From dd5ef3e04d7bb85145a87da4595250d9b08e1508 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Fri, 13 May 2016 08:52:20 -0700 Subject: [PATCH] regenerated registry --- Makefile | 1 + _config.yml | 27 +++-- registry/ontologies.jsonld | 47 ++++++-- registry/ontologies.ttl | 220 +++++++++++++++++++++---------------- registry/ontologies.yml | 27 +++-- registry/publications.md | 2 + 6 files changed, 202 insertions(+), 122 deletions(-) diff --git a/Makefile b/Makefile index 90d1bbbee..7a8f93686 100644 --- a/Makefile +++ b/Makefile @@ -108,6 +108,7 @@ valid-purl-report.txt: registry/ontologies.yml sparql-consistency-report.txt: registry/ontologies.yml ./util/processor.py -i $< sparql-compare > $@.tmp && mv $@.tmp $@ + # output of central OBO build # See FAQ for more details, and also README.md jenkins-output.txt: diff --git a/_config.yml b/_config.yml index 1d9d2a009..eddf56312 100644 --- a/_config.yml +++ b/_config.yml @@ -468,10 +468,7 @@ ontologies: termgenie: http://cl.termgenie.org title: Cell Ontology tracker: https://github.com/obophenotype/cell-ontology/issues -- build: {checkout: 'svn --ignore-externals co http://clo-ontology.googlecode.com/svn/trunk/src/ontology', - method: vcs, post_processing_command: owltools --use-catalog clo.owl --merge-imports-closure - --ni -o -f obo --no-check clo.obo, system: svn} - contact: {email: Sirarat.Sarntivijai@fda.hhs.gov, label: Sirarat Sarntivijai} +- contact: {email: Sirarat.Sarntivijai@fda.hhs.gov, label: Sirarat Sarntivijai} dependencies: - {id: uberon} - {id: cl} @@ -482,6 +479,8 @@ ontologies: homepage: http://www.clo-ontology.org id: clo 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/clo.owl products: - {id: clo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/clo.owl'} @@ -803,6 +802,7 @@ ontologies: page: http://ctdbase.org/downloads/#exposures products: - {id: exo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/exo.owl'} + - {id: exo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/exo.obo'} title: Exposure ontology - build: {insert_ontology_id: true, method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/fungi/fungal_anatomy.obo'} contact: {email: maria@genome.stanford.edu, label: Maria Costanzo} @@ -909,7 +909,8 @@ ontologies: products: - {id: fix.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fix.owl'} title: Physico-chemical methods and properties -- contact: {email: robert.hoehndorf@kaust.edu.sa, label: Robert Hoehndorf} +- build: {method: owl2obo, source_url: 'https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl'} + contact: {email: robert.hoehndorf@kaust.edu.sa, label: Robert Hoehndorf} description: Traits and phenotypes of flowering plants occurring in digitized Floras domain: phenotype homepage: https://github.com/flora-phenotype-ontology/flopoontology @@ -1227,6 +1228,7 @@ ontologies: page: https://rawgit.com/MICommunity/psidev/master/psi/mi/xml/doc/user/index.html products: - {id: mi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mi.owl'} + - {id: mi.obo, ontology_purl: 'http://purl.obolibrary.org/obo/mi.obo'} title: Molecular interactions - contact: {email: hlapp@drycafe.net, label: Hilamr Lapp} description: An application ontology to formalize annotation of phylogenetic data. @@ -1378,8 +1380,9 @@ ontologies: - {id: mro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mro.owl'} title: MHC Restriction Ontology tracker: https://github.com/IEDB/MRO/issues -- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo'} +- 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} @@ -1388,15 +1391,20 @@ ontologies: domain: MS experiments homepage: http://www.psidev.info/groups/controlled-vocabularies id: ms - integration_server: https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/ - label: Mass spectrometry ontology + 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 - browsers: - {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/NBO'} @@ -1717,6 +1725,9 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/poro.owl products: - {id: poro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/poro.owl'} + publications: + - {id: 'http://dx.doi.org/10.1186/2041-1480-5-39', title: 'The Porifera Ontology + (PORO): enhancing sponge systematics with an anatomy ontology'} taxon: {id: 'NCBITaxon:6040', label: Porifera} title: Porifera Ontology tracker: https://github.com/obophenotype/porifera-ontology/issues diff --git a/registry/ontologies.jsonld b/registry/ontologies.jsonld index d76142750..fc0fa4a1e 100644 --- a/registry/ontologies.jsonld +++ b/registry/ontologies.jsonld @@ -932,12 +932,6 @@ "tracker": "https://github.com/obophenotype/cell-ontology/issues" }, { - "build": { - "checkout": "svn --ignore-externals co http://clo-ontology.googlecode.com/svn/trunk/src/ontology", - "method": "vcs", - "post_processing_command": "owltools --use-catalog clo.owl --merge-imports-closure --ni -o -f obo --no-check clo.obo", - "system": "svn" - }, "contact": { "email": "Sirarat.Sarntivijai@fda.hhs.gov", "label": "Sirarat Sarntivijai" @@ -960,6 +954,11 @@ "homepage": "http://www.clo-ontology.org", "id": "clo", "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/clo.owl", "products": [ { @@ -1623,6 +1622,10 @@ { "id": "exo.owl", "ontology_purl": "http://purl.obolibrary.org/obo/exo.owl" + }, + { + "id": "exo.obo", + "ontology_purl": "http://purl.obolibrary.org/obo/exo.obo" } ], "title": "Exposure ontology" @@ -1864,6 +1867,10 @@ "title": "Physico-chemical methods and properties" }, { + "build": { + "method": "owl2obo", + "source_url": "https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl" + }, "contact": { "email": "robert.hoehndorf@kaust.edu.sa", "label": "Robert Hoehndorf" @@ -2515,6 +2522,10 @@ { "id": "mi.owl", "ontology_purl": "http://purl.obolibrary.org/obo/mi.owl" + }, + { + "id": "mi.obo", + "ontology_purl": "http://purl.obolibrary.org/obo/mi.obo" } ], "title": "Molecular interactions" @@ -2836,12 +2847,13 @@ { "build": { "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" + "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" @@ -2854,9 +2866,14 @@ "domain": "MS experiments", "homepage": "http://www.psidev.info/groups/controlled-vocabularies", "id": "ms", - "integration_server": "https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/", - "label": "Mass spectrometry ontology", + "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", @@ -2870,6 +2887,12 @@ "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" }, { @@ -3503,6 +3526,12 @@ "ontology_purl": "http://purl.obolibrary.org/obo/poro.owl" } ], + "publications": [ + { + "id": "http://dx.doi.org/10.1186/2041-1480-5-39", + "title": "The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology" + } + ], "taxon": { "id": "NCBITaxon:6040", "label": "Porifera" diff --git a/registry/ontologies.ttl b/registry/ontologies.ttl index 1211c059a..fb8c1988b 100644 --- a/registry/ontologies.ttl +++ b/registry/ontologies.ttl @@ -1882,6 +1882,12 @@ . + + + "FB" ; + + "FlyBase Browser" . + ; @@ -1920,12 +1926,6 @@ . - - - "FB" ; - - "FlyBase Browser" . - [ @@ -2076,6 +2076,10 @@ . + + + "http://purl.obolibrary.org/obo/exo.obo" . + "http://purl.obolibrary.org/obo/ogsf.owl" . @@ -2216,6 +2220,10 @@ "Uberon, an integrative multi-species anatomy ontology" . + + + "The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology" . + ; @@ -2712,16 +2720,12 @@ , , , ; - - [ - "svn --ignore-externals co http://clo-ontology.googlecode.com/svn/trunk/src/ontology" ; - - "vcs" - ] ; "An ontology to standardize and integrate cell line information and to support computer-assisted reasoning." ; "Cell Line Ontology" ; + + ; "http://purl.obolibrary.org/obo/clo.owl" ; @@ -3059,12 +3063,6 @@ . - - - "FB" ; - - "FlyBase Browser" . - [ @@ -3095,6 +3093,12 @@ . + + + "FB" ; + + "FlyBase Browser" . + "main version" ; @@ -3349,6 +3353,10 @@ . + + + "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary." . + "The pathway ontology - updates and applications." . @@ -3369,7 +3377,7 @@ "http://purl.obolibrary.org/obo/exo.owl" ; - ; + , ; ; @@ -3425,34 +3433,6 @@ "http://purl.obolibrary.org/obo/tgma.owl" . - - - [ - "obo2owl" ; - - "http://anobase.vectorbase.org/miro/miro_release.obo" - ] ; - - ; - - "Application ontology for entities related to insecticide resistance in mosquitos" ; - - "Mosquito insecticide resistance" ; - - "environment" ; - - "http://purl.obolibrary.org/obo/miro.owl" ; - - [ - "C. Louis" ; - - "louis@imbb.forth.gr" - ] ; - - ; - - . - [ @@ -3481,6 +3461,34 @@ . + + + [ + "obo2owl" ; + + "http://anobase.vectorbase.org/miro/miro_release.obo" + ] ; + + ; + + "Application ontology for entities related to insecticide resistance in mosquitos" ; + + "Mosquito insecticide resistance" ; + + "environment" ; + + "http://purl.obolibrary.org/obo/miro.owl" ; + + [ + "C. Louis" ; + + "louis@imbb.forth.gr" + ] ; + + ; + + . + "A formal ontology of genes and genomes of biological organisms." ; @@ -3861,7 +3869,7 @@ "cjmungall@lbl.gov" ] ; - , , , , , , ; + , , , , , , ; , ; @@ -3992,6 +4000,8 @@ "Porifera Ontology" ; ; + + ; "anatomy" ; @@ -4265,38 +4275,6 @@ . - - - "BioPortal" ; - - "BioPortal Browser" . - - - - ; - - "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" ; - - [ - "Robert Hoehndorf" ; - - "robert.hoehndorf@kaust.edu.sa" - ] ; - - ; - - . - , , ; @@ -4331,6 +4309,44 @@ . + + + "BioPortal" ; + + "BioPortal Browser" . + + + + [ + "owl2obo" ; + + "https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl" + ] ; + + ; + + "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" ; + + [ + "Robert Hoehndorf" ; + + "robert.hoehndorf@kaust.edu.sa" + ] ; + + ; + + . + "http://purl.obolibrary.org/obo/omit.owl" . @@ -4438,23 +4454,29 @@ - "Mass spectrometry ontology" ; + "MS" ; - "https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/" ; + "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master" ; , ; [ "obo2owl" ; - "https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" + "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" ] ; "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" ; @@ -4695,6 +4717,10 @@ "An ontology for Xenopus anatomy and development." . + + + "http://purl.obolibrary.org/obo/pato.obo" . + [ @@ -4725,10 +4751,6 @@ . - - - "http://purl.obolibrary.org/obo/pato.obo" . - [ @@ -5165,7 +5187,7 @@ "pporras@ebi.ac.uk, orchard@ebi.ac.uk" ] ; - ; + , ; ; @@ -5183,6 +5205,10 @@ "http://purl.obolibrary.org/obo/fbcv/dpo.owl" . + + + "http://purl.obolibrary.org/obo/mi.obo" . + "http://purl.obolibrary.org/obo/so.owl" . @@ -5247,6 +5273,15 @@ . + + a ; + + "core ontology" ; + + "Uberon" ; + + "http://purl.obolibrary.org/obo/uberon.owl" . + [ @@ -5274,15 +5309,6 @@ . - - a ; - - "core ontology" ; - - "Uberon" ; - - "http://purl.obolibrary.org/obo/uberon.owl" . - "Cephalopod" . diff --git a/registry/ontologies.yml b/registry/ontologies.yml index 76e4baf21..926da8087 100644 --- a/registry/ontologies.yml +++ b/registry/ontologies.yml @@ -458,10 +458,7 @@ ontologies: termgenie: http://cl.termgenie.org title: Cell Ontology tracker: https://github.com/obophenotype/cell-ontology/issues -- build: {checkout: 'svn --ignore-externals co http://clo-ontology.googlecode.com/svn/trunk/src/ontology', - method: vcs, post_processing_command: owltools --use-catalog clo.owl --merge-imports-closure - --ni -o -f obo --no-check clo.obo, system: svn} - contact: {email: Sirarat.Sarntivijai@fda.hhs.gov, label: Sirarat Sarntivijai} +- contact: {email: Sirarat.Sarntivijai@fda.hhs.gov, label: Sirarat Sarntivijai} dependencies: - {id: uberon} - {id: cl} @@ -472,6 +469,8 @@ ontologies: homepage: http://www.clo-ontology.org id: clo 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/clo.owl products: - {id: clo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/clo.owl'} @@ -793,6 +792,7 @@ ontologies: page: http://ctdbase.org/downloads/#exposures products: - {id: exo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/exo.owl'} + - {id: exo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/exo.obo'} title: Exposure ontology - build: {insert_ontology_id: true, method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/fungi/fungal_anatomy.obo'} contact: {email: maria@genome.stanford.edu, label: Maria Costanzo} @@ -899,7 +899,8 @@ ontologies: products: - {id: fix.