object about Earth's moon" Jack Miller obo:RBO_00000016 obo:RBO_00005019 lunar surface lunar surface The area of the lunar landmass exposed to space Jack Miller obo:RBO_00000016 obo:RBO_00005020 cis-mars space cis-Mars space The region of space between the Earth and Mars Jack Miller obo:RBO_00000016 -obo:RBO_00005021 mars orbit Mars orbit A region of space defined by a regular, repeating path of a specified object about Mars Jack Miller obo:RBO_00000016 +obo:RBO_00005021 mars orbit Mars orbit "A region of space defined by a regular, repeating path of a specified object about Mars" Jack Miller obo:RBO_00000016 obo:RBO_00005022 mars surface Mars surface The area of the Mars landmass exposed to the Martian atmosphere Jack Miller obo:RBO_00000016 obo:RBO_00005023 interplanetary space interplanetary space The region of space in the Solar System between planets Jack Miller obo:RBO_00000016 obo:RBO_00005024 planet surface planet surface The outermost solid or liquid area of a planet Jack Miller obo:RBO_00000016 -obo:RBO_00005025 non-irradiated non-irradiated An organism or material entity kept unexposed to radiation, for purposes of comparison to a similar organism or material entity that has been exposed to radiation Jack Miller PATO:0001241 -obo:RBO_00005026 ground analog study ground analog experiment ground analog A study at a ground facility designed so as to replicate one or more conditions in space (e.g. radiation, microgravity, isolation) Jack Miller obo:RBO_00000082 -obo:RBO_00005027 ground control study ground control ground control An study at a ground facility designed so as to replicate conditions in space (e.g. radiation, microgravity, isolation) with the exception of one condition, so as to ascertain the effects of that condition on an organism or instrument Jack Miller obo:RBO_00000082 +obo:RBO_00005025 non-irradiated non-irradiated "An organism or material entity kept unexposed to radiation, for purposes of comparison to a similar organism or material entity that has been exposed to radiation" Jack Miller PATO:0001241 +obo:RBO_00005026 ground analog study ground analog experiment ground analog "A study at a ground facility designed so as to replicate one or more conditions in space (e.g. radiation, microgravity, isolation)" Jack Miller obo:RBO_00000082 +obo:RBO_00005027 ground control study ground control ground control "An study at a ground facility designed so as to replicate conditions in space (e.g. radiation, microgravity, isolation) with the exception of one condition, so as to ascertain the effects of that condition on an organism or instrument" Jack Miller obo:RBO_00000082 obo:RBO_00005028 irradiation protocol irradiation protocol A protocol for administering radiation to a sample Jack Miller OBI:0000272 obo:RBO_00005029 radiation fraction radiation fraction fraction One of the series of individual doses administered to a sample in a fractionated irradiation. Jack Miller dose fraction obo:RBO_00005030 radiation fraction interval radiation fraction interval Time between fractions in a fractionated irradiation. Jack Miller dose rate -obo:RBO_00005031 high altitude high altitude The region of the atmosphere above 8000 feet above sea level. Altitudes above 12000 feet are sometimes referred to as very high altitude, and above 18000 feet as extremely high altitude. https://www.medicinenet.com/high_altitude/definition.htm Jack Miller OBI:0002983 +obo:RBO_00005031 high altitude high altitude "The region of the atmosphere above 8000 feet above sea level. Altitudes above 12000 feet are sometimes referred to as very high altitude, and above 18000 feet as extremely high altitude." https://www.medicinenet.com/high_altitude/definition.htm Jack Miller OBI:0002983 obo:RBO_00005032 sham-irradiated sham A quality of a biotic or abiotic sample or individual which is part of an experiment that tests the effects of radiation on organisms or materials by isolating variables as dictated by the scientific method in order to make a conclusion about the effect of such variables. In sham irradiation the precise treatment of the sample must be identical to that of the experimental samples and should be made explicit in the description of the method. "The class should be used in cases where it is clear that the control sample was treated in precisely the same way as the experimental samples or sham irradiation is specified. It is therefore a more restricted quality definition than ""non-irradiated"". It is likely to be used more often with external radiation exposure or exposure to a beam, and with a biological rather than abiotic sample." Jack Miller non-irradiated obo:RBO_00005033 parabolic flight aircraft parabolic flight Vomit Comet An aircraft which flies a series of parabolic arcs to simulate micrgravity. Jack Miller ENVO:01001488 obo:RBO_00005034 high altitude research aircraft An aircraft which flies at altitudes greater than commercial aircraft altitudes for research purposes. Jack Miller ENVO:01001488 -obo:RBO_00005035 uncrewed aerial vehicle UAV UAV An research aircraft designed to operate without crew members, either autonomously or under control from a ground station Jack Miller ENVO:01001488 +obo:RBO_00005035 uncrewed aerial vehicle UAV UAV "An research aircraft designed to operate without crew members, either autonomously or under control from a ground station" Jack Miller ENVO:01001488 obo:RBO_00005036 highly charged energetic nucleus HZE HZE|highly charged energetic nuclei Fully ionized atomic nucleus with 2 or more protons and energies in excess of tens of MeV per nucleon Jack Miller CHEBI:36347 obo:RBO_00005037 adaptive radiation response study adaptive A study of a response to radiation conditioned by prior administration of radiation of a different type and/or at a different dose or dose rate Jack Miller obo:RBO_00000082 obo:RBO_00005038 average fractionated dose rate The total dose administered in a series of radiation fractions divided by the elapsed time between the beginning of the first exposure fraction and the end of the last exposure fraction Jack Miller dose rate obo:RBO_00005039 gamma irradiator A device which exposes samples to gamma radiation. Jack Miller radiation source obo:RBO_00005040 particle charge charge The electric charge of a particle used in an irradiation Jack Miller UO:0000219 obo:RBO_00005041 radiation dosimetry The measurement of the amount of radiation taken up by a sample. Jack Miller dosimetry -obo:RBO_00005042 microbeam A microbeam is a narrow beam of radiation, of micrometer or sub-micrometer dimensions. Together with integrated imaging techniques, microbeams allow precisely defined quantities of damage to be introduced at precisely defined locations. Wikipedia Jack Miller particle accelerator +obo:RBO_00005042 microbeam "A microbeam is a narrow beam of radiation, of micrometer or sub-micrometer dimensions. Together with integrated imaging techniques, microbeams allow precisely defined quantities of damage to be introduced at precisely defined locations." Wikipedia Jack Miller particle accelerator UO:0000127 IAO:0000003 obo:RBO_00005066 miligray per second mGy/sec mGy/sec A derived absorbed dose unit which is equal to one milligray absorbed per second UO:0000129 UO:0010065 TRUE -obo:RBO_00005067 indirect cellular response to stimulus Indirect cellular response to stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus which acts on another cell and not on the responding cell. The process begins with detection of the stimulus by a cell and ends with a change in state or activity of a different cell Paul Schofield This could be used to describe a tissue response to immune stimulation, so for example an IL2 response of endothelial cells in response to lymphocytes stimulated by pathogen. GO:0051716 -obo:RBO_00005068 indirect cellular response to radiation Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells. Paul Schofield The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 obo:RBO_00005067 -obo:RBO_00005069 indirect cellular response to ionising radiation Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of exposure to ionising radiation which acts on another cell and not on the responding cell. The process begins with detection of the ionising radiation by one cell or cells and ends with a change in state or activity of a different cell or cells. Paul Schofield Directly describes the bystander effect (Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) but can alo sbe used to describe phenomena related to the abscopal effect, manifest in whole organisms where irradiation of one part of the organism causes changes in another un-irradiated component. obo:RBO_00005068 +obo:RBO_00005067 indirect cellular response to stimulus Indirect cellular response to stimulus "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus which acts on another cell and not on the responding cell. The process begins with detection of the stimulus by a cell and ends with a change in state or activity of a different cell" Paul Schofield "This could be used to describe a tissue response to immune stimulation, so for example an IL2 response of endothelial cells in response to lymphocytes stimulated by pathogen." GO:0051716 +obo:RBO_00005068 indirect cellular response to radiation "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells." Paul Schofield "The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671" obo:RBO_00005067 +obo:RBO_00005069 indirect cellular response to ionising radiation "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of exposure to ionising radiation which acts on another cell and not on the responding cell. The process begins with detection of the ionising radiation by one cell or cells and ends with a change in state or activity of a different cell or cells." Paul Schofield "Directly describes the bystander effect (Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) but can alo sbe used to describe phenomena related to the abscopal effect, manifest in whole organisms where irradiation of one part of the organism causes changes in another un-irradiated component." obo:RBO_00005068 obo:RBO_00005070 ionizing radiation device A device for exposing materials or biological organisms to ionizing radiation for research or therapeutic purposes. radiation source -obo:RBO_00005071 high-altitude balloon High-altitude balloons are crewed or uncrewed balloons, usually filled with helium or hydrogen, that are released into the stratosphere, generally attaining between 18 and 37 km (11 and 23 mi; 59,000 and 121,000 ft) above sea level. Wikipedia Jack Miller aircraft +obo:RBO_00005071 high-altitude balloon "High-altitude balloons are crewed or uncrewed balloons, usually filled with helium or hydrogen, that are released into the stratosphere, generally attaining between 18 and 37 km (11 and 23 mi; 59,000 and 121,000 ft) above sea level." Wikipedia Jack Miller aircraft obo:RBO_00005072 space flight spaceflight Travel beyond the Earth's atmosphere Jack Miller PATO:0002062 -obo:RBO_00005074 non-targeted effects of ionising radiation non-targeted effects of ionising radiation NTE|non-targeted effects Non-targeted effects of ionising radiation are characterised by cellular responses that occur in cells in which energy from ionizing radiation has not been deposited. The distinct classes of non-targeted effects include Genomic Instability, and Bystander effect which latter includes Abscopal effects and Bystander-mediated adaptive response. These can also arise non-clonally in the progeny of irradiated somatic or germ cells, resulting in radiation-induced genomic instability and transgenerational genomic instability respectively. (Kadhim M, Salomaa S, Wright E, et al. Non-targeted effects of ionising radiation--implications for low dose risk. Mutat Res. 2013;752(2):84-98. doi:10.1016/j.mrrev.2012.12.001) Paul Schofield ORCID: 0000-0002-5111-7263 obo:RBO_00005069 +obo:RBO_00005074 non-targeted effects of ionising radiation non-targeted effects of ionising radiation NTE|non-targeted effects "Non-targeted effects of ionising radiation are characterised by cellular responses that occur in cells in which energy from ionizing radiation has not been deposited. The distinct classes of non-targeted effects include Genomic Instability, and Bystander effect which latter includes Abscopal effects and Bystander-mediated adaptive response. These can also arise non-clonally in the progeny of irradiated somatic or germ cells, resulting in radiation-induced genomic instability and transgenerational genomic instability respectively. (Kadhim M, Salomaa S, Wright E, et al. Non-targeted effects of ionising radiation--implications for low dose risk. Mutat Res. 2013;752(2):84-98. doi:10.1016/j.mrrev.2012.12.001)" Paul Schofield ORCID: 0000-0002-5111-7263 obo:RBO_00005069 obo:RBO_00002000 radiation exposure Irradiation The process by which an entity is exposed to electromagnetic or acoustic radiation radiation energy internally or externally. 0000-0002-5111-7263 energy transfer process obo:RBO_00002001 accidental radiation exposure Accidental irradiation Unplanned exposure to radiation of any type in any environment or otherwise planned process. 0000-0002-5111-7263 radiation exposure -obo:RBO_00002007 anthropogenic radiation exposure Exposure to human generated radiation Exposure to ionising radiation created by a man-made machine or exposure to a fixed source. For example a cobalt source, an X ray machine, an acceleratororf a nucler weapon. 0000-0002-5111-7263 radiation exposure -obo:RBO_00002002 planned radiation exposure Planned irradiation Planned exposure of an entity to radiation of any type, for example as part of a medical or experimental procedure with the intention of exposing the entity to radiation energy internally or externally. 0000-0002-5111-7263 anthropogenic radiation exposure|OBI:0000011 -obo:RBO_00002003 medical diagnostic radiation exposure Diagnostic irradiation Planned exposure of an organism to radiation of any type, internally or externally, with the intention to effect a diagnosis of disease. 