diff --git a/_config.yml b/_config.yml index c2f4ca2d0..177fc95be 100644 --- a/_config.yml +++ b/_config.yml @@ -342,14 +342,14 @@ ontologies: information from clinical records, via semantic modeling of the processes that generated the data. This makes the discovery of previously unappreciated relations between the data possible for research and for operational tasks. - example: + examples: - description: CYP2C1*2/*2 MI patient taking Clopidogrel url: https://github.com/PennTURBO/Turbo-Documentation/blob/master/IBI_CIC_TURBO_MAM_20190102.pdf user: http://upibi.org/turbo/ - description: The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain. ECO uses OBI to logically describe how the evidence arises from an investigation. - example: + examples: - description: rapid amplification of cDNA ends polymerase chain reaction evidence url: http://purl.obolibrary.org/obo/ECO_0001820 user: http://evidenceontology.org/ @@ -400,8 +400,11 @@ ontologies: - description: PATO is used by the Human Phenotype Ontology (HPO) for logical definitions of phenotypes that facilitate cross-species integration. examples: - - url: https://www.ebi.ac.uk/ols/ontologies/hp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0011017&viewMode=All&siblings=false - reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324074/ + - description: An abnormality in a cellular process. + url: https://www.ebi.ac.uk/ols/ontologies/hp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0011017&viewMode=All&siblings=false + publications: + - id: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324074/ + title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources type: annotation user: https://hpo.jax.org/app/ - activity_status: active @@ -467,11 +470,13 @@ ontologies: user: http://planteome.org/ - description: Maize CELL genomics DB uses PO to annotate images examples: - - url: http://maize.jcvi.org/cellgenomics/geneDB_list.php?filter=3 + - description: LhG4 Promoter Drivers + url: http://maize.jcvi.org/cellgenomics/geneDB_list.php?filter=3 user: http://maize.jcvi.org/ - description: MaizeGDB uses PO for annotation of genes examples: - - url: http://maizegdb.org/gene_center/gene/GRMZM5G863962 + - description: Introduced in gene model set 5b in assembly version RefGen_v2. + url: http://maizegdb.org/gene_center/gene/GRMZM5G863962 user: http://maizegdb.org/ - description: Gramene uses PO for the annotation of plant genes examples: @@ -826,7 +831,7 @@ ontologies: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall - description: An ontology for respresenting spatial concepts, anatomical axes, gradients, + description: An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces domain: anatomy homepage: https://github.com/obophenotype/biological-spatial-ontology @@ -1039,6 +1044,27 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/cido.owl title: Coronavirus Infectious Disease Ontology tracker: https://github.com/cido-ontology/cido/issues +- activity_status: active + contact: + email: bgee@sib.swiss + github: fbastian + label: Frederic Bastian + description: An ontology to capture confidence information about annotations. + homepage: https://github.com/BgeeDB/confidence-information-ontology + id: cio + layout: ontology_detail + license: + label: CC0 + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png + url: https://creativecommons.org/publicdomain/zero/1.0/ + ontology_purl: http://purl.obolibrary.org/obo/cio.owl + products: + - id: cio.owl + ontology_purl: http://purl.obolibrary.org/obo/cio.owl + - id: cio.obo + ontology_purl: http://purl.obolibrary.org/obo/cio.obo + title: Confidence Information Ontology + tracker: https://github.com/BgeeDB/confidence-information-ontology - activity_status: active build: checkout: git clone https://github.com/obophenotype/cell-ontology.git @@ -1117,7 +1143,9 @@ ontologies: research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The ENCODE DCC users Uberon to annotate samples - reference: https://doi.org/10.1093/database/bav010 + publications: + - id: https://doi.org/10.1093/database/bav010 + title: Ontology application and use at the ENCODE DCC seeAlso: https://www.biosharing.org/biodbcore-000034 type: annotation user: https://www.encodeproject.org/ @@ -1498,7 +1526,7 @@ ontologies: tracker: https://github.com/FlyBase/drosophila-phenotype-ontology/issues usages: - description: FlyBase uses dpo for phenotype data annotation in Drosophila - example: + examples: - description: alleles and constructs annotated to pupal lethal in FlyBase url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0002030 user: http://flybase.org @@ -1634,8 +1662,15 @@ ontologies: - description: ECO is used by the Monarch Initiative for evidence types for disease to phenotype annotations. examples: - - url: https://monarchinitiative.org/phenotype/HP%3A0001300#diseases - reference: https://academic.oup.com/nar/article/45/D1/D712/2605791 + - description: 'Parkinsonism: Characteristic neurologic anomaly resulting form + degeneration of dopamine-generating cells in the substantia nigra, a region + of the midbrain, characterized clinically by shaking, rigidity, slowness of + movement and difficulty with walking and gait.' + url: https://monarchinitiative.org/phenotype/HP%3A0001300#disease + publications: + - id: https://academic.oup.com/nar/article/45/D1/D712/2605791 + title: 'The Monarch Initiative: an integrative data and analytic platform connecting + phenotypes to genotypes across species' type: annotation user: https://monarchinitiative.org/ - activity_status: active @@ -1658,7 +1693,8 @@ ontologies: - id: uberon - id: po - id: iao - description: An ontology to provide core semantics for ecological entities. + description: Ecocore is a community ontology for the concise and controlled description + of ecological traits of organisms. domain: ecological functions, ecological interactions homepage: https://github.com/EcologicalSemantics/ecocore id: ecocore @@ -1848,20 +1884,35 @@ ontologies: title: Environment Ontology tracker: https://github.com/EnvironmentOntology/envo/issues/ usages: + - description: describing species habitats + examples: + - description: Pseudobarbus burchelli (Tradou Redfin) is a species of bony fishes + in the family Cyprinidae. They are associated with freshwater habitat. Individuals + can grow to 13.5 cm. They have sexual reproduction. + url: http://eol.org/pages/211700/data + type: data-annotation + user: http://eol.org + - description: describing stomach contents + type: data-annotation + user: http://globalbioticinteractions.org + - description: annotating datasets in data repositories + seeAlso: http://blogs.nature.com/scientificdata/2015/12/17/isa-explorer/ + type: dataset-description + user: http://www.nature.com/sdata/ - description: Samples collected during Tara Oceans expedition are annotated with ENVO - example: + examples: - description: Sample collected during the Tara Oceans expedition (2009-2013) at station TARA_004 (latitudeN=36.5533, longitudeE=-6.5669) url: https://www.ebi.ac.uk/metagenomics/projects/ERP001736/samples/ERS487899 user: http://oceans.taraexpeditions.org/en/ - description: Annotation of habitats of microbes - example: + examples: - description: Annotation of habitat of Pseudovibrio sp. FO-BEG1 to marine environment url: https://www.ncbi.nlm.nih.gov/nuccore/NC_016642 user: https://www.ncbi.nlm.nih.gov/ - description: Annotation and semantic search over microbial data sets - example: + examples: - description: Example metadata of a sample of marine water near Lisboa, taken as part of the Ocean Sampling Day Project (https://www.microb3.eu/osd.html). ENVO is used for the fields environmental feature, material, and biome. @@ -1921,6 +1972,7 @@ ontologies: url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/exo.owl page: http://ctdbase.org/downloads/#exposures + preferredPrefix: ExO products: - id: exo.owl ontology_purl: http://purl.obolibrary.org/obo/exo.owl @@ -2038,13 +2090,15 @@ ontologies: tracker: http://purl.obolibrary.org/obo/fbbt/tracker usages: - description: VFB uses FBbt to annotate brain images - example: + examples: + - description: Ring neuron R2 in VFB + url: http://www.virtualflybrain.org/site/stacks/index.htm?id=FBbt_00003651 - description: genes expressed in ring neuron R2 in VFB url: http://www.virtualflybrain.org/do/gene_list.html?action=geneex&id=FBbt:00003651 user: http://www.virtualflybrain.org/ - description: Flybase uses FBbt for expression and phenotype data annotation in Drosophila - example: + examples: - description: alleles, constructs and insertions annotated to neuron in FlyBase url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBbt:00005106 user: http://flybase.org @@ -2083,7 +2137,7 @@ ontologies: tracker: https://github.com/FlyBase/flybase-controlled-vocabulary/issues usages: - description: FlyBase uses FBcv for phenotype data annotation in Drosophila - example: + examples: - description: alleles and constructs annotated to bang sensitive in FlyBase url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0000391 user: http://flybase.org @@ -2331,7 +2385,7 @@ ontologies: tracker: https://github.com/pombase/fypo/issues usages: - description: Pombase uses fypo for phenotype data annotation in fission yeast - example: + examples: - description: genotypes annotated to abnormal mitotic cell cycle in fission yeast url: https://www.pombase.org/term/FYPO:0000059 user: https://www.pombase.org @@ -2504,7 +2558,7 @@ ontologies: tracker: https://github.com/glygen-glycan-data/GNOme/issues - activity_status: active contact: - email: dwelter@ebi.ac.uk + email: danielle.welter@uni.lu label: Danielle Welter description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide @@ -2519,10 +2573,43 @@ ontologies: url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/hancestro.owl products: - - id: hancestro.owl + - description: The full version of HANCESTRO in OWL format + id: hancestro.owl ontology_purl: http://purl.obolibrary.org/obo/hancestro.owl + title: HANCESTRO + - description: Version of HANCESTRO with BFO upper hierarchy for easier integration + with other ontologies + id: hancestro_bfo.owl + ontology_purl: http://purl.obolibrary.org/obo/hancestro_bfo.owl + title: HANCESTRO BFO title: Human Ancestry Ontology tracker: https://github.com/EBISPOT/ancestro/issues + usages: + - description: The Experimental Factor Ontology (EFO) provides a systematic description + of many experimental variables available in EBI databases, and for external + projects such as the NHGRI GWAS catalogue. It combines parts of several biological + ontologies, such as anatomy, disease and chemical compounds. + examples: + - description: Population category defined using ancestry informative markers + (AIMs) based on genetic/genomic data + url: https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false + user: http://www.ebi.ac.uk/efo + - description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary + to identify, document and research foodborne pathogens and associated outbreaks. + examples: + - description: Population category defined using ancestry informative markers + (AIMs) based on genetic/genomic data + url: https://www.ebi.ac.uk/ols/ontologies/genepio/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false + user: https://genepio.org/ + - description: FoodOn (http://foodon.org) is a consortium-driven project to build + a comprehensive and easily accessible global farm-to-fork ontology about food, + that accurately and consistently describes foods commonly known in cultures + from around the world. + examples: + - description: Population category defined using ancestry informative markers + (AIMs) based on genetic/genomic data + url: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false + user: http://foodon.org - activity_status: active build: checkout: git clone https://github.com/hymao/hao.git @@ -2569,9 +2656,9 @@ ontologies: id: hom layout: ontology_detail license: - label: CC-BY - logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png - url: http://creativecommons.org/licenses/by/3.0/ + label: CC0 + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png + url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/hom.owl products: - id: hom.owl @@ -2596,6 +2683,7 @@ ontologies: url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/hsapdv.owl page: https://github.com/obophenotype/developmental-stage-ontologies + preferredPrefix: HsapDv products: - id: hsapdv.owl ontology_purl: http://purl.obolibrary.org/obo/hsapdv.owl @@ -2603,6 +2691,37 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/hsapdv.obo title: Human Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues +- activity_status: active + contact: + email: fernanda.dorea@sva.se + github: nandadorea + label: Fernanda Dorea + dependencies: + - id: uberon + - id: bfo + - id: ro + - id: obi + - id: ncbitaxon + description: The health Surveillance Ontology (HSO) focuses on "surveillance system + level data", that is, data outputs from surveillance activities, such as number + of samples collected, cases observed, etc. It aims to support One-Health surveillance, + covering animal health, public health and food safety surveillance. + domain: health + homepage: https://w3id.org/hso + id: hso + layout: ontology_detail + license: + label: CC-BY + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png + url: http://creativecommons.org/licenses/by/3.0/ + ontology_purl: http://purl.obolibrary.org/obo/hso.owl + page: https://github.com/SVA-SE/HSO + products: + - homepage: https://w3id.org/hso + id: hso.owl + ontology_purl: http://purl.obolibrary.org/obo/hso.owl + title: Health Surveillance Ontology + tracker: https://github.com/SVA-SE/HSO/issues/ - activity_status: active contact: email: aellenhicks@gmail.com @@ -2641,7 +2760,7 @@ ontologies: license: label: CC-BY 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/iao.owl products: - id: iao.owl @@ -2663,6 +2782,10 @@ ontologies: title: ontology of document acts title: Information Artifact Ontology tracker: https://github.com/information-artifact-ontology/IAO/issues + usages: + - description: IAO is used widely by multiple OBO ontologies for information representation. + type: owl_import + user: http://obofoundry.org - activity_status: active contact: email: liumeng94@sjtu.edu.cn @@ -3131,6 +3254,7 @@ ontologies: url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/mmusdv.owl page: https://github.com/obophenotype/developmental-stage-ontologies + preferredPrefix: MmusDv products: - id: mmusdv.owl ontology_purl: http://purl.obolibrary.org/obo/mmusdv.owl @@ -3142,7 +3266,7 @@ ontologies: build: insert_ontology_id: true method: obo2owl - source_url: https://raw.githubusercontent.com/MICommunity/psidev/master/psi/mod/data/PSI-MOD.obo + source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo contact: email: pierre-alain.binz@chuv.ch label: Pierre-Alain Binz @@ -3158,8 +3282,18 @@ ontologies: url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/mod.owl products: - - id: mod.owl + - description: PSI-MOD Ontology, OWL format + id: mod.owl ontology_purl: http://purl.obolibrary.org/obo/mod.owl + title: PSI-MOD.owl + - description: PSI-MOD Ontology, OBO format + id: mod.obo + ontology_purl: http://purl.obolibrary.org/obo/mod.obo + title: PSI-MOD.obo + publications: + - id: https://pubmed.ncbi.nlm.nih.gov/18688235/ + title: The PSI-MOD community standard for representation of protein modification + data title: Protein modification tracker: https://github.com/HUPO-PSI/psi-mod-CV/issues - activity_status: active @@ -3215,10 +3349,41 @@ ontologies: usages: - description: Mondo is used by the Monarch Initiative for disease annotations. examples: - - url: https://monarchinitiative.org/phenotype/HP:0001300#diseases - reference: https://academic.oup.com/nar/article/45/D1/D712/2605791 + - description: 'Parkinsonism: Characteristic neurologic anomaly resulting form + degeneration of dopamine-generating cells in the substantia nigra, a region + of the midbrain, characterized clinically by shaking, rigidity, slowness of + movement and difficulty with walking and gait.' + url: https://monarchinitiative.org/phenotype/HP:0001300#disease + publications: + - id: https://academic.oup.com/nar/article/45/D1/D712/2605791 + title: 'The Monarch Initiative: an integrative data and analytic platform connecting + phenotypes to genotypes across species ' type: annotation user: https://monarchinitiative.org/ + - description: Mondo is used by the ClinGen for disease curations. + examples: + - description: SCN1A is an autosomal dominant mutation in Dravet syndrome. + url: https://search.clinicalgenome.org/kb/conditions/MONDO_0011794 + type: annotation + user: https://www.clinicalgenome.org/ + - description: Mondo is used by the Kids First Data Resource Portal for disease + annotations. Note, a login is needed to access the portal and view the Mondo-curated + data. + type: annotation + user: https://portal.kidsfirstdrc.org/ + - description: Mondo is used by the Ancestory for some disease curations. + examples: + - description: Some term names in ancestory.com are curated with Mondo, for ease + of use. + url: https://support.ancestry.com/s/article/Disease-Condition-Catalog-Powered-by-MONDO + type: annotation + user: https://www.ancestry.com/ + - description: Mondo is used by the Human Cell Atlas for some disease annotations. + examples: + - description: Disease status specimen is normal, type 2 diabetes mellitus. + url: https://data.humancellatlas.org/explore/projects?filter=%5B%7B%22facetName%22:%22organ%22,%22terms%22:%5B%22kidney%22%5D%7D,%7B%22facetName%22:%22donorDisease%22,%22terms%22:%5B%22acoustic%20neuroma%22,%22acute%20kidney%20tubular%20necrosis%22%5D%7D%5D&catalog=dcp1 + type: annotation + user: https://www.humancellatlas.org/ - activity_status: active build: method: owl2obo @@ -3375,10 +3540,50 @@ ontologies: usages: - description: MRO is used by the The Immune Epitope Database (IEDB) annotations examples: - - url: https://www.iedb.org/assay/1357035 - reference: DOI:10.1093/nar/gky1006 + - description: 'Epitope ID: 59611 based on reference 1003499' + url: https://www.iedb.org/assay/1357035 + publications: + - id: https://doi.org/10.1093/nar/gky1006 + title: 'The Immune Epitope Database (IEDB): 2018 update' type: annotation user: https://www.iedb.org/ +- activity_status: active + build: + method: obo2owl + source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo + contact: + email: gerhard.mayer@rub.de + label: Gerhard Mayer + createdWith: http://oboedit.org + dependencies: + - id: pato + - id: uo + description: A structured controlled vocabulary for the annotation of experiments + concerned with proteomics mass spectrometry. + domain: MS experiments + homepage: http://www.psidev.info/groups/controlled-vocabularies + id: ms + integration_server: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master + label: MS + layout: ontology_detail + license: + label: CC-BY + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png + url: https://creativecommons.org/licenses/by/3.0/ + mailing_list: psidev-ms-vocab@lists.sourceforge.net + ontology_purl: http://purl.obolibrary.org/obo/ms.owl + page: http://www.psidev.info/groups/controlled-vocabularies + products: + - id: ms.obo + ontology_purl: http://purl.obolibrary.org/obo/ms.obo + - id: ms.owl + ontology_purl: http://purl.obolibrary.org/obo/ms.owl + publications: + - id: http://www.ncbi.nlm.nih.gov/pubmed/23482073 + title: The HUPO proteomics standards initiative- mass spectrometry controlled + vocabulary. + title: Mass spectrometry ontology + tracker: https://github.com/HUPO-PSI/psi-ms-CV/issues - activity_status: active browsers: - label: BioPortal @@ -3486,7 +3691,9 @@ ontologies: components, anatomy), supporting cross-ontology reasoning. The current release incorporates CL (cell types) and Uberon (anatomy). id: ncit/ncit-plus.owl - mireots_from: uberon + mireots_from: + - cl + - uberon ontology_purl: http://purl.obolibrary.org/obo/ncit/ncit-plus.owl title: NCIt Plus - description: This is a subset extracted from NCIt Plus, based on the [NCIt Neoplasm @@ -3557,7 +3764,8 @@ ontologies: tracker: https://github.com/SpeciesFileGroup/nomen/issues type: owl:Ontology usages: - - label: TaxonWorks + - description: TaxonWorks is an integrated web-based workbench for taxonomists and + biodiversity scientists. seeAlso: https://github.com/SpeciesFileGroup/taxonworks type: application user: https://taxonworks.org @@ -3840,6 +4048,7 @@ ontologies: url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/olatdv.owl page: https://github.com/obophenotype/developmental-stage-ontologies + preferredPrefix: OlatDv products: - id: olatdv.obo ontology_purl: http://purl.obolibrary.org/obo/olatdv.obo @@ -4011,6 +4220,7 @@ ontologies: domain: nutrition, nutritional studies, nutrition professionals homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies id: ons + label: Ontology for Nutritional Studies layout: ontology_detail license: label: CC-BY @@ -4022,7 +4232,7 @@ ontologies: - id: ons.owl ontology_purl: http://purl.obolibrary.org/obo/ons.owl title: ONS latest release - title: ONS + title: Ontology for Nutritional Studies tracker: https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues - activity_status: active browsers: @@ -4077,6 +4287,7 @@ ontologies: email: preets79@gmail.com label: Priti Parikh description: A reference ontology for parasite life cycle stages. + domain: life cycle stage, parasite organism homepage: https://github.com/OPL-ontology/OPL id: opl layout: ontology_detail @@ -4090,6 +4301,15 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/opl.owl title: Ontology for Parasite LifeCycle tracker: https://github.com/OPL-ontology/OPL/issues + usages: + - description: The ontology for parasite lifecycle is used in the VEuPathDB (Eukaryotic + Pathogen, Vector & Host Informatics Resources) for parasite life cycle annotation. + type: annotation and query + user: https://veupathdb.org + - description: The ontology for parasite lifecycle is used in the GeneDB for parasite + life cycle annotation. + type: annotation and query + user: https://www.genedb.org - activity_status: active contact: email: yongqunh@med.umich.edu @@ -4226,6 +4446,7 @@ ontologies: url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/pdumdv.owl page: https://github.com/obophenotype/developmental-stage-ontologies + preferredPrefix: PdumDv products: - id: pdumdv.owl ontology_purl: http://purl.obolibrary.org/obo/pdumdv.owl @@ -4575,13 +4796,15 @@ ontologies: title: Relation Ontology tracker: https://github.com/oborel/obo-relations/issues usages: - - description: RO is used for annotation extensions in the GO - reference: https://doi.org/10.1186/1471-2105-15-155 - type: annotation - user: http://geneontology.org - - description: RO is used for GO Causal Activity Models + - description: RO is used for annotation extensions in the GO and GO Causal Activity + Models. examples: - - http://model.geneontology.org/56d1143000003402 + - description: wg_biogenesis_FlyBase + url: http://model.geneontology.org/56d1143000003402 + publications: + - id: https://doi.org/10.1186/1471-2105-15-155 + title: A method for increasing expressivity of Gene Ontology annotations using + a compositional approach type: annotation user: http://geneontology.org - activity_status: active @@ -4757,6 +4980,31 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/stato.owl title: The Statistical Methods Ontology tracker: https://github.com/ISA-tools/stato/issues +- activity_status: active + build: + method: owl2obo + source_url: https://raw.githubusercontent.com/allysonlister/swo/master/release/swo_inferred.owl + contact: + email: allyson.lister@oerc.ox.ac.uk + label: Allyson Lister + description: The Software Ontology (SWO) is a resource for describing software tools, + their types, tasks, versions, provenance and associated data. It contains detailed + information on licensing and formats as well as software applications themselves, + mainly (but not limited) to the bioinformatics community. + domain: software + homepage: https://github.com/allysonlister/swo + id: swo + layout: ontology_detail + license: + label: CC BY 4.0 + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png + url: https://creativecommons.org/licenses/by/4.0/ + ontology_purl: http://purl.obolibrary.org/obo/swo.owl + products: + - id: swo.owl + ontology_purl: http://purl.obolibrary.org/obo/swo.owl + title: Software ontology + tracker: https://github.com/allysonlister/swo/issues - activity_status: active build: infallible: 1 @@ -5006,7 +5254,7 @@ ontologies: title: Uberon base ontology - description: Uberon extended id: uberon/ext.owl - mireots_from: ncbitaxon + mireots_from: cl ontology_purl: http://purl.obolibrary.org/obo/uberon/ext.owl title: Uberon edition that includes subsets of other ontologies and axioms connecting to them @@ -5039,14 +5287,21 @@ ontologies: type: BridgeOntology - description: Extended uberon plus all metazoan ontologies id: uberon/composite-metazoan.owl - mireots_from: ehdaa2 ontology_purl: http://purl.obolibrary.org/obo/uberon/composite-metazoan.owl page: https://github.com/obophenotype/uberon/wiki/Multi-species-composite-ontologies taxon: Metazoa title: Uberon composite metazoan ontology type: MergedOntology - id: uberon/composite-vertebrate.owl - mireots_from: ehdaa2 + mireots_from: + - zfa + - xao + - fbbt + - wbbt + - ma + - fma + - emapa + - ehdaa2 ontology_purl: http://purl.obolibrary.org/obo/uberon/composite-vertebrate.owl page: https://github.com/obophenotype/uberon/wiki/Multi-species-composite-ontologies taxon: Metazoa @@ -5088,7 +5343,9 @@ ontologies: research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The ENCODE DCC users Uberon to annotate samples - reference: https://doi.org/10.1093/database/bav010 + publications: + - id: https://doi.org/10.1093/database/bav010 + title: Ontology application and use at the ENCODE DCC seeAlso: https://www.biosharing.org/biodbcore-000034 type: annotation user: https://www.encodeproject.org/ @@ -5102,11 +5359,11 @@ ontologies: - description: Querying expression and phenotype data type: query user: https://monarchinitiative.org/ - - description: Querying for functional annotations relevant to a tissue + - description: GO Database is used for querying for functional annotations relevant + to a tissue examples: - description: GO annotations relevant to the uberon class for brain url: http://amigo.geneontology.org/amigo/term/UBERON:0000955 - label: GO Database type: query user: https://geneontology.org/ - description: The Phenoscape project is both a major driver of and contributor @@ -5116,23 +5373,26 @@ ontologies: Skeletal Anatomy Ontology (VSAO), also created by the Phenoscape group. Phenoscape curators continue to extend the ontology, covering a wide variety of tetrapod structures, with an emphasis on the appendicular system. - label: Phenoscape user: http://phenoscape.org - - label: Neuroscience Information Framework + - description: Searchable collection of neuroscience data and ontology for neuroscience type: Database - url: https://neuinfo.org/ - - label: SciCrunch + user: https://neuinfo.org/ + - description: cooperative data platform to be used by diverse communities in making + data more FAIR. type: Database - url: https://scicrunch.org/ - - label: SCPortalen - reference: https://doi.org/10.1093/nar/gkx949 + user: https://scicrunch.org/ + - description: SCPortalen + publications: + - id: https://doi.org/10.1093/nar/gkx949 + title: 'SCPortalen: human and mouse single-cell centric database' type: Database - url: http://single-cell.clst.riken.jp/ + user: http://single-cell.clst.riken.jp/ - description: ChEMBL uses Uberon to describe organ/tissue information in assays - label: ChEMBL - reference: https://doi.org/10.1093/nar/gky1075 + publications: + - id: https://doi.org/10.1093/nar/gky1075 + title: 'ChEMBL: towards direct deposition of bioassay data' type: Database - url: https://www.ebi.ac.uk/chembl/ + user: https://www.ebi.ac.uk/chembl/ wikidata_template: https://en.wikipedia.org/wiki/Template:Uberon - activity_status: active build: @@ -5190,8 +5450,15 @@ ontologies: usages: - description: uPheno is used by the Monarch Initiative for cross-species inference. examples: - - url: https://monarchinitiative.org/phenotype/HP:0001300#diseases - reference: https://academic.oup.com/nar/article/45/D1/D712/2605791 + - description: Characteristic neurologic anomaly resulting form degeneration of + dopamine-generating cells in the substantia nigra, a region of the midbrain, + characterized clinically by shaking, rigidity, slowness of movement and difficulty + with walking and gait. + url: https://monarchinitiative.org/phenotype/HP:0001300#disease + publications: + - id: https://academic.oup.com/nar/article/45/D1/D712/2605791 + title: 'The Monarch Initiative: an integrative data and analytic platform connecting + phenotypes to genotypes across species ' type: analysis user: https://monarchinitiative.org/ - activity_status: active @@ -5215,6 +5482,28 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/vo.owl title: Vaccine Ontology tracker: https://github.com/vaccineontology/VO/issues +- activity_status: active + build: + checkout: svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt + method: vcs + system: svn + contact: + email: caripark@iastate.edu + label: Carissa Park + description: An ontology of traits covering vertebrates + homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology + id: vt + layout: ontology_detail + license: + label: CC BY 4.0 + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png + url: https://creativecommons.org/licenses/by/4.0/ + ontology_purl: http://purl.obolibrary.org/obo/vt.owl + products: + - id: vt.owl + ontology_purl: http://purl.obolibrary.org/obo/vt.owl + title: Vertebrate trait ontology + tracker: https://github.com/AnimalGenome/vertebrate-trait-ontology/issues - activity_status: active contact: email: balhoff@renci.org @@ -5278,8 +5567,11 @@ ontologies: - description: WormBase uses WBbt to curate anatomical expression patterns and anatomy function annotations, and to allow search and indexing on the WormBase site examples: - - url: http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression - reference: https://academic.oup.com/nar/article/48/D1/D762/5603222 + - description: Expression for gene daf-16 with WormBase ID WBGene00000912 + url: http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression + publications: + - id: https://academic.oup.com/nar/article/48/D1/D762/5603222 + title: 'WormBase: a modern Model Organism Information Resource' type: annotation user: https://www.wormbase.org/ - activity_status: active @@ -5319,8 +5611,11 @@ ontologies: - description: WormBase uses WBls to curate temporal expression patterns, and to allow search and indexing on the WormBase site examples: - - url: http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression - reference: https://academic.oup.com/nar/article/48/D1/D762/5603222 + - description: Expression for daf-16 gene with WormBase ID WBGene00000912. + url: http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression + publications: + - id: https://academic.oup.com/nar/article/48/D1/D762/5603222 + title: 'WormBase: a modern Model Organism Information Resource' type: annotation user: https://www.wormbase.org/ - activity_status: active @@ -5363,15 +5658,23 @@ ontologies: - description: WormBase uses WBPhenotype to curate worm phenotypes, and to allow search and indexing on the WormBase site examples: - - url: http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=phenotype - reference: https://academic.oup.com/nar/article/48/D1/D762/5603222 + - description: Expression for daf-16 gene with WormBase ID WBGene00000912. + url: http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression + publications: + - id: https://academic.oup.com/nar/article/48/D1/D762/5603222 + title: 'WormBase: a modern Model Organism Information Resource' type: annotation user: https://www.wormbase.org/ - description: Monarch integrates phenotype annotations from sources such as WormBase, and allows for querying using the WBPhenotype ontology. examples: - - url: https://monarchinitiative.org/phenotype/WBPhenotype%3A0000370 - reference: https://academic.oup.com/nar/article/45/D1/D712/2605791 + - description: 'Egg long: The fertilized oocytes have a greater than standard + length measured end to end compared to control.' + url: https://monarchinitiative.org/phenotype/WBPhenotype%3A0000370 + publications: + - id: https://academic.oup.com/nar/article/45/D1/D712/2605791 + title: 'The Monarch Initiative: an integrative data and analytic platform connecting + phenotypes to genotypes across species ' type: annotation user: https://monarchinitiative.org/ - activity_status: active @@ -5409,6 +5712,34 @@ ontologies: ontologies: expansion, improvements and new applications.' title: Experimental condition ontology tracker: https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues +- activity_status: active + build: + method: obo2owl + source_url: https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo + contact: + email: gerhard.mayer@rub.de + label: Gerhard Mayer + createdWith: http://oboedit.org + description: A structured controlled vocabulary for cross-linking reagents used + with proteomics mass spectrometry. + domain: MS cross-linker reagents + homepage: http://www.psidev.info/groups/controlled-vocabularies + id: xlmod + integration_server: https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/tree/master/cv + label: xlmod + layout: ontology_detail + license: + label: CC-BY + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png + url: https://creativecommons.org/licenses/by/3.0/ + mailing_list: psidev-ms-vocab@lists.sourceforge.net + ontology_purl: http://purl.obolibrary.org/obo/xlmod.owl + page: http://www.psidev.info/groups/controlled-vocabularies + products: + - id: xlmod.obo + ontology_purl: http://purl.obolibrary.org/obo/xlmod.obo + title: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary + tracker: https://github.com/HUPO-PSI/mzIdentML/issues - activity_status: active build: checkout: git clone https://github.com/obophenotype/xenopus-phenotype-ontology.git @@ -5481,6 +5812,36 @@ ontologies: label: Danio title: Zebrafish Experimental Conditions Ontology tracker: https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues +- activity_status: active + build: + infallible: 1 + method: obo2owl + source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo + contact: + email: van_slyke@zfin.org + label: Ceri Van Slyke + description: Developmental stages of the Zebrafish + domain: anatomy + homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources + id: zfs + in_foundry: false + layout: ontology_detail + license: + label: CC-BY 3.0 + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png + url: http://creativecommons.org/licenses/by/3.0/ + ontology_purl: http://purl.obolibrary.org/obo/zfs.owl + page: https://github.com/obophenotype/developmental-stage-ontologies/wiki/ZFS + products: + - id: zfs.owl + ontology_purl: http://purl.obolibrary.org/obo/zfs.owl + - id: zfs.obo + ontology_purl: http://purl.obolibrary.org/obo/zfs.obo + taxon: + id: NCBITaxon:7954 + label: Danio + title: Zebrafish developmental stages ontology + tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues - activity_status: active build: checkout: git clone https://github.com/obophenotype/zebrafish-phenotype-ontology.git @@ -5522,37 +5883,22 @@ ontologies: - description: Monarch integrates phenotype annotations from sources such as ZFIIN, and allows for querying using the ZP ontology. examples: - - url: https://monarchinitiative.org/phenotype/ZP:0005692 - reference: https://academic.oup.com/nar/article/45/D1/D712/2605791 + - description: 'adaxial cell absent, abnormal: Abnormal(ly) absent (of) adaxial + cell.' + url: https://monarchinitiative.org/phenotype/ZP:0005692 + publications: + - id: https://academic.oup.com/nar/article/45/D1/D712/2605791 + title: 'The Monarch Initiative: an integrative data and analytic platform connecting + phenotypes to genotypes across species' type: annotation user: https://monarchinitiative.org/ -- activity_status: active - contact: - email: bgee@sib.swiss - github: fbastian - label: Frederic Bastian - description: An ontology to capture confidence information about annotations. - homepage: https://github.com/BgeeDB/confidence-information-ontology - id: cio - layout: ontology_detail - license: - label: GNU GPL 3.0 - url: https://www.gnu.org/licenses/gpl-3.0.en.html - ontology_purl: http://purl.obolibrary.org/obo/cio.owl - products: - - id: cio.owl - ontology_purl: http://purl.obolibrary.org/obo/cio.owl - - id: cio.obo - ontology_purl: http://purl.obolibrary.org/obo/cio.obo - title: Confidence Information Ontology - tracker: https://github.com/BgeeDB/confidence-information-ontology - activity_status: active build: method: owl2obo source_url: http://purl.obolibrary.org/obo/ero.owl contact: - email: Juliane_Schneider@hms.harvard.edu - label: Juliane Schneider + email: Marc_Ciriello@hms.harvard.edu + label: Marc Ciriello description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. documentation: https://open.med.harvard.edu/wiki/display/eaglei/Ontology @@ -5707,6 +6053,7 @@ ontologies: - id: kisao.owl ontology_purl: http://purl.obolibrary.org/obo/kisao.owl title: Kinetic Simulation Algorithm Ontology + tracker: https://sourceforge.net/p/kisao/feature-requests/ - activity_status: active build: method: owl2obo @@ -5729,42 +6076,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/mamo.owl title: Mathematical modeling ontology tracker: http://sourceforge.net/p/mamo-ontology/tickets/ -- activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo - contact: - email: gerhard.mayer@rub.de - label: Gerhard Mayer - createdWith: http://oboedit.org - dependencies: - - id: pato - - id: uo - description: A structured controlled vocabulary for the annotation of experiments - concerned with proteomics mass spectrometry. - domain: MS experiments - homepage: http://www.psidev.info/groups/controlled-vocabularies - id: ms - integration_server: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master - label: MS - layout: ontology_detail - license: - label: CC-BY - logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png - url: https://creativecommons.org/licenses/by/3.0/ - mailing_list: psidev-ms-vocab@lists.sourceforge.net - ontology_purl: http://purl.obolibrary.org/obo/ms.owl - page: http://www.psidev.info/groups/controlled-vocabularies - products: - - id: ms.obo - ontology_purl: http://purl.obolibrary.org/obo/ms.obo - - id: ms.owl - ontology_purl: http://purl.obolibrary.org/obo/ms.owl - publications: - - id: http://www.ncbi.nlm.nih.gov/pubmed/23482073 - title: The HUPO proteomics standards initiative- mass spectrometry controlled - vocabulary. - title: Mass spectrometry ontology - activity_status: active build: insert_ontology_id: true @@ -5788,30 +6099,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/sbo.owl title: Systems Biology Ontology tracker: https://sourceforge.net/p/sbo/term-request/ -- activity_status: active - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/allysonlister/swo/master/release/swo_inferred.owl - contact: - email: allyson.lister@oerc.ox.ac.uk - label: Allyson Lister - description: The Software Ontology (SWO) is a resource for describing software tools, - their types, tasks, versions, provenance and associated data. It contains detailed - information on licensing and formats as well as software applications themselves, - mainly (but not limited) to the bioinformatics community. - domain: software - homepage: https://github.com/allysonlister/swo - id: swo - layout: ontology_detail - license: - label: CC BY 4.0 - logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png - url: https://creativecommons.org/licenses/by/4.0/ - ontology_purl: http://purl.obolibrary.org/obo/swo.owl - products: - - id: swo.owl - ontology_purl: http://purl.obolibrary.org/obo/swo.owl - title: Software ontology - activity_status: active browsers: - label: BioPortal @@ -5834,90 +6121,13 @@ ontologies: license: label: CC-BY version 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png - url: http://creativecommons.org/licenses/by/3.0/ + url: https://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/txpo.owl products: - id: txpo.owl ontology_purl: http://purl.obolibrary.org/obo/txpo.owl title: Toxic Process Ontology tracker: https://github.com/txpo-ontology/TXPO/issues -- activity_status: active - build: - checkout: svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt - method: vcs - system: svn - contact: - email: caripark@iastate.edu - label: Carissa Park - description: An ontology of traits covering vertebrates - homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology - id: vt - layout: ontology_detail - license: - label: CC BY 4.0 - logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png - url: https://creativecommons.org/licenses/by/4.0/ - ontology_purl: http://purl.obolibrary.org/obo/vt.owl - products: - - id: vt.owl - ontology_purl: http://purl.obolibrary.org/obo/vt.owl - title: Vertebrate trait ontology -- activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo - contact: - email: gerhard.mayer@rub.de - label: Gerhard Mayer - createdWith: http://oboedit.org - description: A structured controlled vocabulary for cross-linking reagents used - with proteomics mass spectrometry. - domain: MS cross-linker reagents - homepage: http://www.psidev.info/groups/controlled-vocabularies - id: xlmod - integration_server: https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/tree/master/cv - label: xlmod - layout: ontology_detail - license: - label: CC-BY - logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png - url: https://creativecommons.org/licenses/by/3.0/ - mailing_list: psidev-ms-vocab@lists.sourceforge.net - ontology_purl: http://purl.obolibrary.org/obo/xlmod.owl - page: http://www.psidev.info/groups/controlled-vocabularies - products: - - id: xlmod.obo - ontology_purl: http://purl.obolibrary.org/obo/xlmod.obo - title: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary -- activity_status: active - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo - contact: - email: van_slyke@zfin.org - label: Ceri Van Slyke - description: Developmental stages of the Zebrafish - domain: anatomy - homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources - id: zfs - in_foundry: false - layout: ontology_detail - license: - label: CC-BY 3.0 - logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png - url: http://creativecommons.org/licenses/by/3.0/ - ontology_purl: http://purl.obolibrary.org/obo/zfs.owl - page: https://github.com/obophenotype/developmental-stage-ontologies/wiki/ZFS - products: - - id: zfs.owl - ontology_purl: http://purl.obolibrary.org/obo/zfs.owl - - id: zfs.obo - ontology_purl: http://purl.obolibrary.org/obo/zfs.obo - taxon: - id: NCBITaxon:7954 - label: Danio - title: Zebrafish developmental stages ontology - activity_status: orphaned build: checkout: git clone https://github.com/obophenotype/sibo.git @@ -5963,6 +6173,23 @@ ontologies: - id: fix.obo ontology_purl: http://purl.obolibrary.org/obo/fix.obo title: Physico-chemical methods and properties +- activity_status: orphaned + build: + method: obo2owl + source_url: http://variationontology.org/vario_download/vario.obo + contact: + email: mauno.vihinen@med.lu.se + label: Mauno Vihinen + description: Variation Ontology, VariO, is an ontology for standardized, systematic + description of effects, consequences and mechanisms of variations. + homepage: http://variationontology.org + id: vario + layout: ontology_detail + ontology_purl: http://purl.obolibrary.org/obo/vario.owl + products: + - id: vario.owl + ontology_purl: http://purl.obolibrary.org/obo/vario.owl + title: Variation Ontology - activity_status: orphaned description: An ontology that formalizes the genomic element by defining an upper class genetic interval @@ -5989,20 +6216,6 @@ ontologies: - id: rex.owl ontology_purl: http://purl.obolibrary.org/obo/rex.owl title: Physico-chemical process -- activity_status: orphaned - build: - method: obo2owl - source_url: http://variationontology.org/vario_download/vario.obo - description: Variation Ontology, VariO, is an ontology for standardized, systematic - description of effects, consequences and mechanisms of variations. - homepage: http://variationontology.org - id: vario - layout: ontology_detail - ontology_purl: http://purl.obolibrary.org/obo/vario.owl - products: - - id: vario.owl - ontology_purl: http://purl.obolibrary.org/obo/vario.owl - title: Variation Ontology - activity_status: inactive build: checkout: git clone https://github.com/obophenotype/cephalopod-ontology.git diff --git a/registry/obo_context.jsonld b/registry/obo_context.jsonld index df10464f4..c8730115b 100644 --- a/registry/obo_context.jsonld +++ b/registry/obo_context.jsonld @@ -60,7 +60,7 @@ "ERO": "http://purl.obolibrary.org/obo/ERO_", "EUPATH": "http://purl.obolibrary.org/obo/EUPATH_", "EV": "http://purl.obolibrary.org/obo/EV_", - "EXO": "http://purl.obolibrary.org/obo/EXO_", + "ExO": "http://purl.obolibrary.org/obo/ExO_", "FAO": "http://purl.obolibrary.org/obo/FAO_", "FBSP": "http://purl.obolibrary.org/obo/FBSP_", "FBbi": "http://purl.obolibrary.org/obo/FBbi_", @@ -90,8 +90,9 @@ "HAO": "http://purl.obolibrary.org/obo/HAO_", "HOM": "http://purl.obolibrary.org/obo/HOM_", "HP": "http://purl.obolibrary.org/obo/HP_", - "HSAPDV": "http://purl.obolibrary.org/obo/HSAPDV_", + "HSO": "http://purl.obolibrary.org/obo/HSO_", "HTN": "http://purl.obolibrary.org/obo/HTN_", + "HsapDv": "http://purl.obolibrary.org/obo/HsapDv_", "IAO": "http://purl.obolibrary.org/obo/IAO_", "ICEO": "http://purl.obolibrary.org/obo/ICEO_", "ICO": "http://purl.obolibrary.org/obo/ICO_", @@ -122,7 +123,6 @@ "MIRNAO": "http://purl.obolibrary.org/obo/MIRNAO_", "MIRO": "http://purl.obolibrary.org/obo/MIRO_", "MMO": "http://purl.obolibrary.org/obo/MMO_", - "MMUSDV": "http://purl.obolibrary.org/obo/MMUSDV_", "MO": "http://purl.obolibrary.org/obo/MO_", "MOD": "http://purl.obolibrary.org/obo/MOD_", "MONDO": "http://purl.obolibrary.org/obo/MONDO_", @@ -132,6 +132,7 @@ "MPIO": "http://purl.obolibrary.org/obo/MPIO_", "MRO": "http://purl.obolibrary.org/obo/MRO_", "MS": "http://purl.obolibrary.org/obo/MS_", + "MmusDv": "http://purl.obolibrary.org/obo/MmusDv_", "NBO": "http://purl.obolibrary.org/obo/NBO_", "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_", "NCIT": "http://purl.obolibrary.org/obo/NCIT_", @@ -155,7 +156,6 @@ "OHD": "http://purl.obolibrary.org/obo/OHD_", "OHMI": "http://purl.obolibrary.org/obo/OHMI_", "OHPI": "http://purl.obolibrary.org/obo/OHPI_", - "OLATDV": "http://purl.obolibrary.org/obo/OLATDV_", "OMIABIS": "http://purl.obolibrary.org/obo/OMIABIS_", "OMIT": "http://purl.obolibrary.org/obo/OMIT_", "OMO": "http://purl.obolibrary.org/obo/OMO_", @@ -169,11 +169,11 @@ "OPMI": "http://purl.obolibrary.org/obo/OPMI_", "ORNASEQ": "http://purl.obolibrary.org/obo/ORNASEQ_", "OVAE": "http://purl.obolibrary.org/obo/OVAE_", + "OlatDv": "http://purl.obolibrary.org/obo/OlatDv_", "PAO": "http://purl.obolibrary.org/obo/PAO_", "PATO": "http://purl.obolibrary.org/obo/PATO_", "PCO": "http://purl.obolibrary.org/obo/PCO_", "PDRO": "http://purl.obolibrary.org/obo/PDRO_", - "PDUMDV": "http://purl.obolibrary.org/obo/PDUMDV_", "PD_ST": "http://purl.obolibrary.org/obo/PD_ST_", "PECO": "http://purl.obolibrary.org/obo/PECO_", "PGDSO": "http://purl.obolibrary.org/obo/PGDSO_", @@ -189,6 +189,7 @@ "PSDO": "http://purl.obolibrary.org/obo/PSDO_", "PSO": "http://purl.obolibrary.org/obo/PSO_", "PW": "http://purl.obolibrary.org/obo/PW_", + "PdumDv": "http://purl.obolibrary.org/obo/PdumDv_", "RESID": "http://purl.obolibrary.org/obo/RESID_", "REX": "http://purl.obolibrary.org/obo/REX_", "RNAO": "http://purl.obolibrary.org/obo/RNAO_", diff --git a/registry/obo_prefixes.ttl b/registry/obo_prefixes.ttl index 3b431729d..31858ea70 100644 --- a/registry/obo_prefixes.ttl +++ b/registry/obo_prefixes.ttl @@ -27,6 +27,7 @@ ,[ sh:prefix "CHIRO" ; sh:namespace "http://purl.obolibrary.org/obo/CHIRO_"] ,[ sh:prefix "CHMO" ; sh:namespace "http://purl.obolibrary.org/obo/CHMO_"] ,[ sh:prefix "CIDO" ; sh:namespace "http://purl.obolibrary.org/obo/CIDO_"] +,[ sh:prefix "CIO" ; sh:namespace "http://purl.obolibrary.org/obo/CIO_"] ,[ sh:prefix "CL" ; sh:namespace "http://purl.obolibrary.org/obo/CL_"] ,[ sh:prefix "CLAO" ; sh:namespace "http://purl.obolibrary.org/obo/CLAO_"] ,[ sh:prefix "CLO" ; sh:namespace "http://purl.obolibrary.org/obo/CLO_"] @@ -50,7 +51,7 @@ ,[ sh:prefix "EMAPA" ; sh:namespace "http://purl.obolibrary.org/obo/EMAPA_"] ,[ sh:prefix "ENVO" ; sh:namespace "http://purl.obolibrary.org/obo/ENVO_"] ,[ sh:prefix "EUPATH" ; sh:namespace "http://purl.obolibrary.org/obo/EUPATH_"] -,[ sh:prefix "EXO" ; sh:namespace "http://purl.obolibrary.org/obo/EXO_"] +,[ sh:prefix "ExO" ; sh:namespace "http://purl.obolibrary.org/obo/ExO_"] ,[ sh:prefix "FAO" ; sh:namespace "http://purl.obolibrary.org/obo/FAO_"] ,[ sh:prefix "FBbi" ; sh:namespace "http://purl.obolibrary.org/obo/FBbi_"] ,[ sh:prefix "FBbt" ; sh:namespace "http://purl.obolibrary.org/obo/FBbt_"] @@ -71,7 +72,8 @@ ,[ sh:prefix "HANCESTRO" ; sh:namespace "http://purl.obolibrary.org/obo/HANCESTRO_"] ,[ sh:prefix "HAO" ; sh:namespace "http://purl.obolibrary.org/obo/HAO_"] ,[ sh:prefix "HOM" ; sh:namespace "http://purl.obolibrary.org/obo/HOM_"] -,[ sh:prefix "HSAPDV" ; sh:namespace "http://purl.obolibrary.org/obo/HSAPDV_"] +,[ sh:prefix "HsapDv" ; sh:namespace "http://purl.obolibrary.org/obo/HsapDv_"] +,[ sh:prefix "HSO" ; sh:namespace "http://purl.obolibrary.org/obo/HSO_"] ,[ sh:prefix "HTN" ; sh:namespace "http://purl.obolibrary.org/obo/HTN_"] ,[ sh:prefix "IAO" ; sh:namespace "http://purl.obolibrary.org/obo/IAO_"] ,[ sh:prefix "ICEO" ; sh:namespace "http://purl.obolibrary.org/obo/ICEO_"] @@ -90,7 +92,7 @@ ,[ sh:prefix "MIAPA" ; sh:namespace "http://purl.obolibrary.org/obo/MIAPA_"] ,[ sh:prefix "MICRO" ; sh:namespace "http://purl.obolibrary.org/obo/MICRO_"] ,[ sh:prefix "MMO" ; sh:namespace "http://purl.obolibrary.org/obo/MMO_"] -,[ sh:prefix "MMUSDV" ; sh:namespace "http://purl.obolibrary.org/obo/MMUSDV_"] +,[ sh:prefix "MmusDv" ; sh:namespace "http://purl.obolibrary.org/obo/MmusDv_"] ,[ sh:prefix "MOD" ; sh:namespace "http://purl.obolibrary.org/obo/MOD_"] ,[ sh:prefix "MONDO" ; sh:namespace "http://purl.obolibrary.org/obo/MONDO_"] ,[ sh:prefix "MOP" ; sh:namespace "http://purl.obolibrary.org/obo/MOP_"] @@ -98,6 +100,7 @@ ,[ sh:prefix "MPATH" ; sh:namespace "http://purl.obolibrary.org/obo/MPATH_"] ,[ sh:prefix "MPIO" ; sh:namespace "http://purl.obolibrary.org/obo/MPIO_"] ,[ sh:prefix "MRO" ; sh:namespace "http://purl.obolibrary.org/obo/MRO_"] +,[ sh:prefix "MS" ; sh:namespace "http://purl.obolibrary.org/obo/MS_"] ,[ sh:prefix "NBO" ; sh:namespace "http://purl.obolibrary.org/obo/NBO_"] ,[ sh:prefix "NCBITaxon" ; sh:namespace "http://purl.obolibrary.org/obo/NCBITaxon_"] ,[ sh:prefix "NCIT" ; sh:namespace "http://purl.obolibrary.org/obo/NCIT_"] @@ -114,7 +117,7 @@ ,[ sh:prefix "OHD" ; sh:namespace "http://purl.obolibrary.org/obo/OHD_"] ,[ sh:prefix "OHMI" ; sh:namespace "http://purl.obolibrary.org/obo/OHMI_"] ,[ sh:prefix "OHPI" ; sh:namespace "http://purl.obolibrary.org/obo/OHPI_"] -,[ sh:prefix "OLATDV" ; sh:namespace "http://purl.obolibrary.org/obo/OLATDV_"] +,[ sh:prefix "OlatDv" ; sh:namespace "http://purl.obolibrary.org/obo/OlatDv_"] ,[ sh:prefix "OMIABIS" ; sh:namespace "http://purl.obolibrary.org/obo/OMIABIS_"] ,[ sh:prefix "OMIT" ; sh:namespace "http://purl.obolibrary.org/obo/OMIT_"] ,[ sh:prefix "OMO" ; sh:namespace "http://purl.obolibrary.org/obo/OMO_"] @@ -130,7 +133,7 @@ ,[ sh:prefix "OVAE" ; sh:namespace "http://purl.obolibrary.org/obo/OVAE_"] ,[ sh:prefix "PCO" ; sh:namespace "http://purl.obolibrary.org/obo/PCO_"] ,[ sh:prefix "PDRO" ; sh:namespace "http://purl.obolibrary.org/obo/PDRO_"] -,[ sh:prefix "PDUMDV" ; sh:namespace "http://purl.obolibrary.org/obo/PDUMDV_"] +,[ sh:prefix "PdumDv" ; sh:namespace "http://purl.obolibrary.org/obo/PdumDv_"] ,[ sh:prefix "PECO" ; sh:namespace "http://purl.obolibrary.org/obo/PECO_"] ,[ sh:prefix "PHIPO" ; sh:namespace "http://purl.obolibrary.org/obo/PHIPO_"] ,[ sh:prefix "PLANA" ; sh:namespace "http://purl.obolibrary.org/obo/PLANA_"] @@ -147,6 +150,7 @@ ,[ sh:prefix "SO" ; sh:namespace "http://purl.obolibrary.org/obo/SO_"] ,[ sh:prefix "SPD" ; sh:namespace "http://purl.obolibrary.org/obo/SPD_"] ,[ sh:prefix "STATO" ; sh:namespace "http://purl.obolibrary.org/obo/STATO_"] +,[ sh:prefix "SWO" ; sh:namespace "http://purl.obolibrary.org/obo/SWO_"] ,[ sh:prefix "SYMP" ; sh:namespace "http://purl.obolibrary.org/obo/SYMP_"] ,[ sh:prefix "TAXRANK" ; sh:namespace "http://purl.obolibrary.org/obo/TAXRANK_"] ,[ sh:prefix "TO" ; sh:namespace "http://purl.obolibrary.org/obo/TO_"] @@ -156,33 +160,30 @@ ,[ sh:prefix "UO" ; sh:namespace "http://purl.obolibrary.org/obo/UO_"] ,[ sh:prefix "UPHENO" ; sh:namespace "http://purl.obolibrary.org/obo/UPHENO_"] ,[ sh:prefix "VO" ; sh:namespace "http://purl.obolibrary.org/obo/VO_"] +,[ sh:prefix "VT" ; sh:namespace "http://purl.obolibrary.org/obo/VT_"] ,[ sh:prefix "VTO" ; sh:namespace "http://purl.obolibrary.org/obo/VTO_"] ,[ sh:prefix "WBbt" ; sh:namespace "http://purl.obolibrary.org/obo/WBbt_"] ,[ sh:prefix "WBls" ; sh:namespace "http://purl.obolibrary.org/obo/WBls_"] ,[ sh:prefix "WBPhenotype" ; sh:namespace "http://purl.obolibrary.org/obo/WBPhenotype_"] ,[ sh:prefix "XCO" ; sh:namespace "http://purl.obolibrary.org/obo/XCO_"] +,[ sh:prefix "XLMOD" ; sh:namespace "http://purl.obolibrary.org/obo/XLMOD_"] ,[ sh:prefix "XPO" ; sh:namespace "http://purl.obolibrary.org/obo/XPO_"] ,[ sh:prefix "ZECO" ; sh:namespace "http://purl.obolibrary.org/obo/ZECO_"] +,[ sh:prefix "ZFS" ; sh:namespace "http://purl.obolibrary.org/obo/ZFS_"] ,[ sh:prefix "ZP" ; sh:namespace "http://purl.obolibrary.org/obo/ZP_"] -,[ sh:prefix "CIO" ; sh:namespace "http://purl.obolibrary.org/obo/CIO_"] ,[ sh:prefix "ERO" ; sh:namespace "http://purl.obolibrary.org/obo/ERO_"] ,[ sh:prefix "FOBI" ; sh:namespace "http://purl.obolibrary.org/obo/FOBI_"] ,[ sh:prefix "GSSO" ; sh:namespace "http://purl.obolibrary.org/obo/GSSO_"] ,[ sh:prefix "HP" ; sh:namespace "http://purl.obolibrary.org/obo/HP_"] ,[ sh:prefix "KISAO" ; sh:namespace "http://purl.obolibrary.org/obo/KISAO_"] ,[ sh:prefix "MAMO" ; sh:namespace "http://purl.obolibrary.org/obo/MAMO_"] -,[ sh:prefix "MS" ; sh:namespace "http://purl.obolibrary.org/obo/MS_"] ,[ sh:prefix "SBO" ; sh:namespace "http://purl.obolibrary.org/obo/SBO_"] -,[ sh:prefix "SWO" ; sh:namespace "http://purl.obolibrary.org/obo/SWO_"] ,[ sh:prefix "TXPO" ; sh:namespace "http://purl.obolibrary.org/obo/TXPO_"] -,[ sh:prefix "VT" ; sh:namespace "http://purl.obolibrary.org/obo/VT_"] -,[ sh:prefix "XLMOD" ; sh:namespace "http://purl.obolibrary.org/obo/XLMOD_"] -,[ sh:prefix "ZFS" ; sh:namespace "http://purl.obolibrary.org/obo/ZFS_"] ,[ sh:prefix "SIBO" ; sh:namespace "http://purl.obolibrary.org/obo/SIBO_"] ,[ sh:prefix "FIX" ; sh:namespace "http://purl.obolibrary.org/obo/FIX_"] +,[ sh:prefix "VARIO" ; sh:namespace "http://purl.obolibrary.org/obo/VARIO_"] ,[ sh:prefix "OGI" ; sh:namespace "http://purl.obolibrary.org/obo/OGI_"] ,[ sh:prefix "REX" ; sh:namespace "http://purl.obolibrary.org/obo/REX_"] -,[ sh:prefix "VARIO" ; sh:namespace "http://purl.obolibrary.org/obo/VARIO_"] ,[ sh:prefix "CEPH" ; sh:namespace "http://purl.obolibrary.org/obo/CEPH_"] ,[ sh:prefix "EHDAA2" ; sh:namespace "http://purl.obolibrary.org/obo/EHDAA2_"] ,[ sh:prefix "RNAO" ; sh:namespace "http://purl.obolibrary.org/obo/RNAO_"] diff --git a/registry/ontologies.jsonld b/registry/ontologies.jsonld index fb3665a1e..b2ba7a604 100644 --- a/registry/ontologies.jsonld +++ b/registry/ontologies.jsonld @@ -461,7 +461,7 @@ "usages": [ { "description": "PennTURBO accelerates the processes of finding and connecting key information from clinical records, via semantic modeling of the processes that generated the data. This makes the discovery of previously unappreciated relations between the data possible for research and for operational tasks.", - "example": [ + "examples": [ { "description": "CYP2C1*2/*2 MI patient taking Clopidogrel", "url": "https://github.com/PennTURBO/Turbo-Documentation/blob/master/IBI_CIC_TURBO_MAM_20190102.pdf" @@ -471,7 +471,7 @@ }, { "description": "The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain. ECO uses OBI to logically describe how the evidence arises from an investigation.", - "example": [ + "examples": [ { "description": "rapid amplification of cDNA ends polymerase chain reaction evidence", "url": "http://purl.obolibrary.org/obo/ECO_0001820" @@ -548,10 +548,16 @@ "description": "PATO is used by the Human Phenotype Ontology (HPO) for logical definitions of phenotypes that facilitate cross-species integration.", "examples": [ { + "description": "An abnormality in a cellular process.", "url": "https://www.ebi.ac.uk/ols/ontologies/hp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0011017&viewMode=All&siblings=false" } ], - "reference": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324074/", + "publications": [ + { + "id": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324074/", + "title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources" + } + ], "type": "annotation", "user": "https://hpo.jax.org/app/" } @@ -645,6 +651,7 @@ "description": "Maize CELL genomics DB uses PO to annotate images", "examples": [ { + "description": "LhG4 Promoter Drivers", "url": "http://maize.jcvi.org/cellgenomics/geneDB_list.php?filter=3" } ], @@ -654,6 +661,7 @@ "description": "MaizeGDB uses PO for annotation of genes", "examples": [ { + "description": "Introduced in gene model set 5b in assembly version RefGen_v2.", "url": "http://maizegdb.org/gene_center/gene/GRMZM5G863962" } ], @@ -1165,7 +1173,7 @@ "github": "cmungall", "label": "Chris Mungall" }, - "description": "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces", + "description": "An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces", "domain": "anatomy", "homepage": "https://github.com/obophenotype/biological-spatial-ontology", "id": "bspo", @@ -1454,6 +1462,36 @@ "title": "Coronavirus Infectious Disease Ontology", "tracker": "https://github.com/cido-ontology/cido/issues" }, + { + "activity_status": "active", + "contact": { + "email": "bgee@sib.swiss", + "github": "fbastian", + "label": "Frederic Bastian" + }, + "description": "An ontology to capture confidence information about annotations.", + "homepage": "https://github.com/BgeeDB/confidence-information-ontology", + "id": "cio", + "layout": "ontology_detail", + "license": { + "label": "CC0", + "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png", + "url": "https://creativecommons.org/publicdomain/zero/1.0/" + }, + "ontology_purl": "http://purl.obolibrary.org/obo/cio.owl", + "products": [ + { + "id": "cio.owl", + "ontology_purl": "http://purl.obolibrary.org/obo/cio.owl" + }, + { + "id": "cio.obo", + "ontology_purl": "http://purl.obolibrary.org/obo/cio.obo" + } + ], + "title": "Confidence Information Ontology", + "tracker": "https://github.com/BgeeDB/confidence-information-ontology" + }, { "activity_status": "active", "build": { @@ -1559,7 +1597,12 @@ "usages": [ { "description": "The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The ENCODE DCC users Uberon to annotate samples", - "reference": "https://doi.org/10.1093/database/bav010", + "publications": [ + { + "id": "https://doi.org/10.1093/database/bav010", + "title": "Ontology application and use at the ENCODE DCC" + } + ], "seeAlso": "https://www.biosharing.org/biodbcore-000034", "type": "annotation", "user": "https://www.encodeproject.org/" @@ -2090,7 +2133,7 @@ "usages": [ { "description": "FlyBase uses dpo for phenotype data annotation in Drosophila", - "example": [ + "examples": [ { "description": "alleles and constructs annotated to pupal lethal in FlyBase", "url": "http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0002030" @@ -2293,10 +2336,16 @@ "description": "ECO is used by the Monarch Initiative for evidence types for disease to phenotype annotations.", "examples": [ { - "url": "https://monarchinitiative.org/phenotype/HP%3A0001300#diseases" + "description": "Parkinsonism: Characteristic neurologic anomaly resulting form degeneration of dopamine-generating cells in the substantia nigra, a region of the midbrain, characterized clinically by shaking, rigidity, slowness of movement and difficulty with walking and gait.", + "url": "https://monarchinitiative.org/phenotype/HP%3A0001300#disease" + } + ], + "publications": [ + { + "id": "https://academic.oup.com/nar/article/45/D1/D712/2605791", + "title": "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species" } ], - "reference": "https://academic.oup.com/nar/article/45/D1/D712/2605791", "type": "annotation", "user": "https://monarchinitiative.org/" } @@ -2346,7 +2395,7 @@ "id": "iao" } ], - "description": "An ontology to provide core semantics for ecological entities.", + "description": "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.", "domain": "ecological functions, ecological interactions", "homepage": "https://github.com/EcologicalSemantics/ecocore", "id": "ecocore", @@ -2636,9 +2685,31 @@ "title": "Environment Ontology", "tracker": "https://github.com/EnvironmentOntology/envo/issues/", "usages": [ + { + "description": "describing species habitats", + "examples": [ + { + "description": "Pseudobarbus burchelli (Tradou Redfin) is a species of bony fishes in the family Cyprinidae. They are associated with freshwater habitat. Individuals can grow to 13.5 cm. They have sexual reproduction.", + "url": "http://eol.org/pages/211700/data" + } + ], + "type": "data-annotation", + "user": "http://eol.org" + }, + { + "description": "describing stomach contents", + "type": "data-annotation", + "user": "http://globalbioticinteractions.org" + }, + { + "description": "annotating datasets in data repositories", + "seeAlso": "http://blogs.nature.com/scientificdata/2015/12/17/isa-explorer/", + "type": "dataset-description", + "user": "http://www.nature.com/sdata/" + }, { "description": "Samples collected during Tara Oceans expedition are annotated with ENVO", - "example": [ + "examples": [ { "description": "Sample collected during the Tara Oceans expedition (2009-2013) at station TARA_004 (latitudeN=36.5533, longitudeE=-6.5669)", "url": "https://www.ebi.ac.uk/metagenomics/projects/ERP001736/samples/ERS487899" @@ -2648,7 +2719,7 @@ }, { "description": "Annotation of habitats of microbes", - "example": [ + "examples": [ { "description": "Annotation of habitat of Pseudovibrio sp. FO-BEG1 to marine environment", "url": "https://www.ncbi.nlm.nih.gov/nuccore/NC_016642" @@ -2658,7 +2729,7 @@ }, { "description": "Annotation and semantic search over microbial data sets", - "example": [ + "examples": [ { "description": "Example metadata of a sample of marine water near Lisboa, taken as part of the Ocean Sampling Day Project (https://www.microb3.eu/osd.html). ENVO is used for the fields environmental feature, material, and biome.", "url": "https://www.planetmicrobe.org/project/#/samples/200" @@ -2735,6 +2806,7 @@ }, "ontology_purl": "http://purl.obolibrary.org/obo/exo.owl", "page": "http://ctdbase.org/downloads/#exposures", + "preferredPrefix": "ExO", "products": [ { "id": "exo.owl", @@ -2909,7 +2981,11 @@ "usages": [ { "description": "VFB uses FBbt to annotate brain images", - "example": [ + "examples": [ + { + "description": "Ring neuron R2 in VFB", + "url": "http://www.virtualflybrain.org/site/stacks/index.htm?id=FBbt_00003651" + }, { "description": "genes expressed in ring neuron R2 in VFB", "url": "http://www.virtualflybrain.org/do/gene_list.html?action=geneex&id=FBbt:00003651" @@ -2919,7 +2995,7 @@ }, { "description": "Flybase uses FBbt for expression and phenotype data annotation in Drosophila", - "example": [ + "examples": [ { "description": "alleles, constructs and insertions annotated to neuron in FlyBase", "url": "http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBbt:00005106" @@ -2978,7 +3054,7 @@ "usages": [ { "description": "FlyBase uses FBcv for phenotype data annotation in Drosophila", - "example": [ + "examples": [ { "description": "alleles and constructs annotated to bang sensitive in FlyBase", "url": "http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0000391" @@ -3350,7 +3426,7 @@ "usages": [ { "description": "Pombase uses fypo for phenotype data annotation in fission yeast", - "example": [ + "examples": [ { "description": "genotypes annotated to abnormal mitotic cell cycle in fission yeast", "url": "https://www.pombase.org/term/FYPO:0000059" @@ -3591,7 +3667,7 @@ { "activity_status": "active", "contact": { - "email": "dwelter@ebi.ac.uk", + "email": "danielle.welter@uni.lu", "label": "Danielle Welter" }, "description": "The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.", @@ -3607,12 +3683,52 @@ "ontology_purl": "http://purl.obolibrary.org/obo/hancestro.owl", "products": [ { + "description": "The full version of HANCESTRO in OWL format", "id": "hancestro.owl", - "ontology_purl": "http://purl.obolibrary.org/obo/hancestro.owl" + "ontology_purl": "http://purl.obolibrary.org/obo/hancestro.owl", + "title": "HANCESTRO" + }, + { + "description": "Version of HANCESTRO with BFO upper hierarchy for easier integration with other ontologies", + "id": "hancestro_bfo.owl", + "ontology_purl": "http://purl.obolibrary.org/obo/hancestro_bfo.owl", + "title": "HANCESTRO BFO" } ], "title": "Human Ancestry Ontology", - "tracker": "https://github.com/EBISPOT/ancestro/issues" + "tracker": "https://github.com/EBISPOT/ancestro/issues", + "usages": [ + { + "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds.", + "examples": [ + { + "description": "Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data", + "url": "https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false" + } + ], + "user": "http://www.ebi.ac.uk/efo" + }, + { + "description": "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.", + "examples": [ + { + "description": "Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data", + "url": "https://www.ebi.ac.uk/ols/ontologies/genepio/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false" + } + ], + "user": "https://genepio.org/" + }, + { + "description": "FoodOn (http://foodon.org) is a consortium-driven project to build a comprehensive and easily accessible global farm-to-fork ontology about food, that accurately and consistently describes foods commonly known in cultures from around the world.", + "examples": [ + { + "description": "Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data", + "url": "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false" + } + ], + "user": "http://foodon.org" + } + ] }, { "activity_status": "active", @@ -3674,9 +3790,9 @@ "id": "hom", "layout": "ontology_detail", "license": { - "label": "CC-BY", - "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", - "url": "http://creativecommons.org/licenses/by/3.0/" + "label": "CC0", + "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png", + "url": "https://creativecommons.org/publicdomain/zero/1.0/" }, "ontology_purl": "http://purl.obolibrary.org/obo/hom.owl", "products": [ @@ -3710,6 +3826,7 @@ }, "ontology_purl": "http://purl.obolibrary.org/obo/hsapdv.owl", "page": "https://github.com/obophenotype/developmental-stage-ontologies", + "preferredPrefix": "HsapDv", "products": [ { "id": "hsapdv.owl", @@ -3723,6 +3840,52 @@ "title": "Human Developmental Stages", "tracker": "https://github.com/obophenotype/developmental-stage-ontologies/issues" }, + { + "activity_status": "active", + "contact": { + "email": "fernanda.dorea@sva.se", + "github": "nandadorea", + "label": "Fernanda Dorea" + }, + "dependencies": [ + { + "id": "uberon" + }, + { + "id": "bfo" + }, + { + "id": "ro" + }, + { + "id": "obi" + }, + { + "id": "ncbitaxon" + } + ], + "description": "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.", + "domain": "health", + "homepage": "https://w3id.org/hso", + "id": "hso", + "layout": "ontology_detail", + "license": { + "label": "CC-BY", + "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", + "url": "http://creativecommons.org/licenses/by/3.0/" + }, + "ontology_purl": "http://purl.obolibrary.org/obo/hso.owl", + "page": "https://github.com/SVA-SE/HSO", + "products": [ + { + "homepage": "https://w3id.org/hso", + "id": "hso.owl", + "ontology_purl": "http://purl.obolibrary.org/obo/hso.owl" + } + ], + "title": "Health Surveillance Ontology", + "tracker": "https://github.com/SVA-SE/HSO/issues/" + }, { "activity_status": "active", "contact": { @@ -3770,7 +3933,7 @@ "license": { "label": "CC-BY", "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/iao.owl", "products": [ @@ -3801,7 +3964,14 @@ } ], "title": "Information Artifact Ontology", - "tracker": "https://github.com/information-artifact-ontology/IAO/issues" + "tracker": "https://github.com/information-artifact-ontology/IAO/issues", + "usages": [ + { + "description": "IAO is used widely by multiple OBO ontologies for information representation.", + "type": "owl_import", + "user": "http://obofoundry.org" + } + ] }, { "activity_status": "active", @@ -4480,6 +4650,7 @@ }, "ontology_purl": "http://purl.obolibrary.org/obo/mmusdv.owl", "page": "https://github.com/obophenotype/developmental-stage-ontologies", + "preferredPrefix": "MmusDv", "products": [ { "id": "mmusdv.owl", @@ -4498,7 +4669,7 @@ "build": { "insert_ontology_id": true, "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/MICommunity/psidev/master/psi/mod/data/PSI-MOD.obo" + "source_url": "https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo" }, "contact": { "email": "pierre-alain.binz@chuv.ch", @@ -4517,8 +4688,22 @@ "ontology_purl": "http://purl.obolibrary.org/obo/mod.owl", "products": [ { + "description": "PSI-MOD Ontology, OWL format", "id": "mod.owl", - "ontology_purl": "http://purl.obolibrary.org/obo/mod.owl" + "ontology_purl": "http://purl.obolibrary.org/obo/mod.owl", + "title": "PSI-MOD.owl" + }, + { + "description": "PSI-MOD Ontology, OBO format", + "id": "mod.obo", + "ontology_purl": "http://purl.obolibrary.org/obo/mod.obo", + "title": "PSI-MOD.obo" + } + ], + "publications": [ + { + "id": "https://pubmed.ncbi.nlm.nih.gov/18688235/", + "title": "The PSI-MOD community standard for representation of protein modification data" } ], "title": "Protein modification", @@ -4590,12 +4775,56 @@ "description": "Mondo is used by the Monarch Initiative for disease annotations.", "examples": [ { - "url": "https://monarchinitiative.org/phenotype/HP:0001300#diseases" + "description": "Parkinsonism: Characteristic neurologic anomaly resulting form degeneration of dopamine-generating cells in the substantia nigra, a region of the midbrain, characterized clinically by shaking, rigidity, slowness of movement and difficulty with walking and gait.", + "url": "https://monarchinitiative.org/phenotype/HP:0001300#disease" + } + ], + "publications": [ + { + "id": "https://academic.oup.com/nar/article/45/D1/D712/2605791", + "title": "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species " } ], - "reference": "https://academic.oup.com/nar/article/45/D1/D712/2605791", "type": "annotation", "user": "https://monarchinitiative.org/" + }, + { + "description": "Mondo is used by the ClinGen for disease curations.", + "examples": [ + { + "description": "SCN1A is an autosomal dominant mutation in Dravet syndrome.", + "url": "https://search.clinicalgenome.org/kb/conditions/MONDO_0011794" + } + ], + "type": "annotation", + "user": "https://www.clinicalgenome.org/" + }, + { + "description": "Mondo is used by the Kids First Data Resource Portal for disease annotations. Note, a login is needed to access the portal and view the Mondo-curated data.", + "type": "annotation", + "user": "https://portal.kidsfirstdrc.org/" + }, + { + "description": "Mondo is used by the Ancestory for some disease curations.", + "examples": [ + { + "description": "Some term names in ancestory.com are curated with Mondo, for ease of use.", + "url": "https://support.ancestry.com/s/article/Disease-Condition-Catalog-Powered-by-MONDO" + } + ], + "type": "annotation", + "user": "https://www.ancestry.com/" + }, + { + "description": "Mondo is used by the Human Cell Atlas for some disease annotations.", + "examples": [ + { + "description": "Disease status specimen is normal, type 2 diabetes mellitus.", + "url": "https://data.humancellatlas.org/explore/projects?filter=%5B%7B%22facetName%22:%22organ%22,%22terms%22:%5B%22kidney%22%5D%7D,%7B%22facetName%22:%22donorDisease%22,%22terms%22:%5B%22acoustic%20neuroma%22,%22acute%20kidney%20tubular%20necrosis%22%5D%7D%5D&catalog=dcp1" + } + ], + "type": "annotation", + "user": "https://www.humancellatlas.org/" } ] }, @@ -4807,15 +5036,74 @@ "description": "MRO is used by the The Immune Epitope Database (IEDB) annotations", "examples": [ { + "description": "Epitope ID: 59611 based on reference 1003499", "url": "https://www.iedb.org/assay/1357035" } ], - "reference": "DOI:10.1093/nar/gky1006", + "publications": [ + { + "id": "https://doi.org/10.1093/nar/gky1006", + "title": "The Immune Epitope Database (IEDB): 2018 update" + } + ], "type": "annotation", "user": "https://www.iedb.org/" } ] }, + { + "activity_status": "active", + "build": { + "method": "obo2owl", + "source_url": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" + }, + "contact": { + "email": "gerhard.mayer@rub.de", + "label": "Gerhard Mayer" + }, + "createdWith": "http://oboedit.org", + "dependencies": [ + { + "id": "pato" + }, + { + "id": "uo" + } + ], + "description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.", + "domain": "MS experiments", + "homepage": "http://www.psidev.info/groups/controlled-vocabularies", + "id": "ms", + "integration_server": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master", + "label": "MS", + "layout": "ontology_detail", + "license": { + "label": "CC-BY", + "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", + "url": "https://creativecommons.org/licenses/by/3.0/" + }, + "mailing_list": "psidev-ms-vocab@lists.sourceforge.net", + "ontology_purl": "http://purl.obolibrary.org/obo/ms.owl", + "page": "http://www.psidev.info/groups/controlled-vocabularies", + "products": [ + { + "id": "ms.obo", + "ontology_purl": "http://purl.obolibrary.org/obo/ms.obo" + }, + { + "id": "ms.owl", + "ontology_purl": "http://purl.obolibrary.org/obo/ms.owl" + } + ], + "publications": [ + { + "id": "http://www.ncbi.nlm.nih.gov/pubmed/23482073", + "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary." + } + ], + "title": "Mass spectrometry ontology", + "tracker": "https://github.com/HUPO-PSI/psi-ms-CV/issues" + }, { "activity_status": "active", "browsers": [ @@ -4955,7 +5243,10 @@ { "description": "This version replaces NCIt terms with direct references to terms from other domain-specific OBO Library ontologies (e.g. cell types, cellular components, anatomy), supporting cross-ontology reasoning. The current release incorporates CL (cell types) and Uberon (anatomy).", "id": "ncit/ncit-plus.owl", - "mireots_from": "uberon", + "mireots_from": [ + "cl", + "uberon" + ], "ontology_purl": "http://purl.obolibrary.org/obo/ncit/ncit-plus.owl", "title": "NCIt Plus" }, @@ -5045,7 +5336,7 @@ "type": "owl:Ontology", "usages": [ { - "label": "TaxonWorks", + "description": "TaxonWorks is an integrated web-based workbench for taxonomists and biodiversity scientists.", "seeAlso": "https://github.com/SpeciesFileGroup/taxonworks", "type": "application", "user": "https://taxonworks.org" @@ -5418,6 +5709,7 @@ }, "ontology_purl": "http://purl.obolibrary.org/obo/olatdv.owl", "page": "https://github.com/obophenotype/developmental-stage-ontologies", + "preferredPrefix": "OlatDv", "products": [ { "id": "olatdv.obo", @@ -5663,6 +5955,7 @@ "domain": "nutrition, nutritional studies, nutrition professionals", "homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies", "id": "ons", + "label": "Ontology for Nutritional Studies", "layout": "ontology_detail", "license": { "label": "CC-BY", @@ -5678,7 +5971,7 @@ "title": "ONS latest release" } ], - "title": "ONS", + "title": "Ontology for Nutritional Studies", "tracker": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues" }, { @@ -5751,6 +6044,7 @@ "label": "Priti Parikh" }, "description": "A reference ontology for parasite life cycle stages.", + "domain": "life cycle stage, parasite organism", "homepage": "https://github.com/OPL-ontology/OPL", "id": "opl", "layout": "ontology_detail", @@ -5767,7 +6061,19 @@ } ], "title": "Ontology for Parasite LifeCycle", - "tracker": "https://github.com/OPL-ontology/OPL/issues" + "tracker": "https://github.com/OPL-ontology/OPL/issues", + "usages": [ + { + "description": "The ontology for parasite lifecycle is used in the VEuPathDB (Eukaryotic Pathogen, Vector & Host Informatics Resources) for parasite life cycle annotation.", + "type": "annotation and query", + "user": "https://veupathdb.org" + }, + { + "description": "The ontology for parasite lifecycle is used in the GeneDB for parasite life cycle annotation.", + "type": "annotation and query", + "user": "https://www.genedb.org" + } + ] }, { "activity_status": "active", @@ -5964,6 +6270,7 @@ }, "ontology_purl": "http://purl.obolibrary.org/obo/pdumdv.owl", "page": "https://github.com/obophenotype/developmental-stage-ontologies", + "preferredPrefix": "PdumDv", "products": [ { "id": "pdumdv.owl", @@ -6486,15 +6793,18 @@ "tracker": "https://github.com/oborel/obo-relations/issues", "usages": [ { - "description": "RO is used for annotation extensions in the GO", - "reference": "https://doi.org/10.1186/1471-2105-15-155", - "type": "annotation", - "user": "http://geneontology.org" - }, - { - "description": "RO is used for GO Causal Activity Models", + "description": "RO is used for annotation extensions in the GO and GO Causal Activity Models.", "examples": [ - "http://model.geneontology.org/56d1143000003402" + { + "description": "wg_biogenesis_FlyBase", + "url": "http://model.geneontology.org/56d1143000003402" + } + ], + "publications": [ + { + "id": "https://doi.org/10.1186/1471-2105-15-155", + "title": "A method for increasing expressivity of Gene Ontology annotations using a compositional approach" + } ], "type": "annotation", "user": "http://geneontology.org" @@ -6729,17 +7039,47 @@ { "activity_status": "active", "build": { - "infallible": 1, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/symp.obo" + "method": "owl2obo", + "source_url": "https://raw.githubusercontent.com/allysonlister/swo/master/release/swo_inferred.owl" }, "contact": { - "email": "lynn.schriml@gmail.com", - "label": "Lynn Schriml" + "email": "allyson.lister@oerc.ox.ac.uk", + "label": "Allyson Lister" }, - "description": "An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease.", - "domain": "disease", - "homepage": "http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page", + "description": "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.", + "domain": "software", + "homepage": "https://github.com/allysonlister/swo", + "id": "swo", + "layout": "ontology_detail", + "license": { + "label": "CC BY 4.0", + "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, + "ontology_purl": "http://purl.obolibrary.org/obo/swo.owl", + "products": [ + { + "id": "swo.owl", + "ontology_purl": "http://purl.obolibrary.org/obo/swo.owl" + } + ], + "title": "Software ontology", + "tracker": "https://github.com/allysonlister/swo/issues" + }, + { + "activity_status": "active", + "build": { + "infallible": 1, + "method": "obo2owl", + "source_url": "https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/symp.obo" + }, + "contact": { + "email": "lynn.schriml@gmail.com", + "label": "Lynn Schriml" + }, + "description": "An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease.", + "domain": "disease", + "homepage": "http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page", "id": "symp", "layout": "ontology_detail", "license": { @@ -7084,7 +7424,7 @@ { "description": "Uberon extended", "id": "uberon/ext.owl", - "mireots_from": "ncbitaxon", + "mireots_from": "cl", "ontology_purl": "http://purl.obolibrary.org/obo/uberon/ext.owl", "title": "Uberon edition that includes subsets of other ontologies and axioms connecting to them", "type": "owl:Ontology" @@ -7132,7 +7472,6 @@ { "description": "Extended uberon plus all metazoan ontologies", "id": "uberon/composite-metazoan.owl", - "mireots_from": "ehdaa2", "ontology_purl": "http://purl.obolibrary.org/obo/uberon/composite-metazoan.owl", "page": "https://github.com/obophenotype/uberon/wiki/Multi-species-composite-ontologies", "taxon": "Metazoa", @@ -7141,7 +7480,16 @@ }, { "id": "uberon/composite-vertebrate.owl", - "mireots_from": "ehdaa2", + "mireots_from": [ + "zfa", + "xao", + "fbbt", + "wbbt", + "ma", + "fma", + "emapa", + "ehdaa2" + ], "ontology_purl": "http://purl.obolibrary.org/obo/uberon/composite-vertebrate.owl", "page": "https://github.com/obophenotype/uberon/wiki/Multi-species-composite-ontologies", "taxon": "Metazoa", @@ -7195,7 +7543,12 @@ }, { "description": "The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The ENCODE DCC users Uberon to annotate samples", - "reference": "https://doi.org/10.1093/database/bav010", + "publications": [ + { + "id": "https://doi.org/10.1093/database/bav010", + "title": "Ontology application and use at the ENCODE DCC" + } + ], "seeAlso": "https://www.biosharing.org/biodbcore-000034", "type": "annotation", "user": "https://www.encodeproject.org/" @@ -7217,44 +7570,51 @@ "user": "https://monarchinitiative.org/" }, { - "description": "Querying for functional annotations relevant to a tissue", + "description": "GO Database is used for querying for functional annotations relevant to a tissue", "examples": [ { "description": "GO annotations relevant to the uberon class for brain", "url": "http://amigo.geneontology.org/amigo/term/UBERON:0000955" } ], - "label": "GO Database", "type": "query", "user": "https://geneontology.org/" }, { "description": "The Phenoscape project is both a major driver of and contributor to Uberon, contibuting thousands of terms. The teleost (bony fishes) component of Uberon was derived from the Teleost Anatomy Ontology, developed by the Phenoscape group. Most of the high level design of the skeletal system comes from the Vertebrate Skeletal Anatomy Ontology (VSAO), also created by the Phenoscape group. Phenoscape curators continue to extend the ontology, covering a wide variety of tetrapod structures, with an emphasis on the appendicular system.", - "label": "Phenoscape", "user": "http://phenoscape.org" }, { - "label": "Neuroscience Information Framework", + "description": "Searchable collection of neuroscience data and ontology for neuroscience", "type": "Database", - "url": "https://neuinfo.org/" + "user": "https://neuinfo.org/" }, { - "label": "SciCrunch", + "description": "cooperative data platform to be used by diverse communities in making data more FAIR.", "type": "Database", - "url": "https://scicrunch.org/" + "user": "https://scicrunch.org/" }, { - "label": "SCPortalen", - "reference": "https://doi.org/10.1093/nar/gkx949", + "description": "SCPortalen", + "publications": [ + { + "id": "https://doi.org/10.1093/nar/gkx949", + "title": "SCPortalen: human and mouse single-cell centric database" + } + ], "type": "Database", - "url": "http://single-cell.clst.riken.jp/" + "user": "http://single-cell.clst.riken.jp/" }, { "description": "ChEMBL uses Uberon to describe organ/tissue information in assays", - "label": "ChEMBL", - "reference": "https://doi.org/10.1093/nar/gky1075", + "publications": [ + { + "id": "https://doi.org/10.1093/nar/gky1075", + "title": "ChEMBL: towards direct deposition of bioassay data" + } + ], "type": "Database", - "url": "https://www.ebi.ac.uk/chembl/" + "user": "https://www.ebi.ac.uk/chembl/" } ], "wikidata_template": "https://en.wikipedia.org/wiki/Template:Uberon" @@ -7336,10 +7696,16 @@ "description": "uPheno is used by the Monarch Initiative for cross-species inference.", "examples": [ { - "url": "https://monarchinitiative.org/phenotype/HP:0001300#diseases" + "description": "Characteristic neurologic anomaly resulting form degeneration of dopamine-generating cells in the substantia nigra, a region of the midbrain, characterized clinically by shaking, rigidity, slowness of movement and difficulty with walking and gait.", + "url": "https://monarchinitiative.org/phenotype/HP:0001300#disease" + } + ], + "publications": [ + { + "id": "https://academic.oup.com/nar/article/45/D1/D712/2605791", + "title": "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species " } ], - "reference": "https://academic.oup.com/nar/article/45/D1/D712/2605791", "type": "analysis", "user": "https://monarchinitiative.org/" } @@ -7374,6 +7740,36 @@ "title": "Vaccine Ontology", "tracker": "https://github.com/vaccineontology/VO/issues" }, + { + "activity_status": "active", + "build": { + "checkout": "svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt", + "method": "vcs", + "system": "svn" + }, + "contact": { + "email": "caripark@iastate.edu", + "label": "Carissa Park" + }, + "description": "An ontology of traits covering vertebrates", + "homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology", + "id": "vt", + "layout": "ontology_detail", + "license": { + "label": "CC BY 4.0", + "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, + "ontology_purl": "http://purl.obolibrary.org/obo/vt.owl", + "products": [ + { + "id": "vt.owl", + "ontology_purl": "http://purl.obolibrary.org/obo/vt.owl" + } + ], + "title": "Vertebrate trait ontology", + "tracker": "https://github.com/AnimalGenome/vertebrate-trait-ontology/issues" + }, { "activity_status": "active", "contact": { @@ -7465,10 +7861,16 @@ "description": "WormBase uses WBbt to curate anatomical expression patterns and anatomy function annotations, and to allow search and indexing on the WormBase site", "examples": [ { + "description": "Expression for gene daf-16 with WormBase ID WBGene00000912", "url": "http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression" } ], - "reference": "https://academic.oup.com/nar/article/48/D1/D762/5603222", + "publications": [ + { + "id": "https://academic.oup.com/nar/article/48/D1/D762/5603222", + "title": "WormBase: a modern Model Organism Information Resource" + } + ], "type": "annotation", "user": "https://www.wormbase.org/" } @@ -7524,10 +7926,16 @@ "description": "WormBase uses WBls to curate temporal expression patterns, and to allow search and indexing on the WormBase site", "examples": [ { + "description": "Expression for daf-16 gene with WormBase ID WBGene00000912.", "url": "http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression" } ], - "reference": "https://academic.oup.com/nar/article/48/D1/D762/5603222", + "publications": [ + { + "id": "https://academic.oup.com/nar/article/48/D1/D762/5603222", + "title": "WormBase: a modern Model Organism Information Resource" + } + ], "type": "annotation", "user": "https://www.wormbase.org/" } @@ -7587,10 +7995,16 @@ "description": "WormBase uses WBPhenotype to curate worm phenotypes, and to allow search and indexing on the WormBase site", "examples": [ { - "url": "http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=phenotype" + "description": "Expression for daf-16 gene with WormBase ID