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fix.owl'} title: Physico-chemical methods and properties -- contact: {email: robert.hoehndorf@kaust.edu.sa, label: Robert Hoehndorf} +- build: {method: owl2obo, source_url: 'https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl'} + contact: {email: robert.hoehndorf@kaust.edu.sa, label: Robert Hoehndorf} description: Traits and phenotypes of flowering plants occurring in digitized Floras domain: phenotype homepage: https://github.com/flora-phenotype-ontology/flopoontology @@ -1217,6 +1218,7 @@ ontologies: page: https://rawgit.com/MICommunity/psidev/master/psi/mi/xml/doc/user/index.html products: - {id: mi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mi.owl'} + - {id: mi.obo, ontology_purl: 'http://purl.obolibrary.org/obo/mi.obo'} title: Molecular interactions - contact: {email: hlapp@drycafe.net, label: Hilamr Lapp} description: An application ontology to formalize annotation of phylogenetic data. @@ -1368,8 +1370,9 @@ ontologies: - {id: mro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mro.owl'} title: MHC Restriction Ontology tracker: https://github.com/IEDB/MRO/issues -- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo'} +- 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} @@ -1378,15 +1381,20 @@ ontologies: domain: MS experiments homepage: http://www.psidev.info/groups/controlled-vocabularies id: ms - integration_server: https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/ - label: Mass spectrometry ontology + 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 - browsers: - {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/NBO'} @@ -1707,6 +1715,9 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/poro.owl products: - {id: poro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/poro.owl'} + publications: + - {id: 'http://dx.doi.org/10.1186/2041-1480-5-39', title: 'The Porifera Ontology + (PORO): enhancing sponge systematics with an anatomy ontology'} taxon: {id: 'NCBITaxon:6040', label: Porifera} title: Porifera Ontology tracker: https://github.com/obophenotype/porifera-ontology/issues diff --git a/registry/publications.md b/registry/publications.md index 8ab476bda..de08113be 100644 --- a/registry/publications.md +++ b/registry/publications.md @@ -23,11 +23,13 @@ Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Wer - Experimental condition ontology (xco): [Three ontologies to define phenotype measurement data.](http://www.ncbi.nlm.nih.gov/pubmed/22654893) - Human Disease Ontology (doid): [Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data](http://www.ncbi.nlm.nih.gov/pubmed/?term=25348409) - Human developmental anatomy, abstract (ehdaa2): [A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).](http://www.ncbi.nlm.nih.gov/pubmed/22973865) +- Mass spectrometry ontology (ms): [The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.](http://www.ncbi.nlm.nih.gov/pubmed/23482073) - Measurement method ontology (mmo): [Three ontologies to define phenotype measurement data.](http://www.ncbi.nlm.nih.gov/pubmed/22654893) - Pathway ontology (pw): [The Rat Genome Database pathway portal.](http://www.ncbi.nlm.nih.gov/pubmed/21478484) - Plant Environment Ontology (eo): [Ontologies as integrative tools for plant science.](http://www.ncbi.nlm.nih.gov/pubmed/22847540) - 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): [Ontologies as integrative tools for plant science.](http://www.ncbi.nlm.nih.gov/pubmed/22847540) +- Porifera Ontology (poro): [The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology](http://dx.doi.org/10.1186/2041-1480-5-39) - 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 (so): [The Sequence Ontology: a tool for the unification of genome annotations.](http://www.ncbi.nlm.nih.gov/pubmed/15892872) - The Drug-Drug Interactions Ontology (dinto): [DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms.](http://pubs.acs.org/doi/10.1021/acs.jcim.5b00119)