0000-0002-5111-7263 planned anthropogenic radiation exposure +obo:RBO_00002007 anthropogenic radiation exposure Exposure to human generated radiation "Exposure to ionising radiation created by a man-made machine or exposure to a fixed source. For example a cobalt source, an X ray machine, an acceleratororf a nucler weapon." 0000-0002-5111-7263 radiation exposure +obo:RBO_00002002 planned radiation exposure Planned irradiation "Planned exposure of an entity to radiation of any type, for example as part of a medical or experimental procedure with the intention of exposing the entity to radiation energy internally or externally." 0000-0002-5111-7263 anthropogenic radiation exposure|OBI:0000011 +obo:RBO_00002003 medical diagnostic radiation exposure Diagnostic irradiation "Planned exposure of an organism to radiation of any type, internally or externally, with the intention to effect a diagnosis of disease." 0000-0002-5111-7263 planned anthropogenic radiation exposure obo:RBO_00002004 exposure to naturally ocurring radioactive material Environmental irradiation Exposure to naturally occurring radiation (NORM) of any type in any environment . 0000-0002-5111-7263 radiation exposure -obo:RBO_00002005 medical therapeutic radiation exposure Therapeutic irradiation Planned exposure of an organism to radiation of any type, internally or externally, with the intention to effect a cure or mitigation of disease. 0000-0002-5111-7263 planned anthropogenic radiation exposure -obo:RBO_00002006 accidental non-medical anthropogenic radiation exposure Accidental man-made radiation exposure Unplanned exposure to anthropogenic radiation of any type in any environment ; for example radiation from nuclear waste, nuclear industry discharge or weapons. 0000-0002-5111-7263 accidental anthropogenic radiation exposure +obo:RBO_00002005 medical therapeutic radiation exposure Therapeutic irradiation "Planned exposure of an organism to radiation of any type, internally or externally, with the intention to effect a cure or mitigation of disease." 0000-0002-5111-7263 planned anthropogenic radiation exposure +obo:RBO_00002006 accidental non-medical anthropogenic radiation exposure Accidental man-made radiation exposure "Unplanned exposure to anthropogenic radiation of any type in any environment ; for example radiation from nuclear waste, nuclear industry discharge or weapons." 0000-0002-5111-7263 accidental anthropogenic radiation exposure obo:RBO_00002008 planned anthropogenic radiation exposure Planned exposure to radiation generated through a device or exposure to a source emitting ionising radiation 0000-0002-5111-7263 OBI:0000011|anthropogenic radiation exposure obo:RBO_00002009 accidental anthropogenic radiation exposure Accidental or incidental exposure to radiation from a man made process or machine. Covers both radiation accidents and routine occupational exposure. 0000-0002-5111-7263 anthropogenic radiation exposure -obo:RBO_00002010 accidental medical anthropogenic radiation exposure Accidental exposure occurring during medical therapy or diagnostics, for example medical radiation accidents or overdoses. 0000-0002-5111-7263 accidental anthropogenic radiation exposure -obo:RBO_00002011 unplanned naturally occurring radiation exposure Incidental exposure to naturally occurring radiation in a natural or anthropogenic environment, such as geographical areas with high background levels of radiation or specific locations such as Uranium mines. 0000-0002-5111-7263 obo:RBO_00002004 TRUE -obo:RBO_00002012 planned naturally occurring radiation exposure Deliberate or knowing exposure to naturally occurring radiation in a natural or anthropogenic environment, such as a radon spa. 0000-0002-5111-7263 obo:RBO_00002004 +obo:RBO_00002010 accidental medical anthropogenic radiation exposure "Accidental exposure occurring during medical therapy or diagnostics, for example medical radiation accidents or overdoses." 0000-0002-5111-7263 accidental anthropogenic radiation exposure +obo:RBO_00002011 unplanned naturally occurring radiation exposure "Incidental exposure to naturally occurring radiation in a natural or anthropogenic environment, such as geographical areas with high background levels of radiation or specific locations such as Uranium mines." 0000-0002-5111-7263 obo:RBO_00002004 TRUE +obo:RBO_00002012 planned naturally occurring radiation exposure "Deliberate or knowing exposure to naturally occurring radiation in a natural or anthropogenic environment, such as a radon spa." 0000-0002-5111-7263 obo:RBO_00002004 obo:RBO_00002013 social and psychosocial study Studies relating to human society and the interrelation of social and educational factors with individual thought and behaviour including mental illness. 0000-0002-5111-7263 radiobiology study type obo:RBO_00002015 mass media study Studies on the distribution of information or opinion by technological means of communication that reach large numbers of people. 0000-0002-5111-7263 radiobiology study type http://purl.biolontology.org/ontology/CSP/1580-0981 -obo:RBO_00002016 preparedness study Studies on the civil, legal, and political preparedness for accidental or deliberate release of radioactive materials or radiation into the environment. 0000-0002-5111-7263 radiobiology study type -obo:RBO_00002017 clinical study Studies in which research is conducted with human subjects or on material of human origin in which the investigator directly interacts with human subjects, including the dveelopment of new technologies, understanding of the mechanisms of disease, therapy, clinical trials, epidemiology behaviousrand health services research. 0000-0002-5111-7263 radiobiology study type http://purl.bioontology.org/ontology/CSP/4006-0105 -obo:RBO_00002018 legal and governance study Study of the laws, statutes, ordinances, government or international treaty regulations or authoritative guidelines, as well as for legal controversy and court decisions, relating to the regulation of radiation safety, movement and containment of radioactive materials and the consequences for human health or the natural environment of radioactive contamination. 0000-0002-5111-7263 radiobiology study type -obo:RBO_00002019 security and law enforcement study Studies relating to organisations and processes concerned with freedom from or resilience towards potential harm caused by hostile intent or circumstances (for example terrorism and illegal release of radioactive substances or radiation) towards the natural environment or human population, and the enforcement of relevant laws and international treaties. 0000-0002-5111-7263 radiobiology study type -obo:RBO_00002020 cancer study A study whose intention is to discover knowledge concerning the origins, nature diagnosis or therapy for neoplastic disease and cancer. This includes studies in humans, model organisms, the laboratory and in silico. This class includes experimental and epidemiological studies specifically aimed at cancer. 0000-0002-5111-7263 radiobiology study type -obo:RBO_00002021 study modality The specific manner, characteristic, pattern of application, or the employment of any technology, approach or formal procedure to implement the study plan to generate a study type. 0000-0002-5111-7263 obo:PATO_0001236 -obo:RBO_00002022 environmental study Studies of the presence of radiation of any type in the natural or anthropogenic environment and its impact on animals, plants, and microorganisms. This includes studies measuring nuclide transfer in the environment, and interaction with meteorological phenomena. This excludes occupational exposure and the human working environment. 0000-0002-5111-7263 radiobiology study type -obo:RBO_00002023 nuclear industry study Studies concerned with the regulation, monitoring and operation of the nuclear industry. For example nuclear power station and reprocessing plants, isotope purification and manufactore, weapons manufacture and testing. This includes occupation health studies, impact of accidental or deliberate release on the natural or man made environment and impact on organisms specifically affected directly or indirectly by contamination. 0000-0002-5111-7263 radiobiology study type -obo:RBO_00002024 laboratory study Research done in a laboratory. A laboratory study may use special equipment and cells or animals to investigate the effects of an experimental perturbation, discover fundamental molecular mechanisms, assay biological substances, or find out if a drug, procedure, or treatment is likely to be useful in humans. A laboratory investigation is often characterised by a hypothesis and is carried out with controls. 0000-0002-5111-7263 radiobiology study type http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28278 -obo:RBO_00002025 attitudinal study Study of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ethicolegal constructs surrounding radiation and radiation safety and regulation. 0000-0002-5111-7263 social and psychosocial study http://purl.bioontology.org/ontology/CSP/2482-9501 -obo:RBO_00002026 communication study Study concerning exchange or transmission of thoughts, messages, or information between people or between authorities and the general public (for example educational information, risk communication, safety communication) concerning exposure to and use of radiation. 0000-0002-5111-7263 social and psychosocial study -obo:RBO_00002027 community study A study focussed on a set of people with some shared characteristic. The substance of shared element varies widely, from geography to a situation to interest to lives and values. The term is widely used to evoke sense of collectivity. For example communities collectively exposed to radioactive environmental contamination. 0000-0002-5111-7263 social and psychosocial study -obo:RBO_00002028 political and psephological study The study of political involvement in radiation and nuclear regulation, military use, and safety as shown by inclusion in political manifestos and messaging by established or informal groups and its impact on voting patterns and democracy. 0000-0002-5111-7263 social and psychosocial study +obo:RBO_00002016 preparedness study "Studies on the civil, legal, and political preparedness for accidental or deliberate release of radioactive materials or radiation into the environment." 0000-0002-5111-7263 radiobiology study type +obo:RBO_00002017 clinical study "Studies in which research is conducted with human subjects or on material of human origin in which the investigator directly interacts with human subjects, including the dveelopment of new technologies, understanding of the mechanisms of disease, therapy, clinical trials, epidemiology behaviousrand health services research." 0000-0002-5111-7263 radiobiology study type http://purl.bioontology.org/ontology/CSP/4006-0105 +obo:RBO_00002018 legal and governance study "Study of the laws, statutes, ordinances, government or international treaty regulations or authoritative guidelines, as well as for legal controversy and court decisions, relating to the regulation of radiation safety, movement and containment of radioactive materials and the consequences for human health or the natural environment of radioactive contamination." 0000-0002-5111-7263 radiobiology study type +obo:RBO_00002019 security and law enforcement study "Studies relating to organisations and processes concerned with freedom from or resilience towards potential harm caused by hostile intent or circumstances (for example terrorism and illegal release of radioactive substances or radiation) towards the natural environment or human population, and the enforcement of relevant laws and international treaties." 0000-0002-5111-7263 radiobiology study type +obo:RBO_00002020 cancer study "A study whose intention is to discover knowledge concerning the origins, nature diagnosis or therapy for neoplastic disease and cancer. This includes studies in humans, model organisms, the laboratory and in silico. This class includes experimental and epidemiological studies specifically aimed at cancer." 0000-0002-5111-7263 radiobiology study type +obo:RBO_00002021 study modality "The specific manner, characteristic, pattern of application, or the employment of any technology, approach or formal procedure to implement the study plan to generate a study type." 0000-0002-5111-7263 obo:PATO_0001236 +obo:RBO_00002022 environmental study "Studies of the presence of radiation of any type in the natural or anthropogenic environment and its impact on animals, plants, and microorganisms. This includes studies measuring nuclide transfer in the environment, and interaction with meteorological phenomena. This excludes occupational exposure and the human working environment." 0000-0002-5111-7263 radiobiology study type +obo:RBO_00002023 nuclear industry study "Studies concerned with the regulation, monitoring and operation of the nuclear industry. For example nuclear power station and reprocessing plants, isotope purification and manufactore, weapons manufacture and testing. This includes occupation health studies, impact of accidental or deliberate release on the natural or man made environment and impact on organisms specifically affected directly or indirectly by contamination." 0000-0002-5111-7263 radiobiology study type +obo:RBO_00002024 laboratory study "Research done in a laboratory. A laboratory study may use special equipment and cells or animals to investigate the effects of an experimental perturbation, discover fundamental molecular mechanisms, assay biological substances, or find out if a drug, procedure, or treatment is likely to be useful in humans. A laboratory investigation is often characterised by a hypothesis and is carried out with controls." 0000-0002-5111-7263 radiobiology study type http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28278 +obo:RBO_00002025 attitudinal study "Study of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ethicolegal constructs surrounding radiation and radiation safety and regulation." 0000-0002-5111-7263 social and psychosocial study http://purl.bioontology.org/ontology/CSP/2482-9501 +obo:RBO_00002026 communication study "Study concerning exchange or transmission of thoughts, messages, or information between people or between authorities and the general public (for example educational information, risk communication, safety communication) concerning exposure to and use of radiation." 