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Refresh imports #1849

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06adada
Refresh imports
sebastianduesing Jan 16, 2025
e74be5b
Update COB import
sebastianduesing Jan 27, 2025
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2 changes: 1 addition & 1 deletion src/ontology/OntoFox_outputs/CL_imports.owl
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000066"/>
<obo:IAO_0000111>mesothelial cell</obo:IAO_0000111>
<obo:IAO_0000115>A flattened epithelial cell of mesenchymal origin that lines the serous cavity.</obo:IAO_0000115>
<obo:IAO_0000115>A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body&apos;s serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/cl.owl"/>
<rdfs:label>mesothelial cell</rdfs:label>
</owl:Class>
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4 changes: 2 additions & 2 deletions src/ontology/OntoFox_outputs/COB_imports.owl
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000080">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111>complex of molecular entities</obo:IAO_0000111>
<obo:IAO_0000111>complex of molecules</obo:IAO_0000111>
<obo:IAO_0000115>A complex of two or more molecular entities that are not covalently bound.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/cob.owl"/>
<rdfs:label>complex of molecular entities</rdfs:label>
<rdfs:label>complex of molecules</rdfs:label>
</owl:Class>
</rdf:RDF>

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9 changes: 4 additions & 5 deletions src/ontology/OntoFox_outputs/GO_imports.owl
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<!-- http://purl.obolibrary.org/obo/GO_0000785 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0000785">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0032991"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0005575"/>
<obo:IAO_0000111>chromatin</obo:IAO_0000111>
<obo:IAO_0000115>The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
Expand Down Expand Up @@ -111,7 +111,6 @@
<!-- http://purl.obolibrary.org/obo/GO_0001172 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0001172">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0009987"/>
<obo:IAO_0000111>RNA-templated transcription</obo:IAO_0000111>
<obo:IAO_0000115>The synthesis of an RNA transcript from an RNA template.</obo:IAO_0000115>
Expand Down Expand Up @@ -351,7 +350,7 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0003964">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0003824"/>
<obo:IAO_0000111>RNA-directed DNA polymerase activity</obo:IAO_0000111>
<obo:IAO_0000115>Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3&apos;- end of a DNA strand by one deoxynucleotide at a time.</obo:IAO_0000115>
<obo:IAO_0000115>Catalysis of the reaction: a 2&apos;-deoxyribonucleoside 5&apos;-triphosphate + DNA(n) = diphosphate + DNA(n+1); RNA-template-directed extension of the 3&apos;-end of a DNA strand by one deoxynucleotide at a time.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
<rdfs:label>RNA-directed DNA polymerase activity</rdfs:label>
</owl:Class>
Expand All @@ -375,7 +374,7 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0003997">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0003824"/>
<obo:IAO_0000111>acyl-CoA oxidase activity</obo:IAO_0000111>
<obo:IAO_0000115>Catalysis of the reaction: acyl-CoA + O2 = trans-2,3-dehydroacyl-CoA + hydrogen peroxide.</obo:IAO_0000115>
<obo:IAO_0000115>Catalysis of the reaction: a 2,3-saturated acyl-CoA + O2 = a (2E)-enoyl-CoA + H2O2.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
<rdfs:label>acyl-CoA oxidase activity</rdfs:label>
</owl:Class>
Expand Down Expand Up @@ -1431,7 +1430,7 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0034061">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0003824"/>
<obo:IAO_0000111>DNA polymerase activity</obo:IAO_0000111>
<obo:IAO_0000115>Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3&apos;hydroxyl group.</obo:IAO_0000115>
<obo:IAO_0000115>Catalysis of the reaction: a 2&apos;-deoxyribonucleoside 5&apos;-triphosphate + DNA(n) = diphosphate + DNA(n+1).</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
<rdfs:label>DNA polymerase activity</rdfs:label>
</owl:Class>
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2 changes: 2 additions & 0 deletions src/ontology/OntoFox_outputs/NCBITaxon_imports.owl
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<obo:IAO_0000118>Epstein-Barr virus</obo:IAO_0000118>
<obo:IAO_0000118>Epstein-Barr virus EBV</obo:IAO_0000118>
<obo:IAO_0000118>Human herpesvirus 4</obo:IAO_0000118>
<obo:IAO_0000118>Human herpesvirus 4 (Epstein-Barr virus)</obo:IAO_0000118>
<obo:IAO_0000118>Human herpesvirus type 4</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<rdfs:label>human gammaherpesvirus 4</rdfs:label>
Expand Down Expand Up @@ -291,6 +292,7 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_2732406">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2559587"/>
<obo:IAO_0000111>Kitrinoviricota</obo:IAO_0000111>
<obo:IAO_0000118>Tombus-Noda-like virus sp.</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<rdfs:label>Kitrinoviricota</rdfs:label>
</owl:Class>
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58 changes: 45 additions & 13 deletions src/ontology/OntoFox_outputs/PATO_imports.owl
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<!-- http://purl.obolibrary.org/obo/BFO_0000020 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000020">
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/PATO_0000001 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:IAO_0000111>quality</obo:IAO_0000111>
<obo:IAO_0000115>A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
<rdfs:label>quality</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/PATO_0000011 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000011">
Expand Down Expand Up @@ -107,7 +127,7 @@
<!-- http://purl.obolibrary.org/obo/PATO_0000033 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000033">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0002182"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0000070"/>
<obo:IAO_0000111>concentration of</obo:IAO_0000111>
<obo:IAO_0000115>A quality inhering in a substance by virtue of the amount of the bearer&apos;s there is mixed with another substance.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
Expand Down Expand Up @@ -140,6 +160,18 @@



