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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -10,6 +10,9 @@ author: | |
| name: OBO Technical WG | ||
| plugins: | ||
| - jekyll-sitemap | ||
| - jekyll-feed | ||
| feed: | ||
| disable_in_development: true | ||
| ## --Anything above this line can be edited in _config_header.yml -- | ||
| ## --Everything below this line automatically generated in _config.yml -- | ||
| ontologies: | ||
|
|
@@ -796,9 +799,9 @@ ontologies: | |
| label: Alexander Diehl | ||
| orcid: 0000-0001-9990-8331 | ||
| dependencies: | ||
| - id: chebi | ||
| - id: go | ||
| - id: ncbitaxon | ||
| - id: omo | ||
| - id: pato | ||
| - id: pr | ||
| - id: ro | ||
|
|
@@ -826,29 +829,57 @@ ontologies: | |
| ontology_purl: http://purl.obolibrary.org/obo/cl.owl | ||
| title: Main CL OWL edition | ||
| uses: | ||
| - uberon | ||
| - chebi | ||
| - go | ||
| - pr | ||
| - pato | ||
| - ncbitaxon | ||
| - omo | ||
| - pato | ||
| - pr | ||
| - ro | ||
| - uberon | ||
| - derived_from: cl.owl | ||
| description: Complete ontology, plus inter-ontology axioms, and imports modules | ||
| merged in | ||
| format: obo | ||
| id: cl.obo | ||
| ontology_purl: http://purl.obolibrary.org/obo/cl.obo | ||
| title: CL obo format edition | ||
| - derived_from: cl.owl | ||
| description: Complete ontology, plus inter-ontology axioms, and imports modules | ||
| merged in | ||
| format: json | ||
| id: cl.json | ||
| ontology_purl: http://purl.obolibrary.org/obo/cl.json | ||
| title: CL OBOGraph-JSON format edition | ||
| - description: Basic version, no inter-ontology axioms | ||
| format: owl-rdf/xml | ||
| id: cl/cl-basic.owl | ||
| ontology_purl: http://purl.obolibrary.org/obo/cl/cl-basic.owl | ||
| title: Basic CL | ||
| - description: Basic version, no inter-ontology axioms | ||
| format: obo | ||
| id: cl/cl-basic.obo | ||
| ontology_purl: http://purl.obolibrary.org/obo/cl/cl-basic.obo | ||
| title: Basic CL | ||
| title: Basic CL (OBO version) | ||
| - description: Basic version, no inter-ontology axioms | ||
| format: json | ||
| id: cl/cl-basic.json | ||
| ontology_purl: http://purl.obolibrary.org/obo/cl/cl-basic.json | ||
| title: Basic CL (OBOGraph-JSON version) | ||
| - description: complete CL but with no imports or external axioms | ||
| format: owl-rdf/xml | ||
| id: cl/cl-base.owl | ||
| ontology_purl: http://purl.obolibrary.org/obo/cl/cl-base.owl | ||
| title: CL base module | ||
| - description: complete CL but with no imports or external axioms | ||
| format: obo | ||
| id: cl/cl-base.obo | ||
| ontology_purl: http://purl.obolibrary.org/obo/cl/cl-base.obo | ||
| title: CL base module (OBO version) | ||
| - description: complete CL but with no imports or external axioms | ||
| format: json | ||
| id: cl/cl-base.json | ||
| ontology_purl: http://purl.obolibrary.org/obo/cl/cl-base.json | ||
| title: CL base module (OBOGraph-JSON version) | ||
| publications: | ||
| - id: https://www.ncbi.nlm.nih.gov/pubmed/27377652 | ||
| title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology | ||
|
|
@@ -894,6 +925,20 @@ ontologies: | |
| Program.' | ||
| type: annotation | ||
| user: https://hubmapconsortium.org/ | ||
| - description: The single-cell transcriptomics platform CZ CELLxGENE uses CL to | ||
| annotate all cell types. All datasets on CellXGene are annotated according to | ||
| a standard schema that specifies the use of CL to record Cell Type. | ||
| examples: | ||
| - description: A CELLxGENE Cell Guide entry for 'luminal adaptive secretory precursor | ||
| cell of mammary gland', which includes the CL ID (CL:4033057), CL definition | ||
| and a visualizer of CL hierarchy | ||
| url: https://cellxgene.cziscience.com/cellguide/CL:4033057 | ||
| publications: | ||
| - id: https://doi.org/10.1101/2021.04.05.438318 | ||
| title: 'CELLxGENE: a performant, scalable exploration platform for high dimensional | ||
| sparse matrices' | ||