WBGene00000912.", + "url": "http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression" + } + ], + "publications": [ + { + "id": "https://academic.oup.com/nar/article/48/D1/D762/5603222", + "title": "WormBase: a modern Model Organism Information Resource" } ], - "reference": "https://academic.oup.com/nar/article/48/D1/D762/5603222", "type": "annotation", "user": "https://www.wormbase.org/" }, @@ -7598,10 +8012,16 @@ "description": "Monarch integrates phenotype annotations from sources such as WormBase, and allows for querying using the WBPhenotype ontology.", "examples": [ { + "description": "Egg long: The fertilized oocytes have a greater than standard length measured end to end compared to control.", "url": "https://monarchinitiative.org/phenotype/WBPhenotype%3A0000370" } ], - "reference": "https://academic.oup.com/nar/article/45/D1/D712/2605791", + "publications": [ + { + "id": "https://academic.oup.com/nar/article/45/D1/D712/2605791", + "title": "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species " + } + ], "type": "annotation", "user": "https://monarchinitiative.org/" } @@ -7658,6 +8078,41 @@ "title": "Experimental condition ontology", "tracker": "https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues" }, + { + "activity_status": "active", + "build": { + "method": "obo2owl", + "source_url": "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo" + }, + "contact": { + "email": "gerhard.mayer@rub.de", + "label": "Gerhard Mayer" + }, + "createdWith": "http://oboedit.org", + "description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.", + "domain": "MS cross-linker reagents", + "homepage": "http://www.psidev.info/groups/controlled-vocabularies", + "id": "xlmod", + "integration_server": "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/tree/master/cv", + "label": "xlmod", + "layout": "ontology_detail", + "license": { + "label": "CC-BY", + "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", + "url": "https://creativecommons.org/licenses/by/3.0/" + }, + "mailing_list": "psidev-ms-vocab@lists.sourceforge.net", + "ontology_purl": "http://purl.obolibrary.org/obo/xlmod.owl", + "page": "http://www.psidev.info/groups/controlled-vocabularies", + "products": [ + { + "id": "xlmod.obo", + "ontology_purl": "http://purl.obolibrary.org/obo/xlmod.obo" + } + ], + "title": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary", + "tracker": "https://github.com/HUPO-PSI/mzIdentML/issues" + }, { "activity_status": "active", "build": { @@ -7772,6 +8227,47 @@ "title": "Zebrafish Experimental Conditions Ontology", "tracker": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues" }, + { + "activity_status": "active", + "build": { + "infallible": 1, + "method": "obo2owl", + "source_url": "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo" + }, + "contact": { + "email": "van_slyke@zfin.org", + "label": "Ceri Van Slyke" + }, + "description": "Developmental stages of the Zebrafish", + "domain": "anatomy", + "homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources", + "id": "zfs", + "in_foundry": false, + "layout": "ontology_detail", + "license": { + "label": "CC-BY 3.0", + "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", + "url": "http://creativecommons.org/licenses/by/3.0/" + }, + "ontology_purl": "http://purl.obolibrary.org/obo/zfs.owl", + "page": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/ZFS", + "products": [ + { + "id": "zfs.owl", + "ontology_purl": "http://purl.obolibrary.org/obo/zfs.owl" + }, + { + "id": "zfs.obo", + "ontology_purl": "http://purl.obolibrary.org/obo/zfs.obo" + } + ], + "taxon": { + "id": "NCBITaxon:7954", + "label": "Danio" + }, + "title": "Zebrafish developmental stages ontology", + "tracker": "https://github.com/cerivs/zebrafish-anatomical-ontology/issues" + }, { "activity_status": "active", "build": { @@ -7840,44 +8336,21 @@ "description": "Monarch integrates phenotype annotations from sources such as ZFIIN, and allows for querying using the ZP ontology.", "examples": [ { + "description": "adaxial cell absent, abnormal: Abnormal(ly) absent (of) adaxial cell.", "url": "https://monarchinitiative.org/phenotype/ZP:0005692" } ], - "reference": "https://academic.oup.com/nar/article/45/D1/D712/2605791", + "publications": [ + { + "id": "https://academic.oup.com/nar/article/45/D1/D712/2605791", + "title": "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species" + } + ], "type": "annotation", "user": "https://monarchinitiative.org/" } ] }, - { - "activity_status": "active", - "contact": { - "email": "bgee@sib.swiss", - "github": "fbastian", - "label": "Frederic Bastian" - }, - "description": "An ontology to capture confidence information about annotations.", - "homepage": "https://github.com/BgeeDB/confidence-information-ontology", - "id": "cio", - "layout": "ontology_detail", - "license": { - "label": "GNU GPL 3.0", - "url": "https://www.gnu.org/licenses/gpl-3.0.en.html" - }, - "ontology_purl": "http://purl.obolibrary.org/obo/cio.owl", - "products": [ - { - "id": "cio.owl", - "ontology_purl": "http://purl.obolibrary.org/obo/cio.owl" - }, - { - "id": "cio.obo", - "ontology_purl": "http://purl.obolibrary.org/obo/cio.obo" - } - ], - "title": "Confidence Information Ontology", - "tracker": "https://github.com/BgeeDB/confidence-information-ontology" - }, { "activity_status": "active", "build": { @@ -7885,8 +8358,8 @@ "source_url": "http://purl.obolibrary.org/obo/ero.owl" }, "contact": { - "email": "Juliane_Schneider@hms.harvard.edu", - "label": "Juliane Schneider" + "email": "Marc_Ciriello@hms.harvard.edu", + "label": "Marc Ciriello" }, "description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.", "documentation": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology", @@ -8101,7 +8574,8 @@ "ontology_purl": "http://purl.obolibrary.org/obo/kisao.owl" } ], - "title": "Kinetic Simulation Algorithm Ontology" + "title": "Kinetic Simulation Algorithm Ontology", + "tracker": "https://sourceforge.net/p/kisao/feature-requests/" }, { "activity_status": "active", @@ -8131,58 +8605,6 @@ "title": "Mathematical modeling ontology", "tracker": "http://sourceforge.net/p/mamo-ontology/tickets/" }, - { - "activity_status": "active", - "build": { - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" - }, - "contact": { - "email": "gerhard.mayer@rub.de", - "label": "Gerhard Mayer" - }, - "createdWith": "http://oboedit.org", - "dependencies": [ - { - "id": "pato" - }, - { - "id": "uo" - } - ], - "description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.", - "domain": "MS experiments", - "homepage": "http://www.psidev.info/groups/controlled-vocabularies", - "id": "ms", - "integration_server": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master", - "label": "MS", - "layout": "ontology_detail", - "license": { - "label": "CC-BY", - "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", - "url": "https://creativecommons.org/licenses/by/3.0/" - }, - "mailing_list": "psidev-ms-vocab@lists.sourceforge.net", - "ontology_purl": "http://purl.obolibrary.org/obo/ms.owl", - "page": "http://www.psidev.info/groups/controlled-vocabularies", - "products": [ - { - "id": "ms.obo", - "ontology_purl": "http://purl.obolibrary.org/obo/ms.obo" - }, - { - "id": "ms.owl", - "ontology_purl": "http://purl.obolibrary.org/obo/ms.owl" - } - ], - "publications": [ - { - "id": "http://www.ncbi.nlm.nih.gov/pubmed/23482073", - "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary." - } - ], - "title": "Mass spectrometry ontology" - }, { "activity_status": "active", "build": { @@ -8213,35 +8635,6 @@ "title": "Systems Biology Ontology", "tracker": "https://sourceforge.net/p/sbo/term-request/" }, - { - "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "https://raw.githubusercontent.com/allysonlister/swo/master/release/swo_inferred.owl" - }, - "contact": { - "email": "allyson.lister@oerc.ox.ac.uk", - "label": "Allyson Lister" - }, - "description": "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.", - "domain": "software", - "homepage": "https://github.com/allysonlister/swo", - "id": "swo", - "layout": "ontology_detail", - "license": { - "label": "CC BY 4.0", - "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", - "url": "https://creativecommons.org/licenses/by/4.0/" - }, - "ontology_purl": "http://purl.obolibrary.org/obo/swo.owl", - "products": [ - { - "id": "swo.owl", - "ontology_purl": "http://purl.obolibrary.org/obo/swo.owl" - } - ], - "title": "Software ontology" - }, { "activity_status": "active", "browsers": [ @@ -8269,7 +8662,7 @@ "license": { "label": "CC-BY version 3.0", "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", - "url": "http://creativecommons.org/licenses/by/3.0/" + "url": "https://creativecommons.org/licenses/by/3.0/" }, "ontology_purl": "http://purl.obolibrary.org/obo/txpo.owl", "products": [ @@ -8281,109 +8674,6 @@ "title": "Toxic Process Ontology", "tracker": "https://github.com/txpo-ontology/TXPO/issues" }, - { - "activity_status": "active", - "build": { - "checkout": "svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt", - "method": "vcs", - "system": "svn" - }, - "contact": { - "email": "caripark@iastate.edu", - "label": "Carissa Park" - }, - "description": "An ontology of traits covering vertebrates", - "homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology", - "id": "vt", - "layout": "ontology_detail", - "license": { - "label": "CC BY 4.0", - "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", - "url": "https://creativecommons.org/licenses/by/4.0/" - }, - "ontology_purl": "http://purl.obolibrary.org/obo/vt.owl", - "products": [ - { - "id": "vt.owl", - "ontology_purl": "http://purl.obolibrary.org/obo/vt.owl" - } - ], - "title": "Vertebrate trait ontology" - }, - { - "activity_status": "active", - "build": { - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo" - }, - "contact": { - "email": "gerhard.mayer@rub.de", - "label": "Gerhard Mayer" - }, - "createdWith": "http://oboedit.org", - "description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.", - "domain": "MS cross-linker reagents", - "homepage": "http://www.psidev.info/groups/controlled-vocabularies", - "id": "xlmod", - "integration_server": "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/tree/master/cv", - "label": "xlmod", - "layout": "ontology_detail", - "license": { - "label": "CC-BY", - "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", - "url": "https://creativecommons.org/licenses/by/3.0/" - }, - "mailing_list": "psidev-ms-vocab@lists.sourceforge.net", - "ontology_purl": "http://purl.obolibrary.org/obo/xlmod.owl", - "page": "http://www.psidev.info/groups/controlled-vocabularies", - "products": [ - { - "id": "xlmod.obo", - "ontology_purl": "http://purl.obolibrary.org/obo/xlmod.obo" - } - ], - "title": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" - }, - { - "activity_status": "active", - "build": { - "infallible": 1, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo" - }, - "contact": { - "email": "van_slyke@zfin.org", - "label": "Ceri Van Slyke" - }, - "description": "Developmental stages of the Zebrafish", - "domain": "anatomy", - "homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources", - "id": "zfs", - "in_foundry": false, - "layout": "ontology_detail", - "license": { - "label": "CC-BY 3.0", - "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", - "url": "http://creativecommons.org/licenses/by/3.0/" - }, - "ontology_purl": "http://purl.obolibrary.org/obo/zfs.owl", - "page": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/ZFS", - "products": [ - { - "id": "zfs.owl", - "ontology_purl": "http://purl.obolibrary.org/obo/zfs.owl" - }, - { - "id": "zfs.obo", - "ontology_purl": "http://purl.obolibrary.org/obo/zfs.obo" - } - ], - "taxon": { - "id": "NCBITaxon:7954", - "label": "Danio" - }, - "title": "Zebrafish developmental stages ontology" - }, { "activity_status": "orphaned", "build": { @@ -8448,6 +8738,29 @@ ], "title": "Physico-chemical methods and properties" }, + { + "activity_status": "orphaned", + "build": { + "method": "obo2owl", + "source_url": "http://variationontology.org/vario_download/vario.obo" + }, + "contact": { + "email": "mauno.vihinen@med.lu.se", + "label": "Mauno Vihinen" + }, + "description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.", + "homepage": "http://variationontology.org", + "id": "vario", + "layout": "ontology_detail", + "ontology_purl": "http://purl.obolibrary.org/obo/vario.owl", + "products": [ + { + "id": "vario.owl", + "ontology_purl": "http://purl.obolibrary.org/obo/vario.owl" + } + ], + "title": "Variation Ontology" + }, { "activity_status": "orphaned", "description": "An ontology that formalizes the genomic element by defining an upper class genetic interval", @@ -8483,25 +8796,6 @@ ], "title": "Physico-chemical process" }, - { - "activity_status": "orphaned", - "build": { - "method": "obo2owl", - "source_url": "http://variationontology.org/vario_download/vario.obo" - }, - "description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.", - "homepage": "http://variationontology.org", - "id": "vario", - "layout": "ontology_detail", - "ontology_purl": "http://purl.obolibrary.org/obo/vario.owl", - "products": [ - { - "id": "vario.owl", - "ontology_purl": "http://purl.obolibrary.org/obo/vario.owl" - } - ], - "title": "Variation Ontology" - }, { "activity_status": "inactive", "build": { diff --git a/registry/ontologies.nt b/registry/ontologies.nt new file mode 100644 index 000000000..b67edeeef --- /dev/null +++ b/registry/ontologies.nt @@ -0,0 +1,4342 @@ + "active" . + "The upper level ontology upon which OBO Foundry ontologies are built." . + "Basic Formal Ontology" . + . + "upper" . + "https://github.com/BFO-ontology/BFO/issues" . + "https://groups.google.com/forum/#!forum/bfo-discuss" . + . + "http://purl.obolibrary.org/obo/bfo.owl" . + _:B8ec389617ff6109f8024d72aa805a494 . + . + . + . + . + "CC-BY" . + "CC BY 4.0" . + "CC-BY 4.0" . + "BioPortal Browser" . + "BioPortal" . +_:B8ec389617ff6109f8024d72aa805a494 "Barry Smith" . +_:B8ec389617ff6109f8024d72aa805a494 "phismith@buffalo.edu" . + "http://purl.obolibrary.org/obo/bfo.owl" . + "http://purl.obolibrary.org/obo/bfo.obo" . + "ChEBI" . + "active" . + _:B2db3068bb32339a4da1fcf21b49bdd1d . + "A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds." . + "Chemical Entities of Biological Interest" . + . + . + "biochemistry" . + "https://github.com/ebi-chebi/ChEBI/issues" . + . + "http://purl.obolibrary.org/obo/chebi.owl" . + _:Ba11f828d2a06bb4f2fa44f77c8762001 . + . + . + . + . + . + . + . + . +_:B2db3068bb32339a4da1fcf21b49bdd1d "obo2owl" . +_:B2db3068bb32339a4da1fcf21b49bdd1d "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo"^^ . + . + "CC-BY 4.0" . + "CC BY 4.0" . + "CC-BY" . + "ChEBI in 2016: Improved services and an expanding collection of metabolites." . + "EBI CHEBI Browser" . + "CHEBI" . +_:Ba11f828d2a06bb4f2fa44f77c8762001 "Adnan Malik" . +_:Ba11f828d2a06bb4f2fa44f77c8762001 "amalik@ebi.ac.uk" . + "http://purl.obolibrary.org/obo/chebi.owl" . + "http://purl.obolibrary.org/obo/chebi.obo" . + "chebi, compressed owl" . + "http://purl.obolibrary.org/obo/chebi.owl.gz" . + "chebi_lite, no syns or xrefs" . + "http://purl.obolibrary.org/obo/chebi/chebi_lite.obo" . + "chebi_core, no xrefs" . + "http://purl.obolibrary.org/obo/chebi/chebi_core.obo" . + "active" . + _:Bee223fbdfce5b880da97d1ff20e6653c . + . + "An ontology for describing the classification of human diseases organized by etiology." . + "Human Disease Ontology" . + . + . + "disease" . + "https://github.com/DiseaseOntology/HumanDiseaseOntology/issues" . + . + "http://purl.obolibrary.org/obo/doid.owl" . + _:Bfcafa7b5dfaa26dd3911daf2715095b0 . + . + . + . + . + . +_:Bee223fbdfce5b880da97d1ff20e6653c "obo2owl" . +_:Bee223fbdfce5b880da97d1ff20e6653c "https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo"^^ . + "Homo sapiens" . + . + "CC0 1.0 Universal" . + "CC-0" . + "CC0" . + "Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data" . + "DO Browser" . + "DO" . +_:Bfcafa7b5dfaa26dd3911daf2715095b0 "Lynn Schriml" . +_:Bfcafa7b5dfaa26dd3911daf2715095b0 "lynn.schriml@gmail.com" . + "Disease Ontology, OWL format. This file contains DO's is_a asserted hierarchy plus equivalent axioms to other OBO Foundry ontologies." . + "http://purl.obolibrary.org/obo/doid.owl" . + "Disease Ontology, OBO format. This file omits the equivalent axioms." . + "http://purl.obolibrary.org/obo/doid.obo" . + "active" . + "http://build.berkeleybop.org/view/GO" . + . + . + . + . + . + . + "An ontology for describing the function of genes and gene products" . + "Gene Ontology" . + . + "biology" . + "https://github.com/geneontology/go-ontology/issues/" . + "GO" . + . + "http://purl.obolibrary.org/obo/go.owl" . + _:Bccec3161fbc036083e4aac3006f1ef2c . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "active" . + . + . + . + . + _:Be3eb423679d9bc92d65a1e81c2027d33 . + . + "An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies" . + "Uberon multi-species anatomy ontology" . + . + . + . + "anatomy" . + "NIH R24OD011883" . + "NIH R01HG004838" . + "NIH P41HG002273" . + "NSF DEB-0956049" . + . + "https://github.com/obophenotype/uberon/issues" . + "https://lists.sourceforge.net/lists/listinfo/obo-anatomy" . + . + "Uberon" . + "https://www.biosharing.org/bsg-000016" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/uberon.owl" . + _:B97fecff7f8d5dd6785551d850220c0d4 . + . + . + . + . + . + . + . + . + . + . + . + . + "active" . + "http://build.berkeleybop.org/job/build-cl/" . + . + . + . + . + . + _:B601657ebc62b8caaa15d3f328775bd8f . + . + "The Cell Ontology is a structured controlled vocabulary for cell types in animals." . + "Cell Ontology" . + . + . + "cells" . + "https://github.com/obophenotype/cell-ontology/issues" . + "https://groups.google.com/g/cl_edit" . + "Cell Ontology" . + "http://purl.obolibrary.org/obo/cl.owl" . + _:B70446a8a6cef504ca4ae0b425af1bad0 . + . + . + . + . + . + "NCBITaxon" . + "active" . + _:B17f6c1c5c558e683e8ea18d0ffffb1ae . + "An ontology representation of the NCBI organismal taxonomy" . + "http://www.ncbi.nlm.nih.gov/taxonomy" . + "NCBI organismal classification" . + . + "taxonomy" . + "https://github.com/owlcollab/owltools/" . + "ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat" . + "https://github.com/obophenotype/ncbitaxon/issues" . + . + "http://purl.obolibrary.org/obo/ncbitaxon.owl" . + _:B86bd45137e813abfc8c6d49402320d92 . + . + . + . + . + . + . + "active" . + _:B568e2d1c8b6c594d6b3e0869aa17bcdf . + "Relationship types shared across multiple ontologies" . + "Relation Ontology" . + . + "relations" . + "https://github.com/oborel/obo-relations/issues" . + "https://groups.google.com/forum/#!forum/obo-relations" . + "http://purl.obolibrary.org/obo/ro.owl" . + _:B22167dd7d3fdbe3a6790ea3cf30310cc . + . + . + . + . + . + . + . + . + "Bridging axioms between nifstd and go" . + "GO bridge to NIFSTD" . + . + . + "The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments." . + "All life" . + "Gene Ontology AmiGO 2 Browser" . + "AmiGO" . +_:Bccec3161fbc036083e4aac3006f1ef2c "Suzi Aleksander" . +_:Bccec3161fbc036083e4aac3006f1ef2c "suzia@stanford.edu" . + "The main ontology in OWL. This is self contained and does not have connections to other OBO ontologies" . + "GO (OWL edition)" . + "http://purl.obolibrary.org/obo/go.owl" . + . + "Equivalent to go.owl, in obo format" . + "GO (OBO Format edition)" . + "http://purl.obolibrary.org/obo/go.obo" . + . + "Equivalent to go.owl, in obograph json format" . + "GO (JSON edition)" . + "http://purl.obolibrary.org/obo/go.json" . + . + "The main ontology plus axioms connecting to select external ontologies, with subsets of those ontologies" . + "GO-Plus" . + "http://purl.obolibrary.org/obo/go/extensions/go-plus.owl" . + . + "The main ontology plus axioms connecting to select external ontologies, excluding the external ontologies themselves" . + "GO Base Module" . + "http://purl.obolibrary.org/obo/go/go-base.owl" . + . + "As go-plus.owl, in obographs json format" . + "GO-Plus" . + "http://purl.obolibrary.org/obo/go/extensions/go-plus.json" . + . + "Basic version of the GO, filtered such that the graph is guaranteed to be acyclic and annotations can be propagated up the graph. The relations included are is a, part of, regulates, negatively regulates and positively regulates. This version excludes relationships that cross the 3 GO hierarchies." . + "GO-Basic, Filtered, for use with legacy tools" . + "http://purl.obolibrary.org/obo/go/go-basic.obo" . + . + "As go-basic.obo, in json format" . + "GO-Basic, Filtered, for use with legacy tools (JSON)" . + "http://purl.obolibrary.org/obo/go/go-basic.json" . + . + "Classes added to ncbitaxon for groupings such as prokaryotes" . + "GO Taxon Groupings" . + "http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl" . + . + "Equivalent to go.owl, but released daily. Note the snapshot release is not archived." . + "GO (OWL edition), daily snapshot release" . + "http://purl.obolibrary.org/obo/go/snapshot/go.owl" . + . + "Equivalent to go.owl, but released daily. Note the snapshot release is not archived." . + "GO (OBO Format edition), daily snapshot release" . + "http://purl.obolibrary.org/obo/go/snapshot/go.obo" . + . + "active" . + "http://build.berkeleybop.org/job/build-obi/" . + _:B7e41b480491effd4a60afe5d002b81ad . + "An integrated ontology for the description of life-science and clinical investigations" . + "Ontology for Biomedical Investigations" . + . + "experiments" . + "http://purl.obolibrary.org/obo/obi/tracker" . + "http://groups.google.com/group/obi-users" . + . + "http://purl.obolibrary.org/obo/obi.owl" . + _:B16bbaf882ac3e217bbc3fd0de96b7e8b . + . + . + . + . +_:B7e41b480491effd4a60afe5d002b81ad "http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/"^^ . + "BioPortal Browser" . + "BioPortal" . +_:B16bbaf882ac3e217bbc3fd0de96b7e8b "Bjoern Peters" . +_:B16bbaf882ac3e217bbc3fd0de96b7e8b "bpeters@lji.org" . + "The full version of OBI in OWL format" . + "OBI" . + "http://purl.obolibrary.org/obo/obi.owl" . + "The OBO-format version of OBI" . + "OBI in OBO" . + "http://purl.obolibrary.org/obo/obi.obo" . + "A collection of important high-level terms and their relations from OBI and other ontologies" . + "OBI Core" . + "http://purl.obolibrary.org/obo/obi/obi_core.owl" . + "active" . + _:B7ec0e32989aec0993438ddcbb7ae6082 . + "An ontology of phenotypic qualities (properties, attributes or characteristics)" . + "Phenotype And Trait Ontology" . + . + "phenotype" . + "https://github.com/pato-ontology/pato/issues" . + . + "http://purl.obolibrary.org/obo/pato.owl" . + _:B6070669b440f90f696f5b2ab42d758a8 . + . + . + . + . + . +_:B7ec0e32989aec0993438ddcbb7ae6082 "obo2owl" . +_:B7ec0e32989aec0993438ddcbb7ae6082 "https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo"^^ . + . + "CC-BY" . + "CC BY 3.0" . + "CC-BY 3.0" . + "BioPortal Ontology Browser" . + "BioPortal" . +_:B6070669b440f90f696f5b2ab42d758a8 "George Gkoutos" . +_:B6070669b440f90f696f5b2ab42d758a8 "g.gkoutos@gmail.com" . + "http://purl.obolibrary.org/obo/pato.owl" . + "http://purl.obolibrary.org/obo/pato.obo" . + "http://purl.obolibrary.org/obo/pato.json" . + "Includes axioms linking to other ontologies, but no imports of those ontologies" . + "http://purl.obolibrary.org/obo/pato/pato-base.owl" . + "active" . + _:B59d629463ca6c70686071738877415e2 . + . + "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data." . + "Plant Ontology" . + . + . + . + "anatomy and development" . + "https://github.com/Planteome/plant-ontology/issues" . + . + "http://purl.obolibrary.org/obo/po.owl" . + _:Bbbf57d20b40f76832e0ab8b180b04017 . + . + . + . + . + . +_:B59d629463ca6c70686071738877415e2 "git clone https://github.com/Planteome/plant-ontology.git" . +_:B59d629463ca6c70686071738877415e2 "vcs" . + "Viridiplantae" . + "The plant ontology as a tool for comparative plant anatomy and genomic analyses." . + "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics." . + "Planteome browser" . + "Planteome" . +_:Bbbf57d20b40f76832e0ab8b180b04017 "Pankaj Jaiswal" . +_:Bbbf57d20b40f76832e0ab8b180b04017 "jaiswalp@science.oregonstate.edu" . + "http://purl.obolibrary.org/obo/po.owl" . + "http://purl.obolibrary.org/obo/po.obo" . + "active" . + _:Baedf4b7d1d9b71839b1e7240816f3da6 . + "An ontological representation of protein-related entities" . + "PRotein Ontology (PRO)" . + . + . + "proteins" . + "https://github.com/PROconsortium/PRoteinOntology/issues" . + . + . + "http://purl.obolibrary.org/obo/pr.owl" . + _:Bb1dffb7442f2b42f30ec730f0431b243 . + . + . + . +_:Baedf4b7d1d9b71839b1e7240816f3da6 "obo2owl" . +_:Baedf4b7d1d9b71839b1e7240816f3da6 "https://proconsortium.org/download/current/pro_nonreasoned.obo"^^ . + "Publications & Dissemination" . + "BioPortal Browser" . + "BioPortal" . + "PRO Home" . + "PRO" . +_:Bb1dffb7442f2b42f30ec730f0431b243 "Darren Natale" . +_:Bb1dffb7442f2b42f30ec730f0431b243 "dan5@georgetown.edu" . + "PRO after reasoning has been applied, OWL format." . + "pro_reasoned.owl" . + "http://purl.obolibrary.org/obo/pr.owl" . + "PRO after reasoning has been applied, OBO format." . + "pro_reasoned.obo" . + "http://purl.obolibrary.org/obo/pr.obo" . + "active" . + _:B93652a06fd9bbef98da5d62ff9ce067b . + . + "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis." . + "Xenopus Anatomy Ontology" . + . + . + . + "anatomy" . + "https://github.com/xenopus-anatomy/xao/issues" . + "http://purl.obolibrary.org/obo/xao.owl" . + _:B737bcf1c44a6c7406fa76232c02e47b1 . + . + . + . +_:B93652a06fd9bbef98da5d62ff9ce067b "obo2owl" . +_:B93652a06fd9bbef98da5d62ff9ce067b "https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo"^^ . + "Xenopus" . + "An ontology for Xenopus anatomy and development." . + "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase." . +_:B737bcf1c44a6c7406fa76232c02e47b1 "Erik Segerdell" . +_:B737bcf1c44a6c7406fa76232c02e47b1 "esegerd3@gmail.com" . + "http://purl.obolibrary.org/obo/xao.owl" . + "http://purl.obolibrary.org/obo/xao.obo" . + "active" . + _:B0aa5b9318801c9d6b094397e1616c523 . + . + "A structured controlled vocabulary of the anatomy and development of the Zebrafish" . + "Zebrafish anatomy and development ontology" . + . + . + "anatomy" . + "https://github.com/cerivs/zebrafish-anatomical-ontology/issues" . + "http://purl.obolibrary.org/obo/zfa.owl" . + _:Ba3e6e099ac19ccdd9b9c284ee6edced9 . + . + . + . +_:B0aa5b9318801c9d6b094397e1616c523 "obo2owl" . +_:B0aa5b9318801c9d6b094397e1616c523 "https://raw.githubusercontent.com/cerivs/zebrafish-anatomical-ontology/master/src/zebrafish_anatomy.obo"^^ . + "Danio" . + "The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio." . +_:Ba3e6e099ac19ccdd9b9c284ee6edced9 "Ceri Van Slyke" . +_:Ba3e6e099ac19ccdd9b9c284ee6edced9 "van_slyke@zfin.org" . + "http://purl.obolibrary.org/obo/zfa.owl" . + "http://purl.obolibrary.org/obo/zfa.obo" . + "active" . + _:B237b5cb4904c3da92fd3c8ed865b04fd . + "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology" . + "Anatomical Entity Ontology" . + . + "anatomy" . + "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues" . + "http://purl.obolibrary.org/obo/aeo.owl" . + _:B5657cd9b2d7e0a3f2b167890356c3190 . + . + . +_:B237b5cb4904c3da92fd3c8ed865b04fd "git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git" . +_:B237b5cb4904c3da92fd3c8ed865b04fd "vcs" . +_:B5657cd9b2d7e0a3f2b167890356c3190 "Jonathan Bard" . +_:B5657cd9b2d7e0a3f2b167890356c3190 "J.Bard@ed.ac.uk" . + "http://purl.obolibrary.org/obo/aeo.owl" . + "active" . + . + . + . + . + . + . + . + . + . + _:Bb9a606bd2cf050d86292097ce78901c2 . + "Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments" . + "Agronomy Ontology" . + . + "agronomy" . + "https://github.com/AgriculturalSemantics/agro/issues/" . + "https://groups.google.com/group/agronomyOntology" . + "http://purl.obolibrary.org/obo/agro.owl" . + _:Bbcba7847195e6c98872527ee47d95028 . + . + . + "active" . + . + . + . + . + . + . + . + . + _:B561cf75c35e8117dd8976f8706b08022 . + "Ontology of environmental features and habitats" . + "Environment Ontology" . + . + . + . + "environment" . + "https://github.com/EnvironmentOntology/envo/issues/" . + "http://purl.obolibrary.org/obo/envo.owl" . + _:Bee1b8bece7a30f1bafd6a42b6d1e0171 . + . + . + . + . + . + . + . + . + "active" . + _:B2ab2189cdd10a8f697dca5c8e3420277 . + "Metrical units for use in conjunction with PATO" . + "Units of measurement ontology" . + . + "phenotype" . + "https://github.com/bio-ontology-research-group/unit-ontology/issues" . + "http://purl.obolibrary.org/obo/uo.owl" . + _:B608fa056e4c3bdbbab9cb19013df36e4 . + . + . + "active" . + _:B8a7996c83ee849ac063b58e2876451c2 . + "An ontology of information entities." . + "Information Artifact Ontology" . + . + "information" . + "https://github.com/information-artifact-ontology/IAO/issues" . + "http://purl.obolibrary.org/obo/iao.owl" . + _:Beb3906ef594e98a763b5f92bf2813791 . + . + . + . + . + . + "active" . + "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments." . + "Plant Experimental Conditions Ontology" . + . + . + "experimental conditions" . + "https://github.com/Planteome/plant-experimental-conditions-ontology/issues" . + "http://purl.obolibrary.org/obo/peco.owl" . + _:B3fc94925d074e9da51fe50dc30bb9499 . + . + . + . + . +_:Bb9a606bd2cf050d86292097ce78901c2 "git clone https://github.com/AgriculturalSemantics/agro.git" . +_:Bb9a606bd2cf050d86292097ce78901c2 "vcs" . +_:Bbcba7847195e6c98872527ee47d95028 "Marie-Angélique Laporte" . +_:Bbcba7847195e6c98872527ee47d95028 "m.a.laporte@cgiar.org" . + "http://purl.obolibrary.org/obo/agro.owl" . + "active" . + . + _:B01bddc1330a6f2bc298c23f1945c9fe1 . + "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)." . + "The Amphioxus Development and Anatomy Ontology" . + . + "anatomy" . + "https://github.com/EBISPOT/amphx_ontology/issues" . + "http://purl.obolibrary.org/obo/amphx.owl" . + _:B082b80b8e070b8ac273f61780222cdf8 . + . + . + . +_:B01bddc1330a6f2bc298c23f1945c9fe1 "git clone https://github.com/EBISPOT/amphx_ontology.git" . +_:B082b80b8e070b8ac273f61780222cdf8 "Hector Escriva" . +_:B082b80b8e070b8ac273f61780222cdf8 "hescriva@obs-banyuls.fr" . + "http://purl.obolibrary.org/obo/amphx.owl" . + "http://purl.obolibrary.org/obo/amphx.obo" . + "active" . + _:B926fc1f1576bef443ae827fb5c96c5d0 . + . + "A structured controlled vocabulary for the phenotypes of Ascomycete fungi" . + "Ascomycete phenotype ontology" . + . + "phenotype" . + "https://github.com/obophenotype/ascomycete-phenotype-ontology/issues" . + "http://purl.obolibrary.org/obo/apo.owl" . + _:B59499534392539f97df06faed2de773f . + . + . + . +_:B926fc1f1576bef443ae827fb5c96c5d0 "obo2owl" . +_:B926fc1f1576bef443ae827fb5c96c5d0 "https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo"^^ . + "Ascomycota" . +_:B59499534392539f97df06faed2de773f "Stacia R Engel" . +_:B59499534392539f97df06faed2de773f "stacia@stanford.edu" . + "http://purl.obolibrary.org/obo/apo.owl" . + "http://purl.obolibrary.org/obo/apo.obo" . + "active" . + "Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models" . + "Apollo Structured Vocabulary" . + . + "health" . + "https://github.com/ApolloDev/apollo-sv/issues" . + "http://purl.obolibrary.org/obo/apollo_sv.owl" . + _:B4aca588766c5fac93f1000a9a206c8dd . + . + . + . + "CC-BY 3.0" . + "CC-BY" . + "CC-BY version 3.0" . +_:B4aca588766c5fac93f1000a9a206c8dd "Mathias Brochhausen" . +_:B4aca588766c5fac93f1000a9a206c8dd "MBrochhausen@uams.edu" . + "http://purl.obolibrary.org/obo/apollo_sv.owl" . + "active" . + "Antibiotic resistance genes and mutations" . + "Antibiotic Resistance Ontology" . + . + "https://github.com/arpcard/aro/issues" . + "https://mailman.mcmaster.ca/mailman/listinfo/card-l" . + "http://purl.obolibrary.org/obo/aro.owl" . + _:B51e9f3588d59b05d0cfe0934bd68b71e . + . + . +_:B51e9f3588d59b05d0cfe0934bd68b71e "CARD" . +_:B51e9f3588d59b05d0cfe0934bd68b71e "card@mcmaster.ca" . + "http://purl.obolibrary.org/obo/aro.owl" . + "active" . + "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys." . + "Biological Collections Ontology" . + . + "biodiversity collections" . + "https://github.com/tucotuco/bco/issues" . + "http://purl.obolibrary.org/obo/bco.owl" . + _:Be2d33f5dbc1651a237fd40760bffd815 . + . + . +_:Be2d33f5dbc1651a237fd40760bffd815 "Ramona Walls" . +_:Be2d33f5dbc1651a237fd40760bffd815 "rlwalls2008@gmail.com" . + "http://purl.obolibrary.org/obo/bco.owl" . + "active" . + _:B4f4dc08fdbedbe8649998e6ce95a7c84 . + "An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces" . + "Biological Spatial Ontology" . + . + . + "anatomy" . + "https://github.com/obophenotype/biological-spatial-ontology/issues" . + "http://purl.obolibrary.org/obo/bspo.owl" . + _:Bd8f4b6d66fa82318424eef7cdc47c65d . + . + . + . +_:B4f4dc08fdbedbe8649998e6ce95a7c84 "git clone https://github.com/obophenotype/biological-spatial-ontology.git" . +_:B4f4dc08fdbedbe8649998e6ce95a7c84 "vcs" . + "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology." . +_:Bd8f4b6d66fa82318424eef7cdc47c65d "Chris Mungall" . +_:Bd8f4b6d66fa82318424eef7cdc47c65d "cjmungall@lbl.gov" . + "http://purl.obolibrary.org/obo/bspo.owl" . + "http://purl.obolibrary.org/obo/bspo.obo" . + "active" . + _:B7fe72013a47c89db1e67b31d10e754b9 . + "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures." . + "BRENDA tissue / enzyme source" . + . + . + "anatomy" . + "https://github.com/BRENDA-Enzymes/BTO/issues" . + "http://purl.obolibrary.org/obo/bto.owl" . + _:B7ca48cc7cd51b6bfc276a45efcec4e8f . + . + . + . + . + . +_:B7fe72013a47c89db1e67b31d10e754b9 "git clone https://github.com/BRENDA-Enzymes/BTO.git" . + "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources" . +_:B7ca48cc7cd51b6bfc276a45efcec4e8f "Antje Chang" . +_:B7ca48cc7cd51b6bfc276a45efcec4e8f "a.chang@tu-bs.de" . + "http://purl.obolibrary.org/obo/bto.owl" . + "http://purl.obolibrary.org/obo/bto.obo" . + "http://purl.obolibrary.org/obo/bto.json" . + "active" . + _:B6940da5148fc22bd456e2e8cf8c09df7 . + "An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species" . + "Common Anatomy Reference Ontology" . + . + "anatomy" . + "https://github.com/obophenotype/caro/issues" . + "http://purl.obolibrary.org/obo/caro.owl" . + _:B3fd20743efda9aa957ce8f4c335f647f . + . + . +_:B6940da5148fc22bd456e2e8cf8c09df7 "obo2owl" . +_:B6940da5148fc22bd456e2e8cf8c09df7 "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo"^^ . +_:B3fd20743efda9aa957ce8f4c335f647f "Melissa Haendel" . +_:B3fd20743efda9aa957ce8f4c335f647f "haendel@ohsu.edu" . + "http://purl.obolibrary.org/obo/caro.owl" . + "active" . + _:B2ea57db8a18be891d17aed19c1be26be . + "a formalization of concepts and relations relevant to evolutionary comparative analysis" . + "Comparative Data Analysis Ontology" . + . + "https://github.com/evoinfo/cdao/issues" . + "http://purl.obolibrary.org/obo/cdao.owl" . + _:B92a1ef80b9bd1dcb3ad958e6ff107196 . + . + . +_:B2ea57db8a18be891d17aed19c1be26be "owl2obo" . +_:B2ea57db8a18be891d17aed19c1be26be "http://purl.obolibrary.org/obo/cdao.owl"^^ . +_:B92a1ef80b9bd1dcb3ad958e6ff107196 "Jim Balhoff" . +_:B92a1ef80b9bd1dcb3ad958e6ff107196 "balhoff@renci.org" . + "http://purl.obolibrary.org/obo/cdao.owl" . + "active" . + _:Be47ccc4f92b783d63398b5615a182f31 . + "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them." . + "Chemical Information Ontology" . + . + "biochemistry" . + "https://github.com/semanticchemistry/semanticchemistry/issues" . + "https://groups.google.com/forum/#!forum/cheminf-ontology" . + "http://purl.obolibrary.org/obo/cheminf.owl" . + _:B69d80f95d66d70f5c5d1a62b7e97e0c6 . + . + . +_:Be47ccc4f92b783d63398b5615a182f31 "owl2obo" . +_:Be47ccc4f92b783d63398b5615a182f31 "https://raw.githubusercontent.com/semanticchemistry/semanticchemistry/master/ontology/cheminf.owl"^^ . +_:B69d80f95d66d70f5c5d1a62b7e97e0c6 "Egon Willighagen" . +_:B69d80f95d66d70f5c5d1a62b7e97e0c6 "egon.willighagen@gmail.com" . + "http://purl.obolibrary.org/obo/cheminf.owl" . + "active" . + . + . + . + . + . + . + . + _:Bcbe02696364da230faa46a50ba11907b . + "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes." . + "CHEBI Integrated Role Ontology" . + . + "biochemistry" . + "https://github.com/obophenotype/chiro/issues" . + "http://purl.obolibrary.org/obo/chiro.owl" . + _:Bd95eba53688f337a717d94df3be2fd13 . + . + . + . + "active" . + _:Bfb178b44ba804edaf90f21144c383652 . + . + "Standard terms for annotating mammalian phenotypic data." . + "Mammalian Phenotype Ontology" . + . + "phenotype" . + "https://github.com/obophenotype/mammalian-phenotype-ontology/issues" . + "https://groups.google.com/forum/#!forum/phenotype-ontologies-editors" . + . + . + . + "http://purl.obolibrary.org/obo/mp.owl" . + _:B7ed19d6e64b40f8739626d682c69cd2d . + . + . + . + . + . + . + "active" . + _:Bdbfc2d68fb9f243fa397dcb3dbbd51c2 . + . + "A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease." . + "Human Phenotype Ontology" . + . + . + . + . + . + "phenotype" . + "https://github.com/obophenotype/human-phenotype-ontology/issues/" . + "https://groups.io/g/human-phenotype-ontology" . + . + . + "http://purl.obolibrary.org/obo/hp.owl" . + _:Bbbf498b31ec9063ed586b07a804d33ab . + . + . + . + . +_:Bcbe02696364da230faa46a50ba11907b "git clone https://github.com/obophenotype/chiro.git" . + . + "CC-0" . +_:Bd95eba53688f337a717d94df3be2fd13 "Nicole Vasilevsky" . +_:Bd95eba53688f337a717d94df3be2fd13 "vasilevs@ohsu.edu" . + "http://purl.obolibrary.org/obo/chiro.owl" . + "http://purl.obolibrary.org/obo/chiro.obo" . + "active" . + "CHMO, the chemical methods ontology, describes methods used to" . + "Chemical Methods Ontology" . + . + "health" . + "https://github.com/rsc-ontologies/rsc-cmo/issues" . + "chemistry-ontologies@googlegroups.com" . + "http://purl.obolibrary.org/obo/chmo.owl" . + _:B9e8051e6dc85702d6598e00d9788939a . + . + . +_:B9e8051e6dc85702d6598e00d9788939a "Colin Batchelor" . +_:B9e8051e6dc85702d6598e00d9788939a "batchelorc@rsc.org" . + "http://purl.obolibrary.org/obo/chmo.owl" . + "active" . + "The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically represent and standardize various aspects of coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment." . + "Coronavirus Infectious Disease Ontology" . + . + "https://github.com/cido-ontology/cido/issues" . + "cido-discuss@googlegroups.com" . + "http://purl.obolibrary.org/obo/cido.owl" . + _:B9af06e2821025274c828e3bcb6a8c512 . + . + . +_:B9af06e2821025274c828e3bcb6a8c512 "Yongqun Oliver He" . +_:B9af06e2821025274c828e3bcb6a8c512 "yongqunh@med.umich.edu" . + "http://purl.obolibrary.org/obo/cido.owl" . + "active" . + "An ontology to capture confidence information about annotations." . + "Confidence Information Ontology" . + . + "https://github.com/BgeeDB/confidence-information-ontology" . + "http://purl.obolibrary.org/obo/cio.owl" . + _:B0c1deeb8e94482c4628d1a59b26903a7 . + . + . + . +_:B0c1deeb8e94482c4628d1a59b26903a7 "Frederic Bastian" . +_:B0c1deeb8e94482c4628d1a59b26903a7 "bgee@sib.swiss" . + "http://purl.obolibrary.org/obo/cio.owl" . + "http://purl.obolibrary.org/obo/cio.obo" . +_:B601657ebc62b8caaa15d3f328775bd8f "git clone https://github.com/obophenotype/cell-ontology.git" . +_:B601657ebc62b8caaa15d3f328775bd8f "vcs" . + "Metazoa" . + "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability." . +_:B70446a8a6cef504ca4ae0b425af1bad0 "Alexander Diehl" . +_:B70446a8a6cef504ca4ae0b425af1bad0 "addiehl@buffalo.edu" . + "Complete ontology, plus inter-ontology axioms, and imports modules" . + "Main CL OWL edition" . + "owl-rdf/xml" . + "http://purl.obolibrary.org/obo/cl.owl" . + "Complete ontology, plus inter-ontology axioms, and imports modules merged in" . + "CL obo format edition" . + "obo" . + "http://purl.obolibrary.org/obo/cl.obo" . + "Basic version, no inter-ontology axioms" . + "Basic CL" . + "obo" . + "http://purl.obolibrary.org/obo/cl/cl-basic.obo" . + "complete CL but with no imports or external axioms" . + "CL base module" . + "http://purl.obolibrary.org/obo/cl/cl-base.owl" . + "active" . + . + _:B905250a58afa274a95efc1d9ed31f35a . + "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)." . + "Collembola Anatomy Ontology" . + . + "anatomy" . + "https://github.com/luis-gonzalez-m/Collembola/issues" . + "http://purl.obolibrary.org/obo/clao.owl" . + _:B90a3a60176acd0143ae82d42420a5c4e . + . + . + . +_:B905250a58afa274a95efc1d9ed31f35a "git clone https://github.com/luis-gonzalez-m/Collembola.git" . +_:B90a3a60176acd0143ae82d42420a5c4e "Luis González-Montaña" . +_:B90a3a60176acd0143ae82d42420a5c4e "lagonzalezmo@unal.edu.co" . + "http://purl.obolibrary.org/obo/clao.owl" . + "http://purl.obolibrary.org/obo/clao.obo" . + "active" . + . + . + . + . + "An ontology to standardize and integrate cell line information and to support computer-assisted reasoning." . + "Cell Line Ontology" . + . + "https://github.com/CLO-Ontology/CLO/issues" . + "http://purl.obolibrary.org/obo/clo.owl" . + _:B8a5ac4aca284a1c91aff86c3f8f29717 . + . + . +_:B8a5ac4aca284a1c91aff86c3f8f29717 "Sirarat Sarntivijai" . +_:B8a5ac4aca284a1c91aff86c3f8f29717 "siiraa@umich.edu" . + "http://purl.obolibrary.org/obo/clo.owl" . + "active" . + . + . + . + _:B439ac10d6535427af35c17a0d75ef80e . + "The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle." . + "Clytia hemisphaerica Development and Anatomy Ontology" . + . + "anatomy" . + "https://github.com/EBISPOT/clyh_ontology/issues" . + "http://purl.obolibrary.org/obo/clyh.owl" . + _:B3316ac578678cf5461528fb074c93580 . + . + . + . +_:B439ac10d6535427af35c17a0d75ef80e "git clone https://github.com/EBISPOT/clyh_ontology.git" . +_:B3316ac578678cf5461528fb074c93580 "Lucas Leclere" . +_:B3316ac578678cf5461528fb074c93580 "lucas.leclere@obs-vlfr.fr" . + "http://purl.obolibrary.org/obo/clyh.owl" . + "http://purl.obolibrary.org/obo/clyh.obo" . + "active" . + _:B6c1e55eda9d4b1808961841dfeec2e05 . + "Morphological and physiological measurement records generated from clinical and model organism research and health programs." . + "Clinical measurement ontology" . + . + . + . + "clinical" . + "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues" . + . + "http://purl.obolibrary.org/obo/cmo.owl" . + _:B047fc99647b2b35ae05b8465b5454890 . + . + . + . + . +_:B6c1e55eda9d4b1808961841dfeec2e05 "obo2owl" . +_:B6c1e55eda9d4b1808961841dfeec2e05 "ftp://ftp.rgd.mcw.edu/pub/ontology/clinical_measurement/clinical_measurement.obo"^^ . + "Three ontologies to define phenotype measurement data." . + "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications." . + "RGD Ontology Browser" . + "RGD" . +_:B047fc99647b2b35ae05b8465b5454890 "Mary Shimoyama" . +_:B047fc99647b2b35ae05b8465b5454890 "shimoyama@mcw.edu" . + "http://purl.obolibrary.org/obo/cmo.owl" . + "http://purl.obolibrary.org/obo/cmo.obo" . + "active" . + "COB brings together key terms from a wide range of OBO projects to improve interoperability." . + "Core Ontology for Biology and Biomedicine" . + . + "upper" . + "https://github.com/OBOFoundry/COB/issues" . + "http://purl.obolibrary.org/obo/cob.owl" . + _:B4b099d826131a423045180735d021cc9 . + . + . +_:B4b099d826131a423045180735d021cc9 "Bjoern Peters" . +_:B4b099d826131a423045180735d021cc9 "bpeters@lji.org" . + "http://purl.obolibrary.org/obo/cob.owl" . + "active" . + _:B740984ef95c25419d818e411c2ac347a . + "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability." . + "Contributor Role Ontology" . + . + "scholarly contribution roles" . + "https://github.com/data2health/contributor-role-ontology/issues" . + "http://purl.obolibrary.org/obo/cro.owl" . + _:Ba61fadafd1162356756c579c08e9dfbd . + . + . +_:B740984ef95c25419d818e411c2ac347a "git clone https://github.com/data2health/contributor-role-ontology.git" . + . + "CC-BY" . + "CC-BY 2.0" . +_:Ba61fadafd1162356756c579c08e9dfbd "Marijane White" . +_:Ba61fadafd1162356756c579c08e9dfbd "whimar@ohsu.edu" . + "CRO" . + "http://purl.obolibrary.org/obo/cro.owl" . + "active" . + . + . + _:B86a02948f9d09113c2a67dc532ec4e01 . + . + "An anatomical and developmental ontology for ctenophores (Comb Jellies)" . + "Ctenophore Ontology" . + . + "anatomy" . + "https://github.com/obophenotype/ctenophore-ontology/issues" . + "http://purl.obolibrary.org/obo/cteno.owl" . + _:B452816bba8b3c378931861416de6f4e5 . + . + . +_:B86a02948f9d09113c2a67dc532ec4e01 "git clone https://github.com/obophenotype/ctenophore-ontology.git" . +_:B86a02948f9d09113c2a67dc532ec4e01 "vcs" . + "Ctenophore" . +_:B452816bba8b3c378931861416de6f4e5 "Chris Mungall" . +_:B452816bba8b3c378931861416de6f4e5 "cjmungall@lbl.gov" . + "http://purl.obolibrary.org/obo/cteno.owl" . + "active" . + "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials." . + "CTO: Core Ontology of Clinical Trials" . + . + "https://github.com/ClinicalTrialOntology/CTO/issues" . + "http://purl.obolibrary.org/obo/cto.owl" . + _:B1b598e8a84f30d10352ec04b23a0eead . + . + . +_:B1b598e8a84f30d10352ec04b23a0eead "Dr. Alpha Tom Kodamullil" . +_:B1b598e8a84f30d10352ec04b23a0eead "alpha.tom.kodamullil@scai.fraunhofer.de" . + "http://purl.obolibrary.org/obo/cto.owl" . + "active" . + _:Bbc02522d7e3b8f08da90e91a9471515c . + "An ontology to describe entities related to cardiovascular diseases" . + "Cardiovascular Disease Ontology" . + . + "health" . + "https://github.com/OpenLHS/CVDO/issues" . + "http://purl.obolibrary.org/obo/cvdo.owl" . + _:Bc7e52f0c1a472bba46b16b4b921f9667 . + . + . +_:Bbc02522d7e3b8f08da90e91a9471515c "owl2obo" . +_:Bbc02522d7e3b8f08da90e91a9471515c "http://purl.obolibrary.org/obo/cvdo.owl"^^ . +_:Bc7e52f0c1a472bba46b16b4b921f9667 "Paul Fabry" . +_:Bc7e52f0c1a472bba46b16b4b921f9667 "paul.fabry@usherbrooke.ca" . + "http://purl.obolibrary.org/obo/cvdo.owl" . + "active" . + _:Bd06fba0b5fe1dfd6b07eea80df1a1986 . + . + "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum" . + "Dictyostelium discoideum anatomy" . + . + "anatomy" . + "https://github.com/dictyBase/migration-data/issues" . + "http://purl.obolibrary.org/obo/ddanat.owl" . + _:B8f1b1701ef88f5420a338641d6a3290a . + . + . + . + . +_:Bd06fba0b5fe1dfd6b07eea80df1a1986 "obo2owl" . +_:Bd06fba0b5fe1dfd6b07eea80df1a1986 "https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_anatomy.obo"^^ . + "Dictyostelium discoideum" . +_:B8f1b1701ef88f5420a338641d6a3290a "Petra Fey" . +_:B8f1b1701ef88f5420a338641d6a3290a "pfey@northwestern.edu" . + "http://purl.obolibrary.org/obo/ddanat.owl" . + "http://purl.obolibrary.org/obo/ddanat.obo" . + "active" . + _:Bdfe5335d8b42607b0c37d65b6e13b37a . + . + "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum." . + "Dictyostelium discoideum phenotype ontology" . + . + "anatomy" . + "https://github.com/obophenotype/dicty-phenotype-ontology/issues" . + "http://purl.obolibrary.org/obo/ddpheno.owl" . + _:B6505ad8da185b04600e3ed1aba2d726c . + . + . + . + . +_:Bdfe5335d8b42607b0c37d65b6e13b37a "git clone https://github.com/obophenotype/dicty-phenotype-ontology.git" . +_:B6505ad8da185b04600e3ed1aba2d726c "Petra Fey" . +_:B6505ad8da185b04600e3ed1aba2d726c "pfey@northwestern.edu" . + "http://purl.obolibrary.org/obo/ddpheno.owl" . + "http://purl.obolibrary.org/obo/ddpheno.obo" . + "active" . + "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology" . + "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" . + . + "https://github.com/DIDEO/DIDEO/issues" . + "http://purl.obolibrary.org/obo/dideo.owl" . + _:B2d83dcb73fbb4d4e2242af217cf266d1 . + . + . +_:B2d83dcb73fbb4d4e2242af217cf266d1 "Mathias Brochhausen" . +_:B2d83dcb73fbb4d4e2242af217cf266d1 "mbrochhausen@gmail.com" . + "http://purl.obolibrary.org/obo/dideo.owl" . + "FBcv" . + "active" . + _:B68a2ab3b9753a1e38139ffa157c3c990 . + . + "An ontology of commonly encountered and/or high level Drosophila phenotypes." . + "Drosophila Phenotype Ontology" . + . + . + "phenotype" . + "https://github.com/FlyBase/drosophila-phenotype-ontology/issues" . + . + "http://purl.obolibrary.org/obo/dpo.owl" . + _:B85e50440820c37593a1e15ba9b005a29 . + . + . + . + . +_:B68a2ab3b9753a1e38139ffa157c3c990 "git clone https://github.com/FlyBase/drosophila-phenotype-ontolog.git" . + "Drosophila" . + "The Drosophila phenotype ontology." . + "FlyBase Browser" . + "FB" . +_:B85e50440820c37593a1e15ba9b005a29 "Clare Pilgrim" . +_:B85e50440820c37593a1e15ba9b005a29 "cp390@cam.ac.uk" . + "http://purl.obolibrary.org/obo/dpo.owl" . + "http://purl.obolibrary.org/obo/dpo.obo" . + "http://purl.obolibrary.org/obo/dpo.json" . + "FBcv" . + "active" . + _:B734ade8cbdd5002c5f68c7cfb93a748f . + "A structured controlled vocabulary used for various aspects of annotation by FlyBase." . + "FlyBase Controlled Vocabulary" . + . + "organisms" . + "https://github.com/FlyBase/flybase-controlled-vocabulary/issues" . + . + "http://purl.obolibrary.org/obo/fbcv.owl" . + _:B7dc8703b46b27f2019b4d74cf0ef07c4 . + . + . + . + . + "active" . + _:B739ccd83d171c63431c668c8f3e3fa96 . + "An ontology to support comparative effectiveness researchers studying claims data." . + "The Drug Ontology" . + . + "health" . + "https://ontology.atlassian.net/browse/DRON" . + "http://purl.obolibrary.org/obo/dron.owl" . + _:B024888ef1bf84fe22d1277639c0579b5 . + . + . +_:B739ccd83d171c63431c668c8f3e3fa96 "owl2obo" . +_:B739ccd83d171c63431c668c8f3e3fa96 "http://purl.obolibrary.org/obo/dron.owl"^^ . +_:B024888ef1bf84fe22d1277639c0579b5 "William Hogan" . +_:B024888ef1bf84fe22d1277639c0579b5 "hoganwr@gmail.com" . + "http://purl.obolibrary.org/obo/dron.owl" . + "active" . + . + . + _:B0b1bc28f1470d5db436c884be8ce8532 . + "DUO is an ontology which represent data use conditions." . + "Data Use Ontology" . + . + "https://github.com/EBISPOT/DUO/issues" . + "http://purl.obolibrary.org/obo/duo.owl" . + _:B758c605fe718aa42d54d54ceed1371ab . + . + . +_:B0b1bc28f1470d5db436c884be8ce8532 "git clone https://github.com/EBISPOT/duo.git" . +_:B758c605fe718aa42d54d54ceed1371ab "Melanie Courtot" . +_:B758c605fe718aa42d54d54ceed1371ab "mcourtot@gmail.com" . + "http://purl.obolibrary.org/obo/duo.owl" . + "active" . + . + . + . + _:B89224a1c08bfb153e2f745bc163d5824 . + "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586)." . + "The Echinoderm Anatomy and Development Ontology" . + . + "anatomy" . + "https://github.com/echinoderm-ontology/ecao_ontology/issues" . + "http://purl.obolibrary.org/obo/ecao.owl" . + _:B31934bc814965982350ab2b9b9b6d3a8 . + . + . + . +_:B89224a1c08bfb153e2f745bc163d5824 "git clone https://github.com/echinoderm-ontology/ecao_ontology.git" . +_:B31934bc814965982350ab2b9b9b6d3a8 "Charles Ettensohn" . +_:B31934bc814965982350ab2b9b9b6d3a8 "ettensohn@cmu.edu" . + "http://purl.obolibrary.org/obo/ecao.owl" . + "http://purl.obolibrary.org/obo/ecao.obo" . + "active" . + _:B0b55434aed68a2d51e1da9930001b39d . + "An ontology for experimental and other evidence statements." . + "Evidence ontology" . + . + . + . + "experiments" . + "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1458400" . + "https://github.com/evidenceontology/evidenceontology/issues" . + "http://purl.obolibrary.org/obo/eco.owl" . + _:B7e5fcae3dce3c6d9942e20d9eb6db7e8 . + . + . + . +_:B0b55434aed68a2d51e1da9930001b39d "obo2owl" . +_:B0b55434aed68a2d51e1da9930001b39d "https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/eco.obo"^^ . + "ECO, the Evidence & Conclusion Ontology: community standard for evidence information." . + "Standardized description of scientific evidence using the Evidence Ontology (ECO)" . +_:B7e5fcae3dce3c6d9942e20d9eb6db7e8 "Michelle Giglio" . +_:B7e5fcae3dce3c6d9942e20d9eb6db7e8 "mgiglio@som.umaryland.edu" . + "http://purl.obolibrary.org/obo/eco.owl" . + "http://purl.obolibrary.org/obo/eco.obo" . + "active" . + . + . + . + . + . + . + . + . + . + . + _:Bdc332ec616f3d49c847006591db4c694 . + "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms." . + "An ontology of core ecological entities" . + . + "ecological functions, ecological interactions" . + "https://github.com/EcologicalSemantics/ecocore/issues" . + "http://purl.obolibrary.org/obo/ecocore.owl" . + _:Be20427734613f608a54873c3c340b92c . + . + . + . + "active" . + . + . + . + . + . + . + . + . + _:B0e8e0ee16e9376a668cf9ad32ab7c9f3 . + "An ontology about groups of interacting organisms such as populations and communities" . + "Population and Community Ontology" . + . + "collections of organisms" . + "https://github.com/PopulationAndCommunityOntology/pco/issues" . + "http://purl.obolibrary.org/obo/pco.owl" . + _:B17d75ab07c0be4fc148e4ec23dffe82d . + . + . +_:Bdc332ec616f3d49c847006591db4c694 "git clone https://github.com/EcologicalSemantics/ecocore.git" . +_:Be20427734613f608a54873c3c340b92c "Pier Luigi Buttigieg" . +_:Be20427734613f608a54873c3c340b92c "p.buttigieg@gmail.com" . + "http://purl.obolibrary.org/obo/ecocore.owl" . + "http://purl.obolibrary.org/obo/ecocore.obo" . + "active" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + _:Bd396de52df4e18c8febae8710ed29870 . + "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology)." . + "Environmental conditions, treatments and exposures ontology" . + . + "environment" . + "https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues" . + "http://purl.obolibrary.org/obo/ecto.owl" . + _:B34ed28d0ae1a415ab21f1bc3631bdcda . + . + . + . + . + . + . + . + "ExO" . + "active" . + _:Bce4dc2e9f97a07d32a51304ebd30a8f3 . + "Vocabularies for describing exposure data to inform understanding of environmental health." . + "Exposure ontology" . + . + "health" . + "https://github.com/CTDbase/exposure-ontology/issues" . + "http://purl.obolibrary.org/obo/exo.owl" . + _:Bba0bff25157dcbd25ad0d203eb82f7fb . + . + . + . + . + "active" . + . + . + . + . + . + . + _:B02242c6738a8d0b8b9386a00b730b69d . + "Medical Action Ontology is an ontology..." . + "Medical Action Ontology" . + . + "medical" . + "https://github.com/monarch-initiative/MAxO/issues" . + "http://purl.obolibrary.org/obo/maxo.owl" . + _:B5fcc89c4a749a101c8fa169f249247d1 . + . + . + . + . + . + . + . + "active" . + _:Ba6ad3b82e84402c5b7c8001c985fa7c3 . + "An ontology of human and animal behaviours and behavioural phenotypes" . + "Neuro Behavior Ontology" . + . + "behavior" . + "https://github.com/obo-behavior/behavior-ontology/issues" . + . + "http://purl.obolibrary.org/obo/nbo.owl" . + _:Bfd53d633249f7dff0a98051c3c6f1d48 . + . + . + "active" . + "NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental." . + "NCI Thesaurus OBO Edition" . + . + "https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues" . + "http://purl.obolibrary.org/obo/ncit.owl" . + _:B77c03ffa9a8d6f949cddfb3e36ccabbe . + . + . + . + . + . + "active" . + _:Bc1bb827f0e04ac76f898ad15c7ec4653 . + "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms." . + "Experimental condition ontology" . + . + . + . + "clinical" . + "https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues" . + . + "http://purl.obolibrary.org/obo/xco.owl" . + _:Bc2750840ace2cd1fa186d431fe313d23 . + . + . + . +_:Bd396de52df4e18c8febae8710ed29870 "git clone https://github.com/EnvironmentOntology/environmental-exposure-ontology.git" . +_:B34ed28d0ae1a415ab21f1bc3631bdcda "Anne Thessen" . +_:B34ed28d0ae1a415ab21f1bc3631bdcda "annethessen@gmail.com" . + "http://purl.obolibrary.org/obo/ecto.owl" . + "http://purl.obolibrary.org/obo/ecto.obo" . + "http://purl.obolibrary.org/obo/ecto.json" . + "http://purl.obolibrary.org/obo/ecto/ecto-base.owl" . + "http://purl.obolibrary.org/obo/ecto/ecto-base.obo" . + "http://purl.obolibrary.org/obo/ecto/ecto-base.json" . + "active" . + _:B27b9540fb6d9057720074c6df8e7b0e8 . + . + "An ontology for mouse anatomy covering embryonic development and postnatal stages." . + "Mouse Developmental Anatomy Ontology" . + . + "anatomy" . + "https://github.com/obophenotype/mouse-anatomy-ontology/issues" . + "http://purl.obolibrary.org/obo/emapa.owl" . + _:B20731e669a72051b3340e355fe15523e . + . + . + . +_:B27b9540fb6d9057720074c6df8e7b0e8 "obo2owl" . +_:B27b9540fb6d9057720074c6df8e7b0e8 "ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo"^^ . + "Mus" . +_:B20731e669a72051b3340e355fe15523e "Terry Hayamizu" . +_:B20731e669a72051b3340e355fe15523e "Terry.Hayamizu@jax.org" . + "http://purl.obolibrary.org/obo/emapa.owl" . + "http://purl.obolibrary.org/obo/emapa.obo" . + "active" . + . + . + . + . + . + . + . + . + "A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and food webs as well as human-centric categorization and handling of food." . + "FOODON" . + . + "food" . + "https://github.com/FoodOntology/foodon/issues/" . + "http://purl.obolibrary.org/obo/foodon.owl" . + _:Bcba6bf4fc647683fc717118c94bd5b7b . + . + . + . + . +_:B561cf75c35e8117dd8976f8706b08022 "git clone https://github.com/EnvironmentOntology/envo.git" . +_:B561cf75c35e8117dd8976f8706b08022 "vcs" . + "The environment ontology: contextualising biological and biomedical entities" . + "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation" . +_:Bee1b8bece7a30f1bafd6a42b6d1e0171 "Pier Luigi Buttigieg" . +_:Bee1b8bece7a30f1bafd6a42b6d1e0171 "p.buttigieg@gmail.com" . + "main ENVO OWL release" . + "http://purl.obolibrary.org/obo/envo.owl" . + "ENVO in obographs JSON format" . + "http://purl.obolibrary.org/obo/envo.json" . + "ENVO in OBO Format. May be lossy" . + "http://purl.obolibrary.org/obo/envo.obo" . + "OBO-Basic edition of ENVO" . + "http://purl.obolibrary.org/obo/envo/subsets/envo-basic.obo" . + "Earth Microbiome Project subset" . + "http://purl.obolibrary.org/obo/envo/subsets/envoEmpo.owl" . + "GSC Lite subset of ENVO" . + "http://purl.obolibrary.org/obo/envo/subsets/EnvO-Lite-GSC.obo" . + . + "active" . + "An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org)." . + "VEuPathDB ontology" . + . + "functional genomics, population biology, clinical epidemiology, and microbiomes" . + "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues" . + "http://purl.obolibrary.org/obo/eupath.owl" . + _:Bf63c882d32ac2fbe24761f96e1295113 . + . + . +_:Bf63c882d32ac2fbe24761f96e1295113 "Chris Stoeckert" . +_:Bf63c882d32ac2fbe24761f96e1295113 "stoeckrt@pennmedicine.upenn.edu" . + "http://purl.obolibrary.org/obo/eupath.owl" . +_:Bce4dc2e9f97a07d32a51304ebd30a8f3 "obo2owl" . +_:Bce4dc2e9f97a07d32a51304ebd30a8f3 "https://raw.githubusercontent.com/CTDbase/exposure-ontology/master/src/ontology/exo.obo"^^ . +_:Bba0bff25157dcbd25ad0d203eb82f7fb "Carolyn Mattingly" . +_:Bba0bff25157dcbd25ad0d203eb82f7fb "cjmattin@ncsu.edu" . + "http://purl.obolibrary.org/obo/exo.owl" . + "http://purl.obolibrary.org/obo/exo.obo" . + "active" . + _:Bab971bd9b676bc2c9445298f3fee54f9 . + . + "A structured controlled vocabulary for the anatomy of fungi." . + "Fungal gross anatomy" . + . + "anatomy" . + "https://github.com/obophenotype/fungal-anatomy-ontology/issues" . + "http://purl.obolibrary.org/obo/fao.owl" . + _:Bb835540341d55b71e09fe19ccaf72cbc . + . + . + . +_:Bab971bd9b676bc2c9445298f3fee54f9 "git clone https://github.com/obophenotype/fungal-anatomy-ontology.git" . +_:Bab971bd9b676bc2c9445298f3fee54f9 "vcs" . + "Fungal" . +_:Bb835540341d55b71e09fe19ccaf72cbc "Midori Harris" . +_:Bb835540341d55b71e09fe19ccaf72cbc "mah79@cam.ac.uk" . + "http://purl.obolibrary.org/obo/fao.owl" . + "http://purl.obolibrary.org/obo/fao.obo" . + "FBbi" . + "active" . + _:B49c53c51c241af8e81284c539ec618f1 . + "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research." . + "Biological Imaging Methods Ontology" . + . + "imaging experiments" . + "https://github.com/CRBS/Biological_Imaging_Methods_Ontology/issues" . + "http://purl.obolibrary.org/obo/fbbi.owl" . + _:Bd449b94ba9030bcde67bdcebc9c25853 . + . + . +_:B49c53c51c241af8e81284c539ec618f1 "obo2owl" . +_:B49c53c51c241af8e81284c539ec618f1 "https://raw.githubusercontent.com/dosumis/fbbi/master/src/ontology/fbbi.obo"^^ . +_:Bd449b94ba9030bcde67bdcebc9c25853 "David Orloff" . +_:Bd449b94ba9030bcde67bdcebc9c25853 "dorloff@ncmir.ucsd.edu" . + "http://purl.obolibrary.org/obo/fbbi.owl" . + "FBbt" . + "active" . + _:B30f4f0e0db979baa4a60a1fcee52a6fd . + . + "An ontology representing the gross anatomy of Drosophila melanogaster." . + "Drosophila gross anatomy" . + . + . + . + . + . + "Drosophilid anatomy" . + "http://purl.obolibrary.org/obo/fbbt/tracker" . + . + . + . + "http://purl.obolibrary.org/obo/fbbt.owl" . + _:B3247b47ca68303b54c8c197a7726cbf4 . + . + . + . + . + . + . +_:B30f4f0e0db979baa4a60a1fcee52a6fd "git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git" . + "The Drosophila anatomy ontology. [Journal of Biomedical Semantics" . + "A strategy for building neuroanatomy ontologies" . + "The Virtual Fly Brain Browser and Query Interface" . + "FlyBase: anatomical data, images and queries" . + "FlyBase Browser" . + "FB" . + "Virtual Fly Brain" . + "VFB" . + "BioPortal Browser" . + "BioPortal" . +_:B3247b47ca68303b54c8c197a7726cbf4 "Clare Pilgrim" . +_:B3247b47ca68303b54c8c197a7726cbf4 "cp390@cam.ac.uk" . + "http://purl.obolibrary.org/obo/fbbt.owl" . + "http://purl.obolibrary.org/obo/fbbt.obo" . + "http://purl.obolibrary.org/obo/fbbt.json" . + "http://purl.obolibrary.org/obo/fbbt/fbbt-simple.owl" . + "http://purl.obolibrary.org/obo/fbbt/fbbt-simple.obo" . +_:B734ade8cbdd5002c5f68c7cfb93a748f "git clone https://github.com/FlyBase/flybase-controlled-vocabulary.git" . + "FlyBase Browser" . + "FB" . +_:B7dc8703b46b27f2019b4d74cf0ef07c4 "Clare Pilgrim" . +_:B7dc8703b46b27f2019b4d74cf0ef07c4 "cp390@cam.ac.uk" . + "http://purl.obolibrary.org/obo/fbcv.owl" . + "http://purl.obolibrary.org/obo/fbcv.obo" . + "http://purl.obolibrary.org/obo/fbcv.json" . + "FBdv" . + "active" . + _:Bbe9c7550f4e884e13294f07db7ce9aad . + . + "A structured controlled vocabulary of the development of Drosophila melanogaster." . + "Drosophila development" . + . + "development" . + "http://purl.obolibrary.org/obo/fbdv/tracker" . + . + "http://purl.obolibrary.org/obo/fbdv.owl" . + _:B0b355f53014811190a516012e2ed79de . + . + . + . + . + . + . +_:Bbe9c7550f4e884e13294f07db7ce9aad "git clone https://github.com/FlyBase/drosophila-developmental-ontology.git" . + "FlyBase Browser" . + "FB" . +_:B0b355f53014811190a516012e2ed79de "Clare Pilgrim" . +_:B0b355f53014811190a516012e2ed79de "cp390@cam.ac.uk" . + "http://purl.obolibrary.org/obo/fbdv.owl" . + "http://purl.obolibrary.org/obo/fbdv.obo" . + "http://purl.obolibrary.org/obo/fbdv.json" . + "http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl" . + "http://purl.obolibrary.org/obo/fbdv/fbdv-simple.obo" . + "active" . + "Food-Drug interactions automatically extracted from scientific literature" . + "Food Interactions with Drugs Evidence Ontology" . + . + "diet, metabolomics and nutrition" . + "https://github.com/getbordea/fideo/issues" . + "http://purl.obolibrary.org/obo/fideo.owl" . + _:Bb0714cab06a4c16d0371aba85f3bcd33 . + . + . +_:Bb0714cab06a4c16d0371aba85f3bcd33 "Georgeta Bordea" . +_:Bb0714cab06a4c16d0371aba85f3bcd33 "georgeta.bordea@u-bordeaux.fr" . + "http://purl.obolibrary.org/obo/fideo.owl" . + "active" . + _:B1257d580c7d4276cdf6be4ca575b7046 . + . + "Traits and phenotypes of flowering plants occurring in digitized Floras" . + "Flora Phenotype Ontology" . + . + "phenotype" . + "https://github.com/flora-phenotype-ontology/flopoontology/issues" . + "http://purl.obolibrary.org/obo/flopo.owl" . + _:Bfa63115b866a9d429e14f482152a2452 . + . + . +_:B1257d580c7d4276cdf6be4ca575b7046 "owl2obo" . +_:B1257d580c7d4276cdf6be4ca575b7046 "https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl"^^ . +_:Bfa63115b866a9d429e14f482152a2452 "Robert Hoehndorf" . +_:Bfa63115b866a9d429e14f482152a2452 "robert.hoehndorf@kaust.edu.sa" . + "http://purl.obolibrary.org/obo/flopo.owl" . + "active" . + _:B9d1bfea5f4dcef7b50873f01854d5b2f . + . + "This is currently a slimmed down version of FMA" . + "Foundational Model of Anatomy Ontology (subset)" . + . + . + . + . + "anatomy" . + "https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/" . + "http://purl.obolibrary.org/obo/fma.owl" . + _:Ba3b8fa6c2345887bacad4c9b2e99e77b . + . + . + . +_:B9d1bfea5f4dcef7b50873f01854d5b2f "obo2owl" . +_:B9d1bfea5f4dcef7b50873f01854d5b2f "http://svn.code.sf.net/p/obo/svn/fma-conversion/trunk/fma2_obo.obo"^^ . + "Translating the Foundational Model of Anatomy into OWL" . + "The foundational model of anatomy in OWL: Experience and perspectives" . + "Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study" . +_:Ba3b8fa6c2345887bacad4c9b2e99e77b "Onard Mejino" . +_:Ba3b8fa6c2345887bacad4c9b2e99e77b "mejino@u.washington.edu" . + "http://purl.obolibrary.org/obo/fma.owl" . + "inactive" . + _:B60c496d91030621ef8d5a0fe59a77b78 . + "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments." . + "Plant Environment Ontology" . + . + . + "environment" . + "https://github.com/Planteome/plant-environment-ontology/issues" . + _:B52f7f355966cdf65e2d18f15c32b4208 . + . + . + . + . +_:Bcba6bf4fc647683fc717118c94bd5b7b "Damion Dooley" . +_:Bcba6bf4fc647683fc717118c94bd5b7b "damion.dooley@bccdc.ca" . + "FoodOn full ontology including 9000 SIREN indexed food products" . + "owl-rdf/xml" . + "http://purl.obolibrary.org/obo/foodon.owl" . + "FoodOn core ontology (without SIREN)" . + "owl-rdf/xml" . + "http://purl.obolibrary.org/obo/foodon_core.owl" . + "active" . + . + . + . + . + . + . + . + . + _:B3434ee7e95e66bd1d8b95603d7bc629f . + "FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA)." . + "FuTRES Ontology of Vertebrate Traits" . + . + "vertebrate traits" . + "https://github.com/futres/fovt/issues" . + "http://purl.obolibrary.org/obo/fovt.owl" . + _:B1f6cfbdd0e94e7d089fdb3ecf1182232 . + . + . + . + . + . + "active" . + _:Bd9f364456f94b1f4d1bf4e944b621520 . + "A collection of biological attributes (traits) covering all kingdoms of life." . + "Ontology of Biological Attributes" . + . + "phenotype" . + "https://github.com/obophenotype/bio-attribute-ontology/issues" . + "http://purl.obolibrary.org/obo/oba.owl" . + _:B14a26b02fe983bcb66d20d0072418a1d . + . + . + . + . + . +_:B3434ee7e95e66bd1d8b95603d7bc629f "git clone https://github.com/futres/fovt.git" . +_:B1f6cfbdd0e94e7d089fdb3ecf1182232 "FuTRES Ontology of Vertebrate Traits" . +_:B1f6cfbdd0e94e7d089fdb3ecf1182232 "rlwalls2008@gmail.com" . + "http://purl.obolibrary.org/obo/fovt.owl" . + "http://purl.obolibrary.org/obo/fovt.obo" . + "http://purl.obolibrary.org/obo/fovt/fovt-base.owl" . + "http://purl.obolibrary.org/obo/fovt/fovt-base.obo" . + "active" . + _:B28e3ba81e0943989150b4a176173568d . + . + "FYPO is a formal ontology of phenotypes observed in fission yeast." . + "Fission Yeast Phenotype Ontology" . + . + . + "phenotype" . + "https://github.com/pombase/fypo/issues" . + "http://purl.obolibrary.org/obo/fypo.owl" . + _:B1b16ee336ebfe8be2af781d2d1b2a404 . + . + . + . +_:B28e3ba81e0943989150b4a176173568d "obo2owl" . +_:B28e3ba81e0943989150b4a176173568d "https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl"^^ . + "S. pombe" . + "FYPO: The Fission Yeast Phenotype Ontology." . +_:B1b16ee336ebfe8be2af781d2d1b2a404 "Midori Harris" . +_:B1b16ee336ebfe8be2af781d2d1b2a404 "mah79@cam.ac.uk" . + "http://purl.obolibrary.org/obo/fypo.owl" . + "http://purl.obolibrary.org/obo/fypo.obo" . + "active" . + _:Bd50959c2da48160750527fe0879a91b6 . + "A gazetteer constructed on ontological principles" . + "Gazetteer" . + . + "https://github.com/EnvironmentOntology/gaz/issues" . + "https://groups.google.com/forum/#!forum/obo-gazetteer" . + "http://purl.obolibrary.org/obo/gaz.owl" . + _:B012b2a2ce7a4dfe17ad12e1e19e7e978 . + . + . + . +_:Bd50959c2da48160750527fe0879a91b6 "archive" . +_:Bd50959c2da48160750527fe0879a91b6 "http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/*zip*/archive.zip"^^ . +_:B012b2a2ce7a4dfe17ad12e1e19e7e978 "Lynn Schriml" . +_:B012b2a2ce7a4dfe17ad12e1e19e7e978 "lschriml@som.umaryland.edu" . + "http://purl.obolibrary.org/obo/gaz.owl" . + "http://purl.obolibrary.org/obo/gaz.obo" . + "active" . + "An ontology to represent genomics cohort attributes" . + "Genomics Cohorts Knowledge Ontology" . + . + "cohort studies" . + "https://github.com/IHCC-cohorts/GECKO/issues" . + "http://purl.obolibrary.org/obo/gecko.owl" . + _:B7840d78a4e083f15133885dca47abbbc . + . + . +_:B7840d78a4e083f15133885dca47abbbc "Rebecca Jackson" . +_:B7840d78a4e083f15133885dca47abbbc "rbca.jackson@gmail.com" . + "http://purl.obolibrary.org/obo/gecko.owl" . + "active" . + . + . + . + . + . + "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks." . + "Genomic Epidemiology Ontology" . + . + "health" . + "https://github.com/GenEpiO/genepio/issues/" . + "http://purl.obolibrary.org/obo/genepio.owl" . + _:Bf6cce2013d40256dd5a67a3b56f274c0 . + . + . + . +_:Bf6cce2013d40256dd5a67a3b56f274c0 "Damion Dooley" . +_:Bf6cce2013d40256dd5a67a3b56f274c0 "damion.dooley@bccdc.ca" . + "http://purl.obolibrary.org/obo/genepio.owl" . + . + "active" . + _:B8bd030b7633a5d5229a62efd6fe8547c . + "An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases." . + "Genotype Ontology" . + . + "genotype-to-phenotype associations" . + "https://github.com/monarch-initiative/GENO-ontology/issues" . + "http://purl.obolibrary.org/obo/geno.owl" . + _:Bb382e06cd94dfd0f36afa48548279c89 . + . + . +_:B8bd030b7633a5d5229a62efd6fe8547c "git clone https://github.com/monarch-initiative/GENO-ontology.git" . + . + "CC-BY-SA" . +_:Bb382e06cd94dfd0f36afa48548279c89 "Matthew Brush" . +_:Bb382e06cd94dfd0f36afa48548279c89 "mhb120@gmail.com" . + "GENO" . + "http://purl.obolibrary.org/obo/geno.owl" . + "active" . + "An ontology of geographical entities" . + "Geographical Entity Ontology" . + . + "https://ontology.atlassian.net/browse/GEO#selectedTab=com.atlassian.jira.plugin.system.project%3Aissues-panel" . + "http://purl.obolibrary.org/obo/geo.owl" . + _:Bb9f4668fa4b6e1f7c146abd61e5c8287 . + . + . +_:Bb9f4668fa4b6e1f7c146abd61e5c8287 "Bill Hogan" . +_:Bb9f4668fa4b6e1f7c146abd61e5c8287 "hoganwr@gmail.com" . + "http://purl.obolibrary.org/obo/geo.owl" . + "active" . + _:B8b5600c26c6baf231c24c545f456db29 . + "GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels." . + "Glycan Naming and Subsumption Ontology (GNOme)" . + . + "glycan structure" . + "https://github.com/glygen-glycan-data/GNOme/issues" . + . + . + "http://purl.obolibrary.org/obo/gno.owl" . + _:B411c864bf3e4a28a35898f62e32b8406 . + . + . + . + . +_:B8b5600c26c6baf231c24c545f456db29 "git clone https://github.com/glygen-glycan-data/GNOme.git" . + "GNOme Glycan Structure Browser" . + "Structure Browser" . + "GNOme Glycan Composition Browser" . + "Composition Browser" . +_:B411c864bf3e4a28a35898f62e32b8406 "Nathan Edwards" . +_:B411c864bf3e4a28a35898f62e32b8406 "nje5@georgetown.edu" . + "Glycan Naming and Subsumption Ontology, OWL format (primary)" . + "http://purl.obolibrary.org/obo/gno.owl" . + "Glycan Naming and Subsumption Ontology, OBO format (automated conversion from OWL)" . + "http://purl.obolibrary.org/obo/gno.obo" . + "Glycan Naming and Subsumption Ontology, JSON format (automated conversion from OWL)" . + "http://purl.obolibrary.org/obo/gno.json" . + "active" . + "The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies." . + "Human Ancestry Ontology" . + . + "ancestry" . + "https://github.com/EBISPOT/ancestro/issues" . + "http://purl.obolibrary.org/obo/hancestro.owl" . + _:B7d951e6f94d7b61171e55dd5bffc7ee3 . + . + . + . +_:B7d951e6f94d7b61171e55dd5bffc7ee3 "Danielle Welter" . +_:B7d951e6f94d7b61171e55dd5bffc7ee3 "danielle.welter@uni.lu" . + "The full version of HANCESTRO in OWL format" . + "HANCESTRO" . + "http://purl.obolibrary.org/obo/hancestro.owl" . + "Version of HANCESTRO with BFO upper hierarchy for easier integration with other ontologies" . + "HANCESTRO BFO" . + "http://purl.obolibrary.org/obo/hancestro_bfo.owl" . + "active" . + _:B392c8bf47d005a88cdb419918e4f331e . + . + "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)" . + "Hymenoptera Anatomy Ontology" . + . + "anatomy" . + "https://github.com/hymao/hao/issues" . + "http://purl.obolibrary.org/obo/hao.owl" . + _:B28c49ecdcb873188ff2d1d3def55bb4c . + . + . + . + . +_:B392c8bf47d005a88cdb419918e4f331e "git clone https://github.com/hymao/hao.git" . + "Hymenoptera" . +_:B28c49ecdcb873188ff2d1d3def55bb4c "Matt Yoder" . +_:B28c49ecdcb873188ff2d1d3def55bb4c "diapriid@gmail.com" . + "http://purl.obolibrary.org/obo/hao.owl" . + "http://purl.obolibrary.org/obo/hao.obo" . + "http://purl.obolibrary.org/obo/hao/depictions.owl" . + "active" . + _:Bd0dec7372a9a09ecf213fee2210b40e0 . + "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology." . + "Homology Ontology" . + . + "https://github.com/BgeeDB/homology-ontology/issues" . + "http://purl.obolibrary.org/obo/hom.owl" . + _:B2d405e8ea618915b672a46e38fa24ca0 . + . + . +_:Bd0dec7372a9a09ecf213fee2210b40e0 "git clone https://github.com/BgeeDB/homology-ontology.git" . +_:Bd0dec7372a9a09ecf213fee2210b40e0 "vcs" . +_:B2d405e8ea618915b672a46e38fa24ca0 "Frederic Bastian" . +_:B2d405e8ea618915b672a46e38fa24ca0 "bgee@sib.swiss" . + "http://purl.obolibrary.org/obo/hom.owl" . + "HsapDv" . + "active" . + _:B9103b89fdb7e43ea1f347d9503e9337b . + "Life cycle stages for Human" . + "Human Developmental Stages" . + . + "https://github.com/obophenotype/developmental-stage-ontologies/issues" . + "http://purl.obolibrary.org/obo/hsapdv.owl" . + _:B97292444ae7c3cd77ae295ee0840eac9 . + . + . + . + . +_:B9103b89fdb7e43ea1f347d9503e9337b "obo2owl" . +_:B9103b89fdb7e43ea1f347d9503e9337b "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/hsapdv/hsapdv.obo"^^ . +_:B97292444ae7c3cd77ae295ee0840eac9 "bgee" . +_:B97292444ae7c3cd77ae295ee0840eac9 "bgee@sib.swiss" . + "http://purl.obolibrary.org/obo/hsapdv.owl" . + "http://purl.obolibrary.org/obo/hsapdv.obo" . + "active" . + . + . + . + . + . + "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance." . + "Health Surveillance Ontology" . + . + "health" . + "https://github.com/SVA-SE/HSO/issues/" . + "http://purl.obolibrary.org/obo/hso.owl" . + _:Ba0555e846e9bc38476ce36a3e8d47bf3 . + . + . + . +_:Ba0555e846e9bc38476ce36a3e8d47bf3 "Fernanda Dorea" . +_:Ba0555e846e9bc38476ce36a3e8d47bf3 "fernanda.dorea@sva.se" . + "http://purl.obolibrary.org/obo/hso.owl" . + . + "active" . + "https://raw.githubusercontent.com/aellenhicks/htn_owl/master/htn.owl"^^ . + "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines" . + "Hypertension Ontology" . + . + "https://github.com/aellenhicks/htn_owl/issues" . + "http://purl.obolibrary.org/obo/htn.owl" . + _:Bec3cd6e8670f799cec1e58960942aa29 . + . + . +_:Bec3cd6e8670f799cec1e58960942aa29 "Amanda Hicks" . +_:Bec3cd6e8670f799cec1e58960942aa29 "aellenhicks@gmail.com" . + "HTN" . + "http://purl.obolibrary.org/obo/htn.owl" . +_:B8a7996c83ee849ac063b58e2876451c2 "owl2obo" . +_:B8a7996c83ee849ac063b58e2876451c2 "http://purl.obolibrary.org/obo/iao.owl"^^ . +_:Beb3906ef594e98a763b5f92bf2813791 "Jie Zheng" . +_:Beb3906ef594e98a763b5f92bf2813791 "jiezheng@pennmedicine.upenn.edu" . + "http://purl.obolibrary.org/obo/iao.owl" . + "IAO ontology metadata" . + "http://purl.obolibrary.org/obo/iao/ontology-metadata.owl" . + . + "IAO dev" . + "http://purl.obolibrary.org/obo/iao/dev/iao.owl" . + "An ontology based on a theory of document acts describing what people can do with documents" . + "ontology of document acts" . + "http://purl.obolibrary.org/obo/iao/d-acts.owl" . + _:B64591f1a7f35a5657cedd1677a16d333 . +_:B64591f1a7f35a5657cedd1677a16d333 "Mathias Brochhausen" . +_:B64591f1a7f35a5657cedd1677a16d333 "mbrochhausen@gmail.com" . + "active" . + "ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs)." . + "Integrative and Conjugative Element Ontology" . + . + "https://github.com/ontoice/ICEO/issues" . + "http://purl.obolibrary.org/obo/iceo.owl" . + _:B4da392e119981a11a21b9a8246140180 . + . + . +_:B4da392e119981a11a21b9a8246140180 "Meng LIU" . +_:B4da392e119981a11a21b9a8246140180 "liumeng94@sjtu.edu.cn" . + "http://purl.obolibrary.org/obo/iceo.owl" . + "active" . + "An ontology of clinical informed consents" . + "Informed Consent Ontology" . + . + "https://github.com/ICO-ontology/ICO/issues" . + "http://purl.obolibrary.org/obo/ico.owl" . + _:B06957c75dcc8e8fa0b50639f1b2d3ed9 . + . + . +_:B06957c75dcc8e8fa0b50639f1b2d3ed9 "Yongqun Oliver He" . +_:B06957c75dcc8e8fa0b50639f1b2d3ed9 "yongqunh@med.umich.edu" . + "http://purl.obolibrary.org/obo/ico.owl" . + "active" . + _:Bbb7cdc427e285b05dd4ce74052e24bce . + . + "A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain." . + "Infectious Disease Ontology" . + . + "health" . + "https://github.com/infectious-disease-ontology/infectious-disease-ontology/issues" . + "http://purl.obolibrary.org/obo/ido.owl" . + _:Bc633d56ab7eeae0abb10bbb961012989 . + . + . +_:Bbb7cdc427e285b05dd4ce74052e24bce "owl2obo" . +_:Bbb7cdc427e285b05dd4ce74052e24bce "http://purl.obolibrary.org/obo/ido.owl"^^ . +_:Bc633d56ab7eeae0abb10bbb961012989 "Lindsay Cowell" . +_:Bc633d56ab7eeae0abb10bbb961012989 "Lindsay.Cowell@utsouthwestern.edu" . + "http://purl.obolibrary.org/obo/ido.owl" . + "active" . + "An ontology of interactions and interaction networks" . + "Interaction Network Ontology" . + . + "https://github.com/INO-ontology/ino/issues" . + "http://purl.obolibrary.org/obo/ino.owl" . + _:Beb571db0dd7a644145e3bc21d71ee093 . + . + . +_:Beb571db0dd7a644145e3bc21d71ee093 "Yongqun Oliver He" . +_:Beb571db0dd7a644145e3bc21d71ee093 "yongqunh@med.umich.edu" . + "http://purl.obolibrary.org/obo/ino.owl" . + "active" . + . + . + . + . + . + . + . + "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents." . + "clinical LABoratory Ontology" . + . + "clinical documentation" . + "https://github.com/OpenLHS/LABO/issues" . + "http://purl.obolibrary.org/obo/labo.owl" . + _:B0740c5d75144ea709545bb4b8e4c1d3d . + . + . + "active" . + . + "An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities" . + "Ontology for General Medical Science" . + . + "medicine" . + "https://github.com/OGMS/ogms/issues" . + "http://purl.obolibrary.org/obo/ogms.owl" . + _:B2ac000bf5afb14a1be81f29490431840 . + . + . + "active" . + "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)" . + "Ontologized MIABIS" . + . + "health" . + "https://github.com/OMIABIS/omiabis-dev/issues" . + "http://purl.obolibrary.org/obo/omiabis.owl" . + _:B08295f23e5cc8785a6ac40755476b7d1 . + . + . + "active" . + _:B56f0471713cd88618e1a3b12d26be0b6 . + . + "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations." . + "Ontology of Medically Related Social Entities" . + . + "medicine" . + "https://github.com/ufbmi/OMRSE/issues" . + "http://purl.obolibrary.org/obo/omrse.owl" . + _:B2dde413228932ff5606975577c4f3664 . + . + . + "active" . + "The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions." . + "Ontology of Precision Medicine and Investigation" . + . + "https://github.com/OPMI/opmi/issues" . + "http://groups.google.com/group/opmi-discuss" . + "http://purl.obolibrary.org/obo/opmi.owl" . + _:B498d0365b0f6e1272999ee869311cc56 . + . + . +_:B0740c5d75144ea709545bb4b8e4c1d3d "Paul Fabry" . +_:B0740c5d75144ea709545bb4b8e4c1d3d "paul.fabry@usherbrooke.ca" . + "http://purl.obolibrary.org/obo/labo.owl" . + "active" . + _:Bedfb3c2acd9e5daaddc0a384aeaf4bc9 . + . + "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)." . + "Mouse adult gross anatomy" . + . + "anatomy" . + "https://github.com/obophenotype/mouse-anatomy-ontology/issues" . + "http://purl.obolibrary.org/obo/ma.owl" . + _:B60911e95a52876cc83551d37553c03ad . + . + . + . + . +_:Bedfb3c2acd9e5daaddc0a384aeaf4bc9 "obo2owl" . +_:Bedfb3c2acd9e5daaddc0a384aeaf4bc9 "ftp://ftp.informatics.jax.org/pub/reports/adult_mouse_anatomy.obo"^^ . +_:B60911e95a52876cc83551d37553c03ad "Terry Hayamizu" . +_:B60911e95a52876cc83551d37553c03ad "Terry.Hayamizu@jax.org" . + "http://purl.obolibrary.org/obo/ma.owl" . + "http://purl.obolibrary.org/obo/ma.obo" . +_:B02242c6738a8d0b8b9386a00b730b69d "git clone https://github.com/monarch-initiative/MAxO.git" . +_:B5fcc89c4a749a101c8fa169f249247d1 "Leigh Carmody" . +_:B5fcc89c4a749a101c8fa169f249247d1 "Leigh.Carmody@jax.org" . + "http://purl.obolibrary.org/obo/maxo.owl" . + "http://purl.obolibrary.org/obo/maxo.obo" . + "http://purl.obolibrary.org/obo/maxo.json" . + "http://purl.obolibrary.org/obo/maxo/maxo-base.owl" . + "http://purl.obolibrary.org/obo/maxo/maxo-base.obo" . + "http://purl.obolibrary.org/obo/maxo/maxo-base.json" . + "active" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + _:B465d9f2cf47d4e5834d18f922bef58ee . + "Microbial Conditions Ontology is an ontology..." . + "Microbial Conditions Ontology" . + . + "experimental conditions" . + "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology/issues" . + "http://purl.obolibrary.org/obo/mco.owl" . + _:B5a1ca8a79ff2477f7a49c175260e8710 . + . + . + . + "active" . + "An ontology of prokaryotic phenotypic and metabolic characters" . + "Ontology of Prokaryotic Phenotypic and Metabolic Characters" . + . + "phenotype" . + "https://github.com/carrineblank/MicrO/issues" . + "http://purl.obolibrary.org/obo/micro.owl" . + _:B164ecb4de84644ced1fcbcf07752841c . + . + . + "active" . + "Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain" . + "Ontology for MIRNA Target" . + . + "https://github.com/OmniSearch/omit/issues" . + "http://purl.obolibrary.org/obo/omit.owl" . + _:Bfdfe23b1886d174e4fc9157bb8b003ca . + . + . + . + "active" . + _:B5968c778dee4de2417b3ef5d0b2d52d1 . + "An ontology of phenotypes covering microbes" . + "Ontology of Microbial Phenotypes" . + . + "phenotype" . + "https://github.com/microbialphenotypes/OMP-ontology/issues" . + "http://purl.obolibrary.org/obo/omp.owl" . + _:Be97e9c3aa1aecf8b553885c2790340bd . + . + . + . + "active" . + _:Ba25a6e5d7f83b0925a08efd7637169c0 . + . + "Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN" . + "Zebrafish Experimental Conditions Ontology" . + . + "environment" . + "https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues" . + "http://purl.obolibrary.org/obo/zeco.owl" . + _:B2776ad69f6e03d0463aa5a7d1d7cb2f9 . + . + . + . + . +_:B465d9f2cf47d4e5834d18f922bef58ee "git clone https://github.com/microbial-conditions-ontology/microbial-conditions-ontology.git" . +_:B5a1ca8a79ff2477f7a49c175260e8710 "Citlalli Mejía-Almonte" . +_:B5a1ca8a79ff2477f7a49c175260e8710 "citlalli.mejiaalmonte@gmail.com" . + "http://purl.obolibrary.org/obo/mco.owl" . + "http://purl.obolibrary.org/obo/mco.obo" . + "active" . + _:B2211c84a6e95d6ded3b1b8e1b2c8f49d . + "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning." . + "Mental Functioning Ontology" . + . + "health" . + "https://github.com/jannahastings/mental-functioning-ontology/issues" . + "http://purl.obolibrary.org/obo/mf.owl" . + _:B876ab0cf9318fcf0d610c83d8e8250be . + . + . +_:B2211c84a6e95d6ded3b1b8e1b2c8f49d "owl2obo" . +_:B2211c84a6e95d6ded3b1b8e1b2c8f49d "http://purl.obolibrary.org/obo/mf.owl"^^ . +_:B876ab0cf9318fcf0d610c83d8e8250be "Janna Hastings" . +_:B876ab0cf9318fcf0d610c83d8e8250be "janna.hastings@gmail.com" . + "http://purl.obolibrary.org/obo/mf.owl" . + "active" . + . + . + "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors." . + "Mammalian Feeding Muscle Ontology" . + . + "anatomy" . + "https://github.com/RDruzinsky/feedontology/issues" . + "http://purl.obolibrary.org/obo/mfmo.owl" . + _:Be0b14761d0484669cb5abe4907f9fdc7 . + . + . + "Mammalian" . + "Mammalia" . +_:Be0b14761d0484669cb5abe4907f9fdc7 "Robert Druzinsky" . +_:Be0b14761d0484669cb5abe4907f9fdc7 "druzinsk@uic.edu" . + "http://purl.obolibrary.org/obo/mfmo.owl" . + "active" . + _:B096cd62fde9f33a3c52cbce960f1b57e . + "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings." . + "Emotion Ontology" . + . + "health" . + "https://github.com/jannahastings/emotion-ontology/issues" . + "http://purl.obolibrary.org/obo/mfoem.owl" . + _:Bc0a3e23d3a09d1db6203d5e2f90ad266 . + . + . +_:B096cd62fde9f33a3c52cbce960f1b57e "owl2obo" . +_:B096cd62fde9f33a3c52cbce960f1b57e "http://purl.obolibrary.org/obo/mfoem.owl"^^ . +_:Bc0a3e23d3a09d1db6203d5e2f90ad266 "Janna Hastings" . +_:Bc0a3e23d3a09d1db6203d5e2f90ad266 "janna.hastings@gmail.com" . + "http://purl.obolibrary.org/obo/mfoem.owl" . + "active" . + "An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable" . + "Mental Disease Ontology" . + . + "health" . + "https://github.com/jannahastings/mental-functioning-ontology/issues" . + "http://purl.obolibrary.org/obo/mfomd.owl" . + _:B160ab21868b573e86dc283c2ca6109af . + . + . +_:B160ab21868b573e86dc283c2ca6109af "Janna Hastings" . +_:B160ab21868b573e86dc283c2ca6109af "janna.hastings@gmail.com" . + "http://purl.obolibrary.org/obo/mfomd.owl" . + "active" . + _:Bf650e4870edaadc0f4da01d0c4476723 . + "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions." . + "Molecular Interactions Controlled Vocabulary" . + . + "experiments" . + "https://github.com/HUPO-PSI/psi-mi-CV/issues" . + "http://purl.obolibrary.org/obo/mi.owl" . + _:Bda7f00785ad9f782c7f708284074d5a8 . + . + . + . + . +_:Bf650e4870edaadc0f4da01d0c4476723 "obo2owl" . +_:Bf650e4870edaadc0f4da01d0c4476723 "https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo"^^ . +_:Bda7f00785ad9f782c7f708284074d5a8 "Pablo Porras Millán" . +_:Bda7f00785ad9f782c7f708284074d5a8 "pporras@ebi.ac.uk" . + "http://purl.obolibrary.org/obo/mi.owl" . + "http://purl.obolibrary.org/obo/mi.obo" . + "active" . + "An application ontology to formalize annotation of phylogenetic data." . + "MIAPA Ontology" . + . + "https://github.com/evoinfo/miapa/issues" . + "http://groups.google.com/group/miapa-discuss" . + "https://fairsharing.org/FAIRsharing.ca48xs" . + "http://purl.obolibrary.org/obo/miapa.owl" . + _:B3a742a43763397ec3f1bf3c5eab5751b . + . + . +_:B3a742a43763397ec3f1bf3c5eab5751b "Hilmar Lapp" . +_:B3a742a43763397ec3f1bf3c5eab5751b "hilmar.lapp@duke.edu" . + "http://purl.obolibrary.org/obo/miapa.owl" . +_:B164ecb4de84644ced1fcbcf07752841c "Carrine Blank" . +_:B164ecb4de84644ced1fcbcf07752841c "carrine.blank@umontana.edu" . + "http://purl.obolibrary.org/obo/micro.owl" . + "active" . + _:B65b3eae66fdd263b6c1832e078de0b88 . + "A representation of the variety of methods used to make clinical and phenotype measurements. " . + "Measurement method ontology" . + . + . + . + "clinical" . + "https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues" . + . + "http://purl.obolibrary.org/obo/mmo.owl" . + _:Bfc5f3e49f3d5fa12ede0a98f38d3c2ff . + . + . + . + . +_:B65b3eae66fdd263b6c1832e078de0b88 "obo2owl" . +_:B65b3eae66fdd263b6c1832e078de0b88 "ftp://ftp.rgd.mcw.edu/pub/ontology/measurement_method/measurement_method.obo"^^ . + "RGD Ontology Browser" . + "RGD" . +_:Bfc5f3e49f3d5fa12ede0a98f38d3c2ff "Jennifer Smith" . +_:Bfc5f3e49f3d5fa12ede0a98f38d3c2ff "jrsmith@mcw.edu" . + "http://purl.obolibrary.org/obo/mmo.owl" . + "http://purl.obolibrary.org/obo/mmo.obo" . + "MmusDv" . + "active" . + _:B19e9e93765851e097e3ed69f226d718b . + "Life cycle stages for Mus Musculus" . + "Mouse Developmental Stages" . + . + "https://github.com/obophenotype/developmental-stage-ontologies/issues" . + "http://purl.obolibrary.org/obo/mmusdv.owl" . + _:B34a9fc07cdb5cfec3bfc03885230b66a . + . + . + . + . +_:B19e9e93765851e097e3ed69f226d718b "obo2owl" . +_:B19e9e93765851e097e3ed69f226d718b "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/mmusdv/mmusdv.obo"^^ . +_:B34a9fc07cdb5cfec3bfc03885230b66a "bgee" . +_:B34a9fc07cdb5cfec3bfc03885230b66a "bgee@sib.swiss" . + "http://purl.obolibrary.org/obo/mmusdv.owl" . + "http://purl.obolibrary.org/obo/mmusdv.obo" . + "active" . + _:B6492ca55dbf36225a77e78524e0f3ff8 . + "PSI-MOD is an ontology consisting of terms that describe protein chemical modifications" . + "Protein modification" . + . + . + "proteins" . + "https://github.com/HUPO-PSI/psi-mod-CV/issues" . + "http://purl.obolibrary.org/obo/mod.owl" . + _:B479371cdb6485a84f247842a7d4fd6bb . + . + . + . +_:B6492ca55dbf36225a77e78524e0f3ff8 "obo2owl" . +_:B6492ca55dbf36225a77e78524e0f3ff8 "https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo"^^ . + "The PSI-MOD community standard for representation of protein modification data" . +_:B479371cdb6485a84f247842a7d4fd6bb "Pierre-Alain