0000-0002-5111-7263 social and psychosocial study +obo:RBO_00002027 community study "A study focussed on a set of people with some shared characteristic. The substance of shared element varies widely, from geography to a situation to interest to lives and values. The term is widely used to evoke sense of collectivity. For example communities collectively exposed to radioactive environmental contamination." 0000-0002-5111-7263 social and psychosocial study +obo:RBO_00002028 political and psephological study "The study of political involvement in radiation and nuclear regulation, military use, and safety as shown by inclusion in political manifestos and messaging by established or informal groups and its impact on voting patterns and democracy." 0000-0002-5111-7263 social and psychosocial study obo:RBO_00002029 psychometric study "A study measuring ""psychological"" aspects of a person such as knowledge, skills, abilities, attitudes, or personality using defined scales." 0000-0002-5111-7263 social and psychosocial study -obo:RBO_00002030 behavioural study A study of human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology. 0000-0002-5111-7263 social and psychosocial study -obo:RBO_00002031 sociological study A study dealing with group relationships, patterns of collective behavior, and social organization. 0000-0002-5111-7263 social and psychosocial study -obo:RBO_00002032 social science and humanities study Studies involving fields of inquiry into human constructs and concerns as opposed to natural processes . These are traditionally the study of literature, philosophy, and religion. Included in this definition are sociological studies, especially those concerned with the social impact of the humanities. 0000-0002-5111-7263 social and psychosocial study -obo:RBO_00002033 perceptions, expectations and behaviours study Specifically an attitudinal study looking at how perception, for example of risk, and expectations affect behaviour. 0000-0002-5111-7263 social and psychosocial study -obo:RBO_00002034 holistic approaches to governance study Sociological, attitudinal, ethocolegal and regulatory approaches to governance of radiation and radioactive substance use. 0000-0002-5111-7263 social and psychosocial study +obo:RBO_00002030 behavioural study "A study of human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology." 0000-0002-5111-7263 social and psychosocial study +obo:RBO_00002031 sociological study "A study dealing with group relationships, patterns of collective behavior, and social organization." 0000-0002-5111-7263 social and psychosocial study +obo:RBO_00002032 social science and humanities study "Studies involving fields of inquiry into human constructs and concerns as opposed to natural processes . These are traditionally the study of literature, philosophy, and religion. Included in this definition are sociological studies, especially those concerned with the social impact of the humanities." 0000-0002-5111-7263 social and psychosocial study +obo:RBO_00002033 "perceptions, expectations and behaviours study" "Specifically an attitudinal study looking at how perception, for example of risk, and expectations affect behaviour." 0000-0002-5111-7263 social and psychosocial study +obo:RBO_00002034 holistic approaches to governance study "Sociological, attitudinal, ethocolegal and regulatory approaches to governance of radiation and radioactive substance use." 0000-0002-5111-7263 social and psychosocial study obo:RBO_00002035 responsible research and innovation study Studies on policy concerning socially and ethically responsible research and innovation 0000-0002-5111-7263 social and psychosocial study obo:RBO_00002036 stakeholder engagement study Studies of the engagement between an organisational entity and those groups or individuals potentially or actually impacted by the actions of that entity over a range of activities and approaches. 0000-0002-5111-7263 social and psychosocial study -obo:RBO_00002037 risk and health communication study Study concerning the modes, efficacy and response to communication of risk and health impacts of radiation in all aspects. 0000-0002-5111-7263 social and psychosocial study +obo:RBO_00002037 risk and health communication study "Study concerning the modes, efficacy and response to communication of risk and health impacts of radiation in all aspects." 0000-0002-5111-7263 social and psychosocial study obo:RBO_00002038 radiological protection culture study Studies concenring the attitudes to and practices of radiological protection in defined groups of people. For example the nuclear industry of a country or within a specific laboratory. 0000-0002-5111-7263 social and psychosocial study -obo:RBO_00002039 genetic population study Genetic study done at the population level or among population groups, generally to find the cause, incidence or spread of a disease or to see the response to a treatment, nutrition or environment. 0000-0002-5111-7263 epidemiological study http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16160 +obo:RBO_00002039 genetic population study "Genetic study done at the population level or among population groups, generally to find the cause, incidence or spread of a disease or to see the response to a treatment, nutrition or environment." 0000-0002-5111-7263 epidemiological study http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16160 obo:RBO_00002040 prospective study A type of study in which participants are enrolled into the study before they develop the disease or outcome in question. 0000-0002-5111-7263 epidemiological study http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C142646 -obo:RBO_00002041 registry study Observational studies which include an organized system that uses observational methods to collect uniform data (clinical and other) prospectively for a population defined by a particular disorder/disease, condition (including susceptibility to a disorder), or exposure (including products, health care services, and/or procedures) and that serves a predetermined scientific, clinical, or policy purpose. Patient registries may be single purpose or on-going data collection programs that address one or more questions. (AHRQ) An observational study that is also considered to be a Patient Registry. 0000-0002-5111-7263 epidemiological study http://purl.obolibrary.org/obo/NCIT_C129000 +obo:RBO_00002041 registry study "Observational studies which include an organized system that uses observational methods to collect uniform data (clinical and other) prospectively for a population defined by a particular disorder/disease, condition (including susceptibility to a disorder), or exposure (including products, health care services, and/or procedures) and that serves a predetermined scientific, clinical, or policy purpose. Patient registries may be single purpose or on-going data collection programs that address one or more questions. (AHRQ) An observational study that is also considered to be a Patient Registry." 0000-0002-5111-7263 epidemiological study http://purl.obolibrary.org/obo/NCIT_C129000 obo:RBO_00002042 retrospective study A study looking backwards in time using observations collected predominantly prior to subject selection and enrolment 0000-0002-5111-7263 epidemiological study -obo:RBO_00002043 incidence or prevalence study A study of the number of new cases of a given disease during a given period in a specified population. It also is used for the rate at which new events occur in a defined population. this class also includes PREVALENCE, which refers to all cases in the population at a given time. 0000-0002-5111-7263 epidemiological study -obo:RBO_00002044 situation awareness and decision support study Studies concerning the optimisation of situation awareness through gathering and analysing information, and methodologies for making decisions on that awareness, such as estimating the path of a radioactive fallout with respect to weather and population density and making a decision to evacuate a population. 0000-0002-5111-7263 preparedness study -obo:RBO_00002045 civil protection study A study concerning the protection of the population from unexpected radioactive discharge or contamination, such as a dirty bomb, and civil safetyy coningency plans, such as deployment of emergency services and evacuation. 0000-0002-5111-7263 preparedness study -obo:RBO_00002046 disaster planning study Studies on planning for unexpected natural or man-made radiological catastrophe of substantial extent causing significant property damage or destruction, loss of life or sometimes permanent changes to the natural environment. Broader scope than civil protection as may relate to livestock, food and water shortage, disease outbreak and extensive traumas caused by precipitating or consequential damage. 0000-0002-5111-7263 preparedness study +obo:RBO_00002043 incidence or prevalence study "A study of the number of new cases of a given disease during a given period in a specified population. It also is used for the rate at which new events occur in a defined population. this class also includes PREVALENCE, which refers to all cases in the population at a given time." 0000-0002-5111-7263 epidemiological study +obo:RBO_00002044 situation awareness and decision support study "Studies concerning the optimisation of situation awareness through gathering and analysing information, and methodologies for making decisions on that awareness, such as estimating the path of a radioactive fallout with respect to weather and population density and making a decision to evacuate a population." 0000-0002-5111-7263 preparedness study +obo:RBO_00002045 civil protection study "A study concerning the protection of the population from unexpected radioactive discharge or contamination, such as a dirty bomb, and civil safetyy coningency plans, such as deployment of emergency services and evacuation." 0000-0002-5111-7263 preparedness study +obo:RBO_00002046 disaster planning study "Studies on planning for unexpected natural or man-made radiological catastrophe of substantial extent causing significant property damage or destruction, loss of life or sometimes permanent changes to the natural environment. Broader scope than civil protection as may relate to livestock, food and water shortage, disease outbreak and extensive traumas caused by precipitating or consequential damage." 0000-0002-5111-7263 preparedness study obo:RBO_00002047 nuclear accident study Studies on plannig for or analysing a nuclear accident with release of airborn or waterborn contamination into the environment. Narrower than Disaster planning study but may be used to qualify an annotation to Disaster planning study if the source of contamination is a nuclear accident. A nuclear accident is not necessarily a disaster. 0000-0002-5111-7263 preparedness study -obo:RBO_00002048 clinical trial study A controlled study designed to assess the safety and efficacy of new drugs, devices, treatments, or preventive measures in humans by comparing two or more interventions or regimens 0000-0002-5111-7263 clinical study http://purl.bioontology.org/ontology/CSP/0690-6917 -obo:RBO_00002049 medical radiological safety study Study of the effects of radiation used in a medical therapeutic or diagnostic context. Inlcudes radiation accidents in this context, excludes occupational exposure for health professionals. 0000-0002-5111-7263 clinical study -obo:RBO_00002050 occupational health study A study concerned with health and safety policy development, implementation and practice in the workplace including investigating accidents at work, and chronic occupational exposure. Includes monitoring compliance with health and safety legislation and study of the promotion and maintenance of physical and mental health in the work environment. 0000-0002-5111-7263 clinical study -obo:RBO_00002051 radiation based diagnostics study Study on the efficacy, outcomes and adverse consequences of exposure to medical diagnostic procedures using internal or external irradiation. 0000-0002-5111-7263 clinical study -obo:RBO_00002052 radiotherapy study Study of the efficacy, outcomes and adverse consequences of exposure to therapeutic use of ionizing and nonionizing radiation including RADIONUCLIDE THERAPY, therapeutic radiation with visible, laser, or ultraviolet light. Includes technical development of protocols and equipment. 0000-0002-5111-7263 clinical study +obo:RBO_00002048 clinical trial study "A controlled study designed to assess the safety and efficacy of new drugs, devices, treatments, or preventive measures in humans by comparing two or more interventions or regimens" 0000-0002-5111-7263 clinical study http://purl.bioontology.org/ontology/CSP/0690-6917 +obo:RBO_00002049 medical radiological safety study "Study of the effects of radiation used in a medical therapeutic or diagnostic context. Inlcudes radiation accidents in this context, excludes occupational exposure for health professionals." 0000-0002-5111-7263 clinical study +obo:RBO_00002050 occupational health study "A study concerned with health and safety policy development, implementation and practice in the workplace including investigating accidents at work, and chronic occupational exposure. Includes monitoring compliance with health and safety legislation and study of the promotion and maintenance of physical and mental health in the work environment." 0000-0002-5111-7263 clinical study +obo:RBO_00002051 radiation based diagnostics study "Study on the efficacy, outcomes and adverse consequences of exposure to medical diagnostic procedures using internal or external irradiation." 0000-0002-5111-7263 clinical study +obo:RBO_00002052 radiotherapy study "Study of the efficacy, outcomes and adverse consequences of exposure to therapeutic use of ionizing and nonionizing radiation including RADIONUCLIDE THERAPY, therapeutic radiation with visible, laser, or ultraviolet light. Includes technical development of protocols and equipment." 