| type: annotation | ||
| user: https://cellxgene.cziscience.com/ | ||
| - description: The Human Cell Atlas (HCA) is an international group of researchers | ||
| using a combination of these new technologies to create cellular reference maps. | ||
| The HCA use CL to annotate cells in their reference maps. | ||
|
|
@@ -2334,9 +2379,9 @@ ontologies: | |
| id: foodon | ||
| layout: ontology_detail | ||
| license: | ||
| label: CC BY 3.0 | ||
| label: CC BY 4.0 | ||
| logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png | ||
| url: http://creativecommons.org/licenses/by/3.0/ | ||
| url: http://creativecommons.org/licenses/by/4.0/ | ||
| ontology_purl: http://purl.obolibrary.org/obo/foodon.owl | ||
| preferredPrefix: FOODON | ||
| products: | ||
|
|
@@ -2357,6 +2402,27 @@ ontologies: | |
| - food | ||
| title: Food Ontology | ||
| tracker: https://github.com/FoodOntology/foodon/issues/ | ||
| usages: | ||
| - description: FoodData Central nutrition database web portal provided by USDA Agricultural | ||
| Research Service. | ||
| examples: | ||
| - description: An entry for 'Apples, fuji, with skin, raw' from the FoodData Central | ||
| nutrition database which is annotated with the term FOODON:00002862. | ||
| url: https://fdc.nal.usda.gov/fdc-app.html#/food-details/1750340/attributes | ||
| user: https://fdc.nal.usda.gov/ | ||
| - description: FDA GenomeTrackr surveillance program for reporting foodborne pathogen | ||
| biosamples. | ||
| examples: | ||
| - description: An entry from NCBI Biosample that describes a *Samonella enterica* | ||
| sample extracted from Chicken and annotated with the term FOODON:03411457. | ||
| url: https://www.ncbi.nlm.nih.gov/biosample/SAMN03455272 | ||
| user: https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network | ||
| - description: Wiki database consolidating over 30 global food composition databases. | ||
| examples: | ||
| - description: An entry from WikiFCD that describes Walnuts and is annotated with | ||
| the term FOODON:03301364. | ||
| url: https://wikifcd.wikibase.cloud/wiki/Item:Q568877 | ||
| user: https://wikifcd.wikibase.cloud/wiki/Main_Page | ||
| - activity_status: active | ||
| contact: | ||
| email: [email protected] | ||
|
|
@@ -3765,32 +3831,36 @@ ontologies: | |
| ontology_purl: http://purl.obolibrary.org/obo/mondo.owl | ||
| preferredPrefix: MONDO | ||
| products: | ||
| - description: Complete ontology. Uses MONDO IDs. Imports merged. The original mondo.owl | ||
| without merged imports and with equivalence axioms can now be obtained from | ||
| the release pages and is called mondo-with-equivalents. | ||
| - description: Complete ontology with merged imports. | ||
| format: owl-rdf/xml | ||
| id: mondo.owl | ||
| is_canonical: true | ||
| ontology_purl: http://purl.obolibrary.org/obo/mondo.owl | ||
| title: Main OWL edition | ||
| title: Mondo OWL edition | ||
| - derived_from: mondo.owl | ||
| description: As OWL. xrefs can be used as proxy for equivalence. Uses Mondo IDs. | ||
| description: OBO serialization of mondo.owl. | ||
| format: obo | ||
| id: mondo.obo | ||
| ontology_purl: http://purl.obolibrary.org/obo/mondo.obo | ||
| title: obo-format edition | ||
| title: Mondo OBO Format edition | ||
| - derived_from: mondo.owl | ||
| description: Equivalent to the OWL edition. | ||
| description: Obographs serialization of mondo.owl. | ||
| format: obo | ||
| id: mondo.json | ||
| ontology_purl: http://purl.obolibrary.org/obo/mondo.json | ||
| title: json edition | ||
| title: Mondo JSON edition | ||
| - description: The main ontology plus axioms connecting to select external ontologies, | ||
| excluding the external ontologies themselves | ||
| format: owl | ||
| id: mondo/mondo-base.owl | ||
| ontology_purl: http://purl.obolibrary.org/obo/mondo/mondo-base.owl | ||
| title: Mondo Base Module | ||
| title: Mondo Base Release | ||