Binz" . +_:B479371cdb6485a84f247842a7d4fd6bb "pierre-alain.binz@chuv.ch" . + "PSI-MOD Ontology, OWL format" . + "PSI-MOD.owl" . + "http://purl.obolibrary.org/obo/mod.owl" . + "PSI-MOD Ontology, OBO format" . + "PSI-MOD.obo" . + "http://purl.obolibrary.org/obo/mod.obo" . + "active" . + . + "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology." . + "Mondo Disease Ontology" . + . + "disease" . + "https://github.com/monarch-initiative/mondo/issues" . + "https://groups.google.com/group/mondo-users" . + "Mondo" . + . + "http://purl.obolibrary.org/obo/mondo.owl" . + _:B041835e891bde9429c3a5640ac7dbf05 . + . + . + . + . + "Monarch Initiative Disease Browser" . + "Monarch" . +_:B041835e891bde9429c3a5640ac7dbf05 "Nicole Vasilevsky" . +_:B041835e891bde9429c3a5640ac7dbf05 "vasilevs@ohsu.edu" . + "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." . + "Main OWL edition" . + "owl-rdf/xml" . + "http://purl.obolibrary.org/obo/mondo.owl" . + "As OWL. xrefs can be used as proxy for equivalence. Uses Mondo IDs." . + "obo-format edition" . + "obo" . + "http://purl.obolibrary.org/obo/mondo.obo" . + "Equivalent to the OWL edition." . + "json edition" . + "obo" . + "http://purl.obolibrary.org/obo/mondo.json" . + "active" . + _:B3ed4ece5bb2b1d0b5813db3515977435 . + "Processes at the molecular level" . + "Molecular Process Ontology" . + . + "https://github.com/rsc-ontologies/rxno/issues" . + "chemistry-ontologies@googlegroups.com" . + "http://purl.obolibrary.org/obo/mop.owl" . + _:B0aa2fea923be33bb19b31540f60aa7ba . + . + . +_:B3ed4ece5bb2b1d0b5813db3515977435 "owl2obo" . +_:B3ed4ece5bb2b1d0b5813db3515977435 "https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.owl"^^ . +_:B0aa2fea923be33bb19b31540f60aa7ba "Colin Batchelor" . +_:B0aa2fea923be33bb19b31540f60aa7ba "batchelorc@rsc.org" . + "Molecular Process Ontology" . + "http://purl.obolibrary.org/obo/mop.owl" . +_:Bfb178b44ba804edaf90f21144c383652 "git clone https://github.com/obophenotype/mammalian-phenotype-ontology.git" . + "MGI MP Browser" . + "MGI" . + "RGD MP Browser" . + "RGD" . + "Monarch Phenotype Page" . + "Monarch" . +_:B7ed19d6e64b40f8739626d682c69cd2d "JAX phenotype list" . +_:B7ed19d6e64b40f8739626d682c69cd2d "pheno@jax.org" . + "The main ontology in OWL. Contains all MP terms and links to other OBO ontologies." . + "MP (OWL edition)" . + "http://purl.obolibrary.org/obo/mp.owl" . + . + "A direct translation of the MP (OWL edition) into OBO format." . + "MP (OBO edition)" . + "http://purl.obolibrary.org/obo/mp.obo" . + . + "For a description of the format see https://github.com/geneontology/obographs." . + "MP (obographs JSON edition)" . + "http://purl.obolibrary.org/obo/mp.json" . + . + "The main ontology plus axioms connecting to select external ontologies, excluding axioms from the the external ontologies themselves." . + "MP Base Module" . + "http://purl.obolibrary.org/obo/mp/mp-base.owl" . + . + "active" . + _:B6c5460a34916bddd069090f1005f41fb . + . + "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes" . + "Mouse pathology ontology" . + . + "health" . + "https://github.com/PaulNSchofield/mpath/issues" . + "http://purl.obolibrary.org/obo/mpath.owl" . + _:Bd87315ce2b5481de0ce9a171ef7c63fd . + . + . +_:B6c5460a34916bddd069090f1005f41fb "obo2owl" . +_:B6c5460a34916bddd069090f1005f41fb "https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo"^^ . +_:Bd87315ce2b5481de0ce9a171ef7c63fd "Paul Schofield" . +_:Bd87315ce2b5481de0ce9a171ef7c63fd "pns12@hermes.cam.ac.uk" . + "http://purl.obolibrary.org/obo/mpath.owl" . + "active" . + "An ontology of minimum information regarding potential drug-drug interaction information." . + "Minimum PDDI Information Ontology" . + . + "health" . + "https://github.com/MPIO-Developers/MPIO/issues" . + "http://purl.obolibrary.org/obo/mpio.owl" . + _:Be90b62c69fbcbad84db7f74d9ef647f9 . + . + . +_:Be90b62c69fbcbad84db7f74d9ef647f9 "Mathias Brochhausen" . +_:Be90b62c69fbcbad84db7f74d9ef647f9 "mbrochhausen@uams.edu" . + "http://purl.obolibrary.org/obo/mpio.owl" . + "active" . + "An ontology for Major Histocompatibility Complex (MHC) restriction in experiments" . + "MHC Restriction Ontology" . + . + "Major Histocompatibility Complex" . + "https://github.com/IEDB/MRO/issues" . + "http://purl.obolibrary.org/obo/mro.owl" . + _:B3a99242d915480402ca9eb3d34571a92 . + . + . +_:B3a99242d915480402ca9eb3d34571a92 "Bjoern Peters" . +_:B3a99242d915480402ca9eb3d34571a92 "bpeters@lji.org" . + "http://purl.obolibrary.org/obo/mro.owl" . + "active" . + "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master" . + . + . + _:Bc90a28205ecaca40a2bf39836acac641 . + "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry." . + "Mass spectrometry ontology" . + . + . + "MS experiments" . + "http://oboedit.org" . + "https://github.com/HUPO-PSI/psi-ms-CV/issues" . + "psidev-ms-vocab@lists.sourceforge.net" . + "MS" . + "http://purl.obolibrary.org/obo/ms.owl" . + _:B7c1a7da40cc522c8d25dcf0c31c76d5e . + . + . + . + . +_:Bc90a28205ecaca40a2bf39836acac641 "obo2owl" . +_:Bc90a28205ecaca40a2bf39836acac641 "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"^^ . + "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary." . +_:B7c1a7da40cc522c8d25dcf0c31c76d5e "Gerhard Mayer" . +_:B7c1a7da40cc522c8d25dcf0c31c76d5e "gerhard.mayer@rub.de" . + "http://purl.obolibrary.org/obo/ms.obo" . + "http://purl.obolibrary.org/obo/ms.owl" . +_:Ba6ad3b82e84402c5b7c8001c985fa7c3 "owl2obo" . +_:Ba6ad3b82e84402c5b7c8001c985fa7c3 "https://raw.githubusercontent.com/obo-behavior/behavior-ontology/master/nbo.owl"^^ . + "BioPortal Ontology Browser" . + "BioPortal" . +_:Bfd53d633249f7dff0a98051c3c6f1d48 "George Gkoutos" . +_:Bfd53d633249f7dff0a98051c3c6f1d48 "g.gkoutos@bham.ac.uk" . + "http://purl.obolibrary.org/obo/nbo.owl" . +_:B17f6c1c5c558e683e8ea18d0ffffb1ae "archive" . +_:B17f6c1c5c558e683e8ea18d0ffffb1ae "http://build.berkeleybop.org/job/build-ncbitaxon/lastSuccessfulBuild/artifact/*zip*/archive.zip"^^ . + "NCBI Taxonomy Browser" . + "NCBI" . +_:B86bd45137e813abfc8c6d49402320d92 "Frederic Bastian" . +_:B86bd45137e813abfc8c6d49402320d92 "frederic.bastian@unil.ch" . + "Main release" . + "http://purl.obolibrary.org/obo/ncbitaxon.owl" . + "OBO Format version of Main release" . + "http://purl.obolibrary.org/obo/ncbitaxon.obo" . + "taxslim" . + "http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl" . + . + "taxslim disjointness axioms" . + "http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl" . + . +_:B77c03ffa9a8d6f949cddfb3e36ccabbe "Melissa Haendel" . +_:B77c03ffa9a8d6f949cddfb3e36ccabbe "haendel@ohsu.edu" . + "A direct transformation of the standard NCIt content using OBO-style term and ontology IRIs and annotation properties." . + "NCIt OBO Edition OWL format" . + "http://purl.obolibrary.org/obo/ncit.owl" . + "NCIt OBO Edition OBO format" . + "http://purl.obolibrary.org/obo/ncit.obo" . + "This version replaces NCIt terms with direct references to terms from other domain-specific OBO Library ontologies (e.g. cell types, cellular components, anatomy), supporting cross-ontology reasoning. The current release incorporates CL (cell types) and Uberon (anatomy)." . + "NCIt Plus" . + "http://purl.obolibrary.org/obo/ncit/ncit-plus.owl" . + "This is a subset extracted from NCIt Plus, based on the [NCIt Neoplasm Core value set](https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/Neoplasm/About_Core.html) as a starting point." . + "NCIt Plus Neoplasm Core" . + "http://purl.obolibrary.org/obo/ncit/neoplasm-core.owl" . + "active" . + _:Bcf9651e4135d5a6c3f846fca01e8de58 . + "An ontology for non-coding RNA, both of biological origin, and engineered." . + "Non-Coding RNA Ontology" . + . + "experiments" . + "https://github.com/OmniSearch/NCRO-Ontology-Files/issues" . + "ncro-devel@googlegroups.com, ncro-discuss@googlegroups.com" . + "http://purl.obolibrary.org/obo/ncro.owl" . + _:Bcd73ab4725407800cf28a5b500dc6cd9 . + . + . +_:Bcf9651e4135d5a6c3f846fca01e8de58 "owl2obo" . +_:Bcf9651e4135d5a6c3f846fca01e8de58 "http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl"^^ . +_:Bcd73ab4725407800cf28a5b500dc6cd9 "Jingshan Huang" . +_:Bcd73ab4725407800cf28a5b500dc6cd9 "huang@southalabama.edu" . + "NCRO development version" . + "http://purl.obolibrary.org/obo/ncro/dev/ncro.owl" . + "active" . + _:Ba17349a5d256616e6e3b1725a7dd946c . + "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature." . + "NOMEN - A nomenclatural ontology for biological names" . + . + "biological nomenclature" . + "NSF-ABI-1356381" . + "Species File Group" . + "https://github.com/SpeciesFileGroup/nomen/issues" . + "https://groups.google.com/forum/#!forum/nomen-discuss" . + . + "NOMEN" . + "http://purl.obolibrary.org/obo/nomen.owl" . + _:B92ccbbc7c362cf8b344c00b4c230ef3c . + . + . +_:Ba17349a5d256616e6e3b1725a7dd946c "git clone https://github.com/SpeciesFileGroup/nomen.git" . +_:B92ccbbc7c362cf8b344c00b4c230ef3c "Matt Yoder" . +_:B92ccbbc7c362cf8b344c00b4c230ef3c "diapriid@gmail.com" . + "core ontology" . + "NOMEN" . + . + "http://purl.obolibrary.org/obo/nomen.owl" . + "active" . + _:Bc782d101a5a6d369a5c19d291e5de3b5 . + "A biomedical ontology in the domain of adverse events" . + "Ontology of Adverse Events" . + . + "adverse events, health" . + "https://github.com/OAE-ontology/OAE/issues" . + "http://purl.obolibrary.org/obo/oae.owl" . + _:Bcc07e4e5eec864abb7998366d9c3cbe6 . + . + . +_:Bc782d101a5a6d369a5c19d291e5de3b5 "owl2obo" . +_:Bc782d101a5a6d369a5c19d291e5de3b5 "https://raw.githubusercontent.com/OAE-ontology/OAE/master/src/oae_merged.owl"^^ . +_:Bcc07e4e5eec864abb7998366d9c3cbe6 "Yongqunh He" . +_:Bcc07e4e5eec864abb7998366d9c3cbe6 "yongqunh@med.umich.edu" . + "http://purl.obolibrary.org/obo/oae.owl" . + "active" . + "OArCS is an ontology describing the Arthropod ciruclatory system." . + "Ontology of Arthropod Circulatory Systems" . + . + "anatomy" . + "https://github.com/aszool/oarcs/issues" . + "http://purl.obolibrary.org/obo/oarcs.owl" . + _:B41015041cdc25973101d779bd644450d . + . + . +_:B41015041cdc25973101d779bd644450d "Matt Yoder" . +_:B41015041cdc25973101d779bd644450d "mjyoder@illinois.edu" . + "http://purl.obolibrary.org/obo/oarcs.owl" . +_:Bd9f364456f94b1f4d1bf4e944b621520 "git clone https://github.com/obophenotype/bio-attribute-ontology.git" . +_:Bd9f364456f94b1f4d1bf4e944b621520 "vcs" . +_:B14a26b02fe983bcb66d20d0072418a1d "Chris Mungall" . +_:B14a26b02fe983bcb66d20d0072418a1d "cjmungall@lbl.gov" . + "http://purl.obolibrary.org/obo/oba.owl" . + "http://purl.obolibrary.org/obo/oba.obo" . + "http://purl.obolibrary.org/obo/oba/subsets/oba-basic.obo" . + "active" . + "A biomedical ontology in the domain of biological and clinical statistics." . + "Ontology of Biological and Clinical Statistics" . + . + "statistics" . + "https://github.com/obcs/obcs/issues" . + "http://purl.obolibrary.org/obo/obcs.owl" . + _:B67c015d511103b2345e9952c56e98056 . + . + . +_:B67c015d511103b2345e9952c56e98056 "Jie Zheng" . +_:B67c015d511103b2345e9952c56e98056 "jiezheng@pennmedicine.upenn.edu" . + "http://purl.obolibrary.org/obo/obcs.owl" . + "active" . + "An ontology built for annotation and modeling of biobank repository and biobanking administration" . + "Ontology for Biobanking" . + . + "biobanking, specimens, bio-repository, biocuration" . + "https://github.com/biobanking/biobanking/issues" . + "http://purl.obolibrary.org/obo/obib.owl" . + _:B0b0bdef80e98529282b7ec70541195c5 . + . + . +_:B0b0bdef80e98529282b7ec70541195c5 "Jie Zheng" . +_:B0b0bdef80e98529282b7ec70541195c5 "jiezheng@pennmedicine.upenn.edu" . + "http://purl.obolibrary.org/obo/obib.owl" . + "active" . + "A formal ontology of genes and genomes of biological organisms." . + "The Ontology of Genes and Genomes" . + . + "https://bitbucket.org/hegroup/ogg/issues/" . + "http://purl.obolibrary.org/obo/ogg.owl" . + _:B8a0d700869fca054b865769c7a7c076b . + . + . +_:B8a0d700869fca054b865769c7a7c076b "Yongqun Oliver He" . +_:B8a0d700869fca054b865769c7a7c076b "yongqunh@med.umich.edu" . + "http://purl.obolibrary.org/obo/ogg.owl" . +_:B2ac000bf5afb14a1be81f29490431840 "Brian Aevermann" . +_:B2ac000bf5afb14a1be81f29490431840 "baeverma@jcvi.org" . + "http://purl.obolibrary.org/obo/ogms.owl" . + "active" . + "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process." . + "Ontology of Genetic Susceptibility Factor" . + . + "https://github.com/linikujp/OGSF/issues" . + "http://purl.obolibrary.org/obo/ogsf.owl" . + _:B266877dfcab3fab864f72e8e8c56cf62 . + . + . +_:B266877dfcab3fab864f72e8e8c56cf62 "Asiyah Yu Lin" . +_:B266877dfcab3fab864f72e8e8c56cf62 "linikujp@gmail.com" . + "http://purl.obolibrary.org/obo/ogsf.owl" . + "active" . + _:B8f0d8b9e7c6ceeda60bc8dc8d8e61ce5 . + "The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records." . + "The Oral Health and Disease Ontology" . + . + "health" . + "https://purl.obolibrary.org/obo/ohd/issues" . + "http://purl.obolibrary.org/obo/ohd.owl" . + _:B06a05079d62a36db5f1f4c4a35e5d9ba . + . + . + . +_:B8f0d8b9e7c6ceeda60bc8dc8d8e61ce5 "owl2obo" . +_:B8f0d8b9e7c6ceeda60bc8dc8d8e61ce5 "http://purl.obolibrary.org/obo/ohd.owl"^^ . +_:B06a05079d62a36db5f1f4c4a35e5d9ba "Alan Ruttenberg" . +_:B06a05079d62a36db5f1f4c4a35e5d9ba "alanruttenberg@gmail.com" . + "http://purl.obolibrary.org/obo/ohd.owl" . + "OHD dev" . + "http://purl.obolibrary.org/obo/ohd/dev/ohd.owl" . + "active" . + "The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions." . + "Ontology of Host-Microbiome Interactions" . + . + "https://github.com/ohmi-ontology/ohmi/issues" . + "http://groups.google.com/group/ohmi-discuss" . + "http://purl.obolibrary.org/obo/ohmi.owl" . + _:Bd55b4da383ca341cddb3bc4eb862e758 . + . + . +_:Bd55b4da383ca341cddb3bc4eb862e758 "Yongqun Oliver He" . +_:Bd55b4da383ca341cddb3bc4eb862e758 "yongqunh@med.umich.edu" . + "http://purl.obolibrary.org/obo/ohmi.owl" . + "active" . + "OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is developed to represent manually curated HPI knowledge available in the PHIDIAS resource." . + "Ontology of Host Pathogen Interactions" . + . + "https://github.com/OHPI/ohpi/issues" . + "http://groups.google.com/group/ohpi-discuss" . + "http://purl.obolibrary.org/obo/ohpi.owl" . + _:Bc92bc0b6dca734d715106b6094b1789c . + . + . +_:Bc92bc0b6dca734d715106b6094b1789c "Edison Ong" . +_:Bc92bc0b6dca734d715106b6094b1789c "edong@umich.edu" . + "http://purl.obolibrary.org/obo/ohpi.owl" . + "OlatDv" . + "active" . + _:Bdb88b2007039c535d65082442ce70bbe . + "Life cycle stages for Medaka" . + "Medaka Developmental Stages" . + . + "https://github.com/obophenotype/developmental-stage-ontologies/issues" . + "http://purl.obolibrary.org/obo/olatdv.owl" . + _:B112b0500ad08fc31f778d0760954235b . + . + . + . + . +_:Bdb88b2007039c535d65082442ce70bbe "obo2owl" . +_:Bdb88b2007039c535d65082442ce70bbe "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/olatdv/olatdv.obo"^^ . +_:B112b0500ad08fc31f778d0760954235b "bgee" . +_:B112b0500ad08fc31f778d0760954235b "bgee@sib.swiss" . + "http://purl.obolibrary.org/obo/olatdv.obo" . + "http://purl.obolibrary.org/obo/olatdv.owl" . +_:B08295f23e5cc8785a6ac40755476b7d1 "Mathias Brochhausen" . +_:B08295f23e5cc8785a6ac40755476b7d1 "mbrochhausen@gmail.com" . + "http://purl.obolibrary.org/obo/omiabis.owl" . +_:Bfdfe23b1886d174e4fc9157bb8b003ca "Huang, Jingshan" . +_:Bfdfe23b1886d174e4fc9157bb8b003ca "huang@southalabama.edu" . + "http://purl.obolibrary.org/obo/omit.owl" . + "active" . + "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)." . + "OBO Metadata Ontology" . + . + "ontology term annotation" . + "https://github.com/information-artifact-ontology/ontology-metadata/issues" . + "http://purl.obolibrary.org/obo/omo.owl" . + _:B893a0c135cd4127e40258af03add7f3a . + . + . +_:B893a0c135cd4127e40258af03add7f3a "Chris Mungall" . +_:B893a0c135cd4127e40258af03add7f3a "cjmungall@lbl.gov" . + "http://purl.obolibrary.org/obo/omo.owl" . +_:B5968c778dee4de2417b3ef5d0b2d52d1 "obo2owl" . +_:B5968c778dee4de2417b3ef5d0b2d52d1 "https://raw.githubusercontent.com/microbialphenotypes/OMP-ontology-files/master/omp.obo"^^ . +_:Be97e9c3aa1aecf8b553885c2790340bd "James C. Hu" . +_:Be97e9c3aa1aecf8b553885c2790340bd "jimhu@tamu.edu" . + "http://purl.obolibrary.org/obo/omp.owl" . + "http://purl.obolibrary.org/obo/omp.obo" . +_:B56f0471713cd88618e1a3b12d26be0b6 "owl2obo" . +_:B56f0471713cd88618e1a3b12d26be0b6 "https://github.com/ufbmi/OMRSE"^^ . +_:B2dde413228932ff5606975577c4f3664 "Bill Hogan" . +_:B2dde413228932ff5606975577c4f3664 "hoganwr@gmail.com" . + "http://purl.obolibrary.org/obo/omrse.owl" . + "active" . + . + . + . + "An ontology to standardize research output of nutritional epidemiologic studies." . + "Ontology for Nutritional Epidemiology" . + . + "nutritional epidemiology, observational studies, dietary surveys" . + "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies/issues" . + "Ontology for Nutritional Epidemiology" . + "http://purl.obolibrary.org/obo/one.owl" . + _:Be26d8762ac01ac3321312fdfc2169403 . + . + . + . + "active" . + . + . + . + . + . + . + . + . + "An ontology for description of concepts in the nutritional studies domain." . + "Ontology for Nutritional Studies" . + . + "nutrition, nutritional studies, nutrition professionals" . + "https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues" . + "Ontology for Nutritional Studies" . + "http://purl.obolibrary.org/obo/ons.owl" . + _:B2a8340c9ad3718ef7aeac0fc267fc0e9 . + . + . + . +_:Be26d8762ac01ac3321312fdfc2169403 "Chen Yang" . +_:Be26d8762ac01ac3321312fdfc2169403 "chen.yang@ugent.be" . + "http://purl.obolibrary.org/obo/one.owl" . +_:B2a8340c9ad3718ef7aeac0fc267fc0e9 "Francesco Vitali" . +_:B2a8340c9ad3718ef7aeac0fc267fc0e9 "francesco.vitali@ibba.cnr.it" . + "ONS latest release" . + "http://purl.obolibrary.org/obo/ons.owl" . + "active" . + _:Bf2aed6edab91d5c30b0cc7fba4eef48e . + "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby." . + "Obstetric and Neonatal Ontology" . + . + "biomedical, health" . + "https://github.com/ontoneo-project/Ontoneo/issues" . + "http://groups.google.com/group/ontoneo-discuss" . + . + "http://purl.obolibrary.org/obo/ontoneo.owl" . + _:B9358255cf8bca769e8d3bfdf6a5ba3f8 . + . + . +_:Bf2aed6edab91d5c30b0cc7fba4eef48e "http://purl.obolibrary.org/obo/ontoneo/ontoneo.owl"^^ . + "BioPortal Browser" . + "BioPortal" . +_:B9358255cf8bca769e8d3bfdf6a5ba3f8 "Fernanda Farinelli" . +_:B9358255cf8bca769e8d3bfdf6a5ba3f8 "fernanda.farinelli@gmail.com" . + "http://purl.obolibrary.org/obo/ontoneo.owl" . + "active" . + "An ontology built for representating the organizational components of trauma centers and trauma systems." . + "Ontology of Organizational Structures of Trauma centers and Trauma systems" . + . + "health" . + "https://github.com/OOSTT/OOSTT/issues" . + "http://purl.obolibrary.org/obo/oostt.owl" . + _:B4035869911ada77d36fda2af994a3b5a . + . + . +_:B4035869911ada77d36fda2af994a3b5a "Mathias Brochhausen" . +_:B4035869911ada77d36fda2af994a3b5a "mbrochhausen@gmail.com" . + "http://purl.obolibrary.org/obo/oostt.owl" . + "active" . + "A reference ontology for parasite life cycle stages." . + "Ontology for Parasite LifeCycle" . + . + "life cycle stage, parasite organism" . + "https://github.com/OPL-ontology/OPL/issues" . + "http://purl.obolibrary.org/obo/opl.owl" . + _:B24f85a4966b034c9d0ec9044a5269be2 . + . + . +_:B24f85a4966b034c9d0ec9044a5269be2 "Priti Parikh" . +_:B24f85a4966b034c9d0ec9044a5269be2 "preets79@gmail.com" . + "http://purl.obolibrary.org/obo/opl.owl" . +_:B498d0365b0f6e1272999ee869311cc56 "Yongqun Oliver He" . +_:B498d0365b0f6e1272999ee869311cc56 "yongqunh@med.umich.edu" . + "http://purl.obolibrary.org/obo/opmi.owl" . + "active" . + "An application ontology designed to annotate next-generation sequencing experiments performed on RNA." . + "Ontology of RNA Sequencing" . + . + "experiments" . + "https://github.com/safisher/ornaseq/issues" . + "http://purl.obolibrary.org/obo/ornaseq.owl" . + _:B3630ca444374f8a8cbc24acc38b7afb6 . + . + . +_:B3630ca444374f8a8cbc24acc38b7afb6 "Stephen Fisher" . +_:B3630ca444374f8a8cbc24acc38b7afb6 "safisher@upenn.edu" . + "http://purl.obolibrary.org/obo/ornaseq.owl" . + "active" . + "A biomedical ontology in the domain of vaccine adverse events." . + "Ontology of Vaccine Adverse Events" . + . + "https://github.com/OVAE-Ontology/ovae/issues" . + "http://purl.obolibrary.org/obo/ovae.owl" . + _:B16d6fc740b556346c0d04fddb4f2c678 . + . + . +_:B16d6fc740b556346c0d04fddb4f2c678 "Yongqunh He" . +_:B16d6fc740b556346c0d04fddb4f2c678 "yongqunh@med.umich.edu" . + "http://purl.obolibrary.org/obo/ovae.owl" . +_:B0e8e0ee16e9376a668cf9ad32ab7c9f3 "git clone https://github.com/PopulationAndCommunityOntology/pco.git" . +_:B17d75ab07c0be4fc148e4ec23dffe82d "Ramona Walls" . +_:B17d75ab07c0be4fc148e4ec23dffe82d "rlwalls2008@gmail.com" . + "http://purl.obolibrary.org/obo/pco.owl" . + "active" . + _:B45fc81cb96d141eba2ac23d5ffb2fc1d . + "An ontology to describe entities related to prescription of drugs" . + "The Prescription of Drugs Ontology" . + . + "health" . + "https://github.com/OpenLHS/PDRO/issues" . + "http://purl.obolibrary.org/obo/pdro.owl" . + _:B54f2b4e74d8809faeb9e47a74a9431e4 . + . + . +_:B45fc81cb96d141eba2ac23d5ffb2fc1d "owl2obo" . +_:B45fc81cb96d141eba2ac23d5ffb2fc1d "http://purl.obolibrary.org/obo/pdro.owl"^^ . +_:B54f2b4e74d8809faeb9e47a74a9431e4 "Paul Fabry" . +_:B54f2b4e74d8809faeb9e47a74a9431e4 "paul.fabry@usherbrooke.ca" . + "http://purl.obolibrary.org/obo/pdro.owl" . + "PdumDv" . + "active" . + _:B5263f5b6889dbbd29354aa8da42a41f7 . + "Life cycle stages for Platynereis dumerilii" . + "Platynereis Developmental Stages" . + . + "https://github.com/obophenotype/developmental-stage-ontologies/issues" . + "http://purl.obolibrary.org/obo/pdumdv.owl" . + _:B6235a968f9601b9c8d4b7d107b42e458 . + . + . + . + . +_:B5263f5b6889dbbd29354aa8da42a41f7 "obo2owl" . +_:B5263f5b6889dbbd29354aa8da42a41f7 "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/pdumdv/pdumdv.obo"^^ . +_:B6235a968f9601b9c8d4b7d107b42e458 "bgee" . +_:B6235a968f9601b9c8d4b7d107b42e458 "bgee@sib.swiss" . + "http://purl.obolibrary.org/obo/pdumdv.owl" . + "http://purl.obolibrary.org/obo/pdumdv.obo" . +_:B3fc94925d074e9da51fe50dc30bb9499 "Pankaj Jaiswal" . +_:B3fc94925d074e9da51fe50dc30bb9499 "jaiswalp@science.oregonstate.edu" . + "http://purl.obolibrary.org/obo/peco.owl" . + "http://purl.obolibrary.org/obo/peco.obo" . + "active" . + . + _:B7ac90f1cddfbbb01a483ee9a952f910c . + "PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions." . + "Pathogen Host Interaction Phenotype Ontology" . + . + "phenotype" . + "https://github.com/PHI-base/phipo/issues" . + "http://purl.obolibrary.org/obo/phipo.owl" . + _:Bcf495920b90d932cd2e5894346c94e90 . + . + . + . +_:B7ac90f1cddfbbb01a483ee9a952f910c "git clone https://github.com/PHI-base/phipo.git" . +_:Bcf495920b90d932cd2e5894346c94e90 "Alayne Cuzick" . +_:Bcf495920b90d932cd2e5894346c94e90 "alayne.cuzick@rothamsted.ac.uk" . + "http://purl.obolibrary.org/obo/phipo.owl" . + "http://purl.obolibrary.org/obo/phipo.obo" . + "active" . + . + . + _:B86a9957e3151f7be29f6eaf0aa6ffd97 . + "PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes." . + "planaria-ontology" . + . + "anatomy" . + "https://github.com/obophenotype/planaria-ontology/issues" . + "http://purl.obolibrary.org/obo/plana.owl" . + _:B7c1e9598bb37d609bd6de89fbaf2a7e9 . + . + . + . +_:B86a9957e3151f7be29f6eaf0aa6ffd97 "git clone https://github.com/obophenotype/planaria-ontology.git" . +_:B7c1e9598bb37d609bd6de89fbaf2a7e9 "Sofia Robb" . +_:B7c1e9598bb37d609bd6de89fbaf2a7e9 "smr@stowers.org" . + "http://purl.obolibrary.org/obo/plana.owl" . + "http://purl.obolibrary.org/obo/plana.obo" . + "active" . + . + . + . + . + _:B4b228b37f65253c5a08f4d9d7ef5c820 . + "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea." . + "Planarian Phenotype Ontology" . + . + "phenotype" . + "https://github.com/obophenotype/planarian-phenotype-ontology/issues" . + "http://purl.obolibrary.org/obo/planp.owl" . + _:B2faf67db269e78105d75f267566ddfcd . + . + . + . +_:B4b228b37f65253c5a08f4d9d7ef5c820 "git clone https://github.com/obophenotype/planarian-phenotype-ontology.git" . +_:B2faf67db269e78105d75f267566ddfcd "Sofia Robb" . +_:B2faf67db269e78105d75f267566ddfcd "smr@stowers.org" . + "http://purl.obolibrary.org/obo/planp.owl" . + "http://purl.obolibrary.org/obo/planp.obo" . + "active" . + . + . + _:B6d637653045e5a4c8d6b073f3d92d63b . + . + "An ontology covering the anatomy of the taxon Porifera (sponges)" . + "Porifera Ontology" . + . + . + "anatomy" . + "https://github.com/obophenotype/porifera-ontology/issues" . + "http://purl.obolibrary.org/obo/poro.owl" . + _:Bf4ae8413be6ae7dfdb63b0f44bc0a05f . + . + . + . +_:B6d637653045e5a4c8d6b073f3d92d63b "git clone https://github.com/obophenotype/porifera-ontology.git" . +_:B6d637653045e5a4c8d6b073f3d92d63b "vcs" . + "Porifera" . + "The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology" . +_:Bf4ae8413be6ae7dfdb63b0f44bc0a05f "Bob Thacker" . +_:Bf4ae8413be6ae7dfdb63b0f44bc0a05f "robert.thacker@stonybrook.edu" . + "http://purl.obolibrary.org/obo/poro.owl" . + "http://purl.obolibrary.org/obo/poro.obo" . + "active" . + . + "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales." . + "Plant Phenology Ontology" . + . + "plant phenotypes" . + "https://github.com/PlantPhenoOntology/PPO/issues" . + "ppo-discuss@googlegroups.com" . + "http://purl.obolibrary.org/obo/ppo.owl" . + _:Bf70332731b4e26e01712e1c32100585f . + . + . +_:Bf70332731b4e26e01712e1c32100585f "Ramona Walls" . +_:Bf70332731b4e26e01712e1c32100585f "rlwalls2008@gmail.com" . + "http://purl.obolibrary.org/obo/ppo.owl" . + "active" . + . + . + . + . + _:B30d09f433a7e5b02abab5ba888910e8e . + "Ontology to reproducibly study visualizations of clinical performance" . + "Performance Summary Display Ontology" . + . + "learning systems" . + "https://github.com/Display-Lab/psdo/issues" . + "http://purl.obolibrary.org/obo/psdo.owl" . + _:B12e9e263741403ef7c1a110d3ee0dc1e . + . + . + "active" . + "STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of application, and information needed or resulting from statistical methods, such as probability distributions, variables, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results." . + "The Statistical Methods Ontology" . + . + "statistics" . + "https://github.com/ISA-tools/stato/issues" . + "http://purl.obolibrary.org/obo/stato.owl" . + _:B8f422479d4cabc30f3c6e0ee2d1139c2 . + . + . +_:B30d09f433a7e5b02abab5ba888910e8e "https://github.com/Display-Lab/psdo.git" . +_:B12e9e263741403ef7c1a110d3ee0dc1e "Zach Landis-Lewis" . +_:B12e9e263741403ef7c1a110d3ee0dc1e "zachll@umich.edu" . + "http://purl.obolibrary.org/obo/psdo.owl" . + "active" . + . + _:B2bd5246760383e3169d223ded16169ed . + "The Plant Stress Ontology describes..." . + "Plant Stress Ontology" . + . + "plant disease and abiotic stress" . + "https://github.com/Planteome/plant-stress-ontology/issues" . + "http://purl.obolibrary.org/obo/pso.owl" . + _:B814c0ff4ad2960b555dc6ea1089754c1 . + . + . + . +_:B2bd5246760383e3169d223ded16169ed "git clone https://github.com/Planteome/plant-stress-ontology.git" . +_:B814c0ff4ad2960b555dc6ea1089754c1 "Laurel Cooper" . +_:B814c0ff4ad2960b555dc6ea1089754c1 "cooperl@science.oregonstate.edu" . + "http://purl.obolibrary.org/obo/pso.owl" . + "http://purl.obolibrary.org/obo/pso.obo" . + "active" . + _:B4c07feaaa4bed83e54a94578c4581c8f . + "A controlled vocabulary for annotating gene products to pathways." . + "Pathway ontology" . + . + . + . + "biological process" . + "https://github.com/rat-genome-database/PW-Pathway-Ontology/issues" . + . + "http://purl.obolibrary.org/obo/pw.owl" . + _:B10311a227763c1f9eb89578ea067840c . + . + . + . + . +_:B4c07feaaa4bed83e54a94578c4581c8f "obo2owl" . +_:B4c07feaaa4bed83e54a94578c4581c8f "ftp://ftp.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo"^^ . + "The Rat Genome Database pathway portal." . + "The pathway ontology - updates and applications." . + "RGD Ontology Browser" . + "RGD" . +_:B10311a227763c1f9eb89578ea067840c "G. Thomas Hayman" . +_:B10311a227763c1f9eb89578ea067840c "gthayman@mcw.edu" . + "http://purl.obolibrary.org/obo/pw.owl" . + "http://purl.obolibrary.org/obo/pw.obo" . +_:B568e2d1c8b6c594d6b3e0869aa17bcdf "git clone https://github.com/oborel/obo-relations.git" . +_:B568e2d1c8b6c594d6b3e0869aa17bcdf "vcs" . +_:B22167dd7d3fdbe3a6790ea3cf30310cc "Chris Mungall" . +_:B22167dd7d3fdbe3a6790ea3cf30310cc "cjmungall@lbl.gov" . + "Canonical edition" . + "Relation Ontology" . + "http://purl.obolibrary.org/obo/ro.owl" . + "Has imports merged in" . + "Relation Ontology in obo format" . + "http://purl.obolibrary.org/obo/ro.obo" . + "Minimal subset intended to work with BFO-classes" . + "RO Core relations" . + "http://purl.obolibrary.org/obo/ro/core.owl" . + . + "Axioms defined within RO and to be used in imports for other ontologies" . + "RO base ontology" . + "http://purl.obolibrary.org/obo/ro/ro-base.owl" . + . + "For use in ecology and environmental science" . + "Interaction relations" . + "http://purl.obolibrary.org/obo/ro/subsets/ro-interaction.owl" . + "Ecology subset" . + "http://purl.obolibrary.org/obo/ro/subsets/ro-eco.owl" . + "For use in neuroscience" . + "Neuroscience subset" . + "http://purl.obolibrary.org/obo/ro/subsets/ro-neuro.owl" . + . + "active" . + _:B6af8f241924acc66763f224979099586 . + . + "Ontology of rat strains" . + "Rat Strain Ontology" . + . + . + "https://github.com/rat-genome-database/RS-Rat-Strain-Ontology/issues" . + . + "http://purl.obolibrary.org/obo/rs.owl" . + _:B4521c860473ff835c455a8d68e5c746c . + . + . + . + . +_:B6af8f241924acc66763f224979099586 "obo2owl" . +_:B6af8f241924acc66763f224979099586 "ftp://ftp.rgd.mcw.edu/pub/ontology/rat_strain/rat_strain.obo"^^ . + "Rattus" . + "Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD." . + "RGD Ontology Browser" . + "RGD" . +_:B4521c860473ff835c455a8d68e5c746c "Shur-Jen Wang" . +_:B4521c860473ff835c455a8d68e5c746c "sjwang@mcw.edu" . + "http://purl.obolibrary.org/obo/rs.owl" . + "http://purl.obolibrary.org/obo/rs.obo" . + "active" . + _:Bdcd533428d992813c779c7fade27cb98 . + "Connects organic name reactions to their roles in an organic synthesis and to processes in MOP" . + "Name Reaction Ontology" . + . + "https://github.com/rsc-ontologies/rxno/issues" . + "chemistry-ontologies@googlegroups.com" . + "http://purl.obolibrary.org/obo/rxno.owl" . + _:B2b1d387623682f713334ad36f017bc02 . + . + . +_:Bdcd533428d992813c779c7fade27cb98 "owl2obo" . +_:Bdcd533428d992813c779c7fade27cb98 "https://raw.githubusercontent.com/rsc-ontologies/rxno/master/rxno.owl"^^ . +_:B2b1d387623682f713334ad36f017bc02 "Colin Batchelor" . +_:B2b1d387623682f713334ad36f017bc02 "batchelorc@rsc.org" . + "Name Reaction Ontology" . + "http://purl.obolibrary.org/obo/rxno.owl" . + "active" . + _:Be1f56748ffbad264b612afefbd817522 . + "An ontology for representing the provenance of scientific claims and the evidence that supports them." . + "Scientific Evidence and Provenance Information Ontology" . + . + "scientific claims, evidence" . + "https://github.com/monarch-initiative/SEPIO-ontology/issues" . + "http://purl.obolibrary.org/obo/sepio.owl" . + _:B0082f191b1f3cb4fa8a67c1bba79d1c7 . + . + . +_:Be1f56748ffbad264b612afefbd817522 "git clone https://github.com/monarch-initiative/SEPIO-ontology.git" . +_:B0082f191b1f3cb4fa8a67c1bba79d1c7 "Matthew Brush" . +_:B0082f191b1f3cb4fa8a67c1bba79d1c7 "mhb120@gmail.com" . + "SEPIO" . + "http://purl.obolibrary.org/obo/sepio.owl" . + "active" . + _:Baacfd618fc531bd895e74b6ac8c750a3 . + "A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases." . + "Sequence types and features ontology" . + . + . + . + "biological sequence" . + "https://github.com/The-Sequence-Ontology/SO-Ontologies/issues" . + "https://sourceforge.net/p/song/mailman/song-devel/" . + "http://purl.obolibrary.org/obo/so.owl" . + _:Bac426a741538f4d63f09b62ae6b5954f . + . + . + . + . +_:Baacfd618fc531bd895e74b6ac8c750a3 "obo2owl" . +_:Baacfd618fc531bd895e74b6ac8c750a3 "https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so.obo"^^ . + "The Sequence Ontology: a tool for the unification of genome annotations." . + "Evolution of the Sequence Ontology terms and relationships." . +_:Bac426a741538f4d63f09b62ae6b5954f "Karen Eilbeck" . +_:Bac426a741538f4d63f09b62ae6b5954f "keilbeck@genetics.utah.edu" . + "http://purl.obolibrary.org/obo/so.owl" . + "http://purl.obolibrary.org/obo/so.obo" . + "active" . + _:B74d0b4acead4d35f2ddf97756e1613c7 . + . + "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow)." . + "Spider Ontology" . + . + "anatomy" . + "https://github.com/obophenotype/spider-ontology/issues" . + "http://purl.obolibrary.org/obo/spd.owl" . + _:B0a49e4700a11960fd8e4a3944e29dc63 . + . + . +_:B74d0b4acead4d35f2ddf97756e1613c7 "obo2owl" . +_:B74d0b4acead4d35f2ddf97756e1613c7 "https://raw.githubusercontent.com/obophenotype/spider-ontology/master/spider_comparative_biology.obo"^^ . + "spiders" . +_:B0a49e4700a11960fd8e4a3944e29dc63 "Martin Ramirez" . +_:B0a49e4700a11960fd8e4a3944e29dc63 "ramirez@macn.gov.ar" . + "http://purl.obolibrary.org/obo/spd.owl" . +_:B8f422479d4cabc30f3c6e0ee2d1139c2 "Alejandra Gonzalez-Beltran" . +_:B8f422479d4cabc30f3c6e0ee2d1139c2 "alejandra.gonzalez.beltran@gmail.com" . + "http://purl.obolibrary.org/obo/stato.owl" . + "active" . + _:Be4f1cf52b811f7a8f5c55fdb12092fa5 . + "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community." . + "Software ontology" . + . + "software" . + "https://github.com/allysonlister/swo/issues" . + "http://purl.obolibrary.org/obo/swo.owl" . + _:B9179201643c11cf200a33e1796ed723c . + . + . +_:Be4f1cf52b811f7a8f5c55fdb12092fa5 "owl2obo" . +_:Be4f1cf52b811f7a8f5c55fdb12092fa5 "https://raw.githubusercontent.com/allysonlister/swo/master/release/swo_inferred.owl"^^ . +_:B9179201643c11cf200a33e1796ed723c "Allyson Lister" . +_:B9179201643c11cf200a33e1796ed723c "allyson.lister@oerc.ox.ac.uk" . + "http://purl.obolibrary.org/obo/swo.owl" . + "active" . + _:Bf9529dc965c12d57ee43a74afcf2ac18 . + . + "An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease." . + "Symptom Ontology" . + . + "disease" . + "https://github.com/DiseaseOntology/SymptomOntology/issues" . + "http://purl.obolibrary.org/obo/symp.owl" . + _:Bf5ca93820f1b71577938318827d1b0d0 . + . + . + . +_:Bf9529dc965c12d57ee43a74afcf2ac18 "obo2owl" . +_:Bf9529dc965c12d57ee43a74afcf2ac18 "https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/symp.obo"^^ . +_:Bf5ca93820f1b71577938318827d1b0d0 "Lynn Schriml" . +_:Bf5ca93820f1b71577938318827d1b0d0 "lynn.schriml@gmail.com" . + "http://purl.obolibrary.org/obo/symp.owl" . + "http://purl.obolibrary.org/obo/symp.obo" . + "active" . + _:B73e53c7c01a804a8a8900d8a07e3412a . + "A vocabulary of taxonomic ranks (species, family, phylum, etc)" . + "Taxonomic rank vocabulary" . + . + "taxonomy" . + "https://github.com/phenoscape/taxrank/issues" . + "http://purl.obolibrary.org/obo/taxrank.owl" . + _:B1bff654fad3c46ffd27746ffcc1b2799 . + . + . + . +_:B73e53c7c01a804a8a8900d8a07e3412a "git clone https://github.com/phenoscape/taxrank.git" . +_:B1bff654fad3c46ffd27746ffcc1b2799 "Jim Balhoff" . +_:B1bff654fad3c46ffd27746ffcc1b2799 "balhoff@renci.org" . + "http://purl.obolibrary.org/obo/taxrank.owl" . + "http://purl.obolibrary.org/obo/taxrank.obo" . + "active" . + _:B11457a2d35027757e30962929452f33c . + . + "A controlled vocabulary of describe phenotypic traits in plants." . + "Plant Trait Ontology" . + . + . + "phenotype" . + "https://github.com/Planteome/plant-trait-ontology/issues" . + . + "http://purl.obolibrary.org/obo/to.owl" . + _:B1d53e873380b0528244c71165de81675 . + . + . + . + . +_:B11457a2d35027757e30962929452f33c "git clone https://github.com/Planteome/plant-trait-ontology.git" . +_:B11457a2d35027757e30962929452f33c "vcs" . + "Planteome browser" . + "Planteome" . +_:B1d53e873380b0528244c71165de81675 "Pankaj Jaiswal" . +_:B1d53e873380b0528244c71165de81675 "jaiswalp@science.oregonstate.edu" . + "http://purl.obolibrary.org/obo/to.owl" . + "http://purl.obolibrary.org/obo/to.obo" . + "active" . + _:B8c83930335649ef53280db858a68487f . + "An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host." . + "Pathogen Transmission Ontology" . + . + "disease" . + "https://github.com/DiseaseOntology/PathogenTransmissionOntology/issues" . + "http://purl.obolibrary.org/obo/trans.owl" . + _:Bc48b630dc765d636ccaf1bdbe3b99c3d . + . + . + . +_:B8c83930335649ef53280db858a68487f "obo2owl" . +_:B8c83930335649ef53280db858a68487f "https://raw.githubusercontent.com/DiseaseOntology/PathogenTransmissionOntology/master/src/ontology/trans.obo"^^ . +_:Bc48b630dc765d636ccaf1bdbe3b99c3d "Lynn Schriml" . +_:Bc48b630dc765d636ccaf1bdbe3b99c3d "lynn.schriml@gmail.com" . + "http://purl.obolibrary.org/obo/trans.owl" . + "http://purl.obolibrary.org/obo/trans.obo" . + "active" . + . + "An ontology covering the taxonomy of teleosts (bony fish)" . + "Teleost taxonomy ontology" . + . + "taxonomy" . + "https://github.com/phenoscape/teleost-taxonomy-ontology/issues" . + "http://purl.obolibrary.org/obo/tto.owl" . + _:B7173e29a46b22ce016a93446a2148256 . + . + . + . + "Teleostei" . +_:B7173e29a46b22ce016a93446a2148256 "Jim Balhoff" . +_:B7173e29a46b22ce016a93446a2148256 "balhoff@renci.org" . + "http://purl.obolibrary.org/obo/tto.obo" . + "http://purl.obolibrary.org/obo/tto.owl" . +_:Be3eb423679d9bc92d65a1e81c2027d33 "svn --ignore-externals co http://svn.code.sf.net/p/obo/svn/uberon/trunk" . +_:Be3eb423679d9bc92d65a1e81c2027d33 "vcs" . + "Uberon, an integrative multi-species anatomy ontology" . + "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon" . + "Gene Ontology AmiGO 2 Browser" . + "RGD" . + "Gene Ontology AmiGO 2 Browser" . + "AmiGO (SUBSET)" . + "Bgee gene expression queries" . + "Bgee (gene expression)" . + "FANTOM5 Data Portal" . + "FANTOM5" . + "INCF KnowledgeSpace Portal" . + "KnowledgeSpace" . +_:B97fecff7f8d5dd6785551d850220c0d4 "Chris Mungall" . +_:B97fecff7f8d5dd6785551d850220c0d4 "cjmungall@lbl.gov" . + "core ontology" . + "Uberon" . + . + "http://purl.obolibrary.org/obo/uberon.owl" . + "Axioms defined within Uberon and to be used in imports for other ontologies" . + "Uberon base ontology" . + "http://purl.obolibrary.org/obo/uberon/uberon-base.owl" . + . + "Uberon extended" . + "Uberon edition that includes subsets of other ontologies and axioms connecting to them" . + . + "http://purl.obolibrary.org/obo/uberon/ext.owl" . + "Uberon edition that excludes external ontologies and most relations" . + "Uberon basic" . + "obo" . + . + "http://purl.obolibrary.org/obo/uberon/basic.obo" . + "Taxonomic equivalence axioms connecting zebrafish-specific classes to generic uberon counterparts" . + "Uberon bridge to ZFA" . + . + "http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl" . + . + "Taxonomic equivalence axioms connecting adult mouse specific classes to generic uberon counterparts" . + "Uberon bridge to MA" . + . + "http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl" . + . + "Metazoa"^^ . + "Extended uberon plus all metazoan ontologies" . + "Uberon composite metazoan ontology" . + . + "http://purl.obolibrary.org/obo/uberon/composite-metazoan.owl" . + . + "Metazoa"^^ . + "Uberon composite vertebrate ontology" . + . + "http://purl.obolibrary.org/obo/uberon/composite-vertebrate.owl" . + . +_:B2ab2189cdd10a8f697dca5c8e3420277 "obo2owl" . +_:B2ab2189cdd10a8f697dca5c8e3420277 "https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"^^ . +_:B608fa056e4c3bdbbab9cb19013df36e4 "George Gkoutos" . +_:B608fa056e4c3bdbbab9cb19013df36e4 "g.gkoutos@gmail.com" . + "http://purl.obolibrary.org/obo/uo.owl" . + "active" . + _:Bfdf95748c19abd9686daa1ce578eee05 . + "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology." . + "Unified phenotype ontology (uPheno)" . + . + "https://github.com/obophenotype/upheno/issues" . + "https://groups.google.com/forum/#!forum/phenotype-ontologies-editors" . + "http://purl.obolibrary.org/obo/upheno.owl" . + _:B07e5cb70e758cd82da1b248a4a50e7cf . + . + . + . +_:Bfdf95748c19abd9686daa1ce578eee05 "archive" . +_:Bfdf95748c19abd9686daa1ce578eee05 "http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip"^^ . +_:B07e5cb70e758cd82da1b248a4a50e7cf "Nicole Vasilevsky" . +_:B07e5cb70e758cd82da1b248a4a50e7cf "vasilevs@ohsu.edu" . + "http://purl.obolibrary.org/obo/upheno.owl" . + "http://purl.obolibrary.org/obo/upheno/mp-hp-view.owl" . + "active" . + _:Bf39bbd27ba1956fe87333f725e2e77ac . + "VO is a biomedical ontology in the domain of vaccine and vaccination." . + "Vaccine Ontology" . + . + "health" . + "https://github.com/vaccineontology/VO/issues" . + "http://purl.obolibrary.org/obo/vo.owl" . + _:B452b578007dbdbacb1a43f96b3ba670a . + . + . +_:Bf39bbd27ba1956fe87333f725e2e77ac "https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl"^^ . +_:B452b578007dbdbacb1a43f96b3ba670a "Yongqunh He" . +_:B452b578007dbdbacb1a43f96b3ba670a "yongqunh@med.umich.edu" . + "http://purl.obolibrary.org/obo/vo.owl" . + "active" . + _:B945c2b8490c4f6dc9fde59cb057b2c83 . + "An ontology of traits covering vertebrates" . + "Vertebrate trait ontology" . + . + "https://github.com/AnimalGenome/vertebrate-trait-ontology/issues" . + "http://purl.obolibrary.org/obo/vt.owl" . + _:B92501e101adfa36a2f2debc5fc2fa0f1 . + . + . +_:B945c2b8490c4f6dc9fde59cb057b2c83 "svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt" . +_:B945c2b8490c4f6dc9fde59cb057b2c83 "vcs" . +_:B92501e101adfa36a2f2debc5fc2fa0f1 "Carissa Park" . +_:B92501e101adfa36a2f2debc5fc2fa0f1 "caripark@iastate.edu" . + "http://purl.obolibrary.org/obo/vt.owl" . + "active" . + "Comprehensive hierarchy of extinct and extant vertebrate taxa." . + "Vertebrate Taxonomy Ontology" . + . + "https://github.com/phenoscape/vertebrate-taxonomy-ontology/issues" . + "http://purl.obolibrary.org/obo/vto.owl" . + _:B4c41caf8c3eeca30517312a78e2afa64 . + . + . + . +_:B4c41caf8c3eeca30517312a78e2afa64 "Jim Balhoff" . +_:B4c41caf8c3eeca30517312a78e2afa64 "balhoff@renci.org" . + "http://purl.obolibrary.org/obo/vto.owl" . + "http://purl.obolibrary.org/obo/vto.obo" . + "WBbt" . + "active" . + _:Ba54574e2e3e262c0575ae50f6f31ca88 . + . + "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans." . + "C. elegans Gross Anatomy Ontology" . + . + . + "anatomy" . + "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/issues" . + "http://purl.obolibrary.org/obo/wbbt.owl" . + _:Bed1616cfb3ea3ea186b4cadbb1a43686 . + . + . + . +_:Ba54574e2e3e262c0575ae50f6f31ca88 "git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git" . + "Caenorhabditis" . + "Building a cell and anatomy ontology of Caenorhabditis elegans" . +_:Bed1616cfb3ea3ea186b4cadbb1a43686 "Raymond Lee" . +_:Bed1616cfb3ea3ea186b4cadbb1a43686 "raymond@caltech.edu" . + "http://purl.obolibrary.org/obo/wbbt.owl" . + "http://purl.obolibrary.org/obo/wbbt.obo" . + "WBls" . + "active" . + _:Bcb7471f6997b61a54c100fa322cc6566 . + . + "A structured controlled vocabulary of the development of Caenorhabditis elegans." . + "C. elegans development ontology" . + . + . + "developemental life stage" . + "https://github.com/obophenotype/c-elegans-development-ontology/issues" . + "http://purl.obolibrary.org/obo/wbls.owl" . + _:B7ec40202dc46850155e3cd6deaf416ea . + . + . + . +_:Bcb7471f6997b61a54c100fa322cc6566 "git clone https://github.com/obophenotype/c-elegans-development-ontology.git" . + "WormBase: a modern Model Organism Information Resource" . +_:B7ec40202dc46850155e3cd6deaf416ea "Chris Grove" . +_:B7ec40202dc46850155e3cd6deaf416ea "cgrove@caltech.edu" . + "http://purl.obolibrary.org/obo/wbls.owl" . + "http://purl.obolibrary.org/obo/wbls.obo" . + "WBPhenotype" . + "active" . + _:B19b0480b29baa9d4bcf2359a951f0eab . + . + "A structured controlled vocabulary of Caenorhabditis elegans phenotypes" . + "C. elegans phenotype" . + . + . + "phenotype" . + "https://github.com/obophenotype/c-elegans-phenotype-ontology/issues" . + "http://purl.obolibrary.org/obo/wbphenotype.owl" . + _:B123a1354a18c9ba48310fb8e5cc9a844 . + . + . + . + . +_:B19b0480b29baa9d4bcf2359a951f0eab "git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git" . + "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community." . +_:B123a1354a18c9ba48310fb8e5cc9a844 "Chris Grove" . +_:B123a1354a18c9ba48310fb8e5cc9a844 "cgrove@caltech.edu" . + "http://purl.obolibrary.org/obo/wbphenotype.owl" . + "http://purl.obolibrary.org/obo/wbphenotype.obo" . + "http://purl.obolibrary.org/obo/wbphenotype/wbphenotype-base.owl" . +_:Bc1bb827f0e04ac76f898ad15c7ec4653 "obo2owl" . +_:Bc1bb827f0e04ac76f898ad15c7ec4653 "ftp://ftp.rgd.mcw.edu/pub/ontology/experimental_condition/experimental_condition.obo"^^ . + "RGD Ontology Browser" . + "RGD" . +_:Bc2750840ace2cd1fa186d431fe313d23 "Jennifer Smith" . +_:Bc2750840ace2cd1fa186d431fe313d23 "jrsmith@mcw.edu" . + "http://purl.obolibrary.org/obo/xco.owl" . + "http://purl.obolibrary.org/obo/xco.obo" . + "active" . + "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/tree/master/cv" . + _:B54d631bb9a3780b6b4f38963c93e0ff6 . + "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry." . + "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" . + . + "MS cross-linker reagents" . + "http://oboedit.org" . + "https://github.com/HUPO-PSI/mzIdentML/issues" . + "psidev-ms-vocab@lists.sourceforge.net" . + "xlmod" . + "http://purl.obolibrary.org/obo/xlmod.owl" . + _:Babc7b80423dff8df350d58bb2963586d . + . + . + . +_:B54d631bb9a3780b6b4f38963c93e0ff6 "obo2owl" . +_:B54d631bb9a3780b6b4f38963c93e0ff6 "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo"^^ . +_:Babc7b80423dff8df350d58bb2963586d "Gerhard Mayer" . +_:Babc7b80423dff8df350d58bb2963586d "gerhard.mayer@rub.de" . + "http://purl.obolibrary.org/obo/xlmod.obo" . + "active" . + . + . + . + . + . + . + . + . + _:Bfadf94a8acd15785b76966d4b0c76bc9 . + . + "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis." . + "Xenopus Phenotype Ontology" . + . + "phenotype" . + "https://github.com/obophenotype/xenopus-phenotype-ontology/issues" . + "http://purl.obolibrary.org/obo/xpo.owl" . + _:B83c250dded3bfd280c0951f611d8dee4 . + . + . + . +_:Bfadf94a8acd15785b76966d4b0c76bc9 "git clone https://github.com/obophenotype/xenopus-phenotype-ontology.git" . +_:B83c250dded3bfd280c0951f611d8dee4 "Erik Segerdell" . +_:B83c250dded3bfd280c0951f611d8dee4 "esegerd3@gmail.com" . + "http://purl.obolibrary.org/obo/xpo.owl" . + "http://purl.obolibrary.org/obo/xpo.obo" . +_:Ba25a6e5d7f83b0925a08efd7637169c0 "obo2owl" . +_:Ba25a6e5d7f83b0925a08efd7637169c0 "https://raw.githubusercontent.com/ybradford/zebrafish-experimental-conditions-ontology/master/zeco.obo"^^ . +_:B2776ad69f6e03d0463aa5a7d1d7cb2f9 "Yvonne Bradford" . +_:B2776ad69f6e03d0463aa5a7d1d7cb2f9 "ybradford@zfin.org" . + "http://purl.obolibrary.org/obo/zeco.obo" . + "http://purl.obolibrary.org/obo/zeco.owl" . + "http://purl.obolibrary.org/obo/zeco.json" . + "active" . + _:B7fa906ce44d409a41616645229ce2847 . + . + "Developmental stages of the Zebrafish" . + "Zebrafish developmental stages ontology" . + . + "anatomy" . + "https://github.com/cerivs/zebrafish-anatomical-ontology/issues" . + "http://purl.obolibrary.org/obo/zfs.owl" . + _:Bf75f32923523bea657f783b397cca720 . + . + . + . + . +_:B7fa906ce44d409a41616645229ce2847 "obo2owl" . +_:B7fa906ce44d409a41616645229ce2847 "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo"^^ . +_:Bf75f32923523bea657f783b397cca720 "Ceri Van Slyke" . +_:Bf75f32923523bea657f783b397cca720 "van_slyke@zfin.org" . + "http://purl.obolibrary.org/obo/zfs.owl" . + "http://purl.obolibrary.org/obo/zfs.obo" . + "active" . + . + . + . + . + . + . + . + _:Bbb556fb5a753513a59b3151d2e975a81 . + "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism." . + "Zebrafish Phenotype Ontology" . + . + "phenotype" . + "https://github.com/obophenotype/zebrafish-phenotype-ontology/issues" . + "http://purl.obolibrary.org/obo/zp.owl" . + _:B68b5cc971c4959bbc04fd780e7bc7d9e . + . + . + . +_:Bbb556fb5a753513a59b3151d2e975a81 "git clone https://github.com/obophenotype/zebrafish-phenotype-ontology.git" . +_:B68b5cc971c4959bbc04fd780e7bc7d9e "Yvonne Bradford" . +_:B68b5cc971c4959bbc04fd780e7bc7d9e "ybradford@zfin.org" . + "http://purl.obolibrary.org/obo/zp.owl" . + "http://purl.obolibrary.org/obo/zp.obo" . + "active" . + _:B45a8ceb2dc30d46937d37d6fb3600f48 . + "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens." . + "eagle-i resource ontology" . + . + "resources" . + "http://purl.obolibrary.org/obo/ero.owl" . + _:B8f19353e7e46d41a50c28da0d295d8b9 . + . + . +_:B45a8ceb2dc30d46937d37d6fb3600f48 "owl2obo" . +_:B45a8ceb2dc30d46937d37d6fb3600f48 "http://purl.obolibrary.org/obo/ero.owl"^^ . +_:B8f19353e7e46d41a50c28da0d295d8b9 "Marc Ciriello" . +_:B8f19353e7e46d41a50c28da0d295d8b9 "Marc_Ciriello@hms.harvard.edu" . + "http://purl.obolibrary.org/obo/ero.owl" . + "active" . + . + . + "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data" . + "FOBI" . + . + "metabolomics and nutrition" . + "https://github.com/pcastellanoescuder/FoodBiomarkerOntology/issues" . + "http://purl.obolibrary.org/obo/fobi.owl" . + _:B4bd72efd719eb87d13bc531133c0ea97 . + . +_:B4bd72efd719eb87d13bc531133c0ea97 "Pol Castellano Escuder" . +_:B4bd72efd719eb87d13bc531133c0ea97 "polcaes@gmail.com" . + "FOBI is an ontology to represent food intake data and associate it with metabolomic data" . + "owl-rdf/xml" . + "http://purl.obolibrary.org/obo/fobi.owl" . + "active" . + _:Bb95c0db867409ae43d99d80da076d667 . + "The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences." . + "Gender, Sex, and Sexual Orientation (GSSO) ontology" . + . + "organisms" . + "https://github.com/Superraptor/GSSO/issues" . + "http://purl.obolibrary.org/obo/gsso.owl" . + _:B353ebc6f4b22c94ac46b197ba2d750c2 . + . + . + . + . +_:Bb95c0db867409ae43d99d80da076d667 "git clone https://github.com/Superraptor/GSSO.git" . + "Apache 2.0 License" . +_:B353ebc6f4b22c94ac46b197ba2d750c2 "Clair Kronk" . +_:B353ebc6f4b22c94ac46b197ba2d750c2 "kronkcj@mail.uc.edu" . + "http://purl.obolibrary.org/obo/gsso.owl" . + "http://purl.obolibrary.org/obo/gsso.obo" . + "http://purl.obolibrary.org/obo/gsso.json" . +_:Bdbfc2d68fb9f243fa397dcb3dbbd51c2 "archive" . +_:Bdbfc2d68fb9f243fa397dcb3dbbd51c2 "http://compbio.charite.de/hudson/job/hpo/lastSuccessfulBuild/artifact/*zip*/archive.zip"^^ . + "hpo" . + "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease." . + "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease." . + "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data." . + "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources." . + "JAX HPO Browser" . + "HPO" . + "Monarch Phenotype Page" . + "Monarch" . +_:Bbbf498b31ec9063ed586b07a804d33ab "Sebastian Koehler" . +_:Bbbf498b31ec9063ed586b07a804d33ab "dr.sebastian.koehler@gmail.com" . + "http://purl.obolibrary.org/obo/hp.owl" . + "http://purl.obolibrary.org/obo/hp.obo" . + "active" . + _:Bf57c3ea443b62ac36fb8e9607f935e07 . + "A classification of algorithms available for the simulation of models in biology." . + "Kinetic Simulation Algorithm Ontology" . + . + "algorithms" . + "https://sourceforge.net/p/kisao/feature-requests/" . + "http://purl.obolibrary.org/obo/kisao.owl" . + _:Be14c5e2b9235999d30e311319c88e28f . + . + . +_:Bf57c3ea443b62ac36fb8e9607f935e07 "owl2obo" . +_:Bf57c3ea443b62ac36fb8e9607f935e07 "http://svn.code.sf.net/p/kisao/code/tags/kisao-owl-latest/kisao.owl"^^ . + "Artistic License 2.0" . +_:Be14c5e2b9235999d30e311319c88e28f "The Biomodels.net team" . +_:Be14c5e2b9235999d30e311319c88e28f "biomodels-net-support@lists.sf.net" . + "http://purl.obolibrary.org/obo/kisao.owl" . + "active" . + _:B13b6f7d258c17c2e689b0fd7b2c1e1e2 . + "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features." . + "Mathematical modeling ontology" . + . + "http://sourceforge.net/p/mamo-ontology/tickets/" . + "http://purl.obolibrary.org/obo/mamo.owl" . + _:B5d82ec24c7450ccb2c4bd966f5cb53cc . + . + . +_:B13b6f7d258c17c2e689b0fd7b2c1e1e2 "owl2obo" . +_:B13b6f7d258c17c2e689b0fd7b2c1e1e2 "https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl"^^ . +_:B5d82ec24c7450ccb2c4bd966f5cb53cc "Nicolas Le Novere" . +_:B5d82ec24c7450ccb2c4bd966f5cb53cc "n.lenovere@gmail.com" . + "http://purl.obolibrary.org/obo/mamo.owl" . + "active" . + _:Bd89c85da22552f559ff197051f3d336b . + "Terms commonly used in Systems Biology, and in particular in computational modeling." . + "Systems Biology Ontology" . + . + "biochemistry" . + "https://sourceforge.net/p/sbo/term-request/" . + "http://purl.obolibrary.org/obo/sbo.owl" . + _:Ba6836d5094ec5ee46d449159faf7fb65 . + . + . +_:Bd89c85da22552f559ff197051f3d336b "obo2owl" . +_:Bd89c85da22552f559ff197051f3d336b "http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo"^^ . +_:Ba6836d5094ec5ee46d449159faf7fb65 "Rahuman Sheriff" . +_:Ba6836d5094ec5ee46d449159faf7fb65 "sheriff@ebi.ac.uk" . + "http://purl.obolibrary.org/obo/sbo.owl" . + "active" . + "TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity." . + "Toxic Process Ontology" . + . + "toxicity" . + "https://github.com/txpo-ontology/TXPO/issues" . + . + . + "http://purl.obolibrary.org/obo/txpo.owl" . + _:B41f2c6e494685d4c8cf2cc5a83f702a2 . + . + . + "BioPortal Browser" . + "BioPortal" . + "TOXPILOT" . + "TOXPILOT" . +_:B41f2c6e494685d4c8cf2cc5a83f702a2 "Yuki Yamagata" . +_:B41f2c6e494685d4c8cf2cc5a83f702a2 "y-yamagata@nibiohn.go.jp" . + "http://purl.obolibrary.org/obo/txpo.owl" . + "orphaned" . + _:Bb34340418ccd917e4f51b72f700ddcd9 . + "Social Behavior in insects" . + "Social Insect Behavior Ontology" . + . + "behavior" . + "https://github.com/obophenotype/sibo/issues" . + "http://purl.obolibrary.org/obo/sibo.owl" . + _:B83550f9762f325e5e8cf6513e2bd650c . + . + . + . +_:Bb34340418ccd917e4f51b72f700ddcd9 "git clone https://github.com/obophenotype/sibo.git" . +_:Bb34340418ccd917e4f51b72f700ddcd9 "vcs" . +_:B83550f9762f325e5e8cf6513e2bd650c "Chris Mungall" . +_:B83550f9762f325e5e8cf6513e2bd650c "cjmungall@lbl.gov" . + "http://purl.obolibrary.org/obo/sibo.owl" . + "http://purl.obolibrary.org/obo/sibo.obo" . + "orphaned" . + _:B96a0f15c32b6bc5b858194a2179f54cf . + "An ontology of physico-chemical methods and properties." . + "Physico-chemical methods and properties" . + "http://purl.obolibrary.org/obo/fix.owl" . + _:B5f20161078a057b1aaab4d28d728c7ef . + . + . +_:B96a0f15c32b6bc5b858194a2179f54cf "obo2owl" . +_:B96a0f15c32b6bc5b858194a2179f54cf "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/fix.obo"^^ . +_:B5f20161078a057b1aaab4d28d728c7ef "chEBI" . + "http://purl.obolibrary.org/obo/fix.owl" . + "http://purl.obolibrary.org/obo/fix.obo" . + "orphaned" . + _:B2b1635733c9832a04ceeb9b2cb7eca14 . + "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations." . + "Variation Ontology" . + "http://purl.obolibrary.org/obo/vario.owl" . + _:B740097acbfbb355227ff7eb3f413d675 . + . + . +_:B2b1635733c9832a04ceeb9b2cb7eca14 "obo2owl" . +_:B2b1635733c9832a04ceeb9b2cb7eca14 "http://variationontology.org/vario_download/vario.obo"^^ . +_:B740097acbfbb355227ff7eb3f413d675 "Mauno Vihinen" . +_:B740097acbfbb355227ff7eb3f413d675 "mauno.vihinen@med.lu.se" . + "http://purl.obolibrary.org/obo/vario.owl" . + "orphaned" . + "An ontology that formalizes the genomic element by defining an upper class genetic interval" . + "Ontology for genetic interval" . + "https://code.google.com/p/ontology-for-genetic-interval/issues/list" . + "http://purl.obolibrary.org/obo/ogi.owl" . + . + . + "http://purl.obolibrary.org/obo/ogi.owl" . + "orphaned" . + _:Bede46fd87923a1d7eef64a79a79600b9 . + "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time." . + "Physico-chemical process" . + "http://purl.obolibrary.org/obo/rex.owl" . + . +_:Bede46fd87923a1d7eef64a79a79600b9 "obo2owl" . +_:Bede46fd87923a1d7eef64a79a79600b9 "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo"^^ . + "http://purl.obolibrary.org/obo/rex.owl" . + "inactive" . + _:B2b3f70b13dc43ddcd5a6fb1b838087d7 . + . + "An anatomical and developmental ontology for cephalopods" . + "Cephalopod Ontology" . + . + "anatomy" . + "https://github.com/obophenotype/cephalopod-ontology/issues" . + "http://purl.obolibrary.org/obo/ceph.owl" . + _:Bdb22e0b9b3334d76a172cf3834b6746e . + . + . + . +_:B2b3f70b13dc43ddcd5a6fb1b838087d7 "git clone https://github.com/obophenotype/cephalopod-ontology.git" . +_:B2b3f70b13dc43ddcd5a6fb1b838087d7 "vcs" . + "Cephalopod" . +_:Bdb22e0b9b3334d76a172cf3834b6746e "Chris Mungall" . +_:Bdb22e0b9b3334d76a172cf3834b6746e "cjmungall@lbl.gov" . + "main version" . + "http://purl.obolibrary.org/obo/ceph.owl" . + "oboformat edition" . + "http://purl.obolibrary.org/obo/ceph.obo" . + "inactive" . + . + . + . + _:B1d8df54f657953ca1fa7ff135a8d0d65 . + . + "A structured controlled vocabulary of stage-specific anatomical structures of the developing human." . + "Human developmental anatomy, abstract" . + . + . + "anatomy" . + "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues" . + "http://purl.obolibrary.org/obo/ehdaa2.owl" . + _:B36c3b8243f1c633855381a304e78a210 . + . + . + . +_:B1d8df54f657953ca1fa7ff135a8d0d65 "git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git" . +_:B1d8df54f657953ca1fa7ff135a8d0d65 "vcs" . + "A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20)." . +_:B36c3b8243f1c633855381a304e78a210 "Jonathan Bard" . +_:B36c3b8243f1c633855381a304e78a210 "J.Bard@ed.ac.uk" . + "http://purl.obolibrary.org/obo/ehdaa2.owl" . + "http://purl.obolibrary.org/obo/ehdaa2.obo" . + "inactive" . + _:B394fe80b8e6335ff0e2d1f2aaf0bfe39 . + "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures." . + "RNA ontology" . + . + "molecular structure" . + "https://github.com/BGSU-RNA/rnao/issues" . + . + "http://purl.obolibrary.org/obo/rnao.owl" . + _:Bc588fbe909a22c6c1158f9c5c23778ff . + . + . + . +_:B394fe80b8e6335ff0e2d1f2aaf0bfe39 "git clone https://github.com/BGSU-RNA/rnao.git" . +_:B394fe80b8e6335ff0e2d1f2aaf0bfe39 "vcs" . + "RNA Ontology jOWL Browser" . + "RNAO" . +_:Bc588fbe909a22c6c1158f9c5c23778ff "Colin Batchelor" . +_:Bc588fbe909a22c6c1158f9c5c23778ff "BatchelorC@rsc.org" . + "http://purl.obolibrary.org/obo/rnao.owl" . + "http://purl.obolibrary.org/obo/rnao.obo" . + "inactive" . + . + _:B7e4054a7067407e47f3702a0ae34bac3 . + "A manually curated resource for the representation and annotation of metabolic pathways" . + "Unipathway" . + . + . + "pathways" . + "https://github.com/geneontology/unipathway/issues" . + "http://purl.obolibrary.org/obo/upa.owl" . + _:Bd598ea6059ff3a78f085be58307207c2 . + . + . + . +_:B7e4054a7067407e47f3702a0ae34bac3 "git clone https://github.com/geneontology/unipathway.git" . + "UniPathway: a resource for the exploration and annotation of metabolic pathways" . +_:Bd598ea6059ff3a78f085be58307207c2 "Anne Morgat" . +_:Bd598ea6059ff3a78f085be58307207c2 "Anne.Morgat@sib.swiss" . + "http://purl.obolibrary.org/obo/upa.owl" . + "http://purl.obolibrary.org/obo/upa.obo" . + "inactive" . + "CranioMaxilloFacial ontology" . + _:B302c3a3e08bbb350b0a46d0f04ecd0a7 . + . +_:B302c3a3e08bbb350b0a46d0f04ecd0a7 "Mark Engelstad" . +_:B302c3a3e08bbb350b0a46d0f04ecd0a7 "engelsta@ohsu.edu" . + "inactive" . + "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it." . + "Malaria Ontology" . + . + "health" . + "http://purl.obolibrary.org/obo/idomal.owl" . + _:Be6bdde118c4b394060ce51151736f8d3 . + . + . + . +_:Be6bdde118c4b394060ce51151736f8d3 "Pantelis Topalis" . +_:Be6bdde118c4b394060ce51151736f8d3 "topalis@imbb.forth.gr" . + "http://purl.obolibrary.org/obo/idomal.owl" . + "http://purl.obolibrary.org/obo/idomal.obo" . + "inactive" . + . + "Application ontology for entities related to insecticide resistance in mosquitos" . + "Mosquito insecticide resistance" . + "environment" . + "http://purl.obolibrary.org/obo/miro.owl" . + _:B297d9f850e8f2b92e1effdda11337541 . + . + . + "Anopheles" . +_:B297d9f850e8f2b92e1effdda11337541 "C. Louis" . +_:B297d9f850e8f2b92e1effdda11337541 "louis@imbb.forth.gr" . + "http://purl.obolibrary.org/obo/miro.owl" . + "http://purl.obolibrary.org/obo/miro.obo" . + "inactive" . + . + "The anatomy of the Tick, Families: Ixodidae, Argassidae" . + "Tick Anatomy Ontology" . + . + "anatomy" . + "http://purl.obolibrary.org/obo/tads.owl" . + _:B53758603a28f9eabbaf5d610e3d4ec91 . + . + . + . + "Ixodidae" . +_:B53758603a28f9eabbaf5d610e3d4ec91 "Daniel Sonenshine" . +_:B53758603a28f9eabbaf5d610e3d4ec91 "dsonensh@odu.edu" . + "http://purl.obolibrary.org/obo/tads.owl" . + "http://purl.obolibrary.org/obo/tads.obo" . + "inactive" . + . + "A structured controlled vocabulary of the anatomy of mosquitoes." . + "Mosquito gross anatomy ontology" . + . + "anatomy" . + "http://purl.obolibrary.org/obo/tgma.owl" . + _:B9176ef0f7e6f5ef8463006fdca91ea4e . + . + . + . +_:B9176ef0f7e6f5ef8463006fdca91ea4e "Pantelis Topalis" . +_:B9176ef0f7e6f5ef8463006fdca91ea4e "topalis@imbb.forth.gr" . + "http://purl.obolibrary.org/obo/tgma.owl" . + "http://purl.obolibrary.org/obo/tgma.obo" . + "inactive" . + "An application ontology built for beta cell genomics studies." . + "Beta Cell Genomics Ontology" . + . + "https://github.com/obi-bcgo/bcgo/issues" . + _:B3e4c7edf6e2e2a27ca30012fb4ed6d3d . + . + . +_:B3e4c7edf6e2e2a27ca30012fb4ed6d3d "Jie Zheng" . +_:B3e4c7edf6e2e2a27ca30012fb4ed6d3d "jiezheng@pennmedicine.upenn.edu" . + "http://purl.obolibrary.org/obo/bcgo.owl" . + "inactive" . + "A formal represention for drug-drug interactions knowledge." . + "The Drug-Drug Interactions Ontology" . + . + . + "health" . + "https://github.com/labda/DINTO/issues" . + _:B651e64649d98d3f81fa70ef10d8eca88 . + . + . + "DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms." . +_:B651e64649d98d3f81fa70ef10d8eca88 "Maria Herrero" . +_:B651e64649d98d3f81fa70ef10d8eca88 "maria.herrero@kcl.ac.uk" . + "http://purl.obolibrary.org/obo/dinto.owl" . +_:B60c496d91030621ef8d5a0fe59a77b78 "obo2owl" . +_:B60c496d91030621ef8d5a0fe59a77b78 "https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl"^^ . + "Ontologies as integrative tools for plant science." . +_:B52f7f355966cdf65e2d18f15c32b4208 "Pankaj Jaiswal" . +_:B52f7f355966cdf65e2d18f15c32b4208 "jaiswalp@science.oregonstate.edu" . + "http://purl.obolibrary.org/obo/eo.owl" . + "http://purl.obolibrary.org/obo/eo.obo" . + "inactive" . + _:B95ea7bed9161601031ffbc189923dadc . + . + "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa" . + "Teleost Anatomy Ontology" . + . + . + "anatomy" . + "https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3ATAO" . + _:B2b308dcf5c1ecc9bb9e34e6410d8d283 . + . + . +_:B95ea7bed9161601031ffbc189923dadc "obo2owl" . +_:B95ea7bed9161601031ffbc189923dadc "http://purl.obolibrary.org/obo/tao.obo"^^ . + "The teleost anatomy ontology: anatomical representation for the genomics age" . +_:B2b308dcf5c1ecc9bb9e34e6410d8d283 "Wasila Dahdul" . +_:B2b308dcf5c1ecc9bb9e34e6410d8d283 "wasila.dahdul@usd.edu" . + "http://purl.obolibrary.org/obo/tao.owl" . + "inactive" . + . + "Amphibian gross anatomy" . + _:B312ced9203167b611938f9753cba1798 . + . + "Amphibia" . +_:B312ced9203167b611938f9753cba1798 "david.c.blackburn@gmail.com" . +_:B312ced9203167b611938f9753cba1798 "David Blackburn" . + "inactive" . + "Animal natural history and life history" . + _:B13a64bf3d43c084cc74ddf18b7a59a4c . + . +_:B13a64bf3d43c084cc74ddf18b7a59a4c "adw_geeks@umich.edu" . +_:B13a64bf3d43c084cc74ddf18b7a59a4c "Animal Diversity Web technical staff" . + "inactive" . + _:B9e1f44c4e441b75b91e0ccfaea65f684 . + "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events" . + "Adverse Event Reporting Ontology" . + . + "health" . + _:B303edcc002352151b112105eb262a4fe . + . + . +_:B9e1f44c4e441b75b91e0ccfaea65f684 "owl2obo" . +_:B9e1f44c4e441b75b91e0ccfaea65f684 "http://purl.obolibrary.org/obo/aero.owl"^^ . +_:B303edcc002352151b112105eb262a4fe "Melanie Courtot" . +_:B303edcc002352151b112105eb262a4fe "mcourtot@gmail.com" . + "http://purl.obolibrary.org/obo/aero.owl" . + "inactive" . + . + "Amphibian taxonomy" . + _:Bd42214f200f3122ea1062230ffba2ae1 . + . +_:Bd42214f200f3122ea1062230ffba2ae1 "david.c.blackburn@gmail.com" . +_:Bd42214f200f3122ea1062230ffba2ae1 "David Blackburn" . + "inactive" . + _:B26a6a3ce2860abd26714a581389130e9 . + . + "Bilateria anatomy" . + "anatomy" . + _:B9b5a7875fa43f6ad185d28af31c95258 . + . + . +_:B26a6a3ce2860abd26714a581389130e9 "obo2owl" . +_:B26a6a3ce2860abd26714a581389130e9 "http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo"^^ . + "Bilateria" . +_:B9b5a7875fa43f6ad185d28af31c95258 "Thorsten Heinrich" . +_:B9b5a7875fa43f6ad185d28af31c95258 "henrich@embl.de" . + "http://purl.obolibrary.org/obo/bila.owl" . + "inactive" . + "Gene Regulation Ontology" . + _:B30b9da4bbd1c3444fe3d10358015e813 . + . +_:B30b9da4bbd1c3444fe3d10358015e813 "vlee@ebi.ac.uk" . +_:B30b9da4bbd1c3444fe3d10358015e813 "Vivian Lee" . + "inactive" . + . + "Dendritic cell" . + _:B36c4e72dff55ad07eef86d9cca6c7523 . + . +_:B36c4e72dff55ad07eef86d9cca6c7523 "Lindsay.Cowell@utsouthwestern.edu" . +_:B36c4e72dff55ad07eef86d9cca6c7523 "Lindsay Cowell" . + "inactive" . + . + "Human developmental anatomy, timed version" . + _:B73441eda80a19470b62d1a7176ed933e . + . +_:B73441eda80a19470b62d1a7176ed933e "J.Bard@ed.ac.uk" . +_:B73441eda80a19470b62d1a7176ed933e "Jonathan Bard" . + "inactive" . + . + "Human developmental anatomy, abstract version" . + _:Bc63b62001473481f4e8dd4905f3bce90 . +_:Bc63b62001473481f4e8dd4905f3bce90 "J.Bard@ed.ac.uk" . +_:Bc63b62001473481f4e8dd4905f3bce90 "Jonathan Bard" . + "inactive" . + _:B97095f321e1a822f7081dd7c1ace10a6 . + . + "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)." . + "Mouse gross anatomy and development, timed" . + "anatomy" . + _:B003b1d8322ed5a66ddcafb0b1440c0dd . + . + . + . +_:B97095f321e1a822f7081dd7c1ace10a6 "obo2owl" . +_:B97095f321e1a822f7081dd7c1ace10a6 "ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo"^^ . +_:B003b1d8322ed5a66ddcafb0b1440c0dd "Terry Hayamizu" . +_:B003b1d8322ed5a66ddcafb0b1440c0dd "Terry.Hayamizu@jax.org" . + "http://purl.obolibrary.org/obo/emap.owl" . + "inactive" . + "eVOC (Expressed Sequence Annotation for Humans)" . + _:Bd451beb231fe589c2005da98c734d604 . + . +_:Bd451beb231fe589c2005da98c734d604 "evoc@sanbi.ac.za" . +_:Bd451beb231fe589c2005da98c734d604 "eVOC mailing list" . + "inactive" . + _:B5bbd0b0a1119ad078bd748d24aa6ae6e . + . + "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase." . + "Fly taxonomy" . + "taxonomy" . + _:B96371ca59165bf8d95bcffd7c85bb3a7 . + . + . +_:B5bbd0b0a1119ad078bd748d24aa6ae6e "obo2owl" . +_:B5bbd0b0a1119ad078bd748d24aa6ae6e "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo"^^ . +_:B96371ca59165bf8d95bcffd7c85bb3a7 "Marta Costa" . +_:B96371ca59165bf8d95bcffd7c85bb3a7 "mmc46@gen.cam.ac.uk" . + "http://purl.obolibrary.org/obo/fbsp.owl" . + "inactive" . + _:B412073b0d5bef2ee2d99cb412e0ee937 . + "Influenza Ontology" . + "health" . + "http://purl.obolibrary.org/obo/flu/tracker" . + _:B66267214a7d595bfd6e6fc44a69dbe50 . + . + . +_:B412073b0d5bef2ee2d99cb412e0ee937 "owl2obo" . +_:B412073b0d5bef2ee2d99cb412e0ee937 "http://purl.obolibrary.org/obo/flu.owl"^^ . +_:B66267214a7d595bfd6e6fc44a69dbe50 "Burke Squires" . +_:B66267214a7d595bfd6e6fc44a69dbe50 "burkesquires@gmail.com" . + "http://purl.obolibrary.org/obo/flu.owl" . + "inactive" . + "Cereal Plant Gross Anatomy" . + _:B0a762961f5baa12ad8753bb40cd845dd . + . +_:B0a762961f5baa12ad8753bb40cd845dd "Plant Ontology Administrators" . +_:B0a762961f5baa12ad8753bb40cd845dd "po-discuss@plantontology.org" . + "inactive" . + "Habronattus courtship" . + _:B90227699c1d72c0692299c7cc11157c7 . + . +_:B90227699c1d72c0692299c7cc11157c7 "Peter Midford" . +_:B90227699c1d72c0692299c7cc11157c7 "peteremidford@yahoo.com" . + "inactive" . + _:Ba7c7bce02cac8a25c1d0106922dd825b . + "Molecule role (INOH Protein name/family name ontology)" . + _:Ba75d7594869e668101fa7e913a58970a . + . +_:Ba7c7bce02cac8a25c1d0106922dd825b "obo2owl" . +_:Ba7c7bce02cac8a25c1d0106922dd825b "https://web.archive.org/web/20131127090937/http://www.inoh.org/ontologies/MoleculeRoleOntology.obo"^^ . +_:Ba75d7594869e668101fa7e913a58970a "INOH curators" . +_:Ba75d7594869e668101fa7e913a58970a "curator@inoh.org" . + "inactive" . + "Protein Domains" . + _:Bed76db0dd900a9ad33c8fa8c768d94ab . + . +_:Bed76db0dd900a9ad33c8fa8c768d94ab "InterPro Help" . +_:Bed76db0dd900a9ad33c8fa8c768d94ab "interhelp@ebi.ac.uk" . + "inactive" . + _:B93cf4913603085a7d6e613731d8b7917 . + "An ontology representation of the LIPIDMAPS nomenclature classification." . + "Lipid Ontology" . + "lipids" . + _:B24c7afbead999545850036bef2ad95c6 . +_:B93cf4913603085a7d6e613731d8b7917 "owl2obo" . +_:B93cf4913603085a7d6e613731d8b7917 "http://www.lipidprofiles.com/LipidOntology"^^ . +_:B24c7afbead999545850036bef2ad95c6 "Christipher Baker" . +_:B24c7afbead999545850036bef2ad95c6 "bakerc@unb.ca" . + "inactive" . + "Loggerhead nesting" . + _:B6a0192e27d2e33f3873ec18375c67641 . + . +_:B6a0192e27d2e33f3873ec18375c67641 "Peter Midford" . +_:B6a0192e27d2e33f3873ec18375c67641 "peteremidford@yahoo.com" . + "inactive" . + "Multiple alignment" . + _:B5ef0389d030c5f5f80d851d2a5bdf671 . + . +_:B5ef0389d030c5f5f80d851d2a5bdf671 "Julie Thompson" . +_:B5ef0389d030c5f5f80d851d2a5bdf671 "julie@igbmc.u-strasbg.fr" . + "inactive" . + "Minimal anatomical terminology" . + _:B87cdadf6d400fbd1756f18ff08d57923 . +_:B87cdadf6d400fbd1756f18ff08d57923 "Jonathan Bard" . +_:B87cdadf6d400fbd1756f18ff08d57923 "j.bard@ed.ac.uk" . + "inactive" . + . + "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes." . + "Medaka fish anatomy and development" . + "anatomy" . + _:B25e5bb3421564ec49ba2e9cbb504ccda . + . + "Oryzias" . +_:B25e5bb3421564ec49ba2e9cbb504ccda "Thorsten Henrich" . +_:B25e5bb3421564ec49ba2e9cbb504ccda "Thorsten.Henrich@embl-heidelberg.de" . + "http://purl.obolibrary.org/obo/mfo.owl" . + "inactive" . + "An application ontology for use with miRNA databases." . + "microRNA Ontology" . + . + _:B6e360e987d301a01e8acd1cdf75d6127 . + . + . +_:B6e360e987d301a01e8acd1cdf75d6127 "Pantelis Topalis" . +_:B6e360e987d301a01e8acd1cdf75d6127 "topalis@imbb.forth.gr" . + "http://purl.obolibrary.org/obo/mirnao.owl" . + "inactive" . + "A standardized description of a microarray experiment in support of MAGE v.1." . + "Microarray experimental conditions" . + "experiments" . + _:B6741bbb1065d8e8b1b5677b6adb524d2 . + . + . + . +_:B6741bbb1065d8e8b1b5677b6adb524d2 "Chris Stoeckert" . +_:B6741bbb1065d8e8b1b5677b6adb524d2 "stoeckrt@pcbi.upenn.edu" . + "http://purl.obolibrary.org/obo/mo.owl" . + "inactive" . + "Neuronal cell types" . + "NIF Cell" . + _:Bdad84ae922e9fd4a1fb943734286bab8 . + . +_:Bdad84ae922e9fd4a1fb943734286bab8 "Fahim Imam" . +_:Bdad84ae922e9fd4a1fb943734286bab8 "smtifahim@gmail.com" . + "inactive" . + "NIF Dysfunction" . + _:B45954facca8ddb00985fee6c2b1b357d . + . +_:B45954facca8ddb00985fee6c2b1b357d "Fahim Imam" . +_:B45954facca8ddb00985fee6c2b1b357d "smtifahim@gmail.com" . + "inactive" . + "NIF Gross Anatomy" . + _:B327e879658a66be6434463e2f5ec7fe6 . + . +_:B327e879658a66be6434463e2f5ec7fe6 "Fahim Imam" . +_:B327e879658a66be6434463e2f5ec7fe6 "smtifahim@gmail.com" . + "inactive" . + _:Be4c2464fd67f751a4d286f66a5ada11c . + "Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation." . + "NMR-instrument specific component of metabolomics investigations" . + "experiments" . + _:B8cabee3f730d000878514a7e0b02b34c . + . + . + . +_:Be4c2464fd67f751a4d286f66a5ada11c "owl2obo" . +_:Be4c2464fd67f751a4d286f66a5ada11c "https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl"^^ . +_:B8cabee3f730d000878514a7e0b02b34c "Schober Daniel" . +_:B8cabee3f730d000878514a7e0b02b34c "schober@imbi.uni-freiburg.de" . + "http://purl.obolibrary.org/obo/nmr.owl" . + "inactive" . + "OBO relationship types (legacy)" . + _:Bd1fb70ffe5a3b60cc4cb5f378a2ed947 . + . +_:Bd1fb70ffe5a3b60cc4cb5f378a2ed947 "Chris Mungall" . +_:Bd1fb70ffe5a3b60cc4cb5f378a2ed947 "cjmungall@lbl.gov" . + "inactive" . + . + "Plant Anatomy Ontology" . + _:B41ab71adfe5315a510cd52faefd6961a . + . +_:B41ab71adfe5315a510cd52faefd6961a "Pankaj Jaiswal" . +_:B41ab71adfe5315a510cd52faefd6961a "jaiswalp@science.oregonstate.edu" . + "inactive" . + . + "Platynereis stage ontology" . + _:Bd310886c939764aebbd3d5b7283d8e3b . + . + "Platynereis" . +_:Bd310886c939764aebbd3d5b7283d8e3b "Thorsten Heinrich" . +_:Bd310886c939764aebbd3d5b7283d8e3b "henrich@embl.de" . + "inactive" . + . + "Plant Growth and Development Stage" . + _:Bcfebb8a3eb2037b322a208fe350d2d61 . + . +_:Bcfebb8a3eb2037b322a208fe350d2d61 "Plant Ontology Administrators" . +_:Bcfebb8a3eb2037b322a208fe350d2d61 "po-discuss@plantontology.org" . + "inactive" . + "Plasmodium life cycle" . + _:Be6cc05ac532618e2260851c597790d06 . + . +_:Be6cc05ac532618e2260851c597790d06 "Matt Berriman" . +_:Be6cc05ac532618e2260851c597790d06 "mb4@sanger.ac.uk" . + "inactive" . + "Proteomics data and process provenance" . + _:B183729e38a70a80c5ce4364836a35cff . + . +_:B183729e38a70a80c5ce4364836a35cff "Satya S. Sahoo" . +_:B183729e38a70a80c5ce4364836a35cff "satya30@uga.edu" . + "inactive" . + "For the description of covalent bonds in proteins." . + "Protein covalent bond" . + "proteins" . + _:B3d0cdf626d7ad14b22d1d7ffa53ac6bc . + . +_:B3d0cdf626d7ad14b22d1d7ffa53ac6bc "John Garavelli" . +_:B3d0cdf626d7ad14b22d1d7ffa53ac6bc "john.garavelli@ebi.ac.uk" . + "inactive" . + . + "Subcellular anatomy ontology" . + _:Bd4283b1854ed41ec913eddd1d6887496 . + . +_:Bd4283b1854ed41ec913eddd1d6887496 "Stephen Larson" . +_:Bd4283b1854ed41ec913eddd1d6887496 "slarson@ncmir.ucsd.edu" . + "inactive" . + _:Bc7c6a1701bb9f39f4f862313228cc9f2 . + "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments." . + "Sample processing and separation techniques" . + "provenance" . + _:B38f5ce4fa89c4717e927885578d68b53 . + . + . + . +_:Bc7c6a1701bb9f39f4f862313228cc9f2 "obo2owl" . +_:Bc7c6a1701bb9f39f4f862313228cc9f2 "https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo"^^ . +_:B38f5ce4fa89c4717e927885578d68b53 "SEP developers via the PSI and MSI mailing lists" . +_:B38f5ce4fa89c4717e927885578d68b53 "psidev-gps-dev@lists.sourceforge.net" . + "http://purl.obolibrary.org/obo/sep.owl" . + "inactive" . + . + "Suggested Ontology for Pharmacogenomics" . + _:B2aeac92afbd011f5225fab26667a0dc8 . + . +_:B2aeac92afbd011f5225fab26667a0dc8 "Adrien Coulet" . +_:B2aeac92afbd011f5225fab26667a0dc8 "Adrien.Coulet@loria.fr" . + "inactive" . + . + "Terminology of Anatomy of Human Embryology" . + _:Bc33f36ace3c70d79412bb6fcc14fb59f . +_:Bc33f36ace3c70d79412bb6fcc14fb59f "Pierre Sprumont" . +_:Bc33f36ace3c70d79412bb6fcc14fb59f "pierre.sprumont@unifr.ch" . + "inactive" . + . + "Terminology of Anatomy of Human Histology" . + _:B96b8210eade8c7d355b59e0a06357f2e . +_:B96b8210eade8c7d355b59e0a06357f2e "Pierre Sprumont" . +_:B96b8210eade8c7d355b59e0a06357f2e "pierre.sprumont@unifr.ch" . + "inactive" . + _:B6db1b65fe1092253887c7f1d00b1c388 . + . + "Vertebrate skeletal anatomy ontology." . + "Vertebrate Skeletal Anatomy Ontology-" . + "anatomy" . + "https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3AVSAO" . + _:B2141b733570eb293ab8be89aff909f6b . + . + . + . +_:B6db1b65fe1092253887c7f1d00b1c388 "obo2owl" . +_:B6db1b65fe1092253887c7f1d00b1c388 "http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo"^^ . + "Vertebrata" . +_:B2141b733570eb293ab8be89aff909f6b "Wasila Dahdul" . +_:B2141b733570eb293ab8be89aff909f6b "wasila.dahdul@usd.edu" . + "http://purl.obolibrary.org/obo/vsao.owl" . + "inactive" . + . + "Yeast phenotypes" . + _:B7b74b9e0593061b8772a2b6d61b7feb5 . + . + "Saccharomyces cerevisiae" . +_:B7b74b9e0593061b8772a2b6d61b7feb5 "Mike Cherry" . +_:B7b74b9e0593061b8772a2b6d61b7feb5 "cherry@genome.stanford.edu" . + "inactive" . + . + "Maize gross anatomy" . + _:B48b2ad47280b5a768aaba80d38b1fef9 . + . + "Zea" . +_:B48b2ad47280b5a768aaba80d38b1fef9 "Leszek Vincent" . +_:B48b2ad47280b5a768aaba80d38b1fef9 "Leszek@missouri.edu" . + "inactive" . + _:Bbd71bf598f8bde54bab0faf232c36ef9 . + "An ontology designed to support the semantic annotation of epidemiology resources" . + "Epidemiology Ontology" . + . + . +_:Bbd71bf598f8bde54bab0faf232c36ef9 "owl2obo" . +_:Bbd71bf598f8bde54bab0faf232c36ef9 "http://purl.obolibrary.org/obo/epo.owl"^^ . + "http://purl.obolibrary.org/obo/epo.owl" . + "inactive" . + _:B017b26d18ebbeba2850580685acd7a59 . + "Event (INOH pathway ontology)" . + . +_:B017b26d18ebbeba2850580685acd7a59 "obo2owl" . +_:B017b26d18ebbeba2850580685acd7a59 "http://download.baderlab.org/INOH/ontologies/EventOntology_172.obo"^^ . + "inactive" . + "Vertebrate Homologous Ontology Group Ontology" . + . + "http://purl.obolibrary.org/obo/vhog.owl" . diff --git a/registry/ontologies.ttl b/registry/ontologies.ttl index c4443030b..4971587a0 100644 --- a/registry/ontologies.ttl +++ b/registry/ontologies.ttl @@ -436,7 +436,6 @@ _:b16 "obo2owl" ; ; "CC-BY" ; "CC BY 3.0" ; - "CC-BY version 3.0" ; "CC-BY 3.0" . @@ -712,7 +711,7 @@ _:b27 "Jonathan Bard" ; _:b34 ; "An ontology of information entities." ; "Information Artifact Ontology" ; - ; + ; "information" ; "https://github.com/information-artifact-ontology/IAO/issues" ; "http://purl.obolibrary.org/obo/iao.owl" ; @@ -818,7 +817,8 @@ _:b40 "Stacia R Engel" ; ; "CC-BY 3.0" ; - "CC-BY" . + "CC-BY" ; + "CC-BY version 3.0" . _:b41 "Mathias Brochhausen" ; "MBrochhausen@uams.edu" . @@ -865,7 +865,7 @@ _:b43 "Ramona Walls" ; "active" ; _:b44 ; - "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces" ; + "An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces" ; "Biological Spatial Ontology" ; ; ; @@ -1110,6 +1110,27 @@ _:b61 "Yongqun Oliver He" ; "http://purl.obolibrary.org/obo/cido.owl" . + + "active" ; + "An ontology to capture confidence information about annotations." ; + "Confidence Information Ontology" ; + ; + "https://github.com/BgeeDB/confidence-information-ontology" ; + "http://purl.obolibrary.org/obo/cio.owl" ; + _:b62 ; + ; + ; + . + +_:b62 "Frederic Bastian" ; + "bgee@sib.swiss" . + + + "http://purl.obolibrary.org/obo/cio.owl" . + + + "http://purl.obolibrary.org/obo/cio.obo" . + _:b8 "git clone https://github.com/obophenotype/cell-ontology.git" ; "vcs" . @@ -1148,21 +1169,21 @@ _:b9 "Alexander Diehl" ; "active" ; ; - _:b62 ; + _:b63 ; "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)." ; "Collembola Anatomy Ontology" ; ; "anatomy" ; "https://github.com/luis-gonzalez-m/Collembola/issues" ; "http://purl.obolibrary.org/obo/clao.owl" ; - _:b63 ; + _:b64 ; ; ; . -_:b62 "git clone https://github.com/luis-gonzalez-m/Collembola.git" . +_:b63 "git clone https://github.com/luis-gonzalez-m/Collembola.git" . -_:b63 "Luis González-Montaña" ; +_:b64 "Luis González-Montaña" ; "lagonzalezmo@unal.edu.co" . @@ -1182,11 +1203,11 @@ _:b63 "Luis González-Montaña" ; "https://github.com/CLO-Ontology/CLO/issues" ; "http://purl.obolibrary.org/obo/clo.owl" ; - _:b64 ; + _:b65 ; ; . -_:b64 "Sirarat Sarntivijai" ; +_:b65 "Sirarat Sarntivijai" ; "siiraa@umich.edu" . @@ -1197,21 +1218,21 @@ _:b64 "Sirarat Sarntivijai" ; ; ; ; - _:b65 ; + _:b66 ; "The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle." ; "Clytia hemisphaerica Development and Anatomy Ontology" ; ; "anatomy" ; "https://github.com/EBISPOT/clyh_ontology/issues" ; "http://purl.obolibrary.org/obo/clyh.owl" ; - _:b66 ; + _:b67 ; ; ; . -_:b65 "git clone https://github.com/EBISPOT/clyh_ontology.git" . +_:b66 "git clone https://github.com/EBISPOT/clyh_ontology.git" . -_:b66 "Lucas Leclere" ; +_:b67 "Lucas Leclere" ; "lucas.leclere@obs-vlfr.fr" . @@ -1222,7 +1243,7 @@ _:b66 "Lucas Leclere" ; "active" ; - _:b67 ; + _:b68 ; "Morphological and physiological measurement records generated from clinical and model organism research and health programs." ; "Clinical measurement ontology" ; ; @@ -1232,13 +1253,13 @@ _:b66 "Lucas Leclere" ; "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues" ; ; "http://purl.obolibrary.org/obo/cmo.owl" ; - _:b68 ; + _:b69 ; ; ; ; . -_:b67 "obo2owl" ; +_:b68 "obo2owl" ; "ftp://ftp.rgd.mcw.edu/pub/ontology/clinical_measurement/clinical_measurement.obo"^^ . @@ -1251,7 +1272,7 @@ _:b67 "obo2owl" ; "RGD Ontology Browser" ; "RGD" . -_:b68 "Mary Shimoyama" ; +_:b69 "Mary Shimoyama" ; "shimoyama@mcw.edu" . @@ -1268,11 +1289,11 @@ _:b68 "Mary Shimoyama" ; "upper" ; "https://github.com/OBOFoundry/COB/issues" ; "http://purl.obolibrary.org/obo/cob.owl" ; - _:b69 ; + _:b70 ; ; . -_:b69 "Bjoern Peters" ; +_:b70 "Bjoern Peters" ; "bpeters@lji.org" . @@ -1280,25 +1301,25 @@ _:b69 "Bjoern Peters" ; "active" ; - _:b70 ; + _:b71 ; "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability." ; "Contributor Role Ontology" ; ; "scholarly contribution roles" ; "https://github.com/data2health/contributor-role-ontology/issues" ; "http://purl.obolibrary.org/obo/cro.owl" ; - _:b71 ; + _:b72 ; ; . -_:b70 "git clone https://github.com/data2health/contributor-role-ontology.git" . +_:b71 "git clone https://github.com/data2health/contributor-role-ontology.git" . ; "CC-BY" ; "CC-BY 2.0" . -_:b71 "Marijane White" ; +_:b72 "Marijane White" ; "whimar@ohsu.edu" . @@ -1309,7 +1330,7 @@ _:b71 "Marijane White" ; "active" ; ; ; - _:b72 ; + _:b73 ; ; "An anatomical and developmental ontology for ctenophores (Comb Jellies)" ; "Ctenophore Ontology" ; @@ -1317,17 +1338,17 @@ _:b71 "Marijane White" ; "anatomy" ; "https://github.com/obophenotype/ctenophore-ontology/issues" ; "http://purl.obolibrary.org/obo/cteno.owl" ; - _:b73 ; + _:b74 ; ; . -_:b72 "git clone https://github.com/obophenotype/ctenophore-ontology.git" ; +_:b73 "git clone https://github.com/obophenotype/ctenophore-ontology.git" ; "vcs" . "Ctenophore" . -_:b73 "Chris Mungall" ; +_:b74 "Chris Mungall" ; "cjmungall@lbl.gov" . @@ -1340,11 +1361,11 @@ _:b73 "Chris Mungall" ; ; "https://github.com/ClinicalTrialOntology/CTO/issues" ; "http://purl.obolibrary.org/obo/cto.owl" ; - _:b74 ; + _:b75 ; ; . -_:b74 "Dr. Alpha Tom Kodamullil" ; +_:b75 "Dr. Alpha Tom Kodamullil" ; "alpha.tom.kodamullil@scai.fraunhofer.de" . @@ -1352,21 +1373,21 @@ _:b74 "Dr. Alpha Tom Kodamullil" "active" ; - _:b75 ; + _:b76 ; "An ontology to describe entities related to cardiovascular diseases" ; "Cardiovascular Disease Ontology" ; ; "health" ; "https://github.com/OpenLHS/CVDO/issues" ; "http://purl.obolibrary.org/obo/cvdo.owl" ; - _:b76 ; + _:b77 ; ; . -_:b75 "owl2obo" ; +_:b76 "owl2obo" ; "http://purl.obolibrary.org/obo/cvdo.owl"^^ . -_:b76 "Paul Fabry" ; +_:b77 "Paul Fabry" ; "paul.fabry@usherbrooke.ca" . @@ -1374,7 +1395,7 @@ _:b76 "Paul Fabry" ; "active" ; - _:b77 ; + _:b78 ; ; "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum" ; "Dictyostelium discoideum anatomy" ; @@ -1382,19 +1403,19 @@ _:b76 "Paul Fabry" ; "anatomy" ; "https://github.com/dictyBase/migration-data/issues" ; "http://purl.obolibrary.org/obo/ddanat.owl" ; - _:b78 ; + _:b79 ; ; ; ; . -_:b77 "obo2owl" ; +_:b78 "obo2owl" ; "https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_anatomy.obo"^^ . "Dictyostelium discoideum" . -_:b78 "Petra Fey" ; +_:b79 "Petra Fey" ; "pfey@northwestern.edu" . @@ -1405,7 +1426,7 @@ _:b78 "Petra Fey" ; "active" ; - _:b79 ; + _:b80 ; ; "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum." ; "Dictyostelium discoideum phenotype ontology" ; @@ -1413,15 +1434,15 @@ _:b78 "Petra Fey" ; "anatomy" ; "https://github.com/obophenotype/dicty-phenotype-ontology/issues" ; "http://purl.obolibrary.org/obo/ddpheno.owl" ; - _:b80 ; + _:b81 ; ; ; ; . -_:b79 "git clone https://github.com/obophenotype/dicty-phenotype-ontology.git" . +_:b80 "git clone https://github.com/obophenotype/dicty-phenotype-ontology.git" . -_:b80 "Petra Fey" ; +_:b81 "Petra Fey" ; "pfey@northwestern.edu" . @@ -1437,11 +1458,11 @@ _:b80 "Petra Fey" ; ; "https://github.com/DIDEO/DIDEO/issues" ; "http://purl.obolibrary.org/obo/dideo.owl" ; - _:b81 ; + _:b82 ; ; . -_:b81 "Mathias Brochhausen" ; +_:b82 "Mathias Brochhausen" ; "mbrochhausen@gmail.com" . @@ -1450,7 +1471,7 @@ _:b81 "Mathias Brochhausen" ; "FBcv" ; "active" ; - _:b82 ; + _:b83 ; ; "An ontology of commonly encountered and/or high level Drosophila phenotypes." ; "Drosophila Phenotype Ontology" ; @@ -1460,13 +1481,13 @@ _:b81 "Mathias Brochhausen" ; "https://github.com/FlyBase/drosophila-phenotype-ontology/issues" ; ; "http://purl.obolibrary.org/obo/dpo.owl" ; - _:b83 ; + _:b84 ; ; ; ; . -_:b82 "git clone https://github.com/FlyBase/drosophila-phenotype-ontolog.git" . +_:b83 "git clone https://github.com/FlyBase/drosophila-phenotype-ontolog.git" . "Drosophila" . @@ -1478,7 +1499,7 @@ _:b82 "git clone https://gi "FlyBase Browser" ; "FB" . -_:b83 "Clare Pilgrim" ; +_:b84 "Clare Pilgrim" ; "cp390@cam.ac.uk" . @@ -1493,7 +1514,7 @@ _:b83 "Clare Pilgrim" ; "FBcv" ; "active" ; - _:b84 ; + _:b85 ; "A structured controlled vocabulary used for various aspects of annotation by FlyBase." ; "FlyBase Controlled Vocabulary" ; ; @@ -1501,7 +1522,7 @@ _:b83 "Clare Pilgrim" ; "https://github.com/FlyBase/flybase-controlled-vocabulary/issues" ; ; "http://purl.obolibrary.org/obo/fbcv.owl" ; - _:b85 ; + _:b86 ; ; ; ; @@ -1509,21 +1530,21 @@ _:b83 "Clare Pilgrim" ; "active" ; - _:b86 ; + _:b87 ; "An ontology to support comparative effectiveness researchers studying claims data." ; "The Drug Ontology" ; ; "health" ; "https://ontology.atlassian.net/browse/DRON" ; "http://purl.obolibrary.org/obo/dron.owl" ; - _:b87 ; + _:b88 ; ; . -_:b86 "owl2obo" ; +_:b87 "owl2obo" ; "http://purl.obolibrary.org/obo/dron.owl"^^ . -_:b87 "William Hogan" ; +_:b88 "William Hogan" ; "hoganwr@gmail.com" . @@ -1533,19 +1554,19 @@ _:b87 "William Hogan" ; "active" ; ; ; - _:b88 ; + _:b89 ; "DUO is an ontology which represent data use conditions." ; "Data Use Ontology" ; ; "https://github.com/EBISPOT/DUO/issues" ; "http://purl.obolibrary.org/obo/duo.owl" ; - _:b89 ; + _:b90 ; ; . -_:b88 "git clone https://github.com/EBISPOT/duo.git" . +_:b89 "git clone https://github.com/EBISPOT/duo.git" . -_:b89 "Melanie Courtot" ; +_:b90 "Melanie Courtot" ; "mcourtot@gmail.com" . @@ -1556,21 +1577,21 @@ _:b89 "Melanie Courtot" ; ; ; ; - _:b90 ; + _:b91 ; "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586)." ; "The Echinoderm Anatomy and Development Ontology" ; ; "anatomy" ; "https://github.com/echinoderm-ontology/ecao_ontology/issues" ; "http://purl.obolibrary.org/obo/ecao.owl" ; - _:b91 ; + _:b92 ; ; ; . -_:b90 "git clone https://github.com/echinoderm-ontology/ecao_ontology.git" . +_:b91 "git clone https://github.com/echinoderm-ontology/ecao_ontology.git" . -_:b91 "Charles Ettensohn" ; +_:b92 "Charles Ettensohn" ; "ettensohn@cmu.edu" . @@ -1581,7 +1602,7 @@ _:b91 "Charles Ettensohn" ; "active" ; - _:b92 ; + _:b93 ; "An ontology for experimental and other evidence statements." ; "Evidence ontology" ; ; @@ -1591,12 +1612,12 @@ _:b91 "Charles Ettensohn" ; "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1458400" ; "https://github.com/evidenceontology/evidenceontology/issues" ; "http://purl.obolibrary.org/obo/eco.owl" ; - _:b93 ; + _:b94 ; ; ; . -_:b92 "obo2owl" ; +_:b93 "obo2owl" ; "https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/eco.obo"^^ . @@ -1605,7 +1626,7 @@ _:b92 "obo2owl" ; "Standardized description of scientific evidence using the Evidence Ontology (ECO)" . -_:b93 "Michelle Giglio" ; +_:b94 "Michelle Giglio" ; "mgiglio@som.umaryland.edu" . @@ -1626,14 +1647,14 @@ _:b93 "Michelle Giglio" ; ; ; ; - _:b94 ; - "An ontology to provide core semantics for ecological entities." ; + _:b95 ; + "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms." ; "An ontology of core ecological entities" ; ; "ecological functions, ecological interactions" ; "https://github.com/EcologicalSemantics/ecocore/issues" ; "http://purl.obolibrary.org/obo/ecocore.owl" ; - _:b95 ; + _:b96 ; ; ; . @@ -1648,20 +1669,20 @@ _:b93 "Michelle Giglio" ; ; ; ; - _:b96 ; + _:b97 ; "An ontology about groups of interacting organisms such as populations and communities" ; "Population and Community Ontology" ; ; "collections of organisms" ; "https://github.com/PopulationAndCommunityOntology/pco/issues" ; "http://purl.obolibrary.org/obo/pco.owl" ; - _:b97 ; + _:b98 ; ; . -_:b94 "git clone https://github.com/EcologicalSemantics/ecocore.git" . +_:b95 "git clone https://github.com/EcologicalSemantics/ecocore.git" . -_:b95 "Pier Luigi Buttigieg" ; +_:b96 "Pier Luigi Buttigieg" ; "p.buttigieg@gmail.com" . @@ -1686,14 +1707,14 @@ _:b95 "Pier Luigi Buttigieg" ; ; ; ; - _:b98 ; + _:b99 ; "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology)." ; "Environmental conditions, treatments and exposures ontology" ; ; "environment" ; "https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues" ; "http://purl.obolibrary.org/obo/ecto.owl" ; - _:b99 ; + _:b100 ; ; ; ; @@ -1703,15 +1724,16 @@ _:b95 "Pier Luigi Buttigieg" ; . + "ExO" ; "active" ; - _:b100 ; + _:b101 ; "Vocabularies for describing exposure data to inform understanding of environmental health." ; "Exposure ontology" ; ; "health" ; "https://github.com/CTDbase/exposure-ontology/issues" ; "http://purl.obolibrary.org/obo/exo.owl" ; - _:b101 ; + _:b102 ; ; ; ; @@ -1725,14 +1747,14 @@ _:b95 "Pier Luigi Buttigieg" ; ; ; ; - _:b102 ; + _:b103 ; "Medical Action Ontology is an ontology..." ; "Medical Action Ontology" ; ; "medical" ; "https://github.com/monarch-initiative/MAxO/issues" ; "http://purl.obolibrary.org/obo/maxo.owl" ; - _:b103 ; + _:b104 ; ; ; ; @@ -1743,7 +1765,7 @@ _:b95 "Pier Luigi Buttigieg" ; "active" ; - _:b104 ; + _:b105 ; "An ontology of human and animal behaviours and behavioural phenotypes" ; "Neuro Behavior Ontology" ; ; @@ -1751,7 +1773,7 @@ _:b95 "Pier Luigi Buttigieg" ; "https://github.com/obo-behavior/behavior-ontology/issues" ; ; "http://purl.obolibrary.org/obo/nbo.owl" ; - _:b105 ; + _:b106 ; ; . @@ -1762,7 +1784,7 @@ _:b95 "Pier Luigi Buttigieg" ; ; "https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues" ; "http://purl.obolibrary.org/obo/ncit.owl" ; - _:b106 ; + _:b107 ; ; ; ; @@ -1771,7 +1793,7 @@ _:b95 "Pier Luigi Buttigieg" ; "active" ; - _:b107 ; + _:b108 ; "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms." ; "Experimental condition ontology" ; ; @@ -1781,14 +1803,14 @@ _:b95 "Pier Luigi Buttigieg" ; "https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues" ; ; "http://purl.obolibrary.org/obo/xco.owl" ; - _:b108 ; + _:b109 ; ; ; . -_:b98 "git clone https://github.com/EnvironmentOntology/environmental-exposure-ontology.git" . +_:b99 "git clone https://github.com/EnvironmentOntology/environmental-exposure-ontology.git" . -_:b99 "Anne Thessen" ; +_:b100 "Anne Thessen" ; "annethessen@gmail.com" . @@ -1811,7 +1833,7 @@ _:b99 "Anne Thessen" ; "active" ; - _:b109 ; + _:b110 ; ; "An ontology for mouse anatomy covering embryonic development and postnatal stages." ; "Mouse Developmental Anatomy Ontology" ; @@ -1819,18 +1841,18 @@ _:b99 "Anne Thessen" ; "anatomy" ; "https://github.com/obophenotype/mouse-anatomy-ontology/issues" ; "http://purl.obolibrary.org/obo/emapa.owl" ; - _:b110 ; + _:b111 ; ; ; . -_:b109 "obo2owl" ; +_:b110 "obo2owl" ; "ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo"^^ . "Mus" . -_:b110 "Terry Hayamizu" ; +_:b111 "Terry Hayamizu" ; "Terry.Hayamizu@jax.org" . @@ -1855,7 +1877,7 @@ _:b110 "Terry Hayamizu" ; "food" ; "https://github.com/FoodOntology/foodon/issues/" ; "http://purl.obolibrary.org/obo/foodon.owl" ; - _:b111 ; + _:b112 ; ; ; ; @@ -1906,20 +1928,20 @@ _:b31 "Pier Luigi Buttigieg" ; "functional genomics, population biology, clinical epidemiology, and microbiomes" ; "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues" ; "http://purl.obolibrary.org/obo/eupath.owl" ; - _:b112 ; + _:b113 ; ; . -_:b112 "Chris Stoeckert" ; +_:b113 "Chris Stoeckert" ; "stoeckrt@pennmedicine.upenn.edu" . "http://purl.obolibrary.org/obo/eupath.owl" . -_:b100 "obo2owl" ; +_:b101 "obo2owl" ; "https://raw.githubusercontent.com/CTDbase/exposure-ontology/master/src/ontology/exo.obo"^^ . -_:b101 "Carolyn Mattingly" ; +_:b102 "Carolyn Mattingly" ; "cjmattin@ncsu.edu" . @@ -1930,7 +1952,7 @@ _:b101 "Carolyn Mattingly" ; "active" ; - _:b113 ; + _:b114 ; ; "A structured controlled vocabulary for the anatomy of fungi." ; "Fungal gross anatomy" ; @@ -1938,18 +1960,18 @@ _:b101 "Carolyn Mattingly" ; "anatomy" ; "https://github.com/obophenotype/fungal-anatomy-ontology/issues" ; "http://purl.obolibrary.org/obo/fao.owl" ; - _:b114 ; + _:b115 ; ; ; . -_:b113 "git clone https://github.com/obophenotype/fungal-anatomy-ontology.git" ; +_:b114 "git clone https://github.com/obophenotype/fungal-anatomy-ontology.git" ; "vcs" . "Fungal" . -_:b114 "Midori Harris" ; +_:b115 "Midori Harris" ; "mah79@cam.ac.uk" . @@ -1961,21 +1983,21 @@ _:b114 "Midori Harris" ; "FBbi" ; "active" ; - _:b115 ; + _:b116 ; "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research." ; "Biological Imaging Methods Ontology" ; ; "imaging experiments" ; "https://github.com/CRBS/Biological_Imaging_Methods_Ontology/issues" ; "http://purl.obolibrary.org/obo/fbbi.owl" ; - _:b116 ; + _:b117 ; ; . -_:b115 "obo2owl" ; +_:b116 "obo2owl" ; "https://raw.githubusercontent.com/dosumis/fbbi/master/src/ontology/fbbi.obo"^^ . -_:b116 "David Orloff" ; +_:b117 "David Orloff" ; "dorloff@ncmir.ucsd.edu" . @@ -1984,7 +2006,7 @@ _:b116 "David Orloff" ; "FBbt" ; "active" ; - _:b117 ; + _:b118 ; ; "An ontology representing the gross anatomy of Drosophila melanogaster." ; "Drosophila gross anatomy" ; @@ -1999,7 +2021,7 @@ _:b116 "David Orloff" ; ; ; "http://purl.obolibrary.org/obo/fbbt.owl" ; - _:b118 ; + _:b119 ; ; ; ; @@ -2007,7 +2029,7 @@ _:b116 "David Orloff" ; ; . -_:b117 "git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git" . +_:b118 "git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git" . "The Drosophila anatomy ontology. [Journal of Biomedical Semantics" . @@ -2033,7 +2055,7 @@ _:b117 "git clone https://gi "BioPortal Browser" ; "BioPortal" . -_:b118 "Clare Pilgrim" ; +_:b119 "Clare Pilgrim" ; "cp390@cam.ac.uk" . @@ -2051,13 +2073,13 @@ _:b118 "Clare Pilgrim" ; "http://purl.obolibrary.org/obo/fbbt/fbbt-simple.obo" . -_:b84 "git clone https://github.com/FlyBase/flybase-controlled-vocabulary.git" . +_:b85 "git clone https://github.com/FlyBase/flybase-controlled-vocabulary.git" . "FlyBase Browser" ; "FB" . -_:b85 "Clare Pilgrim" ; +_:b86 "Clare Pilgrim" ; "cp390@cam.ac.uk" . @@ -2072,7 +2094,7 @@ _:b85 "Clare Pilgrim" ; "FBdv" ; "active" ; - _:b119 ; + _:b120 ; ; "A structured controlled vocabulary of the development of Drosophila melanogaster." ; "Drosophila development" ; @@ -2081,7 +2103,7 @@ _:b85 "Clare Pilgrim" ; "http://purl.obolibrary.org/obo/fbdv/tracker" ; ; "http://purl.obolibrary.org/obo/fbdv.owl" ; - _:b120 ; + _:b121 ; ; ; ; @@ -2089,13 +2111,13 @@ _:b85 "Clare Pilgrim" ; ; . -_:b119 "git clone https://github.com/FlyBase/drosophila-developmental-ontology.git" . +_:b120 "git clone https://github.com/FlyBase/drosophila-developmental-ontology.git" . "FlyBase Browser" ; "FB" . -_:b120 "Clare Pilgrim" ; +_:b121 "Clare Pilgrim" ; "cp390@cam.ac.uk" . @@ -2121,11 +2143,11 @@ _:b120 "Clare Pilgrim" ; "diet, metabolomics and nutrition" ; "https://github.com/getbordea/fideo/issues" ; "http://purl.obolibrary.org/obo/fideo.owl" ; - _:b121 ; + _:b122 ; ; . -_:b121 "Georgeta Bordea" ; +_:b122 "Georgeta Bordea" ; "georgeta.bordea@u-bordeaux.fr" . @@ -2133,7 +2155,7 @@ _:b121 "Georgeta Bordea" ; "active" ; - _:b122 ; + _:b123 ; ; "Traits and phenotypes of flowering plants occurring in digitized Floras" ; "Flora Phenotype Ontology" ; @@ -2141,14 +2163,14 @@ _:b121 "Georgeta Bordea" ; "phenotype" ; "https://github.com/flora-phenotype-ontology/flopoontology/issues" ; "http://purl.obolibrary.org/obo/flopo.owl" ; - _:b123 ; + _:b124 ; ; . -_:b122 "owl2obo" ; +_:b123 "owl2obo" ; "https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl"^^ . -_:b123 "Robert Hoehndorf" ; +_:b124 "Robert Hoehndorf" ; "robert.hoehndorf@kaust.edu.sa" . @@ -2156,7 +2178,7 @@ _:b123 "Robert Hoehndorf" ; "active" ; - _:b124 ; + _:b125 ; ; "This is currently a slimmed down version of FMA" ; "Foundational Model of Anatomy Ontology (subset)" ; @@ -2167,12 +2189,12 @@ _:b123 "Robert Hoehndorf" ; "anatomy" ; "https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/" ; "http://purl.obolibrary.org/obo/fma.owl" ; - _:b125 ; + _:b126 ; ; ; . -_:b124 "obo2owl" ; +_:b125 "obo2owl" ; "http://svn.code.sf.net/p/obo/svn/fma-conversion/trunk/fma2_obo.obo"^^ . @@ -2184,7 +2206,7 @@ _:b124 "obo2owl" ; "Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study" . -_:b125 "Onard Mejino" ; +_:b126 "Onard Mejino" ; "mejino@u.washington.edu" . @@ -2192,20 +2214,20 @@ _:b125 "Onard Mejino" ; "inactive" ; - _:b126 ; + _:b127 ; "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments." ; "Plant Environment Ontology" ; ; ; "environment" ; "https://github.com/Planteome/plant-environment-ontology/issues" ; - _:b127 ; + _:b128 ; ; ; ; . -_:b111 "Damion Dooley" ; +_:b112 "Damion Dooley" ; "damion.dooley@bccdc.ca" . @@ -2228,14 +2250,14 @@ _:b111 "Damion Dooley" ; ; ; ; - _:b128 ; + _:b129 ; "FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA)." ; "FuTRES Ontology of Vertebrate Traits" ; ; "vertebrate traits" ; "https://github.com/futres/fovt/issues" ; "http://purl.obolibrary.org/obo/fovt.owl" ; - _:b129 ; + _:b130 ; ; ; ; @@ -2244,23 +2266,23 @@ _:b111 "Damion Dooley" ; "active" ; - _:b130 ; + _:b131 ; "A collection of biological attributes (traits) covering all kingdoms of life." ; "Ontology of Biological Attributes" ; ; "phenotype" ; "https://github.com/obophenotype/bio-attribute-ontology/issues" ; "http://purl.obolibrary.org/obo/oba.owl" ; - _:b131 ; + _:b132 ; ; ; ; ; . -_:b128 "git clone https://github.com/futres/fovt.git" . +_:b129 "git clone https://github.com/futres/fovt.git" . -_:b129 "FuTRES Ontology of Vertebrate Traits" ; +_:b130 "FuTRES Ontology of Vertebrate Traits" ; "rlwalls2008@gmail.com" . @@ -2277,7 +2299,7 @@ _:b129 "FuTRES Ontology of Verteb "active" ; - _:b132 ; + _:b133 ; ; "FYPO is a formal ontology of phenotypes observed in fission yeast." ; "Fission Yeast Phenotype Ontology" ; @@ -2286,12 +2308,12 @@ _:b129 "FuTRES Ontology of Verteb "phenotype" ; "https://github.com/pombase/fypo/issues" ; "http://purl.obolibrary.org/obo/fypo.owl" ; - _:b133 ; + _:b134 ; ; ; . -_:b132 "obo2owl" ; +_:b133 "obo2owl" ; "https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl"^^ . @@ -2300,7 +2322,7 @@ _:b132 "obo2owl" ; "FYPO: The Fission Yeast Phenotype Ontology." . -_:b133 "Midori Harris" ; +_:b134 "Midori Harris" ; "mah79@cam.ac.uk" . @@ -2311,22 +2333,22 @@ _:b133 "Midori Harris" ; "active" ; - _:b134 ; + _:b135 ; "A gazetteer constructed on ontological principles" ; "Gazetteer" ; ; "https://github.com/EnvironmentOntology/gaz/issues" ; "https://groups.google.com/forum/#!forum/obo-gazetteer" ; "http://purl.obolibrary.org/obo/gaz.owl" ; - _:b135 ; + _:b136 ; ; ; . -_:b134 "archive" ; +_:b135 "archive" ; "http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/*zip*/archive.zip"^^ . -_:b135 "Lynn Schriml" ; +_:b136 "Lynn Schriml" ; "lschriml@som.umaryland.edu" . @@ -2343,11 +2365,11 @@ _:b135 "Lynn Schriml" ; "cohort studies" ; "https://github.com/IHCC-cohorts/GECKO/issues" ; "http://purl.obolibrary.org/obo/gecko.owl" ; - _:b136 ; + _:b137 ; ; . -_:b136 "Rebecca Jackson" ; +_:b137 "Rebecca Jackson" ; "rbca.jackson@gmail.com" . @@ -2366,12 +2388,12 @@ _:b136 "Rebecca Jackson" ; "health" ; "https://github.com/GenEpiO/genepio/issues/" ; "http://purl.obolibrary.org/obo/genepio.owl" ; - _:b137 ; + _:b138 ; ; ; . -_:b137 "Damion Dooley" ; +_:b138 "Damion Dooley" ; "damion.dooley@bccdc.ca" . @@ -2380,24 +2402,24 @@ _:b137 "Damion Dooley" ; "active" ; - _:b138 ; + _:b139 ; "An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases." ; "Genotype Ontology" ; ; "genotype-to-phenotype associations" ; "https://github.com/monarch-initiative/GENO-ontology/issues" ; "http://purl.obolibrary.org/obo/geno.owl" ; - _:b139 ; + _:b140 ; ; . -_:b138 "git clone https://github.com/monarch-initiative/GENO-ontology.git" . +_:b139 "git clone https://github.com/monarch-initiative/GENO-ontology.git" . ; "CC-BY-SA" . -_:b139 "Matthew Brush" ; +_:b140 "Matthew Brush" ; "mhb120@gmail.com" . @@ -2411,11 +2433,11 @@ _:b139 "Matthew Brush" ; ; "https://ontology.atlassian.net/browse/GEO#selectedTab=com.atlassian.jira.plugin.system.project%3Aissues-panel" ; "http://purl.obolibrary.org/obo/geo.owl" ; - _:b140 ; + _:b141 ; ; . -_:b140 "Bill Hogan" ; +_:b141 "Bill Hogan" ; "hoganwr@gmail.com" . @@ -2423,7 +2445,7 @@ _:b140 "Bill Hogan" ; "active" ; - _:b141 ; + _:b142 ; "GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels." ; "Glycan Naming and Subsumption Ontology (GNOme)" ; ; @@ -2432,13 +2454,13 @@ _:b140 "Bill Hogan" ; ; ; "http://purl.obolibrary.org/obo/gno.owl" ; - _:b142 ; + _:b143 ; ; ; ; . -_:b141 "git clone https://github.com/glygen-glycan-data/GNOme.git" . +_:b142 "git clone https://github.com/glygen-glycan-data/GNOme.git" . "GNOme Glycan Structure Browser" ; @@ -2448,7 +2470,7 @@ _:b141 "git clone https://gi "GNOme Glycan Composition Browser" ; "Composition Browser" . -_:b142 "Nathan Edwards" ; +_:b143 "Nathan Edwards" ; "nje5@georgetown.edu" . @@ -2471,19 +2493,27 @@ _:b142 "Nathan Edwards" ; "ancestry" ; "https://github.com/EBISPOT/ancestro/issues" ; "http://purl.obolibrary.org/obo/hancestro.owl" ; - _:b143 ; + _:b144 ; ; + ; . -_:b143 "Danielle Welter" ; - "dwelter@ebi.ac.uk" . +_:b144 "Danielle Welter" ; + "danielle.welter@uni.lu" . + "The full version of HANCESTRO in OWL format" ; + "HANCESTRO" ; "http://purl.obolibrary.org/obo/hancestro.owl" . + + "Version of HANCESTRO with BFO upper hierarchy for easier integration with other ontologies" ; + "HANCESTRO BFO" ; + "http://purl.obolibrary.org/obo/hancestro_bfo.owl" . + "active" ; - _:b144 ; + _:b145 ; ; "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)" ; "Hymenoptera Anatomy Ontology" ; @@ -2491,18 +2521,18 @@ _:b143 "Danielle Welter" ; "anatomy" ; "https://github.com/hymao/hao/issues" ; "http://purl.obolibrary.org/obo/hao.owl" ; - _:b145 ; + _:b146 ; ; ; ; . -_:b144 "git clone https://github.com/hymao/hao.git" . +_:b145 "git clone https://github.com/hymao/hao.git" . "Hymenoptera" . -_:b145 "Matt Yoder" ; +_:b146 "Matt Yoder" ; "diapriid@gmail.com" . @@ -2516,43 +2546,44 @@ _:b145 "Matt Yoder" ; "active" ; - _:b146 ; + _:b147 ; "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology." ; "Homology Ontology" ; - ; + ; "https://github.com/BgeeDB/homology-ontology/issues" ; "http://purl.obolibrary.org/obo/hom.owl" ; - _:b147 ; + _:b148 ; ; . -_:b146 "git clone https://github.com/BgeeDB/homology-ontology.git" ; +_:b147 "git clone https://github.com/BgeeDB/homology-ontology.git" ; "vcs" . -_:b147 "Frederic Bastian" ; +_:b148 "Frederic Bastian" ; "bgee@sib.swiss" . "http://purl.obolibrary.org/obo/hom.owl" . + "HsapDv" ; "active" ; - _:b148 ; + _:b149 ; "Life cycle stages for Human" ; "Human Developmental Stages" ; ; "https://github.com/obophenotype/developmental-stage-ontologies/issues" ; "http://purl.obolibrary.org/obo/hsapdv.owl" ; - _:b149 ; + _:b150 ; ; ; ; . -_:b148 "obo2owl" ; +_:b149 "obo2owl" ; "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/hsapdv/hsapdv.obo"^^ . -_:b149 "bgee" ; +_:b150 "bgee" ; "bgee@sib.swiss" . @@ -2561,6 +2592,31 @@ _:b149 "bgee" ; "http://purl.obolibrary.org/obo/hsapdv.obo" . + + "active" ; + ; + ; + ; + ; + ; + "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance." ; + "Health Surveillance Ontology" ; + ; + "health" ; + "https://github.com/SVA-SE/HSO/issues/" ; + "http://purl.obolibrary.org/obo/hso.owl" ; + _:b151 ; + ; + ; + . + +_:b151 "Fernanda Dorea" ; + "fernanda.dorea@sva.se" . + + + "http://purl.obolibrary.org/obo/hso.owl" ; + . + "active" ; "https://raw.githubusercontent.com/aellenhicks/htn_owl/master/htn.owl"^^ ; @@ -2569,11 +2625,11 @@ _:b149 "bgee" ; ; "https://github.com/aellenhicks/htn_owl/issues" ; "http://purl.obolibrary.org/obo/htn.owl" ; - _:b150 ; + _:b152 ; ; . -_:b150 "Amanda Hicks" ; +_:b152 "Amanda Hicks" ; "aellenhicks@gmail.com" . @@ -2602,9 +2658,9 @@ _:b35 "Jie Zheng" ; "An ontology based on a theory of document acts describing what people can do with documents" ; "ontology of document acts" ; "http://purl.obolibrary.org/obo/iao/d-acts.owl" ; - _:b151 . + _:b153 . -_:b151 "Mathias Brochhausen" ; +_:b153 "Mathias Brochhausen" ; "mbrochhausen@gmail.com" . @@ -2614,11 +2670,11 @@ _:b151 "Mathias Brochhausen" ; ; "https://github.com/ontoice/ICEO/issues" ; "http://purl.obolibrary.org/obo/iceo.owl" ; - _:b152 ; + _:b154 ; ; . -_:b152 "Meng LIU" ; +_:b154 "Meng LIU" ; "liumeng94@sjtu.edu.cn" . @@ -2631,11 +2687,11 @@ _:b152 "Meng LIU" ; ; "https://github.com/ICO-ontology/ICO/issues" ; "http://purl.obolibrary.org/obo/ico.owl" ; - _:b153 ; + _:b155 ; ; . -_:b153 "Yongqun Oliver He" ; +_:b155 "Yongqun Oliver He" ; "yongqunh@med.umich.edu" . @@ -2643,7 +2699,7 @@ _:b153 "Yongqun Oliver He" ; "active" ; - _:b154 ; + _:b156 ; ; "A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain." ; "Infectious Disease Ontology" ; @@ -2651,14 +2707,14 @@ _:b153 "Yongqun Oliver He" ; "health" ; "https://github.com/infectious-disease-ontology/infectious-disease-ontology/issues" ; "http://purl.obolibrary.org/obo/ido.owl" ; - _:b155 ; + _:b157 ; ; . -_:b154 "owl2obo" ; +_:b156 "owl2obo" ; "http://purl.obolibrary.org/obo/ido.owl"^^ . -_:b155 "Lindsay Cowell" ; +_:b157 "Lindsay Cowell" ; "Lindsay.Cowell@utsouthwestern.edu" . @@ -2671,11 +2727,11 @@ _:b155 "Lindsay Cowell" ; ; "https://github.com/INO-ontology/ino/issues" ; "http://purl.obolibrary.org/obo/ino.owl" ; - _:b156 ; + _:b158 ; ; . -_:b156 "Yongqun Oliver He" ; +_:b158 "Yongqun Oliver He" ; "yongqunh@med.umich.edu" . @@ -2696,7 +2752,7 @@ _:b156 "Yongqun Oliver He" ; "clinical documentation" ; "https://github.com/OpenLHS/LABO/issues" ; "http://purl.obolibrary.org/obo/labo.owl" ; - _:b157 ; + _:b159 ; ; . @@ -2709,7 +2765,7 @@ _:b156 "Yongqun Oliver He" ; "medicine" ; "https://github.com/OGMS/ogms/issues" ; "http://purl.obolibrary.org/obo/ogms.owl" ; - _:b158 ; + _:b160 ; ; . @@ -2721,13 +2777,13 @@ _:b156 "Yongqun Oliver He" ; "health" ; "https://github.com/OMIABIS/omiabis-dev/issues" ; "http://purl.obolibrary.org/obo/omiabis.owl" ; - _:b159 ; + _:b161 ; ; . "active" ; - _:b160 ; + _:b162 ; ; "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations." ; "Ontology of Medically Related Social Entities" ; @@ -2735,7 +2791,7 @@ _:b156 "Yongqun Oliver He" ; "medicine" ; "https://github.com/ufbmi/OMRSE/issues" ; "http://purl.obolibrary.org/obo/omrse.owl" ; - _:b161 ; + _:b163 ; ; . @@ -2747,11 +2803,11 @@ _:b156 "Yongqun Oliver He" ; "https://github.com/OPMI/opmi/issues" ; "http://groups.google.com/group/opmi-discuss" ; "http://purl.obolibrary.org/obo/opmi.owl" ; - _:b162 ; + _:b164 ; ; . -_:b157 "Paul Fabry" ; +_:b159 "Paul Fabry" ; "paul.fabry@usherbrooke.ca" . @@ -2759,7 +2815,7 @@ _:b157 "Paul Fabry" ; "active" ; - _:b163 ; + _:b165 ; ; "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)." ; "Mouse adult gross anatomy" ; @@ -2767,16 +2823,16 @@ _:b157 "Paul Fabry" ; "anatomy" ; "https://github.com/obophenotype/mouse-anatomy-ontology/issues" ; "http://purl.obolibrary.org/obo/ma.owl" ; - _:b164 ; + _:b166 ; ; ; ; . -_:b163 "obo2owl" ; +_:b165 "obo2owl" ; "ftp://ftp.informatics.jax.org/pub/reports/adult_mouse_anatomy.obo"^^ . -_:b164 "Terry Hayamizu" ; +_:b166 "Terry Hayamizu" ; "Terry.Hayamizu@jax.org" . @@ -2785,9 +2841,9 @@ _:b164 "Terry Hayamizu" ; "http://purl.obolibrary.org/obo/ma.obo" . -_:b102 "git clone https://github.com/monarch-initiative/MAxO.git" . +_:b103 "git clone https://github.com/monarch-initiative/MAxO.git" . -_:b103 "Leigh Carmody" ; +_:b104 "Leigh Carmody" ; "Leigh.Carmody@jax.org" . @@ -2824,14 +2880,14 @@ _:b103 "Leigh Carmody" ; ; ; ; - _:b165 ; + _:b167 ; "Microbial Conditions Ontology is an ontology..." ; "Microbial Conditions Ontology" ; ; "experimental conditions" ; "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology/issues" ; "http://purl.obolibrary.org/obo/mco.owl" ; - _:b166 ; + _:b168 ; ; ; . @@ -2844,7 +2900,7 @@ _:b103 "Leigh Carmody" ; "phenotype" ; "https://github.com/carrineblank/MicrO/issues" ; "http://purl.obolibrary.org/obo/micro.owl" ; - _:b167 ; + _:b169 ; ; . @@ -2855,28 +2911,28 @@ _:b103 "Leigh Carmody" ; ; "https://github.com/OmniSearch/omit/issues" ; "http://purl.obolibrary.org/obo/omit.owl" ; - _:b168 ; + _:b170 ; ; ; . "active" ; - _:b169 ; + _:b171 ; "An ontology of phenotypes covering microbes" ; "Ontology of Microbial Phenotypes" ; ; "phenotype" ; "https://github.com/microbialphenotypes/OMP-ontology/issues" ; "http://purl.obolibrary.org/obo/omp.owl" ; - _:b170 ; + _:b172 ; ; ; . "active" ; - _:b171 ; + _:b173 ; ; "Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN" ; "Zebrafish Experimental Conditions Ontology" ; @@ -2884,15 +2940,15 @@ _:b103 "Leigh Carmody" ; "environment" ; "https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues" ; "http://purl.obolibrary.org/obo/zeco.owl" ; - _:b172 ; + _:b174 ; ; ; ; . -_:b165 "git clone https://github.com/microbial-conditions-ontology/microbial-conditions-ontology.git" . +_:b167 "git clone https://github.com/microbial-conditions-ontology/microbial-conditions-ontology.git" . -_:b166 "Citlalli Mejía-Almonte" ; +_:b168 "Citlalli Mejía-Almonte" ; "citlalli.mejiaalmonte@gmail.com" . @@ -2903,21 +2959,21 @@ _:b166 "Citlalli Mejía-Almonte" "active" ; - _:b173 ; + _:b175 ; "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning." ; "Mental Functioning Ontology" ; ; "health" ; "https://github.com/jannahastings/mental-functioning-ontology/issues" ; "http://purl.obolibrary.org/obo/mf.owl" ; - _:b174 ; + _:b176 ; ; . -_:b173 "owl2obo" ; +_:b175 "owl2obo" ; "http://purl.obolibrary.org/obo/mf.owl"^^ . -_:b174 "Janna Hastings" ; +_:b176 "Janna Hastings" ; "janna.hastings@gmail.com" . @@ -2933,7 +2989,7 @@ _:b174 "Janna Hastings" ; "anatomy" ; "https://github.com/RDruzinsky/feedontology/issues" ; "http://purl.obolibrary.org/obo/mfmo.owl" ; - _:b175 ; + _:b177 ; ; . @@ -2941,7 +2997,7 @@ _:b174 "Janna Hastings" ; "Mammalian" ; "Mammalia" . -_:b175 "Robert Druzinsky" ; +_:b177 "Robert Druzinsky" ; "druzinsk@uic.edu" . @@ -2949,21 +3005,21 @@ _:b175 "Robert Druzinsky" ; "active" ; - _:b176 ; + _:b178 ; "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings." ; "Emotion Ontology" ; ; "health" ; "https://github.com/jannahastings/emotion-ontology/issues" ; "http://purl.obolibrary.org/obo/mfoem.owl" ; - _:b177 ; + _:b179 ; ; . -_:b176 "owl2obo" ; +_:b178 "owl2obo" ; "http://purl.obolibrary.org/obo/mfoem.owl"^^ . -_:b177 "Janna Hastings" ; +_:b179 "Janna Hastings" ; "janna.hastings@gmail.com" . @@ -2977,11 +3033,11 @@ _:b177 "Janna Hastings" ; "health" ; "https://github.com/jannahastings/mental-functioning-ontology/issues" ; "http://purl.obolibrary.org/obo/mfomd.owl" ; - _:b178 ; + _:b180 ; ; . -_:b178 "Janna Hastings" ; +_:b180 "Janna Hastings" ; "janna.hastings@gmail.com" . @@ -2989,23 +3045,23 @@ _:b178 "Janna Hastings" ; "active" ; - _:b179 ; + _:b181 ; "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions." ; "Molecular Interactions Controlled Vocabulary" ; ; "experiments" ; "https://github.com/HUPO-PSI/psi-mi-CV/issues" ; "http://purl.obolibrary.org/obo/mi.owl" ; - _:b180 ; + _:b182 ; ; ; ; . -_:b179 "obo2owl" ; +_:b181 "obo2owl" ; "https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo"^^ . -_:b180 "Pablo Porras Millán" ; +_:b182 "Pablo Porras Millán" ; "pporras@ebi.ac.uk" . @@ -3023,17 +3079,17 @@ _:b180 "Pablo Porras Millán" ; "http://groups.google.com/group/miapa-discuss" ; "https://fairsharing.org/FAIRsharing.ca48xs" ; "http://purl.obolibrary.org/obo/miapa.owl" ; - _:b181 ; + _:b183 ; ; . -_:b181 "Hilmar Lapp" ; +_:b183 "Hilmar Lapp" ; "hilmar.lapp@duke.edu" . "http://purl.obolibrary.org/obo/miapa.owl" . -_:b167 "Carrine Blank" ; +_:b169 "Carrine Blank" ; "carrine.blank@umontana.edu" . @@ -3041,7 +3097,7 @@ _:b167 "Carrine Blank" ; "active" ; - _:b182 ; + _:b184 ; "A representation of the variety of methods used to make clinical and phenotype measurements. " ; "Measurement method ontology" ; ; @@ -3051,20 +3107,20 @@ _:b167 "Carrine Blank" ; "https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues" ; ; "http://purl.obolibrary.org/obo/mmo.owl" ; - _:b183 ; + _:b185 ; ; ; ; . -_:b182 "obo2owl" ; +_:b184 "obo2owl" ; "ftp://ftp.rgd.mcw.edu/pub/ontology/measurement_method/measurement_method.obo"^^ . "RGD Ontology Browser" ; "RGD" . -_:b183 "Jennifer Smith" ; +_:b185 "Jennifer Smith" ; "jrsmith@mcw.edu" . @@ -3074,23 +3130,24 @@ _:b183 "Jennifer Smith" ; "http://purl.obolibrary.org/obo/mmo.obo" . + "MmusDv" ; "active" ; - _:b184 ; + _:b186 ; "Life cycle stages for Mus Musculus" ; "Mouse Developmental Stages" ; ; "https://github.com/obophenotype/developmental-stage-ontologies/issues" ; "http://purl.obolibrary.org/obo/mmusdv.owl" ; - _:b185 ; + _:b187 ; ; ; ; . -_:b184 "obo2owl" ; +_:b186 "obo2owl" ; "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/mmusdv/mmusdv.obo"^^ . -_:b185 "bgee" ; +_:b187 "bgee" ; "bgee@sib.swiss" . @@ -3101,26 +3158,38 @@ _:b185 "bgee" ; "active" ; - _:b186 ; + _:b188 ; "PSI-MOD is an ontology consisting of terms that describe protein chemical modifications" ; "Protein modification" ; ; + ; "proteins" ; "https://github.com/HUPO-PSI/psi-mod-CV/issues" ; "http://purl.obolibrary.org/obo/mod.owl" ; - _:b187 ; + _:b189 ; ; + ; . -_:b186 "obo2owl" ; - "https://raw.githubusercontent.com/MICommunity/psidev/master/psi/mod/data/PSI-MOD.obo"^^ . +_:b188 "obo2owl" ; + "https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo"^^ . + + + "The PSI-MOD community standard for representation of protein modification data" . -_:b187 "Pierre-Alain Binz" ; +_:b189 "Pierre-Alain Binz" ; "pierre-alain.binz@chuv.ch" . + "PSI-MOD Ontology, OWL format" ; + "PSI-MOD.owl" ; "http://purl.obolibrary.org/obo/mod.owl" . + + "PSI-MOD Ontology, OBO format" ; + "PSI-MOD.obo" ; + "http://purl.obolibrary.org/obo/mod.obo" . + "active" ; ; @@ -3133,7 +3202,7 @@ _:b187 "Pierre-Alain Binz" ; "Mondo" ; ; "http://purl.obolibrary.org/obo/mondo.owl" ; - _:b188 ; + _:b190 ; ; ; ; @@ -3143,7 +3212,7 @@ _:b187 "Pierre-Alain Binz" ; "Monarch Initiative Disease Browser" ; "Monarch" . -_:b188 "Nicole Vasilevsky" ; +_:b190 "Nicole Vasilevsky" ; "vasilevs@ohsu.edu" . @@ -3166,21 +3235,21 @@ _:b188 "Nicole Vasilevsky" ; "active" ; - _:b189 ; + _:b191 ; "Processes at the molecular level" ; "Molecular Process Ontology" ; ; "https://github.com/rsc-ontologies/rxno/issues" ; "chemistry-ontologies@googlegroups.com" ; "http://purl.obolibrary.org/obo/mop.owl" ; - _:b190 ; + _:b192 ; ; . -_:b189 "owl2obo" ; +_:b191 "owl2obo" ; "https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.owl"^^ . -_:b190 "Colin Batchelor" ; +_:b192 "Colin Batchelor" ; "batchelorc@rsc.org" . @@ -3230,7 +3299,7 @@ _:b57 "JAX phenotype list" ; "active" ; - _:b191 ; + _:b193 ; ; "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes" ; "Mouse pathology ontology" ; @@ -3238,14 +3307,14 @@ _:b57 "JAX phenotype list" ; "health" ; "https://github.com/PaulNSchofield/mpath/issues" ; "http://purl.obolibrary.org/obo/mpath.owl" ; - _:b192 ; + _:b194 ; ; . -_:b191 "obo2owl" ; +_:b193 "obo2owl" ; "https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo"^^ . -_:b192 "Paul Schofield" ; +_:b194 "Paul Schofield" ; "pns12@hermes.cam.ac.uk" . @@ -3259,11 +3328,11 @@ _:b192 "Paul Schofield" ; "health" ; "https://github.com/MPIO-Developers/MPIO/issues" ; "http://purl.obolibrary.org/obo/mpio.owl" ; - _:b193 ; + _:b195 ; ; . -_:b193 "Mathias Brochhausen" ; +_:b195 "Mathias Brochhausen" ; "mbrochhausen@uams.edu" . @@ -3277,24 +3346,61 @@ _:b193 "Mathias Brochhausen" ; "Major Histocompatibility Complex" ; "https://github.com/IEDB/MRO/issues" ; "http://purl.obolibrary.org/obo/mro.owl" ; - _:b194 ; + _:b196 ; ; . -_:b194 "Bjoern Peters" ; +_:b196 "Bjoern Peters" ; "bpeters@lji.org" . "http://purl.obolibrary.org/obo/mro.owl" . -_:b104 "owl2obo" ; + + "active" ; + "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master" ; + ; + ; + _:b197 ; + "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry." ; + "Mass spectrometry ontology" ; + ; + ; + "MS experiments" ; + "http://oboedit.org" ; + "https://github.com/HUPO-PSI/psi-ms-CV/issues" ; + "psidev-ms-vocab@lists.sourceforge.net" ; + "MS" ; + "http://purl.obolibrary.org/obo/ms.owl" ; + _:b198 ; + ; + ; + ; + . + +_:b197 "obo2owl" ; + "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"^^ . + + + "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary." . + +_:b198 "Gerhard Mayer" ; + "gerhard.mayer@rub.de" . + + + "http://purl.obolibrary.org/obo/ms.obo" . + + + "http://purl.obolibrary.org/obo/ms.owl" . + +_:b105 "owl2obo" ; "https://raw.githubusercontent.com/obo-behavior/behavior-ontology/master/nbo.owl"^^ . "BioPortal Ontology Browser" ; "BioPortal" . -_:b105 "George Gkoutos" ; +_:b106 "George Gkoutos" ; "g.gkoutos@bham.ac.uk" . @@ -3328,7 +3434,7 @@ _:b11 "Frederic Bastian" ; "http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl" ; . -_:b106 "Melissa Haendel" ; +_:b107 "Melissa Haendel" ; "haendel@ohsu.edu" . @@ -3352,7 +3458,7 @@ _:b106 "Melissa Haendel" ; "active" ; - _:b195 ; + _:b199 ; "An ontology for non-coding RNA, both of biological origin, and engineered." ; "Non-Coding RNA Ontology" ; ; @@ -3360,14 +3466,14 @@ _:b106 "Melissa Haendel" ; "https://github.com/OmniSearch/NCRO-Ontology-Files/issues" ; "ncro-devel@googlegroups.com, ncro-discuss@googlegroups.com" ; "http://purl.obolibrary.org/obo/ncro.owl" ; - _:b196 ; + _:b200 ; ; . -_:b195 "owl2obo" ; +_:b199 "owl2obo" ; "http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl"^^ . -_:b196 "Jingshan Huang" ; +_:b200 "Jingshan Huang" ; "huang@southalabama.edu" . @@ -3376,7 +3482,7 @@ _:b196 "Jingshan Huang" ; "active" ; - _:b197 ; + _:b201 ; "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature." ; "NOMEN - A nomenclatural ontology for biological names" ; ; @@ -3388,13 +3494,13 @@ _:b196 "Jingshan Huang" ; ; "NOMEN" ; "http://purl.obolibrary.org/obo/nomen.owl" ; - _:b198 ; + _:b202 ; ; . -_:b197 "git clone https://github.com/SpeciesFileGroup/nomen.git" . +_:b201 "git clone https://github.com/SpeciesFileGroup/nomen.git" . -_:b198 "Matt Yoder" ; +_:b202 "Matt Yoder" ; "diapriid@gmail.com" . @@ -3405,21 +3511,21 @@ _:b198 "Matt Yoder" ; "active" ; - _:b199 ; + _:b203 ; "A biomedical ontology in the domain of adverse events" ; "Ontology of Adverse Events" ; ; "adverse events, health" ; "https://github.com/OAE-ontology/OAE/issues" ; "http://purl.obolibrary.org/obo/oae.owl" ; - _:b200 ; + _:b204 ; ; . -_:b199 "owl2obo" ; +_:b203 "owl2obo" ; "https://raw.githubusercontent.com/OAE-ontology/OAE/master/src/oae_merged.owl"^^ . -_:b200 "Yongqunh He" ; +_:b204 "Yongqunh He" ; "yongqunh@med.umich.edu" . @@ -3433,20 +3539,20 @@ _:b200 "Yongqunh He" ; "anatomy" ; "https://github.com/aszool/oarcs/issues" ; "http://purl.obolibrary.org/obo/oarcs.owl" ; - _:b201 ; + _:b205 ; ; . -_:b201 "Matt Yoder" ; +_:b205 "Matt Yoder" ; "mjyoder@illinois.edu" . "http://purl.obolibrary.org/obo/oarcs.owl" . -_:b130 "git clone https://github.com/obophenotype/bio-attribute-ontology.git" ; +_:b131 "git clone https://github.com/obophenotype/bio-attribute-ontology.git" ; "vcs" . -_:b131 "Chris Mungall" ; +_:b132 "Chris Mungall" ; "cjmungall@lbl.gov" . @@ -3466,11 +3572,11 @@ _:b131 "Chris Mungall" ; "statistics" ; "https://github.com/obcs/obcs/issues" ; "http://purl.obolibrary.org/obo/obcs.owl" ; - _:b202 ; + _:b206 ; ; . -_:b202 "Jie Zheng" ; +_:b206 "Jie Zheng" ; "jiezheng@pennmedicine.upenn.edu" . @@ -3484,11 +3590,11 @@ _:b202 "Jie Zheng" ; "biobanking, specimens, bio-repository, biocuration" ; "https://github.com/biobanking/biobanking/issues" ; "http://purl.obolibrary.org/obo/obib.owl" ; - _:b203 ; + _:b207 ; ; . -_:b203 "Jie Zheng" ; +_:b207 "Jie Zheng" ; "jiezheng@pennmedicine.upenn.edu" . @@ -3501,17 +3607,17 @@ _:b203 "Jie Zheng" ; ; "https://bitbucket.org/hegroup/ogg/issues/" ; "http://purl.obolibrary.org/obo/ogg.owl" ; - _:b204 ; + _:b208 ; ; . -_:b204 "Yongqun Oliver He" ; +_:b208 "Yongqun Oliver He" ; "yongqunh@med.umich.edu" . "http://purl.obolibrary.org/obo/ogg.owl" . -_:b158 "Brian Aevermann" ; +_:b160 "Brian Aevermann" ; "baeverma@jcvi.org" . @@ -3524,11 +3630,11 @@ _:b158 "Brian Aevermann" ; ; "https://github.com/linikujp/OGSF/issues" ; "http://purl.obolibrary.org/obo/ogsf.owl" ; - _:b205 ; + _:b209 ; ; . -_:b205 "Asiyah Yu Lin" ; +_:b209 "Asiyah Yu Lin" ; "linikujp@gmail.com" . @@ -3536,22 +3642,22 @@ _:b205 "Asiyah Yu Lin" ; "active" ; - _:b206 ; + _:b210 ; "The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records." ; "The Oral Health and Disease Ontology" ; ; "health" ; "https://purl.obolibrary.org/obo/ohd/issues" ; "http://purl.obolibrary.org/obo/ohd.owl" ; - _:b207 ; + _:b211 ; ; ; . -_:b206 "owl2obo" ; +_:b210 "owl2obo" ; "http://purl.obolibrary.org/obo/ohd.owl"^^ . -_:b207 "Alan Ruttenberg" ; +_:b211 "Alan Ruttenberg" ; "alanruttenberg@gmail.com" . @@ -3569,11 +3675,11 @@ _:b207 "Alan Ruttenberg" ; "https://github.com/ohmi-ontology/ohmi/issues" ; "http://groups.google.com/group/ohmi-discuss" ; "http://purl.obolibrary.org/obo/ohmi.owl" ; - _:b208 ; + _:b212 ; ; . -_:b208 "Yongqun Oliver He" ; +_:b212 "Yongqun Oliver He" ; "yongqunh@med.umich.edu" . @@ -3587,34 +3693,35 @@ _:b208 "Yongqun Oliver He" ; "https://github.com/OHPI/ohpi/issues" ; "http://groups.google.com/group/ohpi-discuss" ; "http://purl.obolibrary.org/obo/ohpi.owl" ; - _:b209 ; + _:b213 ; ; . -_:b209 "Edison Ong" ; +_:b213 "Edison Ong" ; "edong@umich.edu" . "http://purl.obolibrary.org/obo/ohpi.owl" . + "OlatDv" ; "active" ; - _:b210 ; + _:b214 ; "Life cycle stages for Medaka" ; "Medaka Developmental Stages" ; ; "https://github.com/obophenotype/developmental-stage-ontologies/issues" ; "http://purl.obolibrary.org/obo/olatdv.owl" ; - _:b211 ; + _:b215 ; ; ; ; . -_:b210 "obo2owl" ; +_:b214 "obo2owl" ; "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/olatdv/olatdv.obo"^^ . -_:b211 "bgee" ; +_:b215 "bgee" ; "bgee@sib.swiss" . @@ -3623,13 +3730,13 @@ _:b211 "bgee" ; "http://purl.obolibrary.org/obo/olatdv.owl" . -_:b159 "Mathias Brochhausen" ; +_:b161 "Mathias Brochhausen" ; "mbrochhausen@gmail.com" . "http://purl.obolibrary.org/obo/omiabis.owl" . -_:b168 "Huang, Jingshan" ; +_:b170 "Huang, Jingshan" ; "huang@southalabama.edu" . @@ -3643,20 +3750,20 @@ _:b168 "Huang, Jingshan" ; "ontology term annotation" ; "https://github.com/information-artifact-ontology/ontology-metadata/issues" ; "http://purl.obolibrary.org/obo/omo.owl" ; - _:b212 ; + _:b216 ; ; . -_:b212 "Chris Mungall" ; +_:b216 "Chris Mungall" ; "cjmungall@lbl.gov" . "http://purl.obolibrary.org/obo/omo.owl" . -_:b169 "obo2owl" ; +_:b171 "obo2owl" ; "https://raw.githubusercontent.com/microbialphenotypes/OMP-ontology-files/master/omp.obo"^^ . -_:b170 "James C. Hu" ; +_:b172 "James C. Hu" ; "jimhu@tamu.edu" . @@ -3665,10 +3772,10 @@ _:b170 "James C. Hu" ; "http://purl.obolibrary.org/obo/omp.obo" . -_:b160 "owl2obo" ; +_:b162 "owl2obo" ; "https://github.com/ufbmi/OMRSE"^^ . -_:b161 "Bill Hogan" ; +_:b163 "Bill Hogan" ; "hoganwr@gmail.com" . @@ -3686,7 +3793,7 @@ _:b161 "Bill Hogan" ; "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies/issues" ; "Ontology for Nutritional Epidemiology" ; "http://purl.obolibrary.org/obo/one.owl" ; - _:b213 ; + _:b217 ; ; ; . @@ -3702,23 +3809,24 @@ _:b161 "Bill Hogan" ; ; ; "An ontology for description of concepts in the nutritional studies domain." ; - "ONS" ; + "Ontology for Nutritional Studies" ; ; "nutrition, nutritional studies, nutrition professionals" ; "https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues" ; + "Ontology for Nutritional Studies" ; "http://purl.obolibrary.org/obo/ons.owl" ; - _:b214 ; + _:b218 ; ; ; . -_:b213 "Chen Yang" ; +_:b217 "Chen Yang" ; "chen.yang@ugent.be" . "http://purl.obolibrary.org/obo/one.owl" . -_:b214 "Francesco Vitali" ; +_:b218 "Francesco Vitali" ; "francesco.vitali@ibba.cnr.it" . @@ -3727,7 +3835,7 @@ _:b214 "Francesco Vitali" ; "active" ; - _:b215 ; + _:b219 ; "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby." ; "Obstetric and Neonatal Ontology" ; ; @@ -3736,17 +3844,17 @@ _:b214 "Francesco Vitali" ; "http://groups.google.com/group/ontoneo-discuss" ; ; "http://purl.obolibrary.org/obo/ontoneo.owl" ; - _:b216 ; + _:b220 ; ; . -_:b215 "http://purl.obolibrary.org/obo/ontoneo/ontoneo.owl"^^ . +_:b219 "http://purl.obolibrary.org/obo/ontoneo/ontoneo.owl"^^ . "BioPortal Browser" ; "BioPortal" . -_:b216 "Fernanda Farinelli" ; +_:b220 "Fernanda Farinelli" ; "fernanda.farinelli@gmail.com" . @@ -3760,11 +3868,11 @@ _:b216 "Fernanda Farinelli" ; "health" ; "https://github.com/OOSTT/OOSTT/issues" ; "http://purl.obolibrary.org/obo/oostt.owl" ; - _:b217 ; + _:b221 ; ; . -_:b217 "Mathias Brochhausen" ; +_:b221 "Mathias Brochhausen" ; "mbrochhausen@gmail.com" . @@ -3775,19 +3883,20 @@ _:b217 "Mathias Brochhausen" ; "A reference ontology for parasite life cycle stages." ; "Ontology for Parasite LifeCycle" ; ; + "life cycle stage, parasite organism" ; "https://github.com/OPL-ontology/OPL/issues" ; "http://purl.obolibrary.org/obo/opl.owl" ; - _:b218 ; + _:b222 ; ; . -_:b218 "Priti Parikh" ; +_:b222 "Priti Parikh" ; "preets79@gmail.com" . "http://purl.obolibrary.org/obo/opl.owl" . -_:b162 "Yongqun Oliver He" ; +_:b164 "Yongqun Oliver He" ; "yongqunh@med.umich.edu" . @@ -3801,11 +3910,11 @@ _:b162 "Yongqun Oliver He" ; "experiments" ; "https://github.com/safisher/ornaseq/issues" ; "http://purl.obolibrary.org/obo/ornaseq.owl" ; - _:b219 ; + _:b223 ; ; . -_:b219 "Stephen Fisher" ; +_:b223 "Stephen Fisher" ; "safisher@upenn.edu" . @@ -3818,19 +3927,19 @@ _:b219 "Stephen Fisher" ; ; "https://github.com/OVAE-Ontology/ovae/issues" ; "http://purl.obolibrary.org/obo/ovae.owl" ; - _:b220 ; + _:b224 ; ; . -_:b220 "Yongqunh He" ; +_:b224 "Yongqunh He" ; "yongqunh@med.umich.edu" . "http://purl.obolibrary.org/obo/ovae.owl" . -_:b96 "git clone https://github.com/PopulationAndCommunityOntology/pco.git" . +_:b97 "git clone https://github.com/PopulationAndCommunityOntology/pco.git" . -_:b97 "Ramona Walls" ; +_:b98 "Ramona Walls" ; "rlwalls2008@gmail.com" . @@ -3838,44 +3947,45 @@ _:b97 "Ramona Walls" ; "active" ; - _:b221 ; + _:b225 ; "An ontology to describe entities related to prescription of drugs" ; "The Prescription of Drugs Ontology" ; ; "health" ; "https://github.com/OpenLHS/PDRO/issues" ; "http://purl.obolibrary.org/obo/pdro.owl" ; - _:b222 ; + _:b226 ; ; . -_:b221 "owl2obo" ; +_:b225 "owl2obo" ; "http://purl.obolibrary.org/obo/pdro.owl"^^ . -_:b222 "Paul Fabry" ; +_:b226 "Paul Fabry" ; "paul.fabry@usherbrooke.ca" . "http://purl.obolibrary.org/obo/pdro.owl" . + "PdumDv" ; "active" ; - _:b223 ; + _:b227 ; "Life cycle stages for Platynereis dumerilii" ; "Platynereis Developmental Stages" ; ; "https://github.com/obophenotype/developmental-stage-ontologies/issues" ; "http://purl.obolibrary.org/obo/pdumdv.owl" ; - _:b224 ; + _:b228 ; ; ; ; . -_:b223 "obo2owl" ; +_:b227 "obo2owl" ; "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/pdumdv/pdumdv.obo"^^ . -_:b224 "bgee" ; +_:b228 "bgee" ; "bgee@sib.swiss" . @@ -3896,21 +4006,21 @@ _:b36 "Pankaj Jaiswal" ; "active" ; ; - _:b225 ; + _:b229 ; "PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions." ; "Pathogen Host Interaction Phenotype Ontology" ; ; "phenotype" ; "https://github.com/PHI-base/phipo/issues" ; "http://purl.obolibrary.org/obo/phipo.owl" ; - _:b226 ; + _:b230 ; ; ; . -_:b225 "git clone https://github.com/PHI-base/phipo.git" . +_:b229 "git clone https://github.com/PHI-base/phipo.git" . -_:b226 "Alayne Cuzick" ; +_:b230 "Alayne Cuzick" ; "alayne.cuzick@rothamsted.ac.uk" . @@ -3923,21 +4033,21 @@ _:b226 "Alayne Cuzick" ; "active" ; ; ; - _:b227 ; + _:b231 ; "PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes." ; "planaria-ontology" ; ; "anatomy" ; "https://github.com/obophenotype/planaria-ontology/issues" ; "http://purl.obolibrary.org/obo/plana.owl" ; - _:b228 ; + _:b232 ; ; ; . -_:b227 "git clone https://github.com/obophenotype/planaria-ontology.git" . +_:b231 "git clone https://github.com/obophenotype/planaria-ontology.git" . -_:b228 "Sofia Robb" ; +_:b232 "Sofia Robb" ; "smr@stowers.org" . @@ -3952,21 +4062,21 @@ _:b228 "Sofia Robb" ; ; ; ; - _:b229 ; + _:b233 ; "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea." ; "Planarian Phenotype Ontology" ; ; "phenotype" ; "https://github.com/obophenotype/planarian-phenotype-ontology/issues" ; "http://purl.obolibrary.org/obo/planp.owl" ; - _:b230 ; + _:b234 ; ; ; . -_:b229 "git clone https://github.com/obophenotype/planarian-phenotype-ontology.git" . +_:b233 "git clone https://github.com/obophenotype/planarian-phenotype-ontology.git" . -_:b230 "Sofia Robb" ; +_:b234 "Sofia Robb" ; "smr@stowers.org" . @@ -3979,7 +4089,7 @@ _:b230 "Sofia Robb" ; "active" ; ; ; - _:b231 ; + _:b235 ; ; "An ontology covering the anatomy of the taxon Porifera (sponges)" ; "Porifera Ontology" ; @@ -3988,12 +4098,12 @@ _:b230 "Sofia Robb" ; "anatomy" ; "https://github.com/obophenotype/porifera-ontology/issues" ; "http://purl.obolibrary.org/obo/poro.owl" ; - _:b232 ; + _:b236 ; ; ; . -_:b231 "git clone https://github.com/obophenotype/porifera-ontology.git" ; +_:b235 "git clone https://github.com/obophenotype/porifera-ontology.git" ; "vcs" . @@ -4002,7 +4112,7 @@ _:b231 "git clone https://gi "The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology" . -_:b232 "Bob Thacker" ; +_:b236 "Bob Thacker" ; "robert.thacker@stonybrook.edu" . @@ -4021,11 +4131,11 @@ _:b232 "Bob Thacker" ; "https://github.com/PlantPhenoOntology/PPO/issues" ; "ppo-discuss@googlegroups.com" ; "http://purl.obolibrary.org/obo/ppo.owl" ; - _:b233 ; + _:b237 ; ; . -_:b233 "Ramona Walls" ; +_:b237 "Ramona Walls" ; "rlwalls2008@gmail.com" . @@ -4037,14 +4147,14 @@ _:b233 "Ramona Walls" ; ; ; ; - _:b234 ; + _:b238 ; "Ontology to reproducibly study visualizations of clinical performance" ; "Performance Summary Display Ontology" ; ; "learning systems" ; "https://github.com/Display-Lab/psdo/issues" ; "http://purl.obolibrary.org/obo/psdo.owl" ; - _:b235 ; + _:b239 ; ; . @@ -4056,13 +4166,13 @@ _:b233 "Ramona Walls" ; "statistics" ; "https://github.com/ISA-tools/stato/issues" ; "http://purl.obolibrary.org/obo/stato.owl" ; - _:b236 ; + _:b240 ; ; . -_:b234 "https://github.com/Display-Lab/psdo.git" . +_:b238 "https://github.com/Display-Lab/psdo.git" . -_:b235 "Zach Landis-Lewis" ; +_:b239 "Zach Landis-Lewis" ; "zachll@umich.edu" . @@ -4071,21 +4181,21 @@ _:b235 "Zach Landis-Lewis" ; "active" ; ; - _:b237 ; + _:b241 ; "The Plant Stress Ontology describes..." ; "Plant Stress Ontology" ; ; "plant disease and abiotic stress" ; "https://github.com/Planteome/plant-stress-ontology/issues" ; "http://purl.obolibrary.org/obo/pso.owl" ; - _:b238 ; + _:b242 ; ; ; . -_:b237 "git clone https://github.com/Planteome/plant-stress-ontology.git" . +_:b241 "git clone https://github.com/Planteome/plant-stress-ontology.git" . -_:b238 "Laurel Cooper" ; +_:b242 "Laurel Cooper" ; "cooperl@science.oregonstate.edu" . @@ -4096,7 +4206,7 @@ _:b238 "Laurel Cooper" ; "active" ; - _:b239 ; + _:b243 ; "A controlled vocabulary for annotating gene products to pathways." ; "Pathway ontology" ; ; @@ -4106,13 +4216,13 @@ _:b238 "Laurel Cooper" ; "https://github.com/rat-genome-database/PW-Pathway-Ontology/issues" ; ; "http://purl.obolibrary.org/obo/pw.owl" ; - _:b240 ; + _:b244 ; ; ; ; . -_:b239 "obo2owl" ; +_:b243 "obo2owl" ; "ftp://ftp.