0000-0002-5111-7263 clinical study obo:RBO_00002053 therapeutics study A study involvingdevelopment of agents or procedures intended to produce an effect that is intended to mitigate or stop a pathologic process. 0000-0002-5111-7263 clinical study obo:RBO_00002054 histopathologic study A study of the macroscopic and microscopic anatomical changes in diseased tissue. 0000-0002-5111-7263 clinical study http://purl.bioontology.org/ontology/CSP/1448-3909 -obo:RBO_00002055 radiation legislation study Study of legal and statutory instruments and legislation designed to regulate the safety, use and transport of radioactive materials, release of such materials into the environment, or external radiation. 0000-0002-5111-7263 legal and governance study -obo:RBO_00002056 regulatory harmonisation study Study of the policy approaches and their implementation concerned with harmonising regulatory guidelines and legislation dealing with radiation and radioactive substances between legislatures, generally internationally. 0000-0002-5111-7263 legal and governance study -obo:RBO_00002057 nuclear proliferation treaty study Study of the development, implementation and monitoring of nuclear non proliferation treaties between states. 0000-0002-5111-7263 legal and governance study -obo:RBO_00002058 bioterrorism study Studies concerning intentional release of organisms (germs), toxic chemicals, or radioactive substances with intent to harm or kill people or the environment, or to inflict panic within a population. 0000-0002-5111-7263 security and law enforcement study http://purl.bioontology.org/ontology/CSP/5000-0002 -obo:RBO_00002059 military defence study Study of strategies and their implementation towards defence against radiation used as a weapon conducted by military powers and institutions. May also include civil defence where the military has a significant operational role, but not disaster preparedness. 0000-0002-5111-7263 security and law enforcement study -obo:RBO_00002060 dna modification study Study of biological processes that involve adding/removing chemical moieties to/from DNA, including methylation, phosphorylation, dephosphorylation, etc. Includes interventional DNA modification. 0000-0002-5111-7263 study modality -obo:RBO_00002061 histone modification study Study of biological processes that involve adding/removing chemical moieties to/from histones, including methylation, acetylation,phosphorylation, dephosphorylation, etc. 0000-0002-5111-7263 study modality +obo:RBO_00002055 radiation legislation study "Study of legal and statutory instruments and legislation designed to regulate the safety, use and transport of radioactive materials, release of such materials into the environment, or external radiation." 0000-0002-5111-7263 legal and governance study +obo:RBO_00002056 regulatory harmonisation study "Study of the policy approaches and their implementation concerned with harmonising regulatory guidelines and legislation dealing with radiation and radioactive substances between legislatures, generally internationally." 0000-0002-5111-7263 legal and governance study +obo:RBO_00002057 nuclear proliferation treaty study "Study of the development, implementation and monitoring of nuclear non proliferation treaties between states." 0000-0002-5111-7263 legal and governance study +obo:RBO_00002058 bioterrorism study "Studies concerning intentional release of organisms (germs), toxic chemicals, or radioactive substances with intent to harm or kill people or the environment, or to inflict panic within a population." 0000-0002-5111-7263 security and law enforcement study http://purl.bioontology.org/ontology/CSP/5000-0002 +obo:RBO_00002059 military defence study "Study of strategies and their implementation towards defence against radiation used as a weapon conducted by military powers and institutions. May also include civil defence where the military has a significant operational role, but not disaster preparedness." 0000-0002-5111-7263 security and law enforcement study +obo:RBO_00002060 dna modification study "Study of biological processes that involve adding/removing chemical moieties to/from DNA, including methylation, phosphorylation, dephosphorylation, etc. Includes interventional DNA modification." 0000-0002-5111-7263 study modality +obo:RBO_00002061 histone modification study "Study of biological processes that involve adding/removing chemical moieties to/from histones, including methylation, acetylation,phosphorylation, dephosphorylation, etc." 0000-0002-5111-7263 study modality obo:RBO_00002062 interview study Study conducted by means of structured or unstructured interviews of persons of interest. 0000-0002-5111-7263 study modality obo:RBO_00002063 genetic study A study of genetic variation and the inheritance of a trait or traits within a population or an individual including examination of genetic material for the presence or absence of cytogenetic or molecular genetic abnormalities. 0000-0002-5111-7263 study modality -obo:RBO_00002064 imaging study A radiographic study used to evaluate a specific anatomic location for a specific purpose. This may include the assessment of imaging modalities and the development of new techniques. Includes PET, MRI, CT and related techniques. 0000-0002-5111-7263 study modality -obo:RBO_00002065 mathematical modelling study Study concerned with the construction, analysis, evaluation, refinement etc. of mathematical or statistical models of the properties or behaviour of a set of entities, such as molecules, physiological processes, environmental processes such as nuclide transfer, such that functions are developed to reliably predict the behaviour of those entities. 0000-0002-5111-7263 study modality +obo:RBO_00002064 imaging study "A radiographic study used to evaluate a specific anatomic location for a specific purpose. This may include the assessment of imaging modalities and the development of new techniques. Includes PET, MRI, CT and related techniques." 0000-0002-5111-7263 study modality +obo:RBO_00002065 mathematical modelling study "Study concerned with the construction, analysis, evaluation, refinement etc. of mathematical or statistical models of the properties or behaviour of a set of entities, such as molecules, physiological processes, environmental processes such as nuclide transfer, such that functions are developed to reliably predict the behaviour of those entities." 0000-0002-5111-7263 study modality obo:RBO_00002066 model organism study A study usually conducted in a laboratory where non human animals are used to model aspects of a disease process or its therapy to provide insights into human biology or pathobiology. 0000-0002-5111-7263 study modality -obo:RBO_00002067 monitoring technologies and metrology study Study concerning the development, use, calibration or standardisation of technologies for the qualitative or quantitative measurement of radiation and radionuclides. 0000-0002-5111-7263 study modality +obo:RBO_00002067 monitoring technologies and metrology study "Study concerning the development, use, calibration or standardisation of technologies for the qualitative or quantitative measurement of radiation and radionuclides." 0000-0002-5111-7263 study modality obo:RBO_00002068 radiochemistry study Study of the chemistry of radioactive materials including radioactive tracer studies of metabolic processes 0000-0002-5111-7263 study modality obo:RBO_00002069 policy development study Study of the development and implementation of public policy towards issues involving radiation 0000-0002-5111-7263 study modality obo:RBO_00002070 acoustic radiation study Study of the effects of acoustic radiation on cellular and organismal physiology and the effects of acoustic radiation emitted in response to exposure to ionising radiation. 0000-0002-5111-7263 study modality obo:RBO_00002071 environmental study_ abiotic_anthropogenic Study of radiation levels and effects in the human built environment. 0000-0002-5111-7263 environmental study obo:RBO_00002072 natural environment study Study of radiation levels and effects in the natural environment. 0000-0002-5111-7263 environmental study -obo:RBO_00002073 ecological population modelling study The development and use of mathematical models and systems analysis for the description of naturally occurring non-human populations, and applications to measuring the effects of radiological contamination. 0000-0002-5111-7263 environmental study +obo:RBO_00002073 ecological population modelling study "The development and use of mathematical models and systems analysis for the description of naturally occurring non-human populations, and applications to measuring the effects of radiological contamination." 0000-0002-5111-7263 environmental study obo:RBO_00002074 ecotoxicology study The study of environmental contamination with radiation and radioactive substances and the toxic effects on the ecosystem either through chemical toxicity or radiation exposure. 0000-0002-5111-7263 environmental study -obo:RBO_00002075 environmental radon study The study of environmental contamination with radon and the toxic effects on biota including humans. Both natural and anthropogenic environments. Includes radiometrics, safety policies and mitigation technologies. 0000-0002-5111-7263 environmental study -obo:RBO_00002076 radionuclide dispersal modelling study Mathematical modelling of radionuclide transfer and dispersal processes in water, earth or air, either directly or through the mediation of biota. 0000-0002-5111-7263 environmental study -obo:RBO_00002077 naturally occurring radioactive materials study Study of the ocurrence, levels and effects of naturally occurring radioactive materials such as Radon. 0000-0002-5111-7263 environmental study -obo:RBO_00002078 environmental radiation monitoring study Study involving the measurement of radiation levels, or concentration of radionuclides, in the natural or man made environment. Usually in a time series. 0000-0002-5111-7263 environmental study +obo:RBO_00002075 environmental radon study "The study of environmental contamination with radon and the toxic effects on biota including humans. Both natural and anthropogenic environments. Includes radiometrics, safety policies and mitigation technologies." 0000-0002-5111-7263 environmental study +obo:RBO_00002076 radionuclide dispersal modelling study "Mathematical modelling of radionuclide transfer and dispersal processes in water, earth or air, either directly or through the mediation of biota." 0000-0002-5111-7263 environmental study +obo:RBO_00002077 naturally occurring radioactive materials study "Study of the ocurrence, levels and effects of naturally occurring radioactive materials such as Radon." 0000-0002-5111-7263 environmental study +obo:RBO_00002078 environmental radiation monitoring study "Study involving the measurement of radiation levels, or concentration of radionuclides, in the natural or man made environment. Usually in a time series." 0000-0002-5111-7263 environmental study obo:RBO_00002079 environmental radionuclide transfer study Study concerned with the measurement of transfer of radionuclides to biota from the environment. 0000-0002-5111-7263 environmental study -obo:RBO_00002080 non ionising electromagnetic radiation study Any study concenrd with the prevalence or effects on non-ionising radiations such as UV, acoustic, or RF. 0000-0002-5111-7263 environmental study -obo:RBO_00002081 nuclear installation study Study concerning the safety, regulation, activities and engineering of nuclear installations including power stations, waste processing plant, radionuclide generation and purification plant, and military nuclear establishments. May include occupational health studies if broader than just occupationaal health in scope. 0000-0002-5111-7263 nuclear industry study -obo:RBO_00002082 nuclear waste study Study of the process of generation of nuclear waste, its monitoring, regulation, disposal and inadvertent discharge. 0000-0002-5111-7263 nuclear industry study +obo:RBO_00002080 non ionising electromagnetic radiation study "Any study concenrd with the prevalence or effects on non-ionising radiations such as UV, acoustic, or RF." 0000-0002-5111-7263 environmental study +obo:RBO_00002081 nuclear installation study "Study concerning the safety, regulation, activities and engineering of nuclear installations including power stations, waste processing plant, radionuclide generation and purification plant, and military nuclear establishments. May include occupational health studies if broader than just occupationaal health in scope." 0000-0002-5111-7263 nuclear industry study +obo:RBO_00002082 nuclear waste study "Study of the process of generation of nuclear waste, its monitoring, regulation, disposal and inadvertent discharge." 0000-0002-5111-7263 nuclear industry study obo:RBO_00002083 nuclear engineering study Study of the engineering of nuclear installations such as power plants. 0000-0002-5111-7263 nuclear industry study -obo:RBO_00002084 mining study Study of the process, regulation and monitoring of mines where exposure to naturally occurring radiation presents an occupational hazard for workers or the process itself, for example run off water or spoil, constitutes an environmental hazard. 0000-0002-5111-7263 nuclear industry study -obo:RBO_00002085 cell culture study A study using cells derived from an organism grown in artificial culture medium in a laboratory with the aim of understanding some aspect(s) of cell physiology, genetics or behaviour, generally as part of the testing of an hypothesis but also for diagnostic intent. 0000-0002-5111-7263 laboratory study -obo:RBO_00002086 organ culture study A study using an organ, part of an organ or an organoid culture, derived from an organism and grown in artificial culture medium in a laboratory with the aim of understanding some aspect(s) of cell physiology, genetics or behaviour, generally as part of the testing of an hypothesis but also for diagnostic intent. The system differs from cell culture in the generation or maintenance of multiple cell types with the spatial and functional relationship between them derived from or reflecting the normal organisation in vivo. 0000-0002-5111-7263 laboratory study -obo:RBO_00002087 molecular genetic study Any study involving the manipulation, measurement, or characterisation of DNA or RNA in a cell or organism. 