From 01a775611a4850b815b209c533e61a80d1e75259 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Fri, 11 Mar 2022 22:21:59 +0200 Subject: [PATCH] Harmonising domains for all ontologies (#1810) * Harmonising domains for all ontologies * Revert "Harmonising domains for all ontologies" This reverts commit c2a945cdc8f2a811e20b9c645c6b4d5ddb741fac. * Changing to have two spaces * Update registry_schema.json * Update registry_schema.json * Update registry_schema.json * Update registry_schema.json * Update ontology/ontoneo.md Co-authored-by: Charles Tapley Hoyt * Update ontology/oae.md Co-authored-by: Charles Tapley Hoyt * Update ontology/ecocore.md Co-authored-by: Charles Tapley Hoyt * Update ontology/eupath.md Co-authored-by: Charles Tapley Hoyt * Update ontology/opl.md Co-authored-by: Charles Tapley Hoyt * Update ontology/sepio.md Co-authored-by: Charles Tapley Hoyt * Update ontology/obib.md Co-authored-by: Charles Tapley Hoyt * Update ecocore.md * Update ontology/rbo.md Co-authored-by: Charles Tapley Hoyt * Update ontology/one.md Co-authored-by: Charles Tapley Hoyt * Update ontology/lepao.md Co-authored-by: Charles Tapley Hoyt * Update ontology/colao.md Co-authored-by: Charles Tapley Hoyt * Update ontology/fobi.md Co-authored-by: Charles Tapley Hoyt * Update ontology/one.md Co-authored-by: Charles Tapley Hoyt * Update ontology/foodon.md Co-authored-by: Charles Tapley Hoyt * Update ontology/ons.md Co-authored-by: Charles Tapley Hoyt * Update util/schema/registry_schema.json Co-authored-by: Charles Tapley Hoyt * Remove other, add "simulation" * Update pso.md * Fixing two metadata elements * Changes experiments to investigations see https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1225#issuecomment-1062939527 Co-authored-by: Charles Tapley Hoyt --- ontology/aeo.md | 2 +- ontology/agro.md | 4 +++- ontology/aism.md | 2 +- ontology/amphx.md | 2 +- ontology/bco.md | 4 +++- ontology/bila.md | 2 +- ontology/bspo.md | 2 +- ontology/bto.md | 2 +- ontology/caro.md | 2 +- ontology/cdno.md | 2 +- ontology/ceph.md | 2 +- ontology/cl.md | 4 +++- ontology/clao.md | 2 +- ontology/clyh.md | 2 +- ontology/cmo.md | 4 +++- ontology/colao.md | 4 +++- ontology/cro.md | 4 +++- ontology/cteno.md | 2 +- ontology/ddanat.md | 2 +- ontology/ddpheno.md | 2 +- ontology/disdriv.md | 4 +++- ontology/doid.md | 4 +++- ontology/ecao.md | 2 +- ontology/eco.md | 2 +- ontology/ecocore.md | 5 ++++- ontology/ehdaa2.md | 2 +- ontology/emap.md | 2 +- ontology/emapa.md | 2 +- ontology/epio.md | 4 +++- ontology/ero.md | 4 +++- ontology/eupath.md | 7 ++++++- ontology/fao.md | 2 +- ontology/fbbi.md | 4 +++- ontology/fbbt.md | 4 +++- ontology/fbdv.md | 2 +- ontology/fbsp.md | 4 +++- ontology/fideo.md | 2 +- ontology/fma.md | 2 +- ontology/fobi.md | 2 +- ontology/foodon.md | 4 +++- ontology/fovt.md | 4 +++- ontology/gecko.md | 4 +++- ontology/geno.md | 4 +++- ontology/gno.md | 4 +++- ontology/go.md | 4 +++- ontology/hancestro.md | 4 +++- ontology/hao.md | 2 +- ontology/ico.md | 4 +++- ontology/kisao.md | 4 +++- ontology/labo.md | 4 +++- ontology/lepao.md | 4 +++- ontology/lipro.md | 4 +++- ontology/ma.md | 2 +- ontology/maxo.md | 4 +++- ontology/mco.md | 4 +++- ontology/mfmo.md | 2 +- ontology/mfo.md | 2 +- ontology/mi.md | 2 +- ontology/mmo.md | 4 +++- ontology/mo.md | 2 +- ontology/mod.md | 4 +++- ontology/mondo.md | 4 +++- ontology/mro.md | 4 +++- ontology/ms.md | 4 +++- ontology/nbo.md | 4 +++- ontology/ncbitaxon.md | 4 +++- ontology/ncro.md | 2 +- ontology/nmr.md | 2 +- ontology/nomen.md | 4 +++- ontology/oae.md | 4 +++- ontology/oarcs.md | 2 +- ontology/obcs.md | 4 +++- ontology/obi.md | 2 +- ontology/obib.md | 6 +++++- ontology/ogms.md | 4 +++- ontology/omo.md | 4 +++- ontology/omrse.md | 4 +++- ontology/one.md | 6 +++++- ontology/ons.md | 4 +++- ontology/ontoavida.md | 5 ++++- ontology/ontoneo.md | 4 +++- ontology/opl.md | 5 ++++- ontology/ornaseq.md | 2 +- ontology/pco.md | 4 +++- ontology/peco.md | 4 +++- ontology/plana.md | 2 +- ontology/poro.md | 2 +- ontology/ppo.md | 4 +++- ontology/pr.md | 4 +++- ontology/psdo.md | 4 +++- ontology/pso.md | 5 ++++- ontology/pw.md | 4 +++- ontology/rbo.md | 4 +++- ontology/resid.md | 4 +++- ontology/rnao.md | 4 +++- ontology/ro.md | 4 +++- ontology/scdo.md | 4 +++- ontology/sep.md | 4 +++- ontology/sepio.md | 5 ++++- ontology/sibo.md | 4 +++- ontology/so.md | 4 +++- ontology/spd.md | 2 +- ontology/stato.md | 4 +++- ontology/swo.md | 4 +++- ontology/symp.md | 4 +++- ontology/tads.md | 2 +- ontology/tao.md | 2 +- ontology/taxrank.md | 4 +++- ontology/tgma.md | 2 +- ontology/trans.md | 4 +++- ontology/tto.md | 4 +++- ontology/txpo.md | 4 +++- ontology/uberon.md | 2 +- ontology/upa.md | 4 +++- ontology/vsao.md | 2 +- ontology/wbbt.md | 2 +- ontology/wbls.md | 4 +++- ontology/xao.md | 2 +- ontology/xco.md | 4 +++- ontology/xlmod.md | 4 +++- ontology/zfa.md | 2 +- ontology/zfs.md | 2 +- util/schema/registry_schema.json | 30 +++++++++++++++++++++++++++--- 123 files changed, 311 insertions(+), 125 deletions(-) diff --git a/ontology/aeo.md b/ontology/aeo.md index bdc6c1345..7d05dd86e 100644 --- a/ontology/aeo.md +++ b/ontology/aeo.md @@ -8,7 +8,7 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology -domain: anatomy +domain: anatomy and development homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues products: diff --git a/ontology/agro.md b/ontology/agro.md index 9f128933c..ccf777561 100644 --- a/ontology/agro.md +++ b/ontology/agro.md @@ -5,7 +5,9 @@ title: Agronomy Ontology license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 -domain: agronomy +domain: agriculture +tags: + - agronomy build: checkout: git clone https://github.com/AgriculturalSemantics/agro.git system: git diff --git a/ontology/aism.md b/ontology/aism.md index 9454c3ee7..4d4f454f8 100644 --- a/ontology/aism.md +++ b/ontology/aism.md @@ -12,7 +12,7 @@ contact: github: JCGiron orcid: 0000-0002-0851-6883 description: The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology. -domain: anatomy +domain: anatomy and development homepage: https://github.com/insect-morphology/aism products: - id: aism.owl diff --git a/ontology/amphx.md b/ontology/amphx.md index ef31a6cd6..b9bfd0275 100644 --- a/ontology/amphx.md +++ b/ontology/amphx.md @@ -12,7 +12,7 @@ contact: github: hescriva orcid: 0000-0001-7577-5028 description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). -domain: anatomy +domain: anatomy and development homepage: https://github.com/EBISPOT/amphx_ontology products: - id: amphx.owl diff --git a/ontology/bco.md b/ontology/bco.md index f4198213b..8c3c5e5ac 100644 --- a/ontology/bco.md +++ b/ontology/bco.md @@ -11,7 +11,9 @@ license: url: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. -domain: biodiversity collections +domain: organisms +tags: + - biodiversity collections homepage: https://github.com/BiodiversityOntologies/bco products: - id: bco.owl diff --git a/ontology/bila.md b/ontology/bila.md index ab08db100..65b6eff48 100644 --- a/ontology/bila.md +++ b/ontology/bila.md @@ -4,7 +4,7 @@ id: bila contact: email: henrich@embl.de label: Thorsten Heinrich -domain: anatomy +domain: anatomy and development homepage: http://4dx.embl.de/4DXpress products: - id: bila.owl diff --git a/ontology/bspo.md b/ontology/bspo.md index d73e0d691..f03de195d 100644 --- a/ontology/bspo.md +++ b/ontology/bspo.md @@ -7,7 +7,7 @@ contact: github: cmungall orcid: 0000-0002-6601-2165 description: An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces -domain: anatomy +domain: anatomy and development homepage: https://github.com/obophenotype/biological-spatial-ontology products: - id: bspo.owl diff --git a/ontology/bto.md b/ontology/bto.md index 1b789a88e..50fdbd3f8 100644 --- a/ontology/bto.md +++ b/ontology/bto.md @@ -7,7 +7,7 @@ contact: github: chdudek orcid: 0000-0001-9117-7909 description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. -domain: anatomy +domain: anatomy and development homepage: http://www.brenda-enzymes.org tracker: https://github.com/BRENDA-Enzymes/BTO/issues page: https://en.wikipedia.org/wiki/BRENDA_tissue_ontology diff --git a/ontology/caro.md b/ontology/caro.md index 56b9541ee..7f09a884d 100644 --- a/ontology/caro.md +++ b/ontology/caro.md @@ -10,7 +10,7 @@ license: url: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 description: An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species -domain: anatomy +domain: anatomy and development homepage: https://github.com/obophenotype/caro/ products: - id: caro.owl diff --git a/ontology/cdno.md b/ontology/cdno.md index 0ecc9af6a..8bdba8536 100644 --- a/ontology/cdno.md +++ b/ontology/cdno.md @@ -12,7 +12,7 @@ contact: github: LilyAndres orcid: 0000-0002-7696-731X description: CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. -domain: diet, metabolomics and nutrition +domain: diet, metabolomics, and nutrition homepage: https://github.com/Southern-Cross-Plant-Science/cdno products: - id: cdno.owl diff --git a/ontology/ceph.md b/ontology/ceph.md index 0628e6f92..59475380a 100644 --- a/ontology/ceph.md +++ b/ontology/ceph.md @@ -13,7 +13,7 @@ contact: github: cmungall orcid: 0000-0002-6601-2165 description: An anatomical and developmental ontology for cephalopods -domain: anatomy +domain: anatomy and development homepage: https://github.com/obophenotype/cephalopod-ontology products: - id: ceph.owl diff --git a/ontology/cl.md b/ontology/cl.md index 26150d2ab..d4b00ff7f 100644 --- a/ontology/cl.md +++ b/ontology/cl.md @@ -26,7 +26,9 @@ license: taxon: id: NCBITaxon:33208 label: Metazoa -domain: cells +domain: anatomy and development +tags: + - cells tracker: https://github.com/obophenotype/cell-ontology/issues mailing_list: https://groups.google.com/g/cl_edit publications: diff --git a/ontology/clao.md b/ontology/clao.md index 7cc11a3e1..e9b0df51a 100644 --- a/ontology/clao.md +++ b/ontology/clao.md @@ -12,7 +12,7 @@ contact: github: luis-gonzalez-m orcid: 0000-0002-9136-9932 description: "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)." -domain: anatomy +domain: anatomy and development homepage: https://github.com/luis-gonzalez-m/Collembola products: - id: clao.owl diff --git a/ontology/clyh.md b/ontology/clyh.md index f783fa8dd..0c2e5d02d 100644 --- a/ontology/clyh.md +++ b/ontology/clyh.md @@ -12,7 +12,7 @@ contact: github: L-Leclere orcid: 0000-0002-7440-0467 description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle. -domain: anatomy +domain: anatomy and development homepage: https://github.com/EBISPOT/clyh_ontology products: - id: clyh.owl diff --git a/ontology/cmo.md b/ontology/cmo.md index b13d46cda..c40f83c63 100644 --- a/ontology/cmo.md +++ b/ontology/cmo.md @@ -10,7 +10,9 @@ license: url: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. -domain: clinical +domain: health +tags: + - clinical homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html tracker: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues page: https://download.rgd.mcw.edu/ontology/clinical_measurement/ diff --git a/ontology/colao.md b/ontology/colao.md index 36b4cd286..5be3aac63 100644 --- a/ontology/colao.md +++ b/ontology/colao.md @@ -8,7 +8,9 @@ contact: github: JCGiron orcid: 0000-0002-0851-6883 description: "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone." -domain: Insect Anatomy. +domain: anatomy and development +tags: + - insect anatomy homepage: https://github.com/insect-morphology/colao products: - id: colao.owl diff --git a/ontology/cro.md b/ontology/cro.md index 1c0825245..cf993082a 100644 --- a/ontology/cro.md +++ b/ontology/cro.md @@ -3,7 +3,9 @@ layout: ontology_detail id: cro title: Contributor Role Ontology description: 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. -domain: scholarly contribution roles +domain: information +tags: + - scholarly contribution roles homepage: https://github.com/data2health/contributor-role-ontology tracker: https://github.com/data2health/contributor-role-ontology/issues contact: diff --git a/ontology/cteno.md b/ontology/cteno.md index 1e50d5a68..00c24a780 100644 --- a/ontology/cteno.md +++ b/ontology/cteno.md @@ -16,7 +16,7 @@ contact: github: cmungall orcid: 0000-0002-6601-2165 description: An anatomical and developmental ontology for ctenophores (Comb Jellies) -domain: anatomy +domain: anatomy and development homepage: https://github.com/obophenotype/ctenophore-ontology products: - id: cteno.owl diff --git a/ontology/ddanat.md b/ontology/ddanat.md index 09ad7876b..5599bb331 100644 --- a/ontology/ddanat.md +++ b/ontology/ddanat.md @@ -7,7 +7,7 @@ contact: github: pfey03 orcid: 0000-0002-4532-2703 description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum -domain: anatomy +domain: anatomy and development homepage: http://dictybase.org/ twitter: dictybase license: diff --git a/ontology/ddpheno.md b/ontology/ddpheno.md index 4eeb76d96..3612520b2 100644 --- a/ontology/ddpheno.md +++ b/ontology/ddpheno.md @@ -10,7 +10,7 @@ license: url: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. -domain: anatomy +domain: anatomy and development homepage: http://dictybase.org/ tracker: https://github.com/obophenotype/dicty-phenotype-ontology/issues twitter: dictybase diff --git a/ontology/disdriv.md b/ontology/disdriv.md index 26ace6536..6fd580396 100644 --- a/ontology/disdriv.md +++ b/ontology/disdriv.md @@ -8,7 +8,9 @@ contact: orcid: 0000-0001-8910-9851 description: Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI. twitter: diseaseontology -domain: disease +domain: health +tags: + - disease homepage: http://www.disease-ontology.org products: - id: disdriv.owl diff --git a/ontology/doid.md b/ontology/doid.md index dcc9cbcf8..7a8517405 100644 --- a/ontology/doid.md +++ b/ontology/doid.md @@ -9,7 +9,9 @@ contact: orcid: 0000-0001-8910-9851 description: An ontology for describing the classification of human diseases organized by etiology. twitter: diseaseontology -domain: disease +domain: health +tags: + - disease homepage: http://www.disease-ontology.org products: - id: doid.owl diff --git a/ontology/ecao.md b/ontology/ecao.md index d9eac1ad0..eaf17dc5b 100644 --- a/ontology/ecao.md +++ b/ontology/ecao.md @@ -12,7 +12,7 @@ contact: github: ettensohn orcid: 0000-0002-3625-0955 description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586). -domain: anatomy +domain: anatomy and development homepage: https://github.com/echinoderm-ontology/ecao_ontology products: - id: ecao.owl diff --git a/ontology/eco.md b/ontology/eco.md index 27cd8b11e..d2b6799cf 100644 --- a/ontology/eco.md +++ b/ontology/eco.md @@ -2,7 +2,7 @@ layout: ontology_detail id: eco description: An ontology for experimental and other evidence statements. -domain: experiments +domain: investigations homepage: https://github.com/evidenceontology/evidenceontology/ tracker: https://github.com/evidenceontology/evidenceontology/issues products: diff --git a/ontology/ecocore.md b/ontology/ecocore.md index d1888ef3e..9f763724a 100644 --- a/ontology/ecocore.md +++ b/ontology/ecocore.md @@ -15,7 +15,10 @@ contact: github: pbuttigieg orcid: 0000-0002-4366-3088 description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. -domain: ecological functions, ecological interactions +domain: environment +tags: + - ecological functions + - ecological interactions homepage: https://github.com/EcologicalSemantics/ecocore products: - id: ecocore.owl diff --git a/ontology/ehdaa2.md b/ontology/ehdaa2.md index 026967e05..0d6fbee1b 100644 --- a/ontology/ehdaa2.md +++ b/ontology/ehdaa2.md @@ -9,7 +9,7 @@ license: label: CC BY 4.0 description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues -domain: anatomy +domain: anatomy and development homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology products: - id: ehdaa2.owl diff --git a/ontology/emap.md b/ontology/emap.md index 3775490c5..09a8cccee 100644 --- a/ontology/emap.md +++ b/ontology/emap.md @@ -7,7 +7,7 @@ contact: github: tfhayamizu orcid: 0000-0002-0956-8634 description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). -domain: anatomy +domain: anatomy and development homepage: http://emouseatlas.org page: https://www.emouseatlas.org/emap/about/what_is_emap.html products: diff --git a/ontology/emapa.md b/ontology/emapa.md index 04ef6f972..321e9b07f 100644 --- a/ontology/emapa.md +++ b/ontology/emapa.md @@ -10,7 +10,7 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: "An ontology for mouse anatomy covering embryonic development and postnatal stages." -domain: anatomy +domain: anatomy and development homepage: http://www.informatics.jax.org/expression.shtml tracker: https://github.com/obophenotype/mouse-anatomy-ontology/issues products: diff --git a/ontology/epio.md b/ontology/epio.md index 2cb7b897f..b5b93bcfe 100644 --- a/ontology/epio.md +++ b/ontology/epio.md @@ -4,7 +4,9 @@ id: epio label: Epilepsy Ontology title: Epilepsy Ontology description: A application driven Epilepsy Ontology with official terms from the ILAE. -domain: disease +domain: health +tags: + - disease license: url: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 diff --git a/ontology/ero.md b/ontology/ero.md index 37236525f..33d4d9e9d 100644 --- a/ontology/ero.md +++ b/ontology/ero.md @@ -8,7 +8,9 @@ license: url: https://creativecommons.org/licenses/by/2.0/ label: CC BY 2.0 description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. -domain: resources +domain: information +tags: + - resources homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology documentation: https://open.med.harvard.edu/wiki/display/eaglei/Ontology products: diff --git a/ontology/eupath.md b/ontology/eupath.md index ddb4a6a0e..e1d12234f 100644 --- a/ontology/eupath.md +++ b/ontology/eupath.md @@ -10,7 +10,12 @@ license: url: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 depicted_by: https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png -domain: functional genomics, population biology, clinical epidemiology, and microbiomes +domain: organisms +tags: + - functional genomics + - population biology + - clinical epidemiology + - microbiomes description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology products: diff --git a/ontology/fao.md b/ontology/fao.md index 72f10d122..ea5de62a8 100644 --- a/ontology/fao.md +++ b/ontology/fao.md @@ -10,7 +10,7 @@ license: url: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 description: A structured controlled vocabulary for the anatomy of fungi. -domain: anatomy +domain: anatomy and development tracker: https://github.com/obophenotype/fungal-anatomy-ontology/issues homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ products: diff --git a/ontology/fbbi.md b/ontology/fbbi.md index 08e036fdd..a5bba4728 100644 --- a/ontology/fbbi.md +++ b/ontology/fbbi.md @@ -11,7 +11,9 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. -domain: imaging experiments +domain: investigations +tags: + - imaging experiments homepage: http://cellimagelibrary.org/ tracker: https://github.com/CRBS/Biological_Imaging_Methods_Ontology/issues products: diff --git a/ontology/fbbt.md b/ontology/fbbt.md index 5c637524e..eeb216e32 100644 --- a/ontology/fbbt.md +++ b/ontology/fbbt.md @@ -8,7 +8,9 @@ contact: github: Clare72 orcid: 0000-0002-1373-1705 description: An ontology representing the gross anatomy of Drosophila melanogaster. -domain: Drosophilid anatomy +domain: anatomy and development +tags: + - Drosophilid anatomy homepage: http://purl.obolibrary.org/obo/fbbt repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology products: diff --git a/ontology/fbdv.md b/ontology/fbdv.md index ce636aedd..b5efc24e1 100644 --- a/ontology/fbdv.md +++ b/ontology/fbdv.md @@ -8,7 +8,7 @@ contact: github: Clare72 orcid: 0000-0002-1373-1705 description: A structured controlled vocabulary of the development of Drosophila melanogaster. -domain: development +domain: anatomy and development homepage: http://purl.obolibrary.org/obo/fbdv repository: https://github.com/FlyBase/drosophila-developmental-ontology products: diff --git a/ontology/fbsp.md b/ontology/fbsp.md index 2744dba65..5269a3dd3 100644 --- a/ontology/fbsp.md +++ b/ontology/fbsp.md @@ -7,7 +7,9 @@ contact: github: Clare72 orcid: 0000-0002-1373-1705 description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. -domain: taxonomy +domain: organisms +tags: + - taxonomy homepage: http://www.flybase.org/ products: - id: fbsp.owl diff --git a/ontology/fideo.md b/ontology/fideo.md index 3a532d8dd..c484bf468 100644 --- a/ontology/fideo.md +++ b/ontology/fideo.md @@ -3,7 +3,7 @@ layout: ontology_detail id: fideo title: Food Interactions with Drugs Evidence Ontology description: Food-Drug interactions automatically extracted from scientific literature -domain: diet, metabolomics and nutrition +domain: diet, metabolomics, and nutrition homepage: https://gitub.u-bordeaux.fr/erias/fideo contact: email: georgeta.bordea@u-bordeaux.fr diff --git a/ontology/fma.md b/ontology/fma.md index ee9c674eb..493a53d13 100644 --- a/ontology/fma.md +++ b/ontology/fma.md @@ -8,7 +8,7 @@ license: url: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 description: This is currently a slimmed down version of FMA -domain: anatomy +domain: anatomy and development homepage: http://si.washington.edu/projects/fma page: http://en.wikipedia.org/wiki/Foundational_Model_of_Anatomy publications: diff --git a/ontology/fobi.md b/ontology/fobi.md index 3c7b5f29a..f801861b9 100644 --- a/ontology/fobi.md +++ b/ontology/fobi.md @@ -7,7 +7,7 @@ contact: github: pcastellanoescuder orcid: 0000-0001-6466-877X description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data -domain: metabolomics and nutrition +domain: diet, metabolomics, and nutrition license: url: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 diff --git a/ontology/foodon.md b/ontology/foodon.md index d2759041a..29c77e26b 100644 --- a/ontology/foodon.md +++ b/ontology/foodon.md @@ -7,7 +7,9 @@ contact: github: ddooley orcid: 0000-0002-8844-9165 description: A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research -domain: food +domain: diet, metabolomics, and nutrition +tags: + - food homepage: https://foodon.org/ license: url: http://creativecommons.org/licenses/by/3.0/ diff --git a/ontology/fovt.md b/ontology/fovt.md index 7f6ca990f..cc08aaa37 100644 --- a/ontology/fovt.md +++ b/ontology/fovt.md @@ -15,7 +15,9 @@ contact: github: megbalk orcid: 0000-0003-2699-3066 description: 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). -domain: vertebrate traits +domain: phenotype +tags: + - vertebrate traits homepage: https://github.com/futres/fovt products: - id: fovt.owl diff --git a/ontology/gecko.md b/ontology/gecko.md index 1befd6c83..f49096aa2 100644 --- a/ontology/gecko.md +++ b/ontology/gecko.md @@ -3,7 +3,9 @@ layout: ontology_detail id: gecko title: Genomics Cohorts Knowledge Ontology description: An ontology to represent genomics cohort attributes -domain: cohort studies +domain: organisms +tags: + - cohort studies homepage: https://github.com/IHCC-cohorts/GECKO contact: email: rbca.jackson@gmail.com diff --git a/ontology/geno.md b/ontology/geno.md index bd9511d39..300bd010e 100644 --- a/ontology/geno.md +++ b/ontology/geno.md @@ -3,7 +3,9 @@ layout: ontology_detail id: geno title: Genotype Ontology description: An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases. -domain: genotype-to-phenotype associations +domain: biological systems +tags: + - genotype-to-phenotype associations homepage: https://github.com/monarch-initiative/GENO-ontology/ tracker: https://github.com/monarch-initiative/GENO-ontology/issues contact: diff --git a/ontology/gno.md b/ontology/gno.md index 652c06466..704b2a699 100644 --- a/ontology/gno.md +++ b/ontology/gno.md @@ -7,7 +7,9 @@ contact: github: edwardsnj orcid: 0000-0001-5168-3196 description: 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. -domain: glycan structure +domain: biochemistry +tags: + - glycan structure homepage: https://gnome.glyomics.org/ products: - id: gno.owl diff --git a/ontology/go.md b/ontology/go.md index be39da15b..16d4a359a 100644 --- a/ontology/go.md +++ b/ontology/go.md @@ -21,7 +21,9 @@ tracker: https://github.com/geneontology/go-ontology/issues/ taxon: id: NCBITaxon:1 label: All life -domain: biology +domain: biological systems +tags: + - biology integration_server: http://build.berkeleybop.org/view/GO dependencies: - id: uberon diff --git a/ontology/hancestro.md b/ontology/hancestro.md index 1a5c77289..c92362059 100644 --- a/ontology/hancestro.md +++ b/ontology/hancestro.md @@ -10,7 +10,9 @@ title: Human Ancestry Ontology 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. homepage: https://github.com/EBISPOT/ancestro tracker: https://github.com/EBISPOT/ancestro/issues -domain: ancestry +domain: organisms +tags: + - ancestry products: - id: hancestro.owl description: The full version of HANCESTRO in OWL format diff --git a/ontology/hao.md b/ontology/hao.md index e64a88b98..027f8f5ac 100644 --- a/ontology/hao.md +++ b/ontology/hao.md @@ -11,7 +11,7 @@ license: url: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) -domain: anatomy +domain: anatomy and development homepage: http://hymao.org products: - id: hao.owl diff --git a/ontology/ico.md b/ontology/ico.md index 6a868070c..d7fb7c0c5 100644 --- a/ontology/ico.md +++ b/ontology/ico.md @@ -3,7 +3,9 @@ layout: ontology_detail id: ico title: Informed Consent Ontology description: An ontology of clinical informed consents -domain: informed consent +domain: investigations +tags: + - informed consent license: url: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 diff --git a/ontology/kisao.md b/ontology/kisao.md index cd29be1f5..cbbc312a1 100644 --- a/ontology/kisao.md +++ b/ontology/kisao.md @@ -7,7 +7,9 @@ contact: github: jonrkarr orcid: 0000-0002-2605-5080 description: A classification of algorithms for simulating biology and their outputs -domain: algorithms +domain: information technology +tags: + - algorithms homepage: http://co.mbine.org/standards/kisao tracker: https://github.com/SED-ML/KiSAO/issues products: diff --git a/ontology/labo.md b/ontology/labo.md index a9b7cf9be..16ebb127a 100644 --- a/ontology/labo.md +++ b/ontology/labo.md @@ -8,7 +8,9 @@ contact: github: pfabry orcid: 0000-0002-3336-2476 description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. -domain: clinical documentation +domain: information +tags: + - clinical documentation usages: - user: https://griis.ca/ type: database architecture diff --git a/ontology/lepao.md b/ontology/lepao.md index 4a1c3ed3c..4af6a5d76 100644 --- a/ontology/lepao.md +++ b/ontology/lepao.md @@ -8,7 +8,9 @@ contact: github: luis-gonzalez-m orcid: 0000-0002-9136-9932 description: The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research). -domain: Insect Anatomy +domain: anatomy and development +tags: + - insect anatomy homepage: https://github.com/insect-morphology/lepao products: - id: lepao.owl diff --git a/ontology/lipro.md b/ontology/lipro.md index ee7a82d6e..b21c2dde4 100644 --- a/ontology/lipro.md +++ b/ontology/lipro.md @@ -6,7 +6,9 @@ contact: email: bakerc@unb.ca label: Christipher Baker description: An ontology representation of the LIPIDMAPS nomenclature classification. -domain: lipids +domain: biochemistry +tags: + - lipids title: Lipid Ontology build: source_url: http://www.lipidprofiles.com/LipidOntology diff --git a/ontology/ma.md b/ontology/ma.md index a27411f97..4d0f455df 100644 --- a/ontology/ma.md +++ b/ontology/ma.md @@ -10,7 +10,7 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus). -domain: anatomy +domain: anatomy and development homepage: https://github.com/obophenotype/mouse-anatomy-ontology page: http://www.informatics.jax.org/searches/AMA_form.shtml products: diff --git a/ontology/maxo.md b/ontology/maxo.md index 3eefcf8de..25f80a049 100644 --- a/ontology/maxo.md +++ b/ontology/maxo.md @@ -15,7 +15,9 @@ contact: github: LCCarmody orcid: 0000-0001-7941-2961 description: Medical Action Ontology is an ontology... -domain: medical +domain: health +tags: + - medical homepage: https://github.com/monarch-initiative/MAxO products: - id: maxo.owl diff --git a/ontology/mco.md b/ontology/mco.md index 2ce23468b..2daf89633 100644 --- a/ontology/mco.md +++ b/ontology/mco.md @@ -15,7 +15,9 @@ contact: github: citmejia orcid: 0000-0002-0142-5591 description: Microbial Conditions Ontology is an ontology... -domain: experimental conditions +domain: investigations +tags: + - experimental conditions homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology products: - id: mco.owl diff --git a/ontology/mfmo.md b/ontology/mfmo.md index 01460be89..88ab3f878 100644 --- a/ontology/mfmo.md +++ b/ontology/mfmo.md @@ -10,7 +10,7 @@ license: taxon: id: NCBITaxon:40674 label: Mammalian -domain: anatomy +domain: anatomy and development repository: https://github.com/RDruzinsky/feedontology tracker: https://github.com/RDruzinsky/feedontology/issues contact: diff --git a/ontology/mfo.md b/ontology/mfo.md index b21f105de..4536dcf7f 100644 --- a/ontology/mfo.md +++ b/ontology/mfo.md @@ -5,7 +5,7 @@ contact: email: Thorsten.Henrich@embl-heidelberg.de label: Thorsten Henrich description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. -domain: anatomy +domain: anatomy and development products: - id: mfo.owl taxon: diff --git a/ontology/mi.md b/ontology/mi.md index ace97dad7..2dffaedcf 100644 --- a/ontology/mi.md +++ b/ontology/mi.md @@ -11,7 +11,7 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. -domain: experiments +domain: investigations homepage: https://github.com/HUPO-PSI/psi-mi-CV page: https://github.com/HUPO-PSI/psi-mi-CV products: diff --git a/ontology/mmo.md b/ontology/mmo.md index 2d5d41773..eb8617f30 100644 --- a/ontology/mmo.md +++ b/ontology/mmo.md @@ -10,7 +10,9 @@ license: url: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 description: "A representation of the variety of methods used to make clinical and phenotype measurements. " -domain: clinical +domain: health +tags: + - clinical homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 tracker: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues page: https://download.rgd.mcw.edu/ontology/measurement_method/ diff --git a/ontology/mo.md b/ontology/mo.md index 0fc078098..4a52215e4 100644 --- a/ontology/mo.md +++ b/ontology/mo.md @@ -6,7 +6,7 @@ contact: email: stoeckrt@pcbi.upenn.edu label: Chris Stoeckert description: A standardized description of a microarray experiment in support of MAGE v.1. -domain: experiments +domain: investigations homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php page: http://mged.sourceforge.net/software/downloads.php products: diff --git a/ontology/mod.md b/ontology/mod.md index 21771ed06..a76451f5e 100644 --- a/ontology/mod.md +++ b/ontology/mod.md @@ -13,7 +13,9 @@ publications: - id: https://pubmed.ncbi.nlm.nih.gov/18688235/ title: "The PSI-MOD community standard for representation of protein modification data" description: PSI-MOD is an ontology consisting of terms that describe protein chemical modifications -domain: proteins +domain: biochemistry +tags: + - proteins homepage: http://www.psidev.info/MOD tracker: https://github.com/HUPO-PSI/psi-mod-CV/issues products: diff --git a/ontology/mondo.md b/ontology/mondo.md index eb1e86418..56456ea7a 100644 --- a/ontology/mondo.md +++ b/ontology/mondo.md @@ -17,7 +17,9 @@ depicted_by: https://raw.githubusercontent.com/monarch-initiative/mondo/master/d taxon: id: NCBITaxon:33208 label: Metazoa -domain: disease +domain: health +tags: + - disease tracker: https://github.com/monarch-initiative/mondo/issues mailing_list: https://groups.google.com/group/mondo-users canonical: mondo.owl diff --git a/ontology/mro.md b/ontology/mro.md index 0bb16bf51..5b59c2a71 100644 --- a/ontology/mro.md +++ b/ontology/mro.md @@ -5,7 +5,9 @@ title: MHC Restriction Ontology description: An ontology for Major Histocompatibility Complex (MHC) restriction in experiments tracker: https://github.com/IEDB/MRO/issues homepage: https://github.com/IEDB/MRO -domain: Major Histocompatibility Complex +domain: biochemistry +tags: + - Major Histocompatibility Complex contact: label: Bjoern Peters email: bpeters@lji.org diff --git a/ontology/ms.md b/ontology/ms.md index 0f37f6922..322bfeaed 100644 --- a/ontology/ms.md +++ b/ontology/ms.md @@ -10,7 +10,9 @@ contact: github: germa orcid: 0000-0002-1767-2343 integration_server: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master -domain: MS experiments +domain: investigations +tags: + - MS experiments mailing_list: psidev-ms-vocab@lists.sourceforge.net homepage: http://www.psidev.info/groups/controlled-vocabularies tracker: https://github.com/HUPO-PSI/psi-ms-CV/issues diff --git a/ontology/nbo.md b/ontology/nbo.md index 2e4385cb8..a5c04d3f8 100644 --- a/ontology/nbo.md +++ b/ontology/nbo.md @@ -7,7 +7,9 @@ contact: github: gkoutos orcid: 0000-0002-2061-091X description: An ontology of human and animal behaviours and behavioural phenotypes -domain: behavior +domain: biological systems +tags: + - behavior homepage: https://github.com/obo-behavior/behavior-ontology/ products: - id: nbo.owl diff --git a/ontology/ncbitaxon.md b/ontology/ncbitaxon.md index d69e0a9e6..82f3fe851 100644 --- a/ontology/ncbitaxon.md +++ b/ontology/ncbitaxon.md @@ -15,7 +15,9 @@ contact: orcid: 0000-0002-9415-5104 description: An ontology representation of the NCBI organismal taxonomy wasDerivedFrom: ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat -domain: taxonomy +domain: organisms +tags: + - taxonomy homepage: https://github.com/obophenotype/ncbitaxon page: http://www.ncbi.nlm.nih.gov/taxonomy tracker: https://github.com/obophenotype/ncbitaxon/issues diff --git a/ontology/ncro.md b/ontology/ncro.md index ba93ccaf2..555ccfff7 100644 --- a/ontology/ncro.md +++ b/ontology/ncro.md @@ -3,7 +3,7 @@ layout: ontology_detail id: ncro title: Non-Coding RNA Ontology description: An ontology for non-coding RNA, both of biological origin, and engineered. -domain: experiments +domain: investigations homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology mailing_list: ncro-devel@googlegroups.com, ncro-discuss@googlegroups.com tracker: https://github.com/OmniSearch/ncro/issues diff --git a/ontology/nmr.md b/ontology/nmr.md index 8e5fb0e65..30eac2a84 100644 --- a/ontology/nmr.md +++ b/ontology/nmr.md @@ -5,7 +5,7 @@ contact: email: schober@imbi.uni-freiburg.de label: Schober Daniel description: Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation. -domain: experiments +domain: investigations homepage: http://msi-ontology.sourceforge.net/ page: http://msi-ontology.sourceforge.net/ontology/NMR.owlDocument.doc products: diff --git a/ontology/nomen.md b/ontology/nomen.md index a630017d8..4b6f457b8 100644 --- a/ontology/nomen.md +++ b/ontology/nomen.md @@ -12,7 +12,9 @@ license: url: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 description: NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. -domain: biological nomenclature +domain: information +tags: + - biological nomenclature homepage: https://github.com/SpeciesFileGroup/nomen products: - id: nomen.owl diff --git a/ontology/oae.md b/ontology/oae.md index 4ff798e5f..aff61f839 100644 --- a/ontology/oae.md +++ b/ontology/oae.md @@ -7,7 +7,9 @@ contact: github: yongqunh orcid: 0000-0001-9189-9661 description: A biomedical ontology in the domain of adverse events -domain: adverse events, health +domain: health +tags: + - adverse events homepage: https://github.com/OAE-ontology/OAE/ tracker: https://github.com/OAE-ontology/OAE/issues products: diff --git a/ontology/oarcs.md b/ontology/oarcs.md index 0348ac74a..c377ccea2 100644 --- a/ontology/oarcs.md +++ b/ontology/oarcs.md @@ -9,7 +9,7 @@ contact: label: Matt Yoder github: mjy orcid: 0000-0002-5640-5491 -domain: anatomy +domain: anatomy and development repository: https://github.com/aszool/oarcs license: url: http://creativecommons.org/licenses/by/3.0/ diff --git a/ontology/obcs.md b/ontology/obcs.md index 5ff9d7448..c516a913e 100644 --- a/ontology/obcs.md +++ b/ontology/obcs.md @@ -9,7 +9,9 @@ contact: label: Jie Zheng github: zhengj2007 orcid: 0000-0002-2999-0103 -domain: statistics +domain: information technology +tags: + - statistics homepage: https://github.com/obcs/obcs products: - id: obcs.owl diff --git a/ontology/obi.md b/ontology/obi.md index ea2278702..08a251660 100644 --- a/ontology/obi.md +++ b/ontology/obi.md @@ -9,7 +9,7 @@ review: label: PDF link: https://drive.google.com/open?id=0B8vqEgF1N0NIMFlSM3RvdUxGTnc description: An integrated ontology for the description of life-science and clinical investigations -domain: experiments +domain: investigations homepage: http://obi-ontology.org mailing_list: http://groups.google.com/group/obi-users tracker: http://purl.obolibrary.org/obo/obi/tracker diff --git a/ontology/obib.md b/ontology/obib.md index dd5e13dfa..e61724da5 100644 --- a/ontology/obib.md +++ b/ontology/obib.md @@ -8,7 +8,11 @@ contact: github: zhengj2007 orcid: 0000-0002-2999-0103 description: An ontology built for annotation and modeling of biobank repository and biobanking administration -domain: biobanking, specimens, bio-repository, biocuration +domain: investigations +tags: + - biobanking + - specimens + - bio-repository homepage: https://github.com/biobanking/biobanking products: - id: obib.owl diff --git a/ontology/ogms.md b/ontology/ogms.md index 1a71c2d4a..fcde4a5c7 100644 --- a/ontology/ogms.md +++ b/ontology/ogms.md @@ -10,7 +10,9 @@ license: url: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities -domain: medicine +domain: health +tags: + - medicine homepage: https://github.com/OGMS/ogms products: - id: ogms.owl diff --git a/ontology/omo.md b/ontology/omo.md index e30102053..3e12b25e8 100644 --- a/ontology/omo.md +++ b/ontology/omo.md @@ -7,7 +7,9 @@ contact: github: cmungall orcid: 0000-0002-6601-2165 description: 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). -domain: ontology term annotation +domain: information +tags: + - ontology term annotation homepage: https://github.com/information-artifact-ontology/ontology-metadata tracker: https://github.com/information-artifact-ontology/ontology-metadata/issues products: diff --git a/ontology/omrse.md b/ontology/omrse.md index ef2fa0c8c..1d2c3aefe 100644 --- a/ontology/omrse.md +++ b/ontology/omrse.md @@ -10,7 +10,9 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: 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. -domain: medicine +domain: health +tags: + - medicine homepage: https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview tracker: https://github.com/ufbmi/OMRSE/issues products: diff --git a/ontology/one.md b/ontology/one.md index 9d17631c5..93bdf5674 100644 --- a/ontology/one.md +++ b/ontology/one.md @@ -9,7 +9,11 @@ contact: github: cyang0128 orcid: 0000-0001-9202-5309 description: An ontology to standardize research output of nutritional epidemiologic studies. -domain: nutritional epidemiology, observational studies, dietary surveys +domain: diet, metabolomics, and nutrition +tags: + - nutritional epidemiology + - observational studies + - dietary surveys homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies page: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies license: diff --git a/ontology/ons.md b/ontology/ons.md index 0a53859c5..ad86428ef 100644 --- a/ontology/ons.md +++ b/ontology/ons.md @@ -9,7 +9,9 @@ contact: github: FrancescoVit orcid: 0000-0001-9125-4337 description: An ontology for description of concepts in the nutritional studies domain. -domain: nutrition, nutritional studies, nutrition professionals +domain: diet, metabolomics, and nutrition +tags: + - nutrition, nutritional studies, nutrition professionals homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies page: https://github.com/enpadasi/Ontology-for-Nutritional-Studies license: diff --git a/ontology/ontoavida.md b/ontology/ontoavida.md index b73dfb1e3..d621bc054 100644 --- a/ontology/ontoavida.md +++ b/ontology/ontoavida.md @@ -8,7 +8,10 @@ contact: github: miguelfortuna orcid: 0000-0002-8374-1941 description: "OntoAvida develops an integrated vocabulary for the description of the most widely-used computational approach for studying evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment)." -domain: digital evolution, a branch of Artificial Life. +domain: simulation +tags: + - digital evolution + - artificial life homepage: https://gitlab.com/fortunalab/ontoavida products: - id: ontoavida.owl diff --git a/ontology/ontoneo.md b/ontology/ontoneo.md index c87212571..ed2d6165a 100644 --- a/ontology/ontoneo.md +++ b/ontology/ontoneo.md @@ -11,7 +11,9 @@ description: The Obstetric and Neonatal Ontology is a structured controlled voca license: url: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 -domain: biomedical, health +domain: health +tags: + - biomedical homepage: ontoneo.com mailing_list: http://groups.google.com/group/ontoneo-discuss products: diff --git a/ontology/opl.md b/ontology/opl.md index 3b444c11f..db8f89bc5 100644 --- a/ontology/opl.md +++ b/ontology/opl.md @@ -10,7 +10,10 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: A reference ontology for parasite life cycle stages. -domain: life cycle stage, parasite organism +domain: organisms +tags: + - life cycle stage + - parasite organism homepage: https://github.com/OPL-ontology/OPL products: - id: opl.owl diff --git a/ontology/ornaseq.md b/ontology/ornaseq.md index cec57c8d7..0f78649f8 100644 --- a/ontology/ornaseq.md +++ b/ontology/ornaseq.md @@ -8,7 +8,7 @@ contact: github: safisher orcid: 0000-0001-8034-7685 description: An application ontology designed to annotate next-generation sequencing experiments performed on RNA. -domain: experiments +domain: investigations homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml products: - id: ornaseq.owl diff --git a/ontology/pco.md b/ontology/pco.md index 2c5a3d70a..5ff03a631 100644 --- a/ontology/pco.md +++ b/ontology/pco.md @@ -15,7 +15,9 @@ contact: github: ramonawalls orcid: 0000-0001-8815-0078 description: An ontology about groups of interacting organisms such as populations and communities -domain: collections of organisms +domain: environment +tags: + - collections of organisms homepage: https://github.com/PopulationAndCommunityOntology/pco products: - id: pco.owl diff --git a/ontology/peco.md b/ontology/peco.md index 894c86e29..c8d3a0446 100644 --- a/ontology/peco.md +++ b/ontology/peco.md @@ -8,7 +8,9 @@ contact: github: jaiswalp orcid: 0000-0002-1005-8383 description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. -domain: experimental conditions +domain: investigations +tags: + - experimental conditions homepage: http://planteome.org/ page: http://browser.planteome.org/amigo/term/PECO:0007359 products: diff --git a/ontology/plana.md b/ontology/plana.md index f797177e0..ffde6a40e 100644 --- a/ontology/plana.md +++ b/ontology/plana.md @@ -15,7 +15,7 @@ contact: github: srobb1 orcid: 0000-0002-3528-5267 description: PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes. -domain: anatomy +domain: anatomy and development homepage: https://github.com/obophenotype/planaria-ontology products: - id: plana.owl diff --git a/ontology/poro.md b/ontology/poro.md index 9a4de221d..5ba4d107b 100644 --- a/ontology/poro.md +++ b/ontology/poro.md @@ -7,7 +7,7 @@ contact: github: bobthacker orcid: 0000-0002-9654-0073 description: An ontology covering the anatomy of the taxon Porifera (sponges) -domain: anatomy +domain: anatomy and development homepage: https://github.com/obophenotype/porifera-ontology products: - id: poro.owl diff --git a/ontology/ppo.md b/ontology/ppo.md index 4f8c0da22..90d165ef7 100644 --- a/ontology/ppo.md +++ b/ontology/ppo.md @@ -2,7 +2,9 @@ layout: ontology_detail id: ppo title: Plant Phenology Ontology -domain: plant phenotypes +domain: phenotype +tags: + - plant phenotypes description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. homepage: https://github.com/PlantPhenoOntology/PPO contact: diff --git a/ontology/pr.md b/ontology/pr.md index 568a9ce74..edb0e11af 100644 --- a/ontology/pr.md +++ b/ontology/pr.md @@ -8,7 +8,9 @@ contact: github: nataled orcid: 0000-0001-5809-9523 description: An ontological representation of protein-related entities -domain: proteins +domain: biochemistry +tags: + - proteins homepage: http://proconsortium.org documentation: https://proconsortium.org/download/current/pro_readme.txt products: diff --git a/ontology/psdo.md b/ontology/psdo.md index fbff4c508..5d5246bf2 100644 --- a/ontology/psdo.md +++ b/ontology/psdo.md @@ -12,7 +12,9 @@ contact: github: zachll orcid: 0000-0002-9117-9338 description: Ontology to reproducibly study visualizations of clinical performance -domain: learning systems +domain: information +tags: + - learning systems homepage: https://github.com/Display-Lab/psdo products: - id: psdo.owl diff --git a/ontology/pso.md b/ontology/pso.md index be0704746..0def97d4b 100644 --- a/ontology/pso.md +++ b/ontology/pso.md @@ -15,7 +15,10 @@ contact: github: cooperl09 orcid: 0000-0002-6379-8932 description: The Plant Stress Ontology describes... -domain: plant disease and abiotic stress +domain: agriculture +tags: + - plant disease + - abiotic stress homepage: https://github.com/Planteome/plant-stress-ontology products: - id: pso.owl diff --git a/ontology/pw.md b/ontology/pw.md index 71e2d1edb..9c146f764 100644 --- a/ontology/pw.md +++ b/ontology/pw.md @@ -10,7 +10,9 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: A controlled vocabulary for annotating gene products to pathways. -domain: biological process +domain: biological systems +tags: + - biological process homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html tracker: https://github.com/rat-genome-database/PW-Pathway-Ontology/issues page: https://download.rgd.mcw.edu/ontology/pathway/ diff --git a/ontology/rbo.md b/ontology/rbo.md index 944b0bb8a..1f1a537ae 100644 --- a/ontology/rbo.md +++ b/ontology/rbo.md @@ -15,7 +15,9 @@ contact: github: DanBerrios orcid: 0000-0003-4312-9552 description: RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. -domain: radiation biology, the study of the effects of radiation on biological systems +domain: environment +tags: + - radiation biology homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO products: - id: rbo.owl diff --git a/ontology/resid.md b/ontology/resid.md index 278302a99..9dba77a90 100644 --- a/ontology/resid.md +++ b/ontology/resid.md @@ -5,7 +5,9 @@ contact: email: john.garavelli@ebi.ac.uk label: John Garavelli description: For the description of covalent bonds in proteins. -domain: proteins +domain: biochemistry +tags: + - proteins homepage: http://www.ebi.ac.uk/RESID/ title: Protein covalent bond is_obsolete: true diff --git a/ontology/rnao.md b/ontology/rnao.md index 749eb2fd0..693cf64e4 100644 --- a/ontology/rnao.md +++ b/ontology/rnao.md @@ -8,7 +8,9 @@ contact: license: url: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 -domain: molecular structure +domain: biochemistry +tags: + - molecular structure homepage: https://github.com/bgsu-rna/rnao browsers: - label: RNAO diff --git a/ontology/ro.md b/ontology/ro.md index edccd21d8..c5363add1 100644 --- a/ontology/ro.md +++ b/ontology/ro.md @@ -13,7 +13,9 @@ homepage: https://oborel.github.io/ documentation: https://oborel.github.io/obo-relations/ tracker: https://github.com/oborel/obo-relations/issues mailing_list: "https://groups.google.com/forum/#!forum/obo-relations" -domain: relations +domain: upper +tags: + - relations contact: email: cjmungall@lbl.gov label: Chris Mungall diff --git a/ontology/scdo.md b/ontology/scdo.md index d0bb759fd..13d7b1531 100644 --- a/ontology/scdo.md +++ b/ontology/scdo.md @@ -12,7 +12,9 @@ contact: github: JadeHotchkiss orcid: 0000-0002-2193-0704 description: An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. -domain: disease +domain: health +tags: + - disease homepage: https://scdontology.h3abionet.org/ products: - id: scdo.owl diff --git a/ontology/sep.md b/ontology/sep.md index ae3817e31..658955e75 100644 --- a/ontology/sep.md +++ b/ontology/sep.md @@ -5,7 +5,9 @@ contact: email: psidev-gps-dev@lists.sourceforge.net label: SEP developers via the PSI and MSI mailing lists description: A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments. -domain: provenance +domain: investigations +tags: + - provenance homepage: http://psidev.info/index.php?q=node/312 page: http://psidev.info/index.php?q=node/312 products: diff --git a/ontology/sepio.md b/ontology/sepio.md index bcfde3ac2..77f2a8320 100644 --- a/ontology/sepio.md +++ b/ontology/sepio.md @@ -3,7 +3,10 @@ layout: ontology_detail id: sepio title: Scientific Evidence and Provenance Information Ontology description: An ontology for representing the provenance of scientific claims and the evidence that supports them. -domain: scientific claims, evidence +domain: investigations +tags: + - scientific claims + - evidence homepage: https://github.com/monarch-initiative/SEPIO-ontology tracker: https://github.com/monarch-initiative/SEPIO-ontology/issues contact: diff --git a/ontology/sibo.md b/ontology/sibo.md index 775addf48..74be89383 100644 --- a/ontology/sibo.md +++ b/ontology/sibo.md @@ -6,7 +6,9 @@ contact: email: cjmungall@lbl.gov label: Chris Mungall description: Social Behavior in insects -domain: behavior +domain: biological systems +tags: + - behavior homepage: https://github.com/obophenotype/sibo tracker: https://github.com/obophenotype/sibo/issues products: diff --git a/ontology/so.md b/ontology/so.md index b550bf73a..08e23d50c 100644 --- a/ontology/so.md +++ b/ontology/so.md @@ -10,7 +10,9 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. -domain: biological sequence +domain: biochemistry +tags: + - biological sequence homepage: http://www.sequenceontology.org/ mailing_list: https://sourceforge.net/p/song/mailman/song-devel/ page: https://en.wikipedia.org/wiki/Sequence_Ontology diff --git a/ontology/spd.md b/ontology/spd.md index 525173685..ebd22a13b 100644 --- a/ontology/spd.md +++ b/ontology/spd.md @@ -10,7 +10,7 @@ license: url: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 description: 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). -domain: anatomy +domain: anatomy and development homepage: http://research.amnh.org/atol/files/ products: - id: spd.owl diff --git a/ontology/stato.md b/ontology/stato.md index f657352fd..72820626e 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -9,7 +9,9 @@ contact: label: Alejandra Gonzalez-Beltran github: agbeltran orcid: 0000-0003-3499-8262 -domain: statistics +domain: information technology +tags: + - statistics homepage: http://stato-ontology.org/ products: - id: stato.owl diff --git a/ontology/swo.md b/ontology/swo.md index 3d6318e50..46fd79126 100644 --- a/ontology/swo.md +++ b/ontology/swo.md @@ -15,7 +15,9 @@ products: - id: swo.owl title: Software ontology 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 +domain: information technology +tags: + - software build: source_url: https://raw.githubusercontent.com/allysonlister/swo/master/release/swo_inferred.owl method: owl2obo diff --git a/ontology/symp.md b/ontology/symp.md index b2a627a8f..6de131c39 100644 --- a/ontology/symp.md +++ b/ontology/symp.md @@ -7,7 +7,9 @@ contact: github: lschriml orcid: 0000-0001-8910-9851 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 +domain: health +tags: + - disease homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page products: - id: symp.owl diff --git a/ontology/tads.md b/ontology/tads.md index 2ab42af0c..3d4385229 100644 --- a/ontology/tads.md +++ b/ontology/tads.md @@ -8,7 +8,7 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: "The anatomy of the Tick, Families: Ixodidae, Argassidae" -domain: anatomy +domain: anatomy and development homepage: https://www.vectorbase.org/ontology-browser products: - id: tads.owl diff --git a/ontology/tao.md b/ontology/tao.md index 9ae20a798..2ffd42b17 100644 --- a/ontology/tao.md +++ b/ontology/tao.md @@ -6,7 +6,7 @@ contact: email: wasila.dahdul@usd.edu label: Wasila Dahdul description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa -domain: anatomy +domain: anatomy and development homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology products: - id: tao.owl diff --git a/ontology/taxrank.md b/ontology/taxrank.md index 5e7ce892c..23cdfaaca 100644 --- a/ontology/taxrank.md +++ b/ontology/taxrank.md @@ -7,7 +7,9 @@ contact: github: balhoff orcid: 0000-0002-8688-6599 description: A vocabulary of taxonomic ranks (species, family, phylum, etc) -domain: taxonomy +domain: organisms +tags: + - taxonomy homepage: https://github.com/phenoscape/taxrank products: - id: taxrank.owl diff --git a/ontology/tgma.md b/ontology/tgma.md index 57c85d1ad..0dbd25bd6 100644 --- a/ontology/tgma.md +++ b/ontology/tgma.md @@ -8,7 +8,7 @@ license: url: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 description: A structured controlled vocabulary of the anatomy of mosquitoes. -domain: anatomy +domain: anatomy and development homepage: https://www.vectorbase.org/ontology-browser products: - id: tgma.owl diff --git a/ontology/trans.md b/ontology/trans.md index 71cba8b9f..2ee6a5b03 100644 --- a/ontology/trans.md +++ b/ontology/trans.md @@ -7,7 +7,9 @@ contact: github: lschriml orcid: 0000-0001-8910-9851 description: "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." -domain: disease +domain: health +tags: + - disease homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology products: - id: trans.owl diff --git a/ontology/tto.md b/ontology/tto.md index a3b069581..d382f022d 100644 --- a/ontology/tto.md +++ b/ontology/tto.md @@ -7,7 +7,9 @@ contact: github: balhoff orcid: 0000-0002-8688-6599 description: An ontology covering the taxonomy of teleosts (bony fish) -domain: taxonomy +domain: organisms +tags: + - taxonomy homepage: https://github.com/phenoscape/teleost-taxonomy-ontology products: - id: tto.obo diff --git a/ontology/txpo.md b/ontology/txpo.md index 9c1cded17..2154fb12b 100644 --- a/ontology/txpo.md +++ b/ontology/txpo.md @@ -7,7 +7,9 @@ contact: github: yuki-yamagata orcid: 0000-0002-9673-1283 description: TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. -domain: toxicity +domain: biochemistry +tags: + - toxicity homepage: https://toxpilot.nibiohn.go.jp/ tracker: https://github.com/txpo-ontology/TXPO/issues products: diff --git a/ontology/uberon.md b/ontology/uberon.md index 5d8bf048a..d97df37e9 100644 --- a/ontology/uberon.md +++ b/ontology/uberon.md @@ -78,7 +78,7 @@ license: taxon: id: NCBITaxon:33208 label: Metazoa -domain: anatomy +domain: anatomy and development repository: https://github.com/obophenotype/uberon tracker: https://github.com/obophenotype/uberon/issues releases: http://purl.obolibrary.org/obo/uberon/releases/ diff --git a/ontology/upa.md b/ontology/upa.md index 169d0f984..e1142fca3 100644 --- a/ontology/upa.md +++ b/ontology/upa.md @@ -18,7 +18,9 @@ contact: github: amorgat orcid: 0000-0002-1216-2969 description: "A manually curated resource for the representation and annotation of metabolic pathways" -domain: pathways +domain: biological systems +tags: + - pathways homepage: https://github.com/geneontology/unipathway products: - id: upa.owl diff --git a/ontology/vsao.md b/ontology/vsao.md index d5a2b2734..2be7658a9 100644 --- a/ontology/vsao.md +++ b/ontology/vsao.md @@ -6,7 +6,7 @@ contact: email: wasila.dahdul@usd.edu label: Wasila Dahdul description: Vertebrate skeletal anatomy ontology. -domain: anatomy +domain: anatomy and development homepage: https://www.nescent.org/phenoscape/Main_Page page: https://www.phenoscape.org/wiki/Skeletal_Anatomy_Jamboree products: diff --git a/ontology/wbbt.md b/ontology/wbbt.md index f27d65387..cbd65ac23 100644 --- a/ontology/wbbt.md +++ b/ontology/wbbt.md @@ -11,7 +11,7 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. -domain: anatomy +domain: anatomy and development homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology tracker: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/issues products: diff --git a/ontology/wbls.md b/ontology/wbls.md index 9933f5762..177a9e9d7 100644 --- a/ontology/wbls.md +++ b/ontology/wbls.md @@ -11,7 +11,9 @@ license: url: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 description: A structured controlled vocabulary of the development of Caenorhabditis elegans. -domain: developemental life stage +domain: anatomy and development +tags: + - developemental life stage homepage: https://github.com/obophenotype/c-elegans-development-ontology tracker: https://github.com/obophenotype/c-elegans-development-ontology/issues products: diff --git a/ontology/xao.md b/ontology/xao.md index 48c81e724..dd8c30002 100644 --- a/ontology/xao.md +++ b/ontology/xao.md @@ -2,7 +2,7 @@ layout: ontology_detail id: xao description: XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis. -domain: anatomy +domain: anatomy and development homepage: http://www.xenbase.org/anatomy/xao.do?method=display contact: label: Erik Segerdell diff --git a/ontology/xco.md b/ontology/xco.md index f474cf63f..e23d000be 100644 --- a/ontology/xco.md +++ b/ontology/xco.md @@ -9,7 +9,9 @@ license: url: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 description: Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. -domain: clinical +domain: health +tags: + - clinical homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 tracker: https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues page: https://download.rgd.mcw.edu/ontology/experimental_condition/ diff --git a/ontology/xlmod.md b/ontology/xlmod.md index 5fdd5d979..ec884c991 100644 --- a/ontology/xlmod.md +++ b/ontology/xlmod.md @@ -9,7 +9,9 @@ contact: label: Lutz Fischer github: lutzfischer orcid: 0000-0003-4978-0864 -domain: MS cross-linker reagents +domain: biochemistry +tags: + - MS cross-linker reagents mailing_list: psidev-ms-vocab@lists.sourceforge.net homepage: http://www.psidev.info/groups/controlled-vocabularies page: http://www.psidev.info/groups/controlled-vocabularies diff --git a/ontology/zfa.md b/ontology/zfa.md index fa3714b32..64c74274e 100644 --- a/ontology/zfa.md +++ b/ontology/zfa.md @@ -8,7 +8,7 @@ contact: github: cerivs orcid: 0000-0002-2244-7917 description: A structured controlled vocabulary of the anatomy and development of the Zebrafish -domain: anatomy +domain: anatomy and development homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources products: - id: zfa.owl diff --git a/ontology/zfs.md b/ontology/zfs.md index 30e9810cc..5b6f2af4b 100644 --- a/ontology/zfs.md +++ b/ontology/zfs.md @@ -8,7 +8,7 @@ contact: github: cerivs orcid: 0000-0002-2244-7917 description: Developmental stages of the Zebrafish -domain: anatomy +domain: anatomy and development homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources page: https://github.com/obophenotype/developmental-stage-ontologies/wiki/ZFS tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json index 2df6a7f90..84c5bcbaf 100644 --- a/util/schema/registry_schema.json +++ b/util/schema/registry_schema.json @@ -97,9 +97,33 @@ "suggest": false }, "domain": { - "level": "warning", - "description": "'domain' is a recommended field. The value is the scientific topic area addressed by the ontology.", - "type": "string" + "level": "error", + "description": "'domain' is a mandatory field. The value is the scientific topic area addressed by the ontology.", + "type": "string", + "enum": [ + "upper", + "anatomy and development", + "health", + "phenotype", + "investigations", + "environment", + "biochemistry", + "microbiology", + "agriculture", + "diet, metabolomics, and nutrition", + "biological systems", + "information technology", + "organisms", + "information", + "simulation" + ] + }, + "tags": { + "description": "'tags' is an optional field. The value is a list of strings, meant to extend 'domain' by providing more details.", + "type": "array", + "items": { + "type": "string" + } }, "funded_by": { "suggest": false