diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index d186fa7f2..9b9b18b29 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -19,6 +19,10 @@ jobs: with: persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token fetch-depth: 0 # otherwise, you will failed to push refs to dest repo + + - name: "Install uv" + uses: "astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57" # v8.0.0 + - name: Create local changes run: | python -m pip install -r requirements.txt diff --git a/.github/workflows/obo-test.yml b/.github/workflows/obo-test.yml index 15edf2cbb..a53701ec9 100644 --- a/.github/workflows/obo-test.yml +++ b/.github/workflows/obo-test.yml @@ -14,6 +14,10 @@ jobs: if: github.triggering_actor != 'github-actions[bot]' steps: - uses: actions/checkout@v2 + + - name: "Install uv" + uses: "astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57" # v8.0.0 + - uses: actions/setup-python@v2 with: python-version: '3.9' diff --git a/_config.yml b/_config.yml index 68b451c17..81c435cc6 100644 --- a/_config.yml +++ b/_config.yml @@ -763,7 +763,6 @@ ontologies: title: Confidence Information Ontology tracker: https://github.com/BgeeDB/confidence-information-ontology - activity_status: active - canonical: cl.owl contact: email: do12@sanger.ac.uk github: dosumis @@ -783,7 +782,6 @@ ontologies: domain: anatomy and development homepage: https://obophenotype.github.io/cell-ontology/ id: cl - label: Cell Ontology layout: ontology_detail license: label: CC BY 4.0 @@ -1945,7 +1943,6 @@ ontologies: domain: health homepage: https://github.com/SCAI-BIO/EpilepsyOntology id: epio - label: Epilepsy Ontology layout: ontology_detail license: label: CC BY 4.0 @@ -2785,8 +2782,6 @@ ontologies: homepage: http://geneontology.org/ id: go in_foundry_order: 1 - integration_server: http://build.berkeleybop.org/view/GO - label: GO layout: ontology_detail license: label: CC BY 4.0 @@ -3310,7 +3305,6 @@ ontologies: publications: - id: https://doi.org/10.5281/zenodo.6522019 title: 'LABO: An Ontology for Laboratory Test Prescription and Reporting' - releases: https://github.com/OpenLHS/LABO/releases/ repository: https://github.com/OpenLHS/LABO tags: - clinical documentation @@ -3667,7 +3661,6 @@ ontologies: - id: https://doi.org/10.1089/omi.2006.10.231 title: 'Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)' - releases: https://github.com/evoinfo/miapa/releases repository: https://github.com/evoinfo/miapa title: MIAPA Ontology tracker: https://github.com/evoinfo/miapa/issues @@ -3777,7 +3770,6 @@ ontologies: - label: Monarch title: Monarch Initiative Disease Browser url: https://monarchinitiative.org/disease/MONDO:0019609 - canonical: mondo.owl contact: email: Sabrina@tislab.org github: sabrinatoro @@ -3789,7 +3781,6 @@ ontologies: domain: health homepage: https://monarch-initiative.github.io/mondo id: mondo - label: Mondo layout: ontology_detail license: label: CC BY 4.0 @@ -4099,8 +4090,6 @@ ontologies: domain: investigations 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 3.0 @@ -4211,7 +4200,6 @@ ontologies: pertussis as the source organism. url: http://www.iedb.org/assay/1505273 user: https://www.iedb.org - wasDerivedFrom: ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat - activity_status: active contact: email: noreply@example.com @@ -4299,7 +4287,6 @@ ontologies: title: Next Generation Biobanking Ontology tracker: https://github.com/Dalalghamdi/NGBO/issues - activity_status: active - canonical: nomen.owl contact: email: diapriid@gmail.com github: mjy @@ -4313,7 +4300,6 @@ ontologies: title: NSF ABI-1356381 homepage: https://github.com/SpeciesFileGroup/nomen id: nomen - label: NOMEN layout: ontology_detail license: label: CC0 1.0 @@ -4515,7 +4501,6 @@ ontologies: homepage: http://obi-ontology.org id: obi in_foundry_order: 1 - integration_server: http://build.berkeleybop.org/job/build-obi/ layout: ontology_detail license: label: CC BY 4.0 @@ -4965,7 +4950,6 @@ ontologies: domain: diet, metabolomics, and nutrition homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies id: one - label: Ontology for Nutritional Epidemiology layout: ontology_detail license: label: CC BY 4.0 @@ -5004,7 +4988,6 @@ ontologies: domain: diet, metabolomics, and nutrition homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies id: ons - label: Ontology for Nutritional Studies layout: ontology_detail license: label: CC BY 4.0 @@ -5792,7 +5775,6 @@ ontologies: orcid: 0000-0001-5809-9523 depicted_by: https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png description: An ontological representation of protein-related entities - documentation: https://proconsortium.org/download/current/pro_readme.txt domain: chemistry and biochemistry homepage: http://proconsortium.org id: pr @@ -6030,14 +6012,12 @@ ontologies: title: Radiation Biology Ontology tracker: https://github.com/Radiobiology-Informatics-Consortium/RBO/issues - activity_status: active - canonical: ro.owl contact: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 description: Relationship types shared across multiple ontologies - documentation: https://oborel.github.io/obo-relations/ domain: upper homepage: https://oborel.github.io/ id: ro @@ -6724,7 +6704,6 @@ ontologies: - label: KnowledgeSpace title: INCF KnowledgeSpace Portal url: https://knowledge-space.org/index.php/pages/view/UBERON:0000061 - canonical: uberon.owl contact: email: cjmungall@lbl.gov github: cmungall @@ -6758,7 +6737,6 @@ ontologies: title: NSF DEB-0956049 homepage: http://uberon.org id: uberon - label: Uberon layout: ontology_detail license: label: CC BY 3.0 @@ -6823,9 +6801,7 @@ ontologies: - id: https://www.ncbi.nlm.nih.gov/pubmed/25009735 title: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon - releases: http://purl.obolibrary.org/obo/uberon/releases/ repository: https://github.com/obophenotype/uberon - slack: https://obo-communitygroup.slack.com/archives/C01CR698CF2 taxon: id: NCBITaxon:33208 label: Metazoa @@ -6897,7 +6873,6 @@ ontologies: title: 'ChEMBL: towards direct deposition of bioassay data' type: Database user: https://www.ebi.ac.uk/chembl/ - wikidata_template: https://en.wikipedia.org/wiki/Template:Uberon - activity_status: active contact: email: g.gkoutos@gmail.com @@ -7432,7 +7407,6 @@ ontologies: domain: chemistry and biochemistry homepage: http://www.psidev.info/groups/controlled-vocabularies id: xlmod - label: xlmod layout: ontology_detail license: label: CC BY 3.0 @@ -7877,7 +7851,6 @@ ontologies: publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22027554 title: Controlled vocabularies and semantics in systems biology - releases: https://github.com/SED-ML/KiSAO/releases repository: https://github.com/SED-ML/KiSAO tags: - systems biology @@ -8859,7 +8832,6 @@ ontologies: 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 domain: information homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology id: ero diff --git a/ontology/cl.md b/ontology/cl.md index 879055c98..aa621a58e 100644 --- a/ontology/cl.md +++ b/ontology/cl.md @@ -2,7 +2,6 @@ layout: ontology_detail id: cl title: Cell Ontology -canonical: cl.owl contact: email: do12@sanger.ac.uk github: dosumis @@ -20,7 +19,6 @@ depicted_by: /images/CL-logo.jpg description: The Cell Ontology is a structured controlled vocabulary for cell types in animals. domain: anatomy and development homepage: https://obophenotype.github.io/cell-ontology/ -label: Cell Ontology license: label: CC BY 4.0 url: http://creativecommons.org/licenses/by/4.0/ diff --git a/ontology/epio.md b/ontology/epio.md index 384fbd142..3c8e64b2a 100644 --- a/ontology/epio.md +++ b/ontology/epio.md @@ -12,7 +12,6 @@ dependencies: description: A application driven Epilepsy Ontology with official terms from the ILAE. domain: health homepage: https://github.com/SCAI-BIO/EpilepsyOntology -label: Epilepsy Ontology license: label: CC BY 4.0 url: http://creativecommons.org/licenses/by/4.0/ diff --git a/ontology/ero.md b/ontology/ero.md index bfecf9632..45d2b7ef0 100644 --- a/ontology/ero.md +++ b/ontology/ero.md @@ -6,7 +6,6 @@ contact: 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 domain: information homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology is_obsolete: true diff --git a/ontology/go.md b/ontology/go.md index cd5b6279b..b86b756d0 100644 --- a/ontology/go.md +++ b/ontology/go.md @@ -35,8 +35,6 @@ description: An ontology for describing the function of genes and gene products domain: biological systems homepage: http://geneontology.org/ in_foundry_order: 1 -integration_server: http://build.berkeleybop.org/view/GO -label: GO license: label: CC BY 4.0 url: https://creativecommons.org/licenses/by/4.0/ diff --git a/ontology/kisao.md b/ontology/kisao.md index 6350e25df..ca9be6fc2 100644 --- a/ontology/kisao.md +++ b/ontology/kisao.md @@ -34,7 +34,6 @@ products: publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22027554 title: Controlled vocabularies and semantics in systems biology -releases: https://github.com/SED-ML/KiSAO/releases repository: https://github.com/SED-ML/KiSAO tags: - systems biology diff --git a/ontology/labo.md b/ontology/labo.md index 814af94dc..647cffaa5 100644 --- a/ontology/labo.md +++ b/ontology/labo.md @@ -26,7 +26,6 @@ products: publications: - id: https://doi.org/10.5281/zenodo.6522019 title: 'LABO: An Ontology for Laboratory Test Prescription and Reporting' -releases: https://github.com/OpenLHS/LABO/releases/ repository: https://github.com/OpenLHS/LABO tags: - clinical documentation diff --git a/ontology/miapa.md b/ontology/miapa.md index 37d8b5b09..bd3a3d6ad 100644 --- a/ontology/miapa.md +++ b/ontology/miapa.md @@ -20,7 +20,6 @@ products: publications: - id: https://doi.org/10.1089/omi.2006.10.231 title: 'Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)' -releases: https://github.com/evoinfo/miapa/releases repository: https://github.com/evoinfo/miapa tracker: https://github.com/evoinfo/miapa/issues activity_status: active diff --git a/ontology/mondo.md b/ontology/mondo.md index d7e5790c0..b5f6c71dd 100644 --- a/ontology/mondo.md +++ b/ontology/mondo.md @@ -6,7 +6,6 @@ browsers: - title: Monarch Initiative Disease Browser label: Monarch url: https://monarchinitiative.org/disease/MONDO:0019609 -canonical: mondo.owl contact: email: Sabrina@tislab.org github: sabrinatoro @@ -16,7 +15,6 @@ depicted_by: https://raw.githubusercontent.com/monarch-initiative/mondo/master/d description: A global community effort to harmonize multiple disease resources to yield a coherent merged ontology. domain: health homepage: https://monarch-initiative.github.io/mondo -label: Mondo license: label: CC BY 4.0 url: http://creativecommons.org/licenses/by/4.0/ diff --git a/ontology/ms.md b/ontology/ms.md index 3f9acdb34..182a906b4 100644 --- a/ontology/ms.md +++ b/ontology/ms.md @@ -13,8 +13,6 @@ dependencies: description: A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. domain: investigations homepage: http://www.psidev.info/groups/controlled-vocabularies -integration_server: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master -label: MS license: label: CC BY 3.0 url: https://creativecommons.org/licenses/by/3.0/ diff --git a/ontology/ncbitaxon.md b/ontology/ncbitaxon.md index 707efde5b..2d52871ad 100644 --- a/ontology/ncbitaxon.md +++ b/ontology/ncbitaxon.md @@ -42,7 +42,6 @@ usages: - description: A specific assay curated in the IEDB using the NCBITaxon:520 Bordetella pertussis as the source organism. url: http://www.iedb.org/assay/1505273 user: https://www.iedb.org -wasDerivedFrom: ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat activity_status: active --- diff --git a/ontology/nomen.md b/ontology/nomen.md index 05184dad0..189f9d5d7 100644 --- a/ontology/nomen.md +++ b/ontology/nomen.md @@ -2,7 +2,6 @@ layout: ontology_detail id: nomen title: NOMEN - A nomenclatural ontology for biological names -canonical: nomen.owl contact: email: diapriid@gmail.com github: mjy @@ -14,7 +13,6 @@ funded_by: - id: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1356381 title: NSF ABI-1356381 homepage: https://github.com/SpeciesFileGroup/nomen -label: NOMEN license: label: CC0 1.0 url: https://creativecommons.org/publicdomain/zero/1.0/ diff --git a/ontology/obi.md b/ontology/obi.md index 0c4ad9aec..05596336b 100644 --- a/ontology/obi.md +++ b/ontology/obi.md @@ -16,7 +16,6 @@ description: An integrated ontology for the description of life-science and clin domain: investigations homepage: http://obi-ontology.org in_foundry_order: 1 -integration_server: http://build.berkeleybop.org/job/build-obi/ license: label: CC BY 4.0 url: https://creativecommons.org/licenses/by/4.0/ diff --git a/ontology/one.md b/ontology/one.md index 4f88ed9a4..59d9fbb45 100644 --- a/ontology/one.md +++ b/ontology/one.md @@ -14,7 +14,6 @@ dependencies: description: An ontology to standardize research output of nutritional epidemiologic studies. domain: diet, metabolomics, and nutrition homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies -label: Ontology for Nutritional Epidemiology license: label: CC BY 4.0 url: https://creativecommons.org/licenses/by/4.0/ diff --git a/ontology/ons.md b/ontology/ons.md index 68b4b6b61..30cfedc5d 100644 --- a/ontology/ons.md +++ b/ontology/ons.md @@ -19,7 +19,6 @@ dependencies: description: An ontology for description of concepts in the nutritional studies domain. domain: diet, metabolomics, and nutrition homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies -label: Ontology for Nutritional Studies license: label: CC BY 4.0 url: https://creativecommons.org/licenses/by/4.0/ diff --git a/ontology/pr.md b/ontology/pr.md index ecd082ccf..ed2084625 100644 --- a/ontology/pr.md +++ b/ontology/pr.md @@ -16,7 +16,6 @@ contact: orcid: 0000-0001-5809-9523 depicted_by: https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png description: An ontological representation of protein-related entities