0000-0002-5111-7263 laboratory study -obo:RBO_00002088 molecular structural study Elucidation of the physical structure of a macromolecule, protein, carbohydrate, DNA or RNA, its analysis and manipulation based on structure/function considerations. 0000-0002-5111-7263 laboratory study -obo:RBO_00002089 whole organism study A study using an intact organism, plant, animal, or microorganism 0000-0002-5111-7263 laboratory study -obo:RBO_00002090 bystander effect study Study of the cellular phenomenon which radiation energy is not been directly deposited in cells by transfer of medium, proximity/justaposition, or other means, but results in their behaving as if they had been irradiated. 0000-0002-5111-7263 laboratory study +obo:RBO_00002084 mining study "Study of the process, regulation and monitoring of mines where exposure to naturally occurring radiation presents an occupational hazard for workers or the process itself, for example run off water or spoil, constitutes an environmental hazard." 0000-0002-5111-7263 nuclear industry study +obo:RBO_00002085 cell culture study "A study using cells derived from an organism grown in artificial culture medium in a laboratory with the aim of understanding some aspect(s) of cell physiology, genetics or behaviour, generally as part of the testing of an hypothesis but also for diagnostic intent." 0000-0002-5111-7263 laboratory study +obo:RBO_00002086 organ culture study "A study using an organ, part of an organ or an organoid culture, derived from an organism and grown in artificial culture medium in a laboratory with the aim of understanding some aspect(s) of cell physiology, genetics or behaviour, generally as part of the testing of an hypothesis but also for diagnostic intent. The system differs from cell culture in the generation or maintenance of multiple cell types with the spatial and functional relationship between them derived from or reflecting the normal organisation in vivo." 0000-0002-5111-7263 laboratory study +obo:RBO_00002087 molecular genetic study "Any study involving the manipulation, measurement, or characterisation of DNA or RNA in a cell or organism." 0000-0002-5111-7263 laboratory study +obo:RBO_00002088 molecular structural study "Elucidation of the physical structure of a macromolecule, protein, carbohydrate, DNA or RNA, its analysis and manipulation based on structure/function considerations." 0000-0002-5111-7263 laboratory study +obo:RBO_00002089 whole organism study "A study using an intact organism, plant, animal, or microorganism" 0000-0002-5111-7263 laboratory study +obo:RBO_00002090 bystander effect study "Study of the cellular phenomenon which radiation energy is not been directly deposited in cells by transfer of medium, proximity/justaposition, or other means, but results in their behaving as if they had been irradiated." 0000-0002-5111-7263 laboratory study obo:RBO_00002091 epigenetic study A study of heritable phenotype changes that do not involve alterations in the DNA sequence. This may be in intact organisms or in cells and includes population analysis of epigenetic phenomena and molecular analysis of gene expression and epigenetic modifications of chromatin such as DNA methylation and histone acetylation. 0000-0002-5111-7263 laboratory study -obo:RBO_00002092 mutagenesis study Study of the frequency of induction , nature and consequences of the production of genetic or epigenetic alterations by any technique, including chemicals, radiation, recombination, or other molecular biology methods. 0000-0002-5111-7263 laboratory study -obo:RBO_00002093 attitudinal study of nuclear industry risk perception Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or regulation of the nuclear industries. 0000-0002-5111-7263 attitudinal study -obo:RBO_00002094 attitudinal study towards ionising radiation in the environment Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ecological integrity towards natural or anthropogenic ionising radiation in the environment. 0000-0002-5111-7263 attitudinal study -obo:RBO_00002095 attitudinal study towards non-ionising radiation in the environment Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ecological integrity towards natural or anthropogenic non-ionising radiation in the natural environment. 0000-0002-5111-7263 attitudinal study -obo:RBO_00002096 attitudinal study towards medical radiation procedures Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety and efficacy in a clinical context where radiation is used for diagnostic or therapeutic procedures.. 0000-0002-5111-7263 attitudinal study -obo:RBO_00002097 attitudinal study towards radiation in the occupational environment Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety towards natural or anthropogenic non-ionising radiation in the occupational environment. 0000-0002-5111-7263 attitudinal study +obo:RBO_00002092 mutagenesis study "Study of the frequency of induction , nature and consequences of the production of genetic or epigenetic alterations by any technique, including chemicals, radiation, recombination, or other molecular biology methods." 0000-0002-5111-7263 laboratory study +obo:RBO_00002093 attitudinal study of nuclear industry risk perception "Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or regulation of the nuclear industries." 0000-0002-5111-7263 attitudinal study +obo:RBO_00002094 attitudinal study towards ionising radiation in the environment "Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ecological integrity towards natural or anthropogenic ionising radiation in the environment." 0000-0002-5111-7263 attitudinal study +obo:RBO_00002095 attitudinal study towards non-ionising radiation in the environment "Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ecological integrity towards natural or anthropogenic non-ionising radiation in the natural environment." 0000-0002-5111-7263 attitudinal study +obo:RBO_00002096 attitudinal study towards medical radiation procedures "Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety and efficacy in a clinical context where radiation is used for diagnostic or therapeutic procedures.." 0000-0002-5111-7263 attitudinal study +obo:RBO_00002097 attitudinal study towards radiation in the occupational environment "Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety towards natural or anthropogenic non-ionising radiation in the occupational environment." 0000-0002-5111-7263 attitudinal study obo:RBO_00002098 authority trust study Study of social and individual trust in the position and activities of legal or other competent advisory or regulatory authorities. 0000-0002-5111-7263 attitudinal study -obo:RBO_00002099 risk communication study Study on the modality, efficacy and responses to communcation of information or advice to populations or individuals, on the safety and risks of exposure to ionising radiation in any context. 0000-0002-5111-7263 communication study -obo:RBO_00002100 public communication study Study on the modality, efficacy and responses to communication of information or advice to populations or individuals, on the safety and risks of exposure to ionising radiation in any context. 0000-0002-5111-7263 communication study -obo:RBO_00002101 public education study Study on the modality, efficacy and responses to communication of information or advice to populations on any aspect of radiation, conceived of as an educational programme, and including a wider scope than just safety and risk. For example basic nuclear physics, emergency action advice. 0000-0002-5111-7263 communication study -obo:RBO_00002102 social affairs and community health study Study involving attitudes, health status, social organisation of defined communities identified by common characteristics such as occupation type, geography, gender identity, with respect to radiation. 0000-0002-5111-7263 community study -obo:RBO_00002103 community planning study Studies involving creation and assessment of plans for the future physical arrangement, well being, efficiency and condition of a community. It may have the goals of improving health, promoting efficiency in the provision of services and resources on a comprehensive basis for a whole community. In the context of radiation this may be concerned with community planning for dealing with mitigation measures for local NORM, or organised community-wide continegency measures for nuclear accident or recovery from such. 0000-0002-5111-7263 community study -obo:RBO_00002104 community survey study Study concerned with eliciting information in a structured way concerning issues of interest from members of a community defined by common characteristics, for example occupation, geographical location, personal history or gender. 0000-0002-5111-7263 community study -obo:RBO_00002105 individual behaviour study A study concerned with human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology at the level of slected individuals. May be carried out by observation or as individual responses to a questioannaire or interview in the case of humans where the person records their own assessment of their behaviour. 0000-0002-5111-7263 behavioural study -obo:RBO_00002106 population behaviour study A study concerned with human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology within substantial populations of individuals. Likely to be carried out by mass observation or indirect inference. 0000-0002-5111-7263 behavioural study -obo:RBO_00002107 radiotherapeutic modelling study Mathematical modelling for theraputic regime optimisation and for optimal tumor response, for example modelling spatiotemporal dynamics of tumor and blood volume fraction, and predicting response to radiation therapy. Also studies for beam modelling and multiimaging techniques. 0000-0002-5111-7263 therapeutics study +obo:RBO_00002099 risk communication study "Study on the modality, efficacy and responses to communcation of information or advice to populations or individuals, on the safety and risks of exposure to ionising radiation in any context." 0000-0002-5111-7263 communication study +obo:RBO_00002100 public communication study "Study on the modality, efficacy and responses to communication of information or advice to populations or individuals, on the safety and risks of exposure to ionising radiation in any context." 0000-0002-5111-7263 communication study +obo:RBO_00002101 public education study "Study on the modality, efficacy and responses to communication of information or advice to populations on any aspect of radiation, conceived of as an educational programme, and including a wider scope than just safety and risk. For example basic nuclear physics, emergency action advice." 0000-0002-5111-7263 communication study +obo:RBO_00002102 social affairs and community health study "Study involving attitudes, health status, social organisation of defined communities identified by common characteristics such as occupation type, geography, gender identity, with respect to radiation." 0000-0002-5111-7263 community study +obo:RBO_00002103 community planning study "Studies involving creation and assessment of plans for the future physical arrangement, well being, efficiency and condition of a community. It may have the goals of improving health, promoting efficiency in the provision of services and resources on a comprehensive basis for a whole community. In the context of radiation this may be concerned with community planning for dealing with mitigation measures for local NORM, or organised community-wide continegency measures for nuclear accident or recovery from such." 0000-0002-5111-7263 community study +obo:RBO_00002104 community survey study "Study concerned with eliciting information in a structured way concerning issues of interest from members of a community defined by common characteristics, for example occupation, geographical location, personal history or gender." 0000-0002-5111-7263 community study +obo:RBO_00002105 individual behaviour study "A study concerned with human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology at the level of slected individuals. May be carried out by observation or as individual responses to a questioannaire or interview in the case of humans where the person records their own assessment of their behaviour." 0000-0002-5111-7263 behavioural study +obo:RBO_00002106 population behaviour study "A study concerned with human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology within substantial populations of individuals. Likely to be carried out by mass observation or indirect inference." 0000-0002-5111-7263 behavioural study +obo:RBO_00002107 radiotherapeutic modelling study "Mathematical modelling for theraputic regime optimisation and for optimal tumor response, for example modelling spatiotemporal dynamics of tumor and blood volume fraction, and predicting response to radiation therapy. Also studies for beam modelling and multiimaging techniques." 0000-0002-5111-7263 therapeutics study obo:RBO_00002108 building materials radiological safety study Study of the radiolonuclide components and emissions from building materials 0000-0002-5111-7263 environmental study_ abiotic_anthropogenic obo:RBO_00002109 building radiological safety study Studies on radiological safety within buildings. Primary purpose os for buildings not specifially designed to hold radioactive materials but anaylyis and mitigation of risks from radioactive exposure from the local environment or materials. 0000-0002-5111-7263 environmental study_ abiotic_anthropogenic obo:RBO_00002110 meteorology study Study of the weather and atmospheric dynamics mainly with respect to dissemination of radionuclides. 0000-0002-5111-7263 natural environment study -obo:RBO_00002111 environmental study_abiotic Study of non-living objects in the environment, such as soils or rocks. 