| - description: The main ontology classes and their hierarchies, without references | ||
| to external terms. | ||
| format: owl | ||
| id: mondo/mondo-simple.owl | ||
| ontology_purl: http://purl.obolibrary.org/obo/mondo/mondo-simple.owl | ||
| title: Mondo Simple Release | ||
| publications: | ||
| - id: https://www.medrxiv.org/content/10.1101/2022.04.13.22273750 | ||
| title: 'Mondo: Unifying diseases for the world, by the world' | ||
|
|
@@ -3802,7 +3872,6 @@ ontologies: | |
| label: Metazoa | ||
| title: Mondo Disease Ontology | ||
| tracker: https://github.com/monarch-initiative/mondo/issues | ||
| twitter: MonarchInit | ||
| usages: | ||
| - description: Mondo is used by the Monarch Initiative for disease annotations. | ||
| examples: | ||
|
|
@@ -3881,7 +3950,7 @@ ontologies: | |
| title: Monarch Phenotype Page | ||
| url: http://monarchinitiative.org/phenotype/MP:0000001 | ||
| contact: | ||
| email: [email protected] | ||
| email: [email protected] | ||
| github: sbello | ||
| label: Sue Bello | ||
| orcid: 0000-0003-4606-0597 | ||
|
|
@@ -5582,7 +5651,7 @@ ontologies: | |
| github: jaiswalp | ||
| label: Pankaj Jaiswal | ||
| orcid: 0000-0002-1005-8383 | ||
| depicted_by: https://github.com/Planteome/plant-ontology/blob/master/Planteome_profile.jpg | ||
| depicted_by: https://raw.githubusercontent.com/Planteome/plant-ontology/refs/heads/master/Planteome_profile.jpg | ||
| description: The Plant Ontology is a structured vocabulary and database resource | ||
| that links plant anatomy, morphology and growth and development to plant genomics | ||
| data. | ||
|
|
@@ -5737,14 +5806,22 @@ ontologies: | |
| ontology_purl: http://purl.obolibrary.org/obo/pr.owl | ||
| preferredPrefix: PR | ||
| products: | ||
| - description: PRO after reasoning has been applied, OWL format. | ||
| - description: PRO after reasoning has been applied, OWL format. Add '.gz' for compressed. | ||
| id: pr.owl | ||
| ontology_purl: http://purl.obolibrary.org/obo/pr.owl | ||
| title: pro_reasoned.owl | ||
| - description: PRO after reasoning has been applied, OBO format. | ||
| id: pr.obo | ||
| ontology_purl: http://purl.obolibrary.org/obo/pr.obo | ||
| title: pro_reasoned.obo | ||
| - description: PRO without reasoning applied, OWL format. Add '.gz' for compressed. | ||
| id: pr-asserted.owl | ||
| ontology_purl: http://purl.obolibrary.org/obo/pr-asserted.owl | ||
| title: pro_nonreasoned.owl | ||
| - description: PRO without reasoning applied, OBO format. | ||
| id: pr-asserted.obo | ||
| ontology_purl: http://purl.obolibrary.org/obo/pr-asserted.obo | ||
| title: pro_nonreasoned.obo | ||
| publications: | ||
| - id: https://www.ncbi.nlm.nih.gov/pubmed/27899649 | ||
| title: 'Protein Ontology (PRO): enhancing and scaling up the representation of | ||
|
|
@@ -6261,10 +6338,10 @@ ontologies: | |
| tracker: https://github.com/obophenotype/spider-ontology/issues | ||
| - activity_status: active | ||
| contact: | ||
| email: alejandra.gonzalez.beltran@gmail.com | ||
| github: agbeltran | ||
| label: Alejandra Gonzalez-Beltran | ||
| orcid: 0000-0003-3499-8262 | ||
| email: proccaserra@gmail.com | ||
| github: proccaserra | ||
| label: Philippe Rocca-Serra | ||
| orcid: 0000-0001-9853-5668 | ||
| depicted_by: https://raw.githubusercontent.com/ISA-tools/stato/dev/images/stato-logo-3.png | ||
| description: STATO is a general-purpose STATistics Ontology. Its aim is to provide | ||
| coverage for processes such as statistical tests, their conditions of application, | ||
|
|
@@ -6287,11 +6364,43 @@ ontologies: | |
| products: | ||
| - id: stato.owl | ||
| ontology_purl: http://purl.obolibrary.org/obo/stato.owl | ||
| publications: | ||
| - id: https://www.ncbi.nlm.nih.gov/pubmed/31831744 | ||
| title: Experiment design driven FAIRification of omics data matrices, an exemplar | ||
| - id: https://www.ncbi.nlm.nih.gov/pubmed/32109232 | ||
| title: Semantic concept schema of the linear mixed model of experimental observations | ||
| repository: https://github.com/ISA-tools/stato | ||
| tags: | ||
| - statistics | ||
| title: The Statistical Methods Ontology | ||
| tracker: https://github.com/ISA-tools/stato/issues | ||
| usages: | ||
| - description: struct (Statistics in R using Class-based Templates), Struct integrates | ||
| with the STATistics Ontology to ensure consistent reporting and maximizes semantic | ||
| interoperability | ||
| publications: | ||
| - id: https://www.ncbi.nlm.nih.gov/pubmed/33325493 | ||
| title: 'struct: an R/Bioconductor-based framework for standardized metabolomics | ||
| data analysis and beyond' | ||
| type: annotation | ||
| user: https://bioconductor.org/packages/release/bioc/html/struct.html | ||
| - description: Scientific Evidence Code System (SEVCO) on the FEvIR platform. The | ||
| FEvIR Platform includes many Builder Tools to create FHIR Resources without | ||
| requiring expertise in FHIR or JSON, and Converter Tools to convert structured | ||
| data to FHIR Resources | ||
| publications: | ||
| - id: https://www.ncbi.nlm.nih.gov/pubmed/33486066 | ||
| title: 'Making science computable: Developing code systems for statistics, study | ||
| design, and risk of bias' | ||
| type: annotation | ||
| user: https://fevir.net/resources/CodeSystem/27270#STATO:0000039 | ||
| - description: OBCS | ||
| publications: | ||
| - id: https://www.ncbi.nlm.nih.gov/pubmed/27627881 | ||
| title: The Ontology of Biological and Clinical Statistics (OBCS) for standardized | ||
| and reproducible statistical analysis | ||
| type: annotation | ||
| user: https://github.com/obcs/obcs | ||
| - activity_status: active | ||
| contact: | ||
| email: [email protected] | ||
|
|
@@ -6865,10 +6974,10 @@ ontologies: | |
| path: archive/ontology | ||
| source_url: http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip | ||
| contact: | ||
| email: [email protected] | ||
| github: nicolevasilevsky | ||
| label: Nicole Vasilevsky | ||
| orcid: 0000-0001-5208-3432 | ||
| email: [email protected] | ||
| github: jamesamcl | ||
| label: James McLaughlin | ||
| orcid: 0000-0002-8361-2795 | ||
| description: The uPheno ontology integrates multiple phenotype ontologies into a | ||
| unified cross-species phenotype ontology. | ||
| domain: phenotype | ||
|
|
@@ -6895,22 +7004,25 @@ ontologies: | |
| page: https://github.com/obophenotype/upheno/tree/master/hp-mp | ||
| title: uPheno MP-HP equivalence axioms | ||
| - description: The new version of uPheno, along with species independent phenotypes | ||
| amd additional phenotype relations. The ontology is still in Beta status, but | ||
| and additional phenotype relations. The ontology is still in Beta status, but | ||
| we recommend users to migrate their infrastructures to uPheno 2 as uPheno 1 | ||
| is no longer actively maintained. | ||
| id: upheno/v2/upheno.owl | ||
| ontology_purl: http://purl.obolibrary.org/obo/upheno/v2/upheno.owl | ||
| page: https://github.com/obophenotype/upheno-dev | ||
| title: uPheno 2 | ||
| publications: | ||
| - id: https://doi.org/10.1101/2024.09.18.613276 | ||
| title: 'The Unified Phenotype Ontology (uPheno): A framework for cross-species | ||
| integrative phenomics' | ||
| - id: https://zenodo.org/record/2382757 | ||
| title: Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims | ||
| to reconcile logical definitions across species | ||
| - id: https://zenodo.org/record/3352149 | ||
| title: 'Phenotype Ontologies Traversing All The Organisms (POTATO) workshop: 2nd | ||
| edition' | ||
| repository: https://github.com/obophenotype/upheno | ||
| title: Unified phenotype ontology (uPheno) | ||
| title: Unified Phenotype Ontology (uPheno) | ||
| tracker: https://github.com/obophenotype/upheno/issues | ||
| usages: | ||
| - description: uPheno is used by the Monarch Initiative for cross-species inference. | ||
|
|
||
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