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo"^^ . @@ -4125,7 +4235,7 @@ _:b239 "obo2owl" ; "RGD Ontology Browser" ; "RGD" . -_:b240 "G. Thomas Hayman" ; +_:b244 "G. Thomas Hayman" ; "gthayman@mcw.edu" . @@ -4179,7 +4289,7 @@ _:b13 "Chris Mungall" ; "active" ; - _:b241 ; + _:b245 ; ; "Ontology of rat strains" ; "Rat Strain Ontology" ; @@ -4188,13 +4298,13 @@ _:b13 "Chris Mungall" ; "https://github.com/rat-genome-database/RS-Rat-Strain-Ontology/issues" ; ; "http://purl.obolibrary.org/obo/rs.owl" ; - _:b242 ; + _:b246 ; ; ; ; . -_:b241 "obo2owl" ; +_:b245 "obo2owl" ; "ftp://ftp.rgd.mcw.edu/pub/ontology/rat_strain/rat_strain.obo"^^ . @@ -4207,7 +4317,7 @@ _:b241 "obo2owl" ; "RGD Ontology Browser" ; "RGD" . -_:b242 "Shur-Jen Wang" ; +_:b246 "Shur-Jen Wang" ; "sjwang@mcw.edu" . @@ -4218,21 +4328,21 @@ _:b242 "Shur-Jen Wang" ; "active" ; - _:b243 ; + _:b247 ; "Connects organic name reactions to their roles in an organic synthesis and to processes in MOP" ; "Name Reaction Ontology" ; ; "https://github.com/rsc-ontologies/rxno/issues" ; "chemistry-ontologies@googlegroups.com" ; "http://purl.obolibrary.org/obo/rxno.owl" ; - _:b244 ; + _:b248 ; ; . -_:b243 "owl2obo" ; +_:b247 "owl2obo" ; "https://raw.githubusercontent.com/rsc-ontologies/rxno/master/rxno.owl"^^ . -_:b244 "Colin Batchelor" ; +_:b248 "Colin Batchelor" ; "batchelorc@rsc.org" . @@ -4241,20 +4351,20 @@ _:b244 "Colin Batchelor" ; "active" ; - _:b245 ; + _:b249 ; "An ontology for representing the provenance of scientific claims and the evidence that supports them." ; "Scientific Evidence and Provenance Information Ontology" ; ; "scientific claims, evidence" ; "https://github.com/monarch-initiative/SEPIO-ontology/issues" ; "http://purl.obolibrary.org/obo/sepio.owl" ; - _:b246 ; + _:b250 ; ; . -_:b245 "git clone https://github.com/monarch-initiative/SEPIO-ontology.git" . +_:b249 "git clone https://github.com/monarch-initiative/SEPIO-ontology.git" . -_:b246 "Matthew Brush" ; +_:b250 "Matthew Brush" ; "mhb120@gmail.com" . @@ -4263,7 +4373,7 @@ _:b246 "Matthew Brush" ; "active" ; - _:b247 ; + _:b251 ; "A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases." ; "Sequence types and features ontology" ; ; @@ -4273,13 +4383,13 @@ _:b246 "Matthew Brush" ; "https://github.com/The-Sequence-Ontology/SO-Ontologies/issues" ; "https://sourceforge.net/p/song/mailman/song-devel/" ; "http://purl.obolibrary.org/obo/so.owl" ; - _:b248 ; + _:b252 ; ; ; ; . -_:b247 "obo2owl" ; +_:b251 "obo2owl" ; "https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so.obo"^^ . @@ -4288,7 +4398,7 @@ _:b247 "obo2owl" ; "Evolution of the Sequence Ontology terms and relationships." . -_:b248 "Karen Eilbeck" ; +_:b252 "Karen Eilbeck" ; "keilbeck@genetics.utah.edu" . @@ -4299,7 +4409,7 @@ _:b248 "Karen Eilbeck" ; "active" ; - _:b249 ; + _:b253 ; ; "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow)." ; "Spider Ontology" ; @@ -4307,47 +4417,69 @@ _:b248 "Karen Eilbeck" ; "anatomy" ; "https://github.com/obophenotype/spider-ontology/issues" ; "http://purl.obolibrary.org/obo/spd.owl" ; - _:b250 ; + _:b254 ; ; . -_:b249 "obo2owl" ; +_:b253 "obo2owl" ; "https://raw.githubusercontent.com/obophenotype/spider-ontology/master/spider_comparative_biology.obo"^^ . "spiders" . -_:b250 "Martin Ramirez" ; +_:b254 "Martin Ramirez" ; "ramirez@macn.gov.ar" . "http://purl.obolibrary.org/obo/spd.owl" . -_:b236 "Alejandra Gonzalez-Beltran" ; +_:b240 "Alejandra Gonzalez-Beltran" ; "alejandra.gonzalez.beltran@gmail.com" . "http://purl.obolibrary.org/obo/stato.owl" . - + "active" ; - _:b251 ; - ; - "An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease." ; - "Symptom Ontology" ; - ; - "disease" ; - "https://github.com/DiseaseOntology/SymptomOntology/issues" ; - "http://purl.obolibrary.org/obo/symp.owl" ; - _:b252 ; + _:b255 ; + "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community." ; + "Software ontology" ; + ; + "software" ; + "https://github.com/allysonlister/swo/issues" ; + "http://purl.obolibrary.org/obo/swo.owl" ; + _:b256 ; + ; + . + +_:b255 "owl2obo" ; + "https://raw.githubusercontent.com/allysonlister/swo/master/release/swo_inferred.owl"^^ . + +_:b256 "Allyson Lister" ; + "allyson.lister@oerc.ox.ac.uk" . + + + "http://purl.obolibrary.org/obo/swo.owl" . + + + "active" ; + _:b257 ; + ; + "An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease." ; + "Symptom Ontology" ; + ; + "disease" ; + "https://github.com/DiseaseOntology/SymptomOntology/issues" ; + "http://purl.obolibrary.org/obo/symp.owl" ; + _:b258 ; ; ; . -_:b251 "obo2owl" ; +_:b257 "obo2owl" ; "https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/symp.obo"^^ . -_:b252 "Lynn Schriml" ; +_:b258 "Lynn Schriml" ; "lynn.schriml@gmail.com" . @@ -4358,21 +4490,21 @@ _:b252 "Lynn Schriml" ; "active" ; - _:b253 ; + _:b259 ; "A vocabulary of taxonomic ranks (species, family, phylum, etc)" ; "Taxonomic rank vocabulary" ; ; "taxonomy" ; "https://github.com/phenoscape/taxrank/issues" ; "http://purl.obolibrary.org/obo/taxrank.owl" ; - _:b254 ; + _:b260 ; ; ; . -_:b253 "git clone https://github.com/phenoscape/taxrank.git" . +_:b259 "git clone https://github.com/phenoscape/taxrank.git" . -_:b254 "Jim Balhoff" ; +_:b260 "Jim Balhoff" ; "balhoff@renci.org" . @@ -4383,7 +4515,7 @@ _:b254 "Jim Balhoff" ; "active" ; - _:b255 ; + _:b261 ; ; "A controlled vocabulary of describe phenotypic traits in plants." ; "Plant Trait Ontology" ; @@ -4393,20 +4525,20 @@ _:b254 "Jim Balhoff" ; "https://github.com/Planteome/plant-trait-ontology/issues" ; ; "http://purl.obolibrary.org/obo/to.owl" ; - _:b256 ; + _:b262 ; ; ; ; . -_:b255 "git clone https://github.com/Planteome/plant-trait-ontology.git" ; +_:b261 "git clone https://github.com/Planteome/plant-trait-ontology.git" ; "vcs" . "Planteome browser" ; "Planteome" . -_:b256 "Pankaj Jaiswal" ; +_:b262 "Pankaj Jaiswal" ; "jaiswalp@science.oregonstate.edu" . @@ -4417,22 +4549,22 @@ _:b256 "Pankaj Jaiswal" ; "active" ; - _:b257 ; + _:b263 ; "An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host." ; "Pathogen Transmission Ontology" ; ; "disease" ; "https://github.com/DiseaseOntology/PathogenTransmissionOntology/issues" ; "http://purl.obolibrary.org/obo/trans.owl" ; - _:b258 ; + _:b264 ; ; ; . -_:b257 "obo2owl" ; +_:b263 "obo2owl" ; "https://raw.githubusercontent.com/DiseaseOntology/PathogenTransmissionOntology/master/src/ontology/trans.obo"^^ . -_:b258 "Lynn Schriml" ; +_:b264 "Lynn Schriml" ; "lynn.schriml@gmail.com" . @@ -4450,7 +4582,7 @@ _:b258 "Lynn Schriml" ; "taxonomy" ; "https://github.com/phenoscape/teleost-taxonomy-ontology/issues" ; "http://purl.obolibrary.org/obo/tto.owl" ; - _:b259 ; + _:b265 ; ; ; . @@ -4458,7 +4590,7 @@ _:b258 "Lynn Schriml" ; "Teleostei" . -_:b259 "Jim Balhoff" ; +_:b265 "Jim Balhoff" ; "balhoff@renci.org" . @@ -4564,22 +4696,22 @@ _:b33 "George Gkoutos" ; "active" ; - _:b260 ; + _:b266 ; "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology." ; "Unified phenotype ontology (uPheno)" ; ; "https://github.com/obophenotype/upheno/issues" ; "https://groups.google.com/forum/#!forum/phenotype-ontologies-editors" ; "http://purl.obolibrary.org/obo/upheno.owl" ; - _:b261 ; + _:b267 ; ; ; . -_:b260 "archive" ; +_:b266 "archive" ; "http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip"^^ . -_:b261 "Nicole Vasilevsky" ; +_:b267 "Nicole Vasilevsky" ; "vasilevs@ohsu.edu" . @@ -4590,25 +4722,46 @@ _:b261 "Nicole Vasilevsky" ; "active" ; - _:b262 ; + _:b268 ; "VO is a biomedical ontology in the domain of vaccine and vaccination." ; "Vaccine Ontology" ; ; "health" ; "https://github.com/vaccineontology/VO/issues" ; "http://purl.obolibrary.org/obo/vo.owl" ; - _:b263 ; + _:b269 ; ; . -_:b262 "https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl"^^ . +_:b268 "https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl"^^ . -_:b263 "Yongqunh He" ; +_:b269 "Yongqunh He" ; "yongqunh@med.umich.edu" . "http://purl.obolibrary.org/obo/vo.owl" . + + "active" ; + _:b270 ; + "An ontology of traits covering vertebrates" ; + "Vertebrate trait ontology" ; + ; + "https://github.com/AnimalGenome/vertebrate-trait-ontology/issues" ; + "http://purl.obolibrary.org/obo/vt.owl" ; + _:b271 ; + ; + . + +_:b270 "svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt" ; + "vcs" . + +_:b271 "Carissa Park" ; + "caripark@iastate.edu" . + + + "http://purl.obolibrary.org/obo/vt.owl" . + "active" ; "Comprehensive hierarchy of extinct and extant vertebrate taxa." ; @@ -4616,12 +4769,12 @@ _:b263 "Yongqunh He" ; ; "https://github.com/phenoscape/vertebrate-taxonomy-ontology/issues" ; "http://purl.obolibrary.org/obo/vto.owl" ; - _:b264 ; + _:b272 ; ; ; . -_:b264 "Jim Balhoff" ; +_:b272 "Jim Balhoff" ; "balhoff@renci.org" . @@ -4633,7 +4786,7 @@ _:b264 "Jim Balhoff" ; "WBbt" ; "active" ; - _:b265 ; + _:b273 ; ; "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans." ; "C. elegans Gross Anatomy Ontology" ; @@ -4642,12 +4795,12 @@ _:b264 "Jim Balhoff" ; "anatomy" ; "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/issues" ; "http://purl.obolibrary.org/obo/wbbt.owl" ; - _:b266 ; + _:b274 ; ; ; . -_:b265 "git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git" . +_:b273 "git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git" . "Caenorhabditis" . @@ -4655,7 +4808,7 @@ _:b265 "git clone https://gi "Building a cell and anatomy ontology of Caenorhabditis elegans" . -_:b266 "Raymond Lee" ; +_:b274 "Raymond Lee" ; "raymond@caltech.edu" . @@ -4667,7 +4820,7 @@ _:b266 "Raymond Lee" ; "WBls" ; "active" ; - _:b267 ; + _:b275 ; ; "A structured controlled vocabulary of the development of Caenorhabditis elegans." ; "C. elegans development ontology" ; @@ -4676,17 +4829,17 @@ _:b266 "Raymond Lee" ; "developemental life stage" ; "https://github.com/obophenotype/c-elegans-development-ontology/issues" ; "http://purl.obolibrary.org/obo/wbls.owl" ; - _:b268 ; + _:b276 ; ; ; . -_:b267 "git clone https://github.com/obophenotype/c-elegans-development-ontology.git" . +_:b275 "git clone https://github.com/obophenotype/c-elegans-development-ontology.git" . "WormBase: a modern Model Organism Information Resource" . -_:b268 "Chris Grove" ; +_:b276 "Chris Grove" ; "cgrove@caltech.edu" . @@ -4698,7 +4851,7 @@ _:b268 "Chris Grove" ; "WBPhenotype" ; "active" ; - _:b269 ; + _:b277 ; ; "A structured controlled vocabulary of Caenorhabditis elegans phenotypes" ; "C. elegans phenotype" ; @@ -4707,18 +4860,18 @@ _:b268 "Chris Grove" ; "phenotype" ; "https://github.com/obophenotype/c-elegans-phenotype-ontology/issues" ; "http://purl.obolibrary.org/obo/wbphenotype.owl" ; - _:b270 ; + _:b278 ; ; ; ; . -_:b269 "git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git" . +_:b277 "git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git" . "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community." . -_:b270 "Chris Grove" ; +_:b278 "Chris Grove" ; "cgrove@caltech.edu" . @@ -4730,14 +4883,14 @@ _:b270 "Chris Grove" ; "http://purl.obolibrary.org/obo/wbphenotype/wbphenotype-base.owl" . -_:b107 "obo2owl" ; +_:b108 "obo2owl" ; "ftp://ftp.rgd.mcw.edu/pub/ontology/experimental_condition/experimental_condition.obo"^^ . "RGD Ontology Browser" ; "RGD" . -_:b108 "Jennifer Smith" ; +_:b109 "Jennifer Smith" ; "jrsmith@mcw.edu" . @@ -4746,6 +4899,33 @@ _:b108 "Jennifer Smith" ; "http://purl.obolibrary.org/obo/xco.obo" . + + "active" ; + "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/tree/master/cv" ; + _:b279 ; + "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry." ; + "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" ; + ; + "MS cross-linker reagents" ; + "http://oboedit.org" ; + "https://github.com/HUPO-PSI/mzIdentML/issues" ; + "psidev-ms-vocab@lists.sourceforge.net" ; + "xlmod" ; + "http://purl.obolibrary.org/obo/xlmod.owl" ; + _:b280 ; + ; + ; + . + +_:b279 "obo2owl" ; + "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo"^^ . + +_:b280 "Gerhard Mayer" ; + "gerhard.mayer@rub.de" . + + + "http://purl.obolibrary.org/obo/xlmod.obo" . + "active" ; ; @@ -4756,7 +4936,7 @@ _:b108 "Jennifer Smith" ; ; ; ; - _:b271 ; + _:b281 ; ; "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis." ; "Xenopus Phenotype Ontology" ; @@ -4764,14 +4944,14 @@ _:b108 "Jennifer Smith" ; "phenotype" ; "https://github.com/obophenotype/xenopus-phenotype-ontology/issues" ; "http://purl.obolibrary.org/obo/xpo.owl" ; - _:b272 ; + _:b282 ; ; ; . -_:b271 "git clone https://github.com/obophenotype/xenopus-phenotype-ontology.git" . +_:b281 "git clone https://github.com/obophenotype/xenopus-phenotype-ontology.git" . -_:b272 "Erik Segerdell" ; +_:b282 "Erik Segerdell" ; "esegerd3@gmail.com" . @@ -4780,10 +4960,10 @@ _:b272 "Erik Segerdell" ; "http://purl.obolibrary.org/obo/xpo.obo" . -_:b171 "obo2owl" ; +_:b173 "obo2owl" ; "https://raw.githubusercontent.com/ybradford/zebrafish-experimental-conditions-ontology/master/zeco.obo"^^ . -_:b172 "Yvonne Bradford" ; +_:b174 "Yvonne Bradford" ; "ybradford@zfin.org" . @@ -4795,6 +4975,34 @@ _:b172 "Yvonne Bradford" ; "http://purl.obolibrary.org/obo/zeco.json" . + + "active" ; + _:b283 ; + ; + "Developmental stages of the Zebrafish" ; + "Zebrafish developmental stages ontology" ; + ; + "anatomy" ; + "https://github.com/cerivs/zebrafish-anatomical-ontology/issues" ; + "http://purl.obolibrary.org/obo/zfs.owl" ; + _:b284 ; + ; + ; + ; + . + +_:b283 "obo2owl" ; + "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo"^^ . + +_:b284 "Ceri Van Slyke" ; + "van_slyke@zfin.org" . + + + "http://purl.obolibrary.org/obo/zfs.owl" . + + + "http://purl.obolibrary.org/obo/zfs.obo" . + "active" ; ; @@ -4804,21 +5012,21 @@ _:b172 "Yvonne Bradford" ; ; ; ; - _:b273 ; + _:b285 ; "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism." ; "Zebrafish Phenotype Ontology" ; ; "phenotype" ; "https://github.com/obophenotype/zebrafish-phenotype-ontology/issues" ; "http://purl.obolibrary.org/obo/zp.owl" ; - _:b274 ; + _:b286 ; ; ; . -_:b273 "git clone https://github.com/obophenotype/zebrafish-phenotype-ontology.git" . +_:b285 "git clone https://github.com/obophenotype/zebrafish-phenotype-ontology.git" . -_:b274 "Yvonne Bradford" ; +_:b286 "Yvonne Bradford" ; "ybradford@zfin.org" . @@ -4827,47 +5035,23 @@ _:b274 "Yvonne Bradford" ; "http://purl.obolibrary.org/obo/zp.obo" . - - "active" ; - "An ontology to capture confidence information about annotations." ; - "Confidence Information Ontology" ; - ; - "https://github.com/BgeeDB/confidence-information-ontology" ; - "http://purl.obolibrary.org/obo/cio.owl" ; - _:b275 ; - ; - ; - . - - - "GNU GPL 3.0" . - -_:b275 "Frederic Bastian" ; - "bgee@sib.swiss" . - - - "http://purl.obolibrary.org/obo/cio.owl" . - - - "http://purl.obolibrary.org/obo/cio.obo" . - "active" ; - _:b276 ; + _:b287 ; "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens." ; "eagle-i resource ontology" ; ; "resources" ; "http://purl.obolibrary.org/obo/ero.owl" ; - _:b277 ; + _:b288 ; ; . -_:b276 "owl2obo" ; +_:b287 "owl2obo" ; "http://purl.obolibrary.org/obo/ero.owl"^^ . -_:b277 "Juliane Schneider" ; - "Juliane_Schneider@hms.harvard.edu" . +_:b288 "Marc Ciriello" ; + "Marc_Ciriello@hms.harvard.edu" . "http://purl.obolibrary.org/obo/ero.owl" . @@ -4882,10 +5066,10 @@ _:b277 "Juliane Schneider" ; "metabolomics and nutrition" ; "https://github.com/pcastellanoescuder/FoodBiomarkerOntology/issues" ; "http://purl.obolibrary.org/obo/fobi.owl" ; - _:b278 ; + _:b289 ; . -_:b278 "Pol Castellano Escuder" ; +_:b289 "Pol Castellano Escuder" ; "polcaes@gmail.com" . @@ -4895,25 +5079,25 @@ _:b278 "Pol Castellano Escuder" ; "active" ; - _:b279 ; + _:b290 ; "The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences." ; "Gender, Sex, and Sexual Orientation (GSSO) ontology" ; ; "organisms" ; "https://github.com/Superraptor/GSSO/issues" ; "http://purl.obolibrary.org/obo/gsso.owl" ; - _:b280 ; + _:b291 ; ; ; ; . -_:b279 "git clone https://github.com/Superraptor/GSSO.git" . +_:b290 "git clone https://github.com/Superraptor/GSSO.git" . "Apache 2.0 License" . -_:b280 "Clair Kronk" ; +_:b291 "Clair Kronk" ; "kronkcj@mail.uc.edu" . @@ -4962,23 +5146,24 @@ _:b59 "Sebastian Koehler" ; "active" ; - _:b281 ; + _:b292 ; "A classification of algorithms available for the simulation of models in biology." ; "Kinetic Simulation Algorithm Ontology" ; ; "algorithms" ; + "https://sourceforge.net/p/kisao/feature-requests/" ; "http://purl.obolibrary.org/obo/kisao.owl" ; - _:b282 ; + _:b293 ; ; . -_:b281 "owl2obo" ; +_:b292 "owl2obo" ; "http://svn.code.sf.net/p/kisao/code/tags/kisao-owl-latest/kisao.owl"^^ . "Artistic License 2.0" . -_:b282 "The Biomodels.net team" ; +_:b293 "The Biomodels.net team" ; "biomodels-net-support@lists.sf.net" . @@ -4986,115 +5171,58 @@ _:b282 "The Biomodels.net team" ; "active" ; - _:b283 ; + _:b294 ; "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features." ; "Mathematical modeling ontology" ; ; "http://sourceforge.net/p/mamo-ontology/tickets/" ; "http://purl.obolibrary.org/obo/mamo.owl" ; - _:b284 ; + _:b295 ; ; . -_:b283 "owl2obo" ; +_:b294 "owl2obo" ; "https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl"^^ . -_:b284 "Nicolas Le Novere" ; +_:b295 "Nicolas Le Novere" ; "n.lenovere@gmail.com" . "http://purl.obolibrary.org/obo/mamo.owl" . - - "active" ; - "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master" ; - ; - ; - _:b285 ; - "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry." ; - "Mass spectrometry ontology" ; - ; - ; - "MS experiments" ; - "http://oboedit.org" ; - "psidev-ms-vocab@lists.sourceforge.net" ; - "MS" ; - "http://purl.obolibrary.org/obo/ms.owl" ; - _:b286 ; - ; - ; - ; - . - -_:b285 "obo2owl" ; - "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"^^ . - - - "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary." . - -_:b286 "Gerhard Mayer" ; - "gerhard.mayer@rub.de" . - - - "http://purl.obolibrary.org/obo/ms.obo" . - - - "http://purl.obolibrary.org/obo/ms.owl" . - "active" ; - _:b287 ; + _:b296 ; "Terms commonly used in Systems Biology, and in particular in computational modeling." ; "Systems Biology Ontology" ; ; "biochemistry" ; "https://sourceforge.net/p/sbo/term-request/" ; "http://purl.obolibrary.org/obo/sbo.owl" ; - _:b288 ; + _:b297 ; ; . -_:b287 "obo2owl" ; +_:b296 "obo2owl" ; "http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo"^^ . -_:b288 "Rahuman Sheriff" ; +_:b297 "Rahuman Sheriff" ; "sheriff@ebi.ac.uk" . "http://purl.obolibrary.org/obo/sbo.owl" . - - "active" ; - _:b289 ; - "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community." ; - "Software ontology" ; - ; - "software" ; - "http://purl.obolibrary.org/obo/swo.owl" ; - _:b290 ; - ; - . - -_:b289 "owl2obo" ; - "https://raw.githubusercontent.com/allysonlister/swo/master/release/swo_inferred.owl"^^ . - -_:b290 "Allyson Lister" ; - "allyson.lister@oerc.ox.ac.uk" . - - - "http://purl.obolibrary.org/obo/swo.owl" . - "active" ; "TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity." ; "Toxic Process Ontology" ; - ; + ; "toxicity" ; "https://github.com/txpo-ontology/TXPO/issues" ; ; ; "http://purl.obolibrary.org/obo/txpo.owl" ; - _:b291 ; + _:b298 ; ; . @@ -5106,103 +5234,30 @@ _:b290 "Allyson Lister" ; "TOXPILOT" ; "TOXPILOT" . -_:b291 "Yuki Yamagata" ; +_:b298 "Yuki Yamagata" ; "y-yamagata@nibiohn.go.jp" . "http://purl.obolibrary.org/obo/txpo.owl" . - - "active" ; - _:b292 ; - "An ontology of traits covering vertebrates" ; - "Vertebrate trait ontology" ; - ; - "http://purl.obolibrary.org/obo/vt.owl" ; - _:b293 ; - ; - . - -_:b292 "svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt" ; - "vcs" . - -_:b293 "Carissa Park" ; - "caripark@iastate.edu" . - - - "http://purl.obolibrary.org/obo/vt.owl" . - - - "active" ; - "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/tree/master/cv" ; - _:b294 ; - "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry." ; - "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" ; - ; - "MS cross-linker reagents" ; - "http://oboedit.org" ; - "psidev-ms-vocab@lists.sourceforge.net" ; - "xlmod" ; - "http://purl.obolibrary.org/obo/xlmod.owl" ; - _:b295 ; - ; - ; - . - -_:b294 "obo2owl" ; - "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo"^^ . - -_:b295 "Gerhard Mayer" ; - "gerhard.mayer@rub.de" . - - - "http://purl.obolibrary.org/obo/xlmod.obo" . - - - "active" ; - _:b296 ; - ; - "Developmental stages of the Zebrafish" ; - "Zebrafish developmental stages ontology" ; - ; - "anatomy" ; - "http://purl.obolibrary.org/obo/zfs.owl" ; - _:b297 ; - ; - ; - ; - . - -_:b296 "obo2owl" ; - "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo"^^ . - -_:b297 "Ceri Van Slyke" ; - "van_slyke@zfin.org" . - - - "http://purl.obolibrary.org/obo/zfs.owl" . - - - "http://purl.obolibrary.org/obo/zfs.obo" . - "orphaned" ; - _:b298 ; + _:b299 ; "Social Behavior in insects" ; "Social Insect Behavior Ontology" ; ; "behavior" ; "https://github.com/obophenotype/sibo/issues" ; "http://purl.obolibrary.org/obo/sibo.owl" ; - _:b299 ; + _:b300 ; ; ; . -_:b298 "git clone https://github.com/obophenotype/sibo.git" ; +_:b299 "git clone https://github.com/obophenotype/sibo.git" ; "vcs" . -_:b299 "Chris Mungall" ; +_:b300 "Chris Mungall" ; "cjmungall@lbl.gov" . @@ -5213,18 +5268,18 @@ _:b299 "Chris Mungall" ; "orphaned" ; - _:b300 ; + _:b301 ; "An ontology of physico-chemical methods and properties." ; "Physico-chemical methods and properties" ; "http://purl.obolibrary.org/obo/fix.owl" ; - _:b301 ; + _:b302 ; ; . -_:b300 "obo2owl" ; +_:b301 "obo2owl" ; "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/fix.obo"^^ . -_:b301 "chEBI" . +_:b302 "chEBI" . "http://purl.obolibrary.org/obo/fix.owl" . @@ -5232,6 +5287,25 @@ _:b301 "chEBI" . "http://purl.obolibrary.org/obo/fix.obo" . + + "orphaned" ; + _:b303 ; + "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations." ; + "Variation Ontology" ; + "http://purl.obolibrary.org/obo/vario.owl" ; + _:b304 ; + ; + . + +_:b303 "obo2owl" ; + "http://variationontology.org/vario_download/vario.obo"^^ . + +_:b304 "Mauno Vihinen" ; + "mauno.vihinen@med.lu.se" . + + + "http://purl.obolibrary.org/obo/vario.owl" . + "orphaned" ; "An ontology that formalizes the genomic element by defining an upper class genetic interval" ; @@ -5246,36 +5320,21 @@ _:b301 "chEBI" . "orphaned" ; - _:b302 ; + _:b305 ; "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time." ; "Physico-chemical process" ; "http://purl.obolibrary.org/obo/rex.owl" ; . -_:b302 "obo2owl" ; +_:b305 "obo2owl" ; "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo"^^ . "http://purl.obolibrary.org/obo/rex.owl" . - - "orphaned" ; - _:b303 ; - "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations." ; - "Variation Ontology" ; - "http://purl.obolibrary.org/obo/vario.owl" ; - ; - . - -_:b303 "obo2owl" ; - "http://variationontology.org/vario_download/vario.obo"^^ . - - - "http://purl.obolibrary.org/obo/vario.owl" . - "inactive" ; - _:b304 ; + _:b306 ; ; "An anatomical and developmental ontology for cephalopods" ; "Cephalopod Ontology" ; @@ -5283,18 +5342,18 @@ _:b303 "obo2owl" ; "anatomy" ; "https://github.com/obophenotype/cephalopod-ontology/issues" ; "http://purl.obolibrary.org/obo/ceph.owl" ; - _:b305 ; + _:b307 ; ; ; . -_:b304 "git clone https://github.com/obophenotype/cephalopod-ontology.git" ; +_:b306 "git clone https://github.com/obophenotype/cephalopod-ontology.git" ; "vcs" . "Cephalopod" . -_:b305 "Chris Mungall" ; +_:b307 "Chris Mungall" ; "cjmungall@lbl.gov" . @@ -5310,7 +5369,7 @@ _:b305 "Chris Mungall" ; ; ; ; - _:b306 ; + _:b308 ; ; "A structured controlled vocabulary of stage-specific anatomical structures of the developing human." ; "Human developmental anatomy, abstract" ; @@ -5319,18 +5378,18 @@ _:b305 "Chris Mungall" ; "anatomy" ; "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues" ; "http://purl.obolibrary.org/obo/ehdaa2.owl" ; - _:b307 ; + _:b309 ; ; ; . -_:b306 "git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git" ; +_:b308 "git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git" ; "vcs" . "A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20)." . -_:b307 "Jonathan Bard" ; +_:b309 "Jonathan Bard" ; "J.Bard@ed.ac.uk" . @@ -5341,7 +5400,7 @@ _:b307 "Jonathan Bard" ; "inactive" ; - _:b308 ; + _:b310 ; "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures." ; "RNA ontology" ; ; @@ -5349,19 +5408,19 @@ _:b307 "Jonathan Bard" ; "https://github.com/BGSU-RNA/rnao/issues" ; ; "http://purl.obolibrary.org/obo/rnao.owl" ; - _:b309 ; + _:b311 ; ; ; . -_:b308 "git clone https://github.com/BGSU-RNA/rnao.git" ; +_:b310 "git clone https://github.com/BGSU-RNA/rnao.git" ; "vcs" . "RNA Ontology jOWL Browser" ; "RNAO" . -_:b309 "Colin Batchelor" ; +_:b311 "Colin Batchelor" ; "BatchelorC@rsc.org" . @@ -5373,7 +5432,7 @@ _:b309 "Colin Batchelor" ; "inactive" ; ; - _:b310 ; + _:b312 ; "A manually curated resource for the representation and annotation of metabolic pathways" ; "Unipathway" ; ; @@ -5381,17 +5440,17 @@ _:b309 "Colin Batchelor" ; "pathways" ; "https://github.com/geneontology/unipathway/issues" ; "http://purl.obolibrary.org/obo/upa.owl" ; - _:b311 ; + _:b313 ; ; ; . -_:b310 "git clone https://github.com/geneontology/unipathway.git" . +_:b312 "git clone https://github.com/geneontology/unipathway.git" . "UniPathway: a resource for the exploration and annotation of metabolic pathways" . -_:b311 "Anne Morgat" ; +_:b313 "Anne Morgat" ; "Anne.Morgat@sib.swiss" . @@ -5403,10 +5462,10 @@ _:b311 "Anne Morgat" ; "inactive" ; "CranioMaxilloFacial ontology" ; - _:b312 ; + _:b314 ; . -_:b312 "Mark Engelstad" ; +_:b314 "Mark Engelstad" ; "engelsta@ohsu.edu" . @@ -5416,12 +5475,12 @@ _:b312 "Mark Engelstad" ; ; "health" ; "http://purl.obolibrary.org/obo/idomal.owl" ; - _:b313 ; + _:b315 ; ; ; . -_:b313 "Pantelis Topalis" ; +_:b315 "Pantelis Topalis" ; "topalis@imbb.forth.gr" . @@ -5437,14 +5496,14 @@ _:b313 "Pantelis Topalis" ; "Mosquito insecticide resistance" ; "environment" ; "http://purl.obolibrary.org/obo/miro.owl" ; - _:b314 ; + _:b316 ; ; . "Anopheles" . -_:b314 "C. Louis" ; +_:b316 "C. Louis" ; "louis@imbb.forth.gr" . @@ -5461,7 +5520,7 @@ _:b314 "C. Louis" ; ; "anatomy" ; "http://purl.obolibrary.org/obo/tads.owl" ; - _:b315 ; + _:b317 ; ; ; . @@ -5469,7 +5528,7 @@ _:b314 "C. Louis" ; "Ixodidae" . -_:b315 "Daniel Sonenshine" ; +_:b317 "Daniel Sonenshine" ; "dsonensh@odu.edu" . @@ -5486,12 +5545,12 @@ _:b315 "Daniel Sonenshine" ; ; "anatomy" ; "http://purl.obolibrary.org/obo/tgma.owl" ; - _:b316 ; + _:b318 ; ; ; . -_:b316 "Pantelis Topalis" ; +_:b318 "Pantelis Topalis" ; "topalis@imbb.forth.gr" . @@ -5506,11 +5565,11 @@ _:b316 "Pantelis Topalis" ; "Beta Cell Genomics Ontology" ; ; "https://github.com/obi-bcgo/bcgo/issues" ; - _:b317 ; + _:b319 ; ; . -_:b317 "Jie Zheng" ; +_:b319 "Jie Zheng" ; "jiezheng@pennmedicine.upenn.edu" . @@ -5524,26 +5583,26 @@ _:b317 "Jie Zheng" ; ; "health" ; "https://github.com/labda/DINTO/issues" ; - _:b318 ; + _:b320 ; ; . "DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms." . -_:b318 "Maria Herrero" ; +_:b320 "Maria Herrero" ; "maria.herrero@kcl.ac.uk" . "http://purl.obolibrary.org/obo/dinto.owl" . -_:b126 "obo2owl" ; +_:b127 "obo2owl" ; "https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl"^^ . "Ontologies as integrative tools for plant science." . -_:b127 "Pankaj Jaiswal" ; +_:b128 "Pankaj Jaiswal" ; "jaiswalp@science.oregonstate.edu" . @@ -5554,7 +5613,7 @@ _:b127 "Pankaj Jaiswal" ; "inactive" ; - _:b319 ; + _:b321 ; ; "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa" ; "Teleost Anatomy Ontology" ; @@ -5562,17 +5621,17 @@ _:b127 "Pankaj Jaiswal" ; ; "anatomy" ; "https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3ATAO" ; - _:b320 ; + _:b322 ; ; . -_:b319 "obo2owl" ; +_:b321 "obo2owl" ; "http://purl.obolibrary.org/obo/tao.obo"^^ . "The teleost anatomy ontology: anatomical representation for the genomics age" . -_:b320 "Wasila Dahdul" ; +_:b322 "Wasila Dahdul" ; "wasila.dahdul@usd.edu" . @@ -5582,39 +5641,39 @@ _:b320 "Wasila Dahdul" ; "inactive" ; ; "Amphibian gross anatomy" ; - _:b321 ; + _:b323 ; . "Amphibia" . -_:b321 "david.c.blackburn@gmail.com" ; +_:b323 "david.c.blackburn@gmail.com" ; "David Blackburn" . "inactive" ; "Animal natural history and life history" ; - _:b322 ; + _:b324 ; . -_:b322 "adw_geeks@umich.edu" ; +_:b324 "adw_geeks@umich.edu" ; "Animal Diversity Web technical staff" . "inactive" ; - _:b323 ; + _:b325 ; "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events" ; "Adverse Event Reporting Ontology" ; ; "health" ; - _:b324 ; + _:b326 ; ; . -_:b323 "owl2obo" ; +_:b325 "owl2obo" ; "http://purl.obolibrary.org/obo/aero.owl"^^ . -_:b324 "Melanie Courtot" ; +_:b326 "Melanie Courtot" ; "mcourtot@gmail.com" . @@ -5624,29 +5683,29 @@ _:b324 "Melanie Courtot" ; "inactive" ; ; "Amphibian taxonomy" ; - _:b325 ; + _:b327 ; . -_:b325 "david.c.blackburn@gmail.com" ; +_:b327 "david.c.blackburn@gmail.com" ; "David Blackburn" . "inactive" ; - _:b326 ; + _:b328 ; ; "Bilateria anatomy" ; "anatomy" ; - _:b327 ; + _:b329 ; ; . -_:b326 "obo2owl" ; +_:b328 "obo2owl" ; "http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo"^^ . "Bilateria" . -_:b327 "Thorsten Heinrich" ; +_:b329 "Thorsten Heinrich" ; "henrich@embl.de" . @@ -5655,57 +5714,57 @@ _:b327 "Thorsten Heinrich" ; "inactive" ; "Gene Regulation Ontology" ; - _:b328 ; + _:b330 ; . -_:b328 "vlee@ebi.ac.uk" ; +_:b330 "vlee@ebi.ac.uk" ; "Vivian Lee" . "inactive" ; ; "Dendritic cell" ; - _:b329 ; + _:b331 ; . -_:b329 "Lindsay.Cowell@utsouthwestern.edu" ; +_:b331 "Lindsay.Cowell@utsouthwestern.edu" ; "Lindsay Cowell" . "inactive" ; ; "Human developmental anatomy, timed version" ; - _:b330 ; + _:b332 ; . -_:b330 "J.Bard@ed.ac.uk" ; +_:b332 "J.Bard@ed.ac.uk" ; "Jonathan Bard" . "inactive" ; ; "Human developmental anatomy, abstract version" ; - _:b331 . + _:b333 . -_:b331 "J.Bard@ed.ac.uk" ; +_:b333 "J.Bard@ed.ac.uk" ; "Jonathan Bard" . "inactive" ; - _:b332 ; + _:b334 ; ; "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)." ; "Mouse gross anatomy and development, timed" ; "anatomy" ; - _:b333 ; + _:b335 ; ; ; . -_:b332 "obo2owl" ; +_:b334 "obo2owl" ; "ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo"^^ . -_:b333 "Terry Hayamizu" ; +_:b335 "Terry Hayamizu" ; "Terry.Hayamizu@jax.org" . @@ -5714,27 +5773,27 @@ _:b333 "Terry Hayamizu" ; "inactive" ; "eVOC (Expressed Sequence Annotation for Humans)" ; - _:b334 ; + _:b336 ; . -_:b334 "evoc@sanbi.ac.za" ; +_:b336 "evoc@sanbi.ac.za" ; "eVOC mailing list" . "inactive" ; - _:b335 ; + _:b337 ; ; "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase." ; "Fly taxonomy" ; "taxonomy" ; - _:b336 ; + _:b338 ; ; . -_:b335 "obo2owl" ; +_:b337 "obo2owl" ; "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo"^^ . -_:b336 "Marta Costa" ; +_:b338 "Marta Costa" ; "mmc46@gen.cam.ac.uk" . @@ -5742,18 +5801,18 @@ _:b336 "Marta Costa" ; "inactive" ; - _:b337 ; + _:b339 ; "Influenza Ontology" ; "health" ; "http://purl.obolibrary.org/obo/flu/tracker" ; - _:b338 ; + _:b340 ; ; . -_:b337 "owl2obo" ; +_:b339 "owl2obo" ; "http://purl.obolibrary.org/obo/flu.owl"^^ . -_:b338 "Burke Squires" ; +_:b340 "Burke Squires" ; "burkesquires@gmail.com" . @@ -5762,81 +5821,81 @@ _:b338 "Burke Squires" ; "inactive" ; "Cereal Plant Gross Anatomy" ; - _:b339 ; + _:b341 ; . -_:b339 "Plant Ontology Administrators" ; +_:b341 "Plant Ontology Administrators" ; "po-discuss@plantontology.org" . "inactive" ; "Habronattus courtship" ; - _:b340 ; + _:b342 ; . -_:b340 "Peter Midford" ; +_:b342 "Peter Midford" ; "peteremidford@yahoo.com" . "inactive" ; - _:b341 ; + _:b343 ; "Molecule role (INOH Protein name/family name ontology)" ; - _:b342 ; + _:b344 ; . -_:b341 "obo2owl" ; +_:b343 "obo2owl" ; "https://web.archive.org/web/20131127090937/http://www.inoh.org/ontologies/MoleculeRoleOntology.obo"^^ . -_:b342 "INOH curators" ; +_:b344 "INOH curators" ; "curator@inoh.org" . "inactive" ; "Protein Domains" ; - _:b343 ; + _:b345 ; . -_:b343 "InterPro Help" ; +_:b345 "InterPro Help" ; "interhelp@ebi.ac.uk" . "inactive" ; - _:b344 ; + _:b346 ; "An ontology representation of the LIPIDMAPS nomenclature classification." ; "Lipid Ontology" ; "lipids" ; - _:b345 . + _:b347 . -_:b344 "owl2obo" ; +_:b346 "owl2obo" ; "http://www.lipidprofiles.com/LipidOntology"^^ . -_:b345 "Christipher Baker" ; +_:b347 "Christipher Baker" ; "bakerc@unb.ca" . "inactive" ; "Loggerhead nesting" ; - _:b346 ; + _:b348 ; . -_:b346 "Peter Midford" ; +_:b348 "Peter Midford" ; "peteremidford@yahoo.com" . "inactive" ; "Multiple alignment" ; - _:b347 ; + _:b349 ; . -_:b347 "Julie Thompson" ; +_:b349 "Julie Thompson" ; "julie@igbmc.u-strasbg.fr" . "inactive" ; "Minimal anatomical terminology" ; - _:b348 . + _:b350 . -_:b348 "Jonathan Bard" ; +_:b350 "Jonathan Bard" ; "j.bard@ed.ac.uk" . @@ -5845,13 +5904,13 @@ _:b348 "Jonathan Bard" ; "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes." ; "Medaka fish anatomy and development" ; "anatomy" ; - _:b349 ; + _:b351 ; . "Oryzias" . -_:b349 "Thorsten Henrich" ; +_:b351 "Thorsten Henrich" ; "Thorsten.Henrich@embl-heidelberg.de" . @@ -5862,11 +5921,11 @@ _:b349 "Thorsten Henrich" ; "An application ontology for use with miRNA databases." ; "microRNA Ontology" ; ; - _:b350 ; + _:b352 ; ; . -_:b350 "Pantelis Topalis" ; +_:b352 "Pantelis Topalis" ; "topalis@imbb.forth.gr" . @@ -5877,12 +5936,12 @@ _:b350 "Pantelis Topalis" ; "A standardized description of a microarray experiment in support of MAGE v.1." ; "Microarray experimental conditions" ; "experiments" ; - _:b351 ; + _:b353 ; ; ; . -_:b351 "Chris Stoeckert" ; +_:b353 "Chris Stoeckert" ; "stoeckrt@pcbi.upenn.edu" . @@ -5892,45 +5951,45 @@ _:b351 "Chris Stoeckert" ; "inactive" ; "Neuronal cell types" ; "NIF Cell" ; - _:b352 ; + _:b354 ; . -_:b352 "Fahim Imam" ; +_:b354 "Fahim Imam" ; "smtifahim@gmail.com" . "inactive" ; "NIF Dysfunction" ; - _:b353 ; + _:b355 ; . -_:b353 "Fahim Imam" ; +_:b355 "Fahim Imam" ; "smtifahim@gmail.com" . "inactive" ; "NIF Gross Anatomy" ; - _:b354 ; + _:b356 ; . -_:b354 "Fahim Imam" ; +_:b356 "Fahim Imam" ; "smtifahim@gmail.com" . "inactive" ; - _:b355 ; + _:b357 ; "Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation." ; "NMR-instrument specific component of metabolomics investigations" ; "experiments" ; - _:b356 ; + _:b358 ; ; ; . -_:b355 "owl2obo" ; +_:b357 "owl2obo" ; "https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl"^^ . -_:b356 "Schober Daniel" ; +_:b358 "Schober Daniel" ; "schober@imbi.uni-freiburg.de" . @@ -5939,61 +5998,61 @@ _:b356 "Schober Daniel" ; "inactive" ; "OBO relationship types (legacy)" ; - _:b357 ; + _:b359 ; . -_:b357 "Chris Mungall" ; +_:b359 "Chris Mungall" ; "cjmungall@lbl.gov" . "inactive" ; ; "Plant Anatomy Ontology" ; - _:b358 ; + _:b360 ; . -_:b358 "Pankaj Jaiswal" ; +_:b360 "Pankaj Jaiswal" ; "jaiswalp@science.oregonstate.edu" . "inactive" ; ; "Platynereis stage ontology" ; - _:b359 ; + _:b361 ; . "Platynereis" . -_:b359 "Thorsten Heinrich" ; +_:b361 "Thorsten Heinrich" ; "henrich@embl.de" . "inactive" ; ; "Plant Growth and Development Stage" ; - _:b360 ; + _:b362 ; . -_:b360 "Plant Ontology Administrators" ; +_:b362 "Plant Ontology Administrators" ; "po-discuss@plantontology.org" . "inactive" ; "Plasmodium life cycle" ; - _:b361 ; + _:b363 ; . -_:b361 "Matt Berriman" ; +_:b363 "Matt Berriman" ; "mb4@sanger.ac.uk" . "inactive" ; "Proteomics data and process provenance" ; - _:b362 ; + _:b364 ; . -_:b362 "Satya S. Sahoo" ; +_:b364 "Satya S. Sahoo" ; "satya30@uga.edu" . @@ -6001,37 +6060,37 @@ _:b362 "Satya S. Sahoo" ; "For the description of covalent bonds in proteins." ; "Protein covalent bond" ; "proteins" ; - _:b363 ; + _:b365 ; . -_:b363 "John Garavelli" ; +_:b365 "John Garavelli" ; "john.garavelli@ebi.ac.uk" . "inactive" ; ; "Subcellular anatomy ontology" ; - _:b364 ; + _:b366 ; . -_:b364 "Stephen Larson" ; +_:b366 "Stephen Larson" ; "slarson@ncmir.ucsd.edu" . "inactive" ; - _:b365 ; + _:b367 ; "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments." ; "Sample processing and separation techniques" ; "provenance" ; - _:b366 ; + _:b368 ; ; ; . -_:b365 "obo2owl" ; +_:b367 "obo2owl" ; "https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo"^^ . -_:b366 "SEP developers via the PSI and MSI mailing lists" ; +_:b368 "SEP developers via the PSI and MSI mailing lists" ; "psidev-gps-dev@lists.sourceforge.net" . @@ -6041,50 +6100,50 @@ _:b366 "SEP developers via the PS "inactive" ; ; "Suggested Ontology for Pharmacogenomics" ; - _:b367 ; + _:b369 ; . -_:b367 "Adrien Coulet" ; +_:b369 "Adrien Coulet" ; "Adrien.Coulet@loria.fr" . "inactive" ; ; "Terminology of Anatomy of Human Embryology" ; - _:b368 . + _:b370 . -_:b368 "Pierre Sprumont" ; +_:b370 "Pierre Sprumont" ; "pierre.sprumont@unifr.ch" . "inactive" ; ; "Terminology of Anatomy of Human Histology" ; - _:b369 . + _:b371 . -_:b369 "Pierre Sprumont" ; +_:b371 "Pierre Sprumont" ; "pierre.sprumont@unifr.ch" . "inactive" ; - _:b370 ; + _:b372 ; ; "Vertebrate skeletal anatomy ontology." ; "Vertebrate Skeletal Anatomy Ontology-" ; "anatomy" ; "https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3AVSAO" ; - _:b371 ; + _:b373 ; ; ; . -_:b370 "obo2owl" ; +_:b372 "obo2owl" ; "http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo"^^ . "Vertebrata" . -_:b371 "Wasila Dahdul" ; +_:b373 "Wasila Dahdul" ; "wasila.dahdul@usd.edu" . @@ -6094,37 +6153,37 @@ _:b371 "Wasila Dahdul" ; "inactive" ; ; "Yeast phenotypes" ; - _:b372 ; + _:b374 ; . "Saccharomyces cerevisiae" . -_:b372 "Mike Cherry" ; +_:b374 "Mike Cherry" ; "cherry@genome.stanford.edu" . "inactive" ; ; "Maize gross anatomy" ; - _:b373 ; + _:b375 ; . "Zea" . -_:b373 "Leszek Vincent" ; +_:b375 "Leszek Vincent" ; "Leszek@missouri.edu" . "inactive" ; - _:b374 ; + _:b376 ; "An ontology designed to support the semantic annotation of epidemiology resources" ; "Epidemiology Ontology" ; ; . -_:b374 "owl2obo" ; +_:b376 "owl2obo" ; "http://purl.obolibrary.org/obo/epo.owl"^^ . @@ -6132,11 +6191,11 @@ _:b374 "owl2obo" ; "inactive" ; - _:b375 ; + _:b377 ; "Event (INOH pathway ontology)" ; . -_:b375 "obo2owl" ; +_:b377 "obo2owl" ; "http://download.baderlab.org/INOH/ontologies/EventOntology_172.obo"^^ . diff --git a/registry/ontologies.yml b/registry/ontologies.yml index 6a2571901..4aa35e69e 100644 --- a/registry/ontologies.yml +++ b/registry/ontologies.yml @@ -819,7 +819,7 @@ ontologies: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall - description: An ontology for respresenting spatial concepts, anatomical axes, gradients, + description: An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces domain: anatomy homepage: https://github.com/obophenotype/biological-spatial-ontology @@ -3348,6 +3348,30 @@ ontologies: phenotypes to genotypes across species ' type: annotation user: https://monarchinitiative.org/ + - description: Mondo is used by the ClinGen for disease curations. + examples: + - description: SCN1A is an autosomal dominant mutation in Dravet syndrome. + url: https://search.clinicalgenome.org/kb/conditions/MONDO_0011794 + type: annotation + user: https://www.clinicalgenome.org/ + - description: Mondo is used by the Kids First Data Resource Portal for disease + annotations. Note, a login is needed to access the portal and view the Mondo-curated + data. + type: annotation + user: https://portal.kidsfirstdrc.org/ + - description: Mondo is used by the Ancestory for some disease curations. + examples: + - description: Some term names in ancestory.com are curated with Mondo, for ease + of use. + url: https://support.ancestry.com/s/article/Disease-Condition-Catalog-Powered-by-MONDO + type: annotation + user: https://www.ancestry.com/ + - description: Mondo is used by the Human Cell Atlas for some disease annotations. + examples: + - description: Disease status specimen is normal, type 2 diabetes mellitus. + url: https://data.humancellatlas.org/explore/projects?filter=%5B%7B%22facetName%22:%22organ%22,%22terms%22:%5B%22kidney%22%5D%7D,%7B%22facetName%22:%22donorDisease%22,%22terms%22:%5B%22acoustic%20neuroma%22,%22acute%20kidney%20tubular%20necrosis%22%5D%7D%5D&catalog=dcp1 + type: annotation + user: https://www.humancellatlas.org/ - activity_status: active build: method: owl2obo @@ -5776,6 +5800,36 @@ ontologies: label: Danio title: Zebrafish Experimental Conditions Ontology tracker: https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues +- activity_status: active + build: + infallible: 1 + method: obo2owl + source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo + contact: + email: van_slyke@zfin.org + label: Ceri Van Slyke + description: Developmental stages of the Zebrafish + domain: anatomy + homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources + id: zfs + in_foundry: false + layout: ontology_detail + license: + label: CC-BY 3.0 + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png + url: http://creativecommons.org/licenses/by/3.0/ + ontology_purl: http://purl.obolibrary.org/obo/zfs.owl + page: https://github.com/obophenotype/developmental-stage-ontologies/wiki/ZFS + products: + - id: zfs.owl + ontology_purl: http://purl.obolibrary.org/obo/zfs.owl + - id: zfs.obo + ontology_purl: http://purl.obolibrary.org/obo/zfs.obo + taxon: + id: NCBITaxon:7954 + label: Danio + title: Zebrafish developmental stages ontology + tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues - activity_status: active build: checkout: git clone https://github.com/obophenotype/zebrafish-phenotype-ontology.git @@ -5831,8 +5885,8 @@ ontologies: method: owl2obo source_url: http://purl.obolibrary.org/obo/ero.owl contact: - email: Juliane_Schneider@hms.harvard.edu - label: Juliane Schneider + email: Marc_Ciriello@hms.harvard.edu + label: Marc Ciriello description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. documentation: https://open.med.harvard.edu/wiki/display/eaglei/Ontology @@ -5987,6 +6041,7 @@ ontologies: - id: kisao.owl ontology_purl: http://purl.obolibrary.org/obo/kisao.owl title: Kinetic Simulation Algorithm Ontology + tracker: https://sourceforge.net/p/kisao/feature-requests/ - activity_status: active build: method: owl2obo @@ -6061,35 +6116,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/txpo.owl title: Toxic Process Ontology tracker: https://github.com/txpo-ontology/TXPO/issues -- activity_status: active - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo - contact: - email: van_slyke@zfin.org - label: Ceri Van Slyke - description: Developmental stages of the Zebrafish - domain: anatomy - homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources - id: zfs - in_foundry: false - layout: ontology_detail - license: - label: CC-BY 3.0 - logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png - url: http://creativecommons.org/licenses/by/3.0/ - ontology_purl: http://purl.obolibrary.org/obo/zfs.owl - page: https://github.com/obophenotype/developmental-stage-ontologies/wiki/ZFS - products: - - id: zfs.owl - ontology_purl: http://purl.obolibrary.org/obo/zfs.owl - - id: zfs.obo - ontology_purl: http://purl.obolibrary.org/obo/zfs.obo - taxon: - id: NCBITaxon:7954 - label: Danio - title: Zebrafish developmental stages ontology - activity_status: orphaned build: checkout: git clone https://github.com/obophenotype/sibo.git diff --git a/registry/publications.md b/registry/publications.md index aac794fc3..37d927d1d 100644 --- a/registry/publications.md +++ b/registry/publications.md @@ -40,6 +40,7 @@ Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Wer - Plant Ontology (po): [The plant ontology as a tool for comparative plant anatomy and genomic analyses.](http://www.ncbi.nlm.nih.gov/pubmed/23220694) - Plant Trait Ontology (to): [The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.](https://doi.org/10.1093/nar/gkx1152) - Porifera Ontology (poro): [The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology](https://doi.org/10.1186/2041-1480-5-39) +- Protein modification (mod): [The PSI-MOD community standard for representation of protein modification data](https://pubmed.ncbi.nlm.nih.gov/18688235/) - Rat Strain Ontology (rs): [Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.](http://www.ncbi.nlm.nih.gov/pubmed/24267899) - Sequence types and features ontology (so): [The Sequence Ontology: a tool for the unification of genome annotations.](http://www.ncbi.nlm.nih.gov/pubmed/15892872) - Teleost Anatomy Ontology (tao): [The teleost anatomy ontology: anatomical representation for the genomics age](https://www.ncbi.nlm.nih.gov/pubmed/20547776)