0000-0002-5111-7263 natural environment study +obo:RBO_00002111 environmental study_abiotic "Study of non-living objects in the environment, such as soils or rocks." 0000-0002-5111-7263 natural environment study obo:RBO_00002112 environmental study_biota ( non human) Study of non-human biota in the natural environment. 0000-0002-5111-7263 natural environment study obo:RBO_00002113 environmental study_panbiota (all) Study which may include human and non-human biota in the environment. 0000-0002-5111-7263 natural environment study -obo:RBO_00002114 wireless communication radiation study Study of the measurement, effects and regulation of wireless communication signals, for example mobile phone radiation and microwave communication. 0000-0002-5111-7263 non ionising electromagnetic radiation study +obo:RBO_00002114 wireless communication radiation study "Study of the measurement, effects and regulation of wireless communication signals, for example mobile phone radiation and microwave communication." 0000-0002-5111-7263 non ionising electromagnetic radiation study obo:RBO_00002115 gamma ray photon Photons having energies that are greater than tens of thousands of electron volts (eV). Britannica.com The sample was irradiated with Cs-137 gamma ray photons. CHEBI:30212 obo:RBO_00002116 x-ray photon A photon with energies from about 100 eV (electron volts) to 1 MeV (million electron volts). Britannica.com The sample was irradiated with x-ray photons. CHEBI:30212 obo:RBO_00002117 irradiation An energy transfer process in which energy in the form of particles or waves is transferred from one entity to another Jack Miller Irradiation of the sample was with x-ray photons. 0000-0003-1741-8297 http://purl.obolibrary.org/obo/ENVO_01001852 obo:RBO_0002000 TRUE @@ -292,37 +300,43 @@ obo:RBO_00002125 anthropogenic environment radiation monitoring Monitoring fo obo:RBO_00002126 natural environment radiation monitoring Monitoring for radiation dose or quality within a natural environment. obo:RBO_00002122|obo:RBO_00002123 obo:RBO_00015000 radiation That energy which is transferred in space and time as part of the process of radiation (ENVO:01001023). obo:BFO_0000040 obo:RBO_00015001 neutral particle radiation Uncharged particles with kinetic energy imparted by natural or artificial means (such as by a particle accelerator) obo:RBO_00015000 -obo:RBO_00015002 nanodosimetry assay An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at nm scale obo:RBO_00005041 -obo:RBO_00015003 microdosimetry assay An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at micrometre scale obo:RBO_00005041 +obo:RBO_00015002 nanodosimetry assay An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." Usually a track structure assay at nm scale obo:RBO_00005041 +obo:RBO_00015003 microdosimetry assay An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers "See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006." Usually a track structure assay at micrometre scale obo:RBO_00005041 obo:RBO_00015004 alpha decay Nuclear decay in which an alpha particle is emitted. https://goldbook.iupac.org/terms/view/A00005 obo:RBO_00002118 alpha-decay http://purl.obolibrary.org/obo/REX_0000017 obo:RBO_00015005 beta decay Radioactive decay in which a beta particle is emitted or in which orbital electron capture occurs. http://goldbook.iupac.org/B00572.html obo:RBO_00002118 beta-decay http://purl.obolibrary.org/obo/REX_0000007 obo:RBO_00015006 subatomic process Processes in which electrons or components of the atomic nucleus are participants. BFO:0000015 obo:RBO_00015007 nanodosimetric measurement datum Measurement of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers obo:RBO_010016 -obo:RBO_00015008 specific energy measurement datum In microdosimetry the specific energy, z, is the energy deposited by radiation ( in one or more deposition events) in a specified micrometric (or smaller) site divided my the mass of the site. Measured in Gy. obo:RBO_010016 -obo:RBO_00015009 particle track The path of a particle in matter, delineated by sites where the particle deposits energy. obo:IAO_0000030 +obo:RBO_00015008 specific energy measurement datum "In microdosimetry the specific energy, z, is the energy deposited by radiation ( in one or more deposition events) in a specified micrometric (or smaller) site divided my the mass of the site. Measured in Gy." obo:RBO_010016 +obo:RBO_00015009 particle track "The path of a particle in matter, delineated by sites where the particle deposits energy." obo:IAO_0000030 obo:RBO_00015010 nanodosimetry A pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers. PATO:0001241 obo:RBO_00015011 particle track structure The complete set of spatial coordinates of energy deposition events along a particle track in matter PATO:0001236 -obo:RBO_00015012 ionization cluster A group of ionization events closely related in time and space, occurring in a specified target volume and originating from a single primary ionizing particle. UBERON:0000000 +obo:RBO_00015012 ionization cluster "A group of ionization events closely related in time and space, occurring in a specified target volume and originating from a single primary ionizing particle." UBERON:0000000 obo:RBO_00015013 microdosimetric measurement datum Measurement of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers. obo:RBO_010016 obo:RBO_00015014 micrometric volume "A volume of matter characterised by linear dimensions of the order of 0.5- 10's of microns, referred to as the ""site"" in microdosimetry." PATO:0001241 -obo:RBO_00015015 control specimen role A control specimen role of a biotic or abiotic sample or individual describes a specimen by its purpose, and therefore treatment, within a planned experimental process that tests hypotheses by isolating variables as dictated by the scientific method in order to make a conclusion about the effect of such variables. The quality of control inhering in the sample role exists as a result of the historical treatment of the sample. In a controlled experiment, two or more virtually identical experiments are conducted, but the factor being tested is varied in only one of them. This serves to isolate any causal phenomena. A control may have been subject to treatments during the experiment that might alter its state or behaviour and is therefore distinguishable from the sample as initial input into the experiment. However such treatments should in all cases but that of the variable under scrutiny, be the same as the experimental sample. OBI:0000112 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C64355 -obo:RBO_00015016 approximate sham irradiation Sham irradiation in which an identical irradiation protocol (with the exception of the administration of the radiation exposure) is not followed in every respect. Use approximate sham irradiation when at least one aspect of the irradiation (with the exception of the administration of the radiation exposure) is not followed precisely. For example, Not placing an organism or sample in a beam line for the same length of time as the irradiated organism(s) or sample(s) were left in the beam. obo:RBO_00005015 -obo:RBO_00015017 internal radiation exposure Exposure to an inhaled, ingested, injected or implanted source of radiation of any origin as part of a planned or accidental process. Experimental internal radiation exposure of rodents to radon gas through inhalation. obo:RBO_00002000 +obo:RBO_00015015 control specimen role "A control specimen role of a biotic or abiotic sample or individual describes a specimen by its purpose, and therefore treatment, within a planned experimental process that tests hypotheses by isolating variables as dictated by the scientific method in order to make a conclusion about the effect of such variables. The quality of control inhering in the sample role exists as a result of the historical treatment of the sample. In a controlled experiment, two or more virtually identical experiments are conducted, but the factor being tested is varied in only one of them. This serves to isolate any causal phenomena. A control may have been subject to treatments during the experiment that might alter its state or behaviour and is therefore distinguishable from the sample as initial input into the experiment. However such treatments should in all cases but that of the variable under scrutiny, be the same as the experimental sample." OBI:0000112 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C64355 +obo:RBO_00015016 approximate sham irradiation Sham irradiation in which an identical irradiation protocol (with the exception of the administration of the radiation exposure) is not followed in every respect. "Use approximate sham irradiation when at least one aspect of the irradiation (with the exception of the administration of the radiation exposure) is not followed precisely. For example, Not placing an organism or sample in a beam line for the same length of time as the irradiated organism(s) or sample(s) were left in the beam." obo:RBO_00005015 +obo:RBO_00015017 internal radiation exposure "Exposure to an inhaled, ingested, injected or implanted source of radiation of any origin as part of a planned or accidental process." Experimental internal radiation exposure of rodents to radon gas through inhalation. obo:RBO_00002000 obo:RBO_00015018 external radiation exposure Exposure to an external source of radiation of any origin or type. Mice exposed to external radiation from a Sr source. https://orcid.org/0000-0002-5111-7263 obo:RBO_00002000 -obo:RBO_00015019 complete sham irradiation Sham irradiation in which an identical irradiation protocol is followed in every respect, with the exception of the administration of the radiation exposure. Use complete sham irradiation when all steps of an irradiation protocol are followed for sham control group (with the exception of administration of the radiation exposure). obo:RBO_00005015 -obo:RBO_00015020 internal experimental radiation exposure Planned exposure of an entity to radiation of any type, for example as part of a medical or experimental procedure with the intention of exposing the entity to radiation energy internally by the ingestion, inhalation or implantation of a source of radiation. https://orcid.org/0000-0002-5111-7263 Research subjects participating in a clinical trial using an internally implanted radiation source have an internal experimental radiation exposure obo:RBO_00002008|obo:RBO_00015017 +obo:RBO_00015019 complete sham irradiation "Sham irradiation in which an identical irradiation protocol is followed in every respect, with the exception of the administration of the radiation exposure." Use complete sham irradiation when all steps of an irradiation protocol are followed for sham control group (with the exception of administration of the radiation exposure). obo:RBO_00005015 +obo:RBO_00015020 internal experimental radiation exposure "Planned exposure of an entity to radiation of any type, for example as part of a medical or experimental procedure with the intention of exposing the entity to radiation energy internally by the ingestion, inhalation or implantation of a source of radiation." https://orcid.org/0000-0002-5111-7263 Research subjects participating in a clinical trial using an internally implanted radiation source have an internal experimental radiation exposure obo:RBO_00002008|obo:RBO_00015017 obo:RBO_00015021 energy deposition event The direct or indirect transfer of energy from radiation to a medium through ionisation or excitation of the atoms of the medium. obo:RBO_00015006 obo:RBO_00015022 track formation http://purl.obolibrary.org/obo/BFO_0000015 -obo:RBO_00015023 mixed irradiation study A mixed irradiation study typically involves exposing a sample or system to a combination of different types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00000082 -obo:RBO_00015024 mixed ion and photon irradiation study A mixed ion and photon irradiation study typically involves exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00015023 -obo:RBO_00015025 mixed ion and photon simultaneous irradiation study A mixed ion and photon simultaneous irradiation study typically involves simultaneously exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00015024 -obo:RBO_00015026 mixed ion and photon sequential irradiation study A mixed ion and photon sequential irradiation study typically involves sequentially exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00015024 +obo:RBO_00015023 mixed irradiation study "A mixed irradiation study typically involves exposing a sample or system to a combination of different types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation." http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00000082 +obo:RBO_00015024 mixed ion and photon irradiation study "A mixed ion and photon irradiation study typically involves exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation." http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00015023 +obo:RBO_00015025 mixed ion and photon simultaneous irradiation study "A mixed ion and photon simultaneous irradiation study typically involves simultaneously exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation." http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00015024 +obo:RBO_00015026 mixed ion and photon sequential irradiation study "A mixed ion and photon sequential irradiation study typically involves sequentially exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation." http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00015024 obo:RBO_00015027 multiple ion irradiation study multiple ion mixed irradiation study A multiple ion irradiation study typically involves exposing a sample or system to a combination of different types of charged particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00015023 -obo:RBO_00015028 multiple ion simultaneous irradiation study A multiple ion simultaneous irradiation study typically involves simultaneously exposing a sample or system to a combination of ions. This could include exposure to various forms of particle radiation, for example ion beams. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00015027 +obo:RBO_00015028 multiple ion simultaneous irradiation study "A multiple ion simultaneous irradiation study typically involves simultaneously exposing a sample or system to a combination of ions. This could include exposure to various forms of particle radiation, for example ion beams. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation." http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00015027 obo:RBO_00015029 multiple ion sequential irradiation study A multiple ion sequential irradiation study involves exposing a sample or system to a combination of different ions. This could include exposure to various forms of particle radiation such as ion beams. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00015027 -obo:RBO_00015030 anthropogenic background radiation Radiation present in an experimental or therapeutic process, other than that produced as part of that planned process. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00000013 background radiation|ambient radiation -obo:RBO_00015031 natural background radiation Radiation originating in the terrestrial or extra-terrestrial environment. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00000013 -obo:RBO_00015032 radiation beam composition beam composition The types and characteristics of particles or waves that make up the radiation produced or emitted by a radiation source for use in a particular exposure context or protocol. The source may be artificial as in a particle accelerator or natural, in a controlled environment, such as a collimated beam from a radioactive isotope. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:PATO_0000025|obo:PATO_0001739 -obo:RBO_00015033 space radiation field The mix of charged and neutral atomic and subatomic particles and electromagnetic radiation suffusing a defined volume in an extraterrestrial environment at a given time. The space radiation field in the solar system consists of particle and electromagnetic radiation from the sun, electromagnetic radiation originating from extra-solar sources, and galactic cosmic radiation. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 http://purl.obolibrary.org/obo/BFO_0000027 -obo:RBO_00015034 multiple ion irradiation multiple ion mixed irradiation|mixed irradiation with multiple ions The process by an entity is exposed to two or more species of accelerated ions sequentially or simultaneously. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670|http://orcid.org/0000-0003-4312-9552|https://orcid.org/0000-0003-1741-8297|Mark H. Phillips The term is often used as jargon, in which cases it is taken to imply sequential exposure to multiple ion types, and not parallel exposures. (perhaps include reference to NSRL) obo:RBO_00002000 -obo:RBO_00015035 radiation field composition Radiation field composition refers to the spectrum of types and characteristics of radiation present in a specific area or region where radiation is being used, emitted, absorbed, or measured. It describes the combination of different types of particles or waves that make up the radiation in a given field. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670|http://orcid.org/0000-0003-4312-9552|https://orcid.org/0000-0003-1741-8297 obo:PATO_0000025 +obo:RBO_00015030 anthropogenic ionizing background radiation "Radiation present in an experimental or therapeutic process, other than that produced as part of that planned process." http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00000013 background radiation|ambient radiation +obo:RBO_00015031 natural ionizing background radiation Radiation originating in the terrestrial or extra-terrestrial environment. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:RBO_00000013 +obo:RBO_00015032 radiation beam composition beam composition "The types and characteristics of particles or waves that make up the radiation produced or emitted by a radiation source for use in a particular exposure context or protocol. The source may be artificial as in a particle accelerator or natural, in a controlled environment, such as a collimated beam from a radioactive isotope." http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 obo:PATO_0000025|obo:PATO_0001739 +obo:RBO_00015033 space radiation field The mix of charged and neutral atomic and subatomic particles and electromagnetic radiation suffusing a defined volume in an extraterrestrial environment at a given time. "The space radiation field in the solar system consists of particle and electromagnetic radiation from the sun, electromagnetic radiation originating from extra-solar sources, and galactic cosmic radiation." http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670 http://purl.obolibrary.org/obo/BFO_0000027 +obo:RBO_00015034 multiple ion irradiation multiple ion mixed irradiation|mixed irradiation with multiple ions The process by an entity is exposed to two or more species of accelerated ions sequentially or simultaneously. http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670|http://orcid.org/0000-0003-4312-9552|https://orcid.org/0000-0003-1741-8297|Mark H. Phillips "The term is often used as jargon, in which cases it is taken to imply sequential exposure to multiple ion types, and not parallel exposures. (perhaps include reference to NSRL)" obo:RBO_00002000 +obo:RBO_00015035 radiation field composition "Radiation field composition refers to the spectrum of types and characteristics of radiation present in a specific area or region where radiation is being used, emitted, absorbed, or measured. It describes the combination of different types of particles or waves that make up the radiation in a given field." http://orcid.org/0000-0002-5111-7263|https://orcid.org/0000-0001-9227-0670|http://orcid.org/0000-0003-4312-9552|https://orcid.org/0000-0003-1741-8297 obo:PATO_0000025 +obo:RBO_00015036 thermal neutron thermal neutron "A neutron that has (by collision with other particles) reached an energy state equal to that of its surroundings, typically on the order of 0.025 eV." https://www.nrc.gov/reading-rm/basic-ref/glossary/neutron-thermal.html "http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670" neutral particle radiation +obo:RBO_00015037 epithermal neutron epithermal neutron "a neutron with energy greater than a thermal neutron, but less than a fast neutron. The approximate energy range is 0.025-0.4 eV." https://ns.ph.liv.ac.uk/~ajb/radiometrics/glossary/epithermal_neutron.html "http://orcid.org/0000-0002-5111-7263,https://orcid.org/0000-0001-9227-0670" neutral particle radiation +obo:RBO_00015038 background radiation background radiation The ambient radiation in a defined environment emanating from natural or anthropogenic sources. "For uses involving experimentation or radiation therapy, use ""anthropogenic background radiation"" instead. Use this concept to indicate source is a mixture of anthropogenic and naturally occurring (ambient), or unknown or if the discrimination is not sought." "http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670" obo:RBO_00015000 +obo:RBO_00015039 non-ionizing background radiation non-ionizing background radiation Background radiation that does not result in ionization of target material "http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670" obo:RBO_00015038 +obo:RBO_00015040 anthropogenic non-ionizing background radiation anthropogenic non-ionizing background radiation Non-ionizing background radiation that is the result of a human planned process. "http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670" obo:RBO_00015039 +obo:RBO_00015041 natural non-ionizing background radiation natural non-ionizing background radiation Non-ionizing background radiation that is not the result of a human planned process. "http://orcid.org/0000-0002-5111-7263, https://orcid.org/0000-0001-9227-0670" obo:RBO_00015039 diff --git a/src/templates/RBO_individuals.owl b/src/templates/RBO_individuals.owl index c81cef9..06cdfc5 100644 --- a/src/templates/RBO_individuals.owl +++ b/src/templates/RBO_individuals.owl @@ -157,11 +157,11 @@ - NSRL GCRSim - The samples were irradiated using the NSRL Galactic Cosmic Ray Simulation. - The NSRL Galactic Cosmic Ray Simulation is comprised of seven different species of ion, and fourteen different energies of H and He for 33 separate beams in a single GCRSim exposure. (https://www.bnl.gov/nsrl/userguide/GCRSim.php) - NSRL GCRSim - NSRL Galactic Cosmic Ray Simulation + NSRL GCRSim + The samples were irradiated using the NSRL Galactic Cosmic Ray Simulation. + The NSRL Galactic Cosmic Ray Simulation is comprised of seven different species of ion, and fourteen different energies of H and He for 33 separate beams in a single GCRSim exposure. (https://www.bnl.gov/nsrl/userguide/GCRSim.php) + NSRL GCRSim + NSRL Galactic Cosmic Ray Simulation @@ -170,12 +170,12 @@ - NSRL - The experiment was conducted at the NSRL - A particle accelerator beamline located at Brookhaven National Laboratory - Jack Miller - NSRL - NASA Space Radiation Laboratory + NSRL + The experiment was conducted at the NSRL + A particle accelerator beamline located at Brookhaven National Laboratory + Jack Miller + NSRL + NASA Space Radiation Laboratory @@ -184,11 +184,11 @@ - HIMAC - The experiment was carried out at HIMAC - A particle accelerator at the National Institute of Radiological Sciences in Chiba, Japan - HIMAC; NIRS-HIMAC - Heavy Ion Medical Accelerator at Chiba + HIMAC + The experiment was carried out at HIMAC + A particle accelerator at the National Institute of Radiological Sciences in Chiba, Japan + HIMAC; NIRS-HIMAC + Heavy Ion Medical Accelerator at Chiba @@ -197,13 +197,13 @@ - ISS - The experiment was conducted aboard the International Space Station - An instance of an Earth-orbiting space station that went operational in the year 2000. - Jack Miller - term editor - ISS - International Space Station + ISS + The experiment was conducted aboard the International Space Station + An instance of an Earth-orbiting space station that went operational in the year 2000. + Jack Miller + term editor + ISS + International Space Station @@ -212,10 +212,10 @@ - The experiment was conducted on the Mir space station - An instance of an Earth-orbiting space station, operational from1986 to 2001, operated by the Soviet Union and later by Russia. - Wikipedia - Mir + The experiment was conducted on the Mir space station + An instance of an Earth-orbiting space station, operational from1986 to 2001, operated by the Soviet Union and later by Russia. + Wikipedia + Mir @@ -224,10 +224,10 @@ - The biological payload was carried into orbit by the Space Shuttle - An instance of a reusable spacecraft designed to carry passengers and equipment into low Earth orbit and return to Earth. Operated by the United States and operational from 1981 to 2011. - Wikipedia - Space Shuttle + The biological payload was carried into orbit by the Space Shuttle + An instance of a reusable spacecraft designed to carry passengers and equipment into low Earth orbit and return to Earth. Operated by the United States and operational from 1981 to 2011. + Wikipedia + Space Shuttle @@ -236,11 +236,11 @@ - The experiment was conducted aboard the Bion-MI satellite. - An instance of a Russian-operated Earth satellite carrying biological samples. Launched April 19, 2013 and returned to Earth May 19, 2013 - Jack Miller - Wikipedia - Bion-M1 + The experiment was conducted aboard the Bion-MI satellite. + An instance of a Russian-operated Earth satellite carrying biological samples. Launched April 19, 2013 and returned to Earth May 19, 2013 + Jack Miller + Wikipedia + Bion-M1 @@ -249,10 +249,10 @@ - The samples were flown on the Foton-M4 satellite - An instance of a Russian-operated Earth satellite carrying biological samples. Launched July 19, 2014 and returned to Earth September 1, 2014 - Wikipedia - Foton-M4 + The samples were flown on the Foton-M4 satellite + An instance of a Russian-operated Earth satellite carrying biological samples. Launched July 19, 2014 and returned to Earth September 1, 2014 + Wikipedia + Foton-M4 @@ -261,10 +261,10 @@ - The experiment was conducted on the Shenzhou-8 space station - An instance of a Chinese-operated Earth satellite carrying biological samples. Launched October 31, 2011 and returned to Earth November 17, 2011. - Wikipedia - Shenzhou-8 + The experiment was conducted on the Shenzhou-8 space station + An instance of a Chinese-operated Earth satellite carrying biological samples. Launched October 31, 2011 and returned to Earth November 17, 2011. + Wikipedia + Shenzhou-8 @@ -273,12 +273,12 @@ - US Lab - The experiment was conducted in the US Laboratory on the ISS - An instance of a module on the International Space Station, operated by the United States - Wikipedia - Destiny|US Lab - ISS-US Laboratory + US Lab + The experiment was conducted in the US Laboratory on the ISS + An instance of a module on the International Space Station, operated by the United States + Wikipedia + Destiny|US Lab + ISS-US Laboratory @@ -287,12 +287,12 @@ - JEM - The experiment was conducted on the Japanese Experiment Module - A Japanese science module for the International Space Station developed by JAXA. It is the largest single ISS module, and is attached to the Harmony module. The first two pieces of the module were launched on Space Shuttle missions STS-123 and STS-124. - Wikipedia - JEM|Kibo - ISS-Japanese Experiment Module + JEM + The experiment was conducted on the Japanese Experiment Module + A Japanese science module for the International Space Station developed by JAXA. It is the largest single ISS module, and is attached to the Harmony module. The first two pieces of the module were launched on Space Shuttle missions STS-123 and STS-124. + Wikipedia + JEM|Kibo + ISS-Japanese Experiment Module @@ -301,12 +301,12 @@ - Columbus - The experiment was conducted on the Columbus module on the ISS - An instance of a module on the International Space Station, operated by the European Space Agency. - Wikipedia - Columbus laboratory - ISS-Columbus + Columbus + The experiment was conducted on the Columbus module on the ISS + An instance of a module on the International Space Station, operated by the European Space Agency. + Wikipedia + Columbus laboratory + ISS-Columbus @@ -315,12 +315,12 @@ - Zvezda - The experiment was conducted in the Zvezda module of the ISS. - An instance of a module on the International Space Station, operated by the Russian Space Agency. - Wikipedia - Russian Service Module - ISS-Zvezda + Zvezda + The experiment was conducted in the Zvezda module of the ISS. + An instance of a module on the International Space Station, operated by the Russian Space Agency. + Wikipedia + Russian Service Module + ISS-Zvezda @@ -329,9 +329,9 @@ - The experiment was carried out at the SIS-18 accelerator. - An particle accelerator located at the GSI Helmholtz Centre for Heavy Ion Research, Darmstadt, Germay. - SIS18 + The experiment was carried out at the SIS-18 accelerator. + An particle accelerator located at the GSI Helmholtz Centre for Heavy Ion Research, Darmstadt, Germay. + SIS18 @@ -340,11 +340,11 @@ - NSRL SPESim - The samples were irradiated using the NSRL Solar Particle Event Simulation. - The NSRL SPE simulatoris based on the fluence of the August 1972 event, with an energy spectrum similar to the March 1989 event. The majority of the protons are at very low energies, below 1 MeV, and pose little to no risk to astronauts in a space craft or space suit. The SPESim begins with 50 MeV protons, which amounts to 91.66% of the total dose. Then the beam energy increments in steps of 10 MeV up to 150 MeV where 0.14% of the total dose is delivered. - NSRL SPESim - NSRL Solar Particle Event Simulation + NSRL SPESim + The samples were irradiated using the NSRL Solar Particle Event Simulation. + The NSRL SPE simulatoris based on the fluence of the August 1972 event, with an energy spectrum similar to the March 1989 event. The majority of the protons are at very low energies, below 1 MeV, and pose little to no risk to astronauts in a space craft or space suit. The SPESim begins with 50 MeV protons, which amounts to 91.66% of the total dose. Then the beam energy increments in steps of 10 MeV up to 150 MeV where 0.14% of the total dose is delivered. + NSRL SPESim + NSRL Solar Particle Event Simulation @@ -353,11 +353,11 @@ - NSRL SimGCRSim - The samples were irradiated using the NSRL Simplified Galactic Cosmic Ray Simulation. - The NSRL Simplified Galactic Cosmic Ray Simulation uses 6 beams and 5 different ions including protons at two different energies. https://www.bnl.gov/nsrl/userguide/SimGCRSim.php - NSRL SimGCRSim - NSRL Simplified Galactic Cosmic Ray Simulation + NSRL SimGCRSim + The samples were irradiated using the NSRL Simplified Galactic Cosmic Ray Simulation. + The NSRL Simplified Galactic Cosmic Ray Simulation uses 6 beams and 5 different ions including protons at two different energies. https://www.bnl.gov/nsrl/userguide/SimGCRSim.php + NSRL SimGCRSim + NSRL Simplified Galactic Cosmic Ray Simulation @@ -366,11 +366,11 @@ - KUR-HWNIF - The samples were irradiated with thermal neutrons at the KUR-HWNIF - A heavy water tank of approximately 2 m3 adjacent to the core of the Kyoto University Research Reactor (KUR), a light-water moderated tank-type reactor. - KUR-HWNIF - Kyoto University Research Reactor-Heavy Water Neutron Irradiation Facility + KUR-HWNIF + The samples were irradiated with thermal neutrons at the KUR-HWNIF + A heavy water tank of approximately 2 m3 adjacent to the core of the Kyoto University Research Reactor (KUR), a light-water moderated tank-type reactor. + KUR-HWNIF + Kyoto University Research Reactor-Heavy Water Neutron Irradiation Facility @@ -379,11 +379,11 @@ - HIRRAC - The samples were irradiated with fast neutrons at the HIRRAC. - A neutron generator at the Research Institute for Radiation Biology and Medicine, Hiroshima University (RIRBM). Monoenergetic neutrons of which energy is less than 1.3 MeV are generated by the 7Li(p,n)7 Be reaction at proton energies up to 3 MeV. - HIRRAC - Hiroshima University Radiobiological Research Accelerator + HIRRAC + The samples were irradiated with fast neutrons at the HIRRAC. + A neutron generator at the Research Institute for Radiation Biology and Medicine, Hiroshima University (RIRBM). Monoenergetic neutrons of which energy is less than 1.3 MeV are generated by the 7Li(p,n)7 Be reaction at proton energies up to 3 MeV. + HIRRAC + Hiroshima University Radiobiological Research Accelerator @@ -392,11 +392,11 @@ - BNL GRSF - The Gamma Radiation Facility known as GRSF houses a cesium-137 gamma ray source which can provide gamma rays at a variety of dose rates. The gamma source is an industry standar dJ.L. Shepherd Mark I Model 68A 137Cs ? Irradiator. The photon energy from the source is 662 keV, with a Lineal Energy Transfer (LET) in water of approximately 0.8 keV/um. (https://www.bnl.gov/nsrl/grsf/) - Jack Miller - BNL GRSF - Brookhaven National Laboratory Gamma Radiation Source Facility + BNL GRSF + The Gamma Radiation Facility known as GRSF houses a cesium-137 gamma ray source which can provide gamma rays at a variety of dose rates. The gamma source is an industry standar dJ.L. Shepherd Mark I Model 68A 137Cs ? Irradiator. The photon energy from the source is 662 keV, with a Lineal Energy Transfer (LET) in water of approximately 0.8 keV/um. (https://www.bnl.gov/nsrl/grsf/) + Jack Miller + BNL GRSF + Brookhaven National Laboratory Gamma Radiation Source Facility @@ -405,8 +405,8 @@ - http://www.theratronics.ca/PDFs/GC40_BTMB_8008GC40E_2_v112013_webSECURE.pdf - Gammacell 40 + http://www.theratronics.ca/PDFs/GC40_BTMB_8008GC40E_2_v112013_webSECURE.pdf + Gammacell 40 @@ -415,8 +415,8 @@ - https://www.crr.columbia.edu/services/ion-beam-and-neutron-core-facility - RARAF 5.5 MV microbeam + https://www.crr.columbia.edu/services/ion-beam-and-neutron-core-facility + RARAF 5.5 MV microbeam @@ -425,8 +425,8 @@ - https://www.nasa.gov/feature/ames/nasa-small-business-partnership-prepares-drone-for-30-day-science-flights - Swift HALE + https://www.nasa.gov/feature/ames/nasa-small-business-partnership-prepares-drone-for-30-day-science-flights + Swift HALE @@ -435,8 +435,8 @@ - https://www.nasa.gov/centers/armstrong/aircraft/ER-2/index.html - ER-2 + https://www.nasa.gov/centers/armstrong/aircraft/ER-2/index.html + ER-2 @@ -445,8 +445,8 @@ - https://airbornescience.nasa.gov/aircraft/WB-57_-_JSC - WB-57 + https://airbornescience.nasa.gov/aircraft/WB-57_-_JSC + WB-57 @@ -455,8 +455,8 @@ - doi: 10.2349/biij.2.1.e1 - Faxitron CP160 + doi: 10.2349/biij.2.1.e1 + Faxitron CP160 @@ -465,12 +465,12 @@ - https://precisionxray.com/x-rad/xrad-320/ - X-Rad320 + https://precisionxray.com/x-rad/xrad-320/ + X-Rad320 - + diff --git a/src/templates/RBO_nuclei.owl b/src/templates/RBO_nuclei.owl index 68ab75c..3a87bb7 100644 --- a/src/templates/RBO_nuclei.owl +++ b/src/templates/RBO_nuclei.owl @@ -45,11 +45,11 @@ - + - + - has atomic number + has atomic number @@ -59,7 +59,7 @@ - mass number + mass number @@ -79,8 +79,8 @@ - Atomic nuclei, each with 26 protons and 30 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - Fe-56 ion radiation + Atomic nuclei, each with 26 protons and 30 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + Fe-56 ion radiation @@ -89,8 +89,8 @@ - Atomic nuclei, each with 6 protons and 6 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - C-12 ion radiation + Atomic nuclei, each with 6 protons and 6 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + C-12 ion radiation @@ -99,8 +99,8 @@ - Atomic nuclei, each with 14 protons and 14 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - Si-28 ion radiation + Atomic nuclei, each with 14 protons and 14 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + Si-28 ion radiation @@ -109,8 +109,8 @@ - Atomic nuclei, each with 2 protons and 2 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - He-4 ion radiation + Atomic nuclei, each with 2 protons and 2 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + He-4 ion radiation @@ -119,8 +119,8 @@ - Atomic nuclei, each with 10 protons and 10 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - Ne-20 ion radiation + Atomic nuclei, each with 10 protons and 10 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + Ne-20 ion radiation @@ -129,8 +129,8 @@ - Atomic nuclei, each with 8 protons and 8 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - O-16 ion radiation + Atomic nuclei, each with 8 protons and 8 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + O-16 ion radiation @@ -139,8 +139,8 @@ - Atomic nuclei, each with 18 protons and 22 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - Ar-40 ion radiation + Atomic nuclei, each with 18 protons and 22 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + Ar-40 ion radiation @@ -149,8 +149,8 @@ - Atomic nuclei, each with 22 protons and 26 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - Ti-48 ion radiation + Atomic nuclei, each with 22 protons and 26 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + Ti-48 ion radiation @@ -159,8 +159,8 @@ - Atomic nuclei, each with 36 protons and 48 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - Kr-84 ion radiation + Atomic nuclei, each with 36 protons and 48 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + Kr-84 ion radiation @@ -169,8 +169,8 @@ - Atomic nuclei, each with 41 protons and 52 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - Nb-93 ion radiation + Atomic nuclei, each with 41 protons and 52 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + Nb-93 ion radiation @@ -179,8 +179,8 @@ - Atomic nuclei, each with 47 protons and 60 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - Ag-107 ion radiation + Atomic nuclei, each with 47 protons and 60 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + Ag-107 ion radiation @@ -189,8 +189,8 @@ - Atomic nuclei, each with 54 protons and 75 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - Xe-129 ion radiation + Atomic nuclei, each with 54 protons and 75 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + Xe-129 ion radiation @@ -199,8 +199,8 @@ - Atomic nuclei, each with 73 protons and 108 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - Ta-181 ion radiation + Atomic nuclei, each with 73 protons and 108 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + Ta-181 ion radiation @@ -209,8 +209,8 @@ - Atomic nuclei, each with 79 protons and 118 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - Au-197 ion radiation + Atomic nuclei, each with 79 protons and 118 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + Au-197 ion radiation @@ -219,8 +219,8 @@ - Atomic nuclei, each with 7 protons and 7 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator - N-14 ion radiation + Atomic nuclei, each with 7 protons and 7 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator + N-14 ion radiation @@ -241,9 +241,9 @@ - An atomic nucleus with 26 protons and 30 neutrons - Fe-56 ion;Fe-56 nucleus;Fe-56 - Iron-56 nucleus + An atomic nucleus with 26 protons and 30 neutrons + Fe-56 ion;Fe-56 nucleus;Fe-56 + Iron-56 nucleus @@ -252,9 +252,9 @@ - An atomic nucleus with 14 protons and 14 neutrons - Si-28 ion;Si-28 nucleus;Si-28 - Silicon-28 nucleus + An atomic nucleus with 14 protons and 14 neutrons + Si-28 ion;Si-28 nucleus;Si-28 + Silicon-28 nucleus @@ -263,9 +263,9 @@ - An atomic nucleus with 6 protons and 6 neutrons - C-12 ion;C-12 nucleus;C-12 - Carbon-12 nucleus + An atomic nucleus with 6 protons and 6 neutrons + C-12 ion;C-12 nucleus;C-12 + Carbon-12 nucleus @@ -274,9 +274,9 @@ - An atomic nucleus with 2 protons and 2 neutrons - He-4 ion;He-4 nucleus;He-4 - Helium-4 nucleus + An atomic nucleus with 2 protons and 2 neutrons + He-4 ion;He-4 nucleus;He-4 + Helium-4 nucleus @@ -285,9 +285,9 @@ - An atomic nucleus with 10 protons and 10 neutrons - Ne-20 ion;Ne-20 nucleus;Ne-20 - Neon-20 nucleus + An atomic nucleus with 10 protons and 10 neutrons + Ne-20 ion;Ne-20 nucleus;Ne-20 + Neon-20 nucleus @@ -296,9 +296,9 @@ - An atomic nucleus with 41 protons and 52 neutrons - Nb-93 ion;Nb-93 nucleus;Nb-93 - Niobium-93 nucleus + An atomic nucleus with 41 protons and 52 neutrons + Nb-93 ion;Nb-93 nucleus;Nb-93 + Niobium-93 nucleus @@ -307,9 +307,9 @@ - An atomic nucleus with 47 protons and 60 neutrons - Ag-107 ion;Ag-107 nucleus;Ag-107 - Silver-107 nucleus + An atomic nucleus with 47 protons and 60 neutrons + Ag-107 ion;Ag-107 nucleus;Ag-107 + Silver-107 nucleus @@ -318,9 +318,9 @@ - An atomic nucleus with 54 protons and 75 neutrons - Xe-129 ion;Xe-129 nucleus;Xe-129 - Xenon-129 nucleus + An atomic nucleus with 54 protons and 75 neutrons + Xe-129 ion;Xe-129 nucleus;Xe-129 + Xenon-129 nucleus @@ -329,9 +329,9 @@ - An atomic nucleus with 73 protons and 108 neutrons - Ta-181 ion;Ta-181 nucleus;Ta-181 - Tantalum-181 nucleus + An atomic nucleus with 73 protons and 108 neutrons + Ta-181 ion;Ta-181 nucleus;Ta-181 + Tantalum-181 nucleus @@ -340,9 +340,9 @@ - An atomic nucleus with 79 protons and 118 neutrons - Au-197 ion;Au-197 nucleus;Au-197 - Gold-197 nucleus + An atomic nucleus with 79 protons and 118 neutrons + Au-197 ion;Au-197 nucleus;Au-197 + Gold-197 nucleus @@ -351,9 +351,9 @@ - An atomic nucleus with 7 protons and 7 neutrons - N-14 ion;N-14 nucleus;N-14 - Nitrogen-14 nucleus + An atomic nucleus with 7 protons and 7 neutrons + N-14 ion;N-14 nucleus;N-14 + Nitrogen-14 nucleus @@ -362,9 +362,9 @@ - An atomic nucleus with 8 protons and 8 neutrons - O-16 ion;O-16 nucleus;O-16 - Oxygen-16 nucleus + An atomic nucleus with 8 protons and 8 neutrons + O-16 ion;O-16 nucleus;O-16 + Oxygen-16 nucleus @@ -373,9 +373,9 @@ - An atomic nucleus with 18 protons and 22 neutrons - Ar-40 ion;Ar-40 nucleus;Ar-40 - Argon-40 nucleus + An atomic nucleus with 18 protons and 22 neutrons + Ar-40 ion;Ar-40 nucleus;Ar-40 + Argon-40 nucleus @@ -384,9 +384,9 @@ - An atomic nucleus with 22 protons and 26 neutrons - Ti-48 ion;Ti-48 nucleus;Ti-48 - Titanium-48 nucleus + An atomic nucleus with 22 protons and 26 neutrons + Ti-48 ion;Ti-48 nucleus;Ti-48 + Titanium-48 nucleus @@ -395,9 +395,9 @@ - An atomic nucleus with 36 protons and 48 neutrons - Kr-84 ion;Kr-84 nucleus;Kr-84 - Krypton-84 nucleus + An atomic nucleus with 36 protons and 48 neutrons + Kr-84 ion;Kr-84 nucleus;Kr-84 + Krypton-84 nucleus @@ -409,5 +409,5 @@ - +