<!-- http://purl.obolibrary.org/obo/PATO_0000070 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000070">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0103000"/>
<obo:IAO_0000111>amount</obo:IAO_0000111>
<obo:IAO_0000115>The number of entities of this type that are part of the whole organism.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
<rdfs:label>amount</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/PATO_0000117 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000117">
Expand Down Expand Up @@ -896,18 +928,6 @@



<!-- http://purl.obolibrary.org/obo/PATO_0002182 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0002182">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0001241"/>
<obo:IAO_0000111>molecular quality</obo:IAO_0000111>
<obo:IAO_0000115>A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
<rdfs:label>molecular quality</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/PATO_0002198 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0002198">
Expand Down Expand Up @@ -1001,6 +1021,18 @@
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
<rdfs:label>quality of interaction of a substance with electromagnetic radiation</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/PATO_0103000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0103000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0000001"/>
<obo:IAO_0000111>quantitative</obo:IAO_0000111>
<obo:IAO_0000115>A quality of an entity that can be represented numerically, including anything that can be counted, measured, or given a numerical value.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
<rdfs:label>quantitative</rdfs:label>
</owl:Class>
</rdf:RDF>


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4 changes: 2 additions & 2 deletions src/ontology/templates/assays.tsv
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Expand Up @@ -107,7 +107,7 @@ OBI:0001030 RNASE T1 structure mapping assay ready for release single nucleotid
OBI:0001035 Nuclease S1 structure mapping assay ready for release single nucleotide resolution mapping assay using Nuclease S1 A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe. RNA ontology PMID:363143 Philippe Rocca-Serra subclass single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing RNA extract nuclease S1 secondary structure of sequence macromolecule
OBI:0001038 Ruthenium structure mapping assay ready for release A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe RNA Ontology PMID:3016894 Philippe Rocca-Serra subclass single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing ('deoxyribonucleic acid' or 'ribonucleic acid') measurement datum secondary structure of RNA molecule
OBI:0001039 inline probing RNA structure mapping assay ready for release A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity RNA ontology PMID:10573122 and PMID: 18369975 Philippe Rocca-Serra subclass single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing RNA extract measurement datum secondary structure of RNA molecule
OBI:0001145 3D structure determination of bound molecular complex assay A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration. IEDB Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody. IEDB equivalent 3D molecular structure determination assay 3D structural organization datum complex of molecular entities
OBI:0001145 3D structure determination of bound molecular complex assay A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration. IEDB Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody. IEDB equivalent 3D molecular structure determination assay 3D structural organization datum complex of molecules
OBI:0001146 binding assay An assay with the objective to characterize the disposition of two or more material entities to form a complex. Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. Bjoern Peters|Randi Vita|Jason Greenbaum subclass assay binding datum binding
OBI:0001158 age determination assay metadata complete age measurement assay An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted). OBI group Alan Ruttenberg This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. subclass assay organism age measurement datum
OBI:0001170 reverse transcription polymerase chain reaction assay metadata complete An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. Penn Group Chris Stoeckert|Jie Zheng subclass assay reverse transcribed polymerase chain reaction RNA extract RNA extract information content entity gene expression
Expand Down Expand Up @@ -486,7 +486,7 @@ OBI:0003112 Olink assay A proximity extension assay that uses quantitative po
OBI:0003113 proximity extension assay An analyte assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of an analyte or analyte complex. Bjoern Peters Bjoern Peters|Randi Vita|Hector Guzman-Orozco ImmPort https://github.com/obi-ontology/obi/issues/1308 subclass analyte assay polymerase chain reaction assay
OBI:0003115 antigen detection by cytometric bead array assay A cytometric bead array assay in which a series of beads are coated with antibodies specific to antigens of interest. Antigens of interest attach to antibodies on the beads. Fluorescent labeled secondary antibodies are used to detect the antigens of interest. CMI-PB CMI-PB https://github.com/obi-ontology/obi/issues/1399 subclass cytometric bead array assay antigen
OBI:0003116 antibody detection by cytometric bead array assay A cytometric bead array assay that detects antigen-specific antibodies. In the assay a series of beads are coated with antigens which capture antibodies specific to the antigens. Fluorescent labeled secondary antibodies are used to detect the antibodies of interest. CMI-PB CMI-PB https://github.com/obi-ontology/obi/issues/1399 subclass cytometric bead array assay immunoglobulin complex
OBI:0003117 3D molecular structure determination assay An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex. IEDB Bjoern Peters|Hector Guzman-Orozco https://github.com/obi-ontology/obi/issues/1380 equivalent 3D structure determination assay 3D structural organization datum ('molecular entity' or 'complex of molecular entities')
OBI:0003117 3D molecular structure determination assay An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex. IEDB Bjoern Peters|Hector Guzman-Orozco https://github.com/obi-ontology/obi/issues/1380 equivalent 3D structure determination assay 3D structural organization datum ('molecular entity' or 'complex of molecules')
OBI:0003118 electron-microscopy 3D molecular structure determination assay A 3D molecular structure determination assay that uses electron microscopy imaging. IEDB Bjoern Peters|Hector Guzman-Orozco https://github.com/obi-ontology/obi/issues/1380 subclass 3D molecular structure determination assay electron microscope
OBI:0003122 3D cell structure determination assay A 3D structure determination assay that determines the 3-dimensional configuration of a cell. Hector Guzman-Orozco|Patrick Ray Hector Guzman-Orozco|Patrick Ray https://github.com/obi-ontology/obi/issues/1364 equivalent 3D structure determination assay cell 3D structural organization datum cell
OBI:0003123 3D neural cell structure determination assay A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell. Hector Guzman-Orozco|Patrick Ray Hector Guzman-Orozco|Patrick Ray Allen Institute for Brain Science https://github.com/obi-ontology/obi/issues/1364 equivalent 3D cell structure determination assay 3D structural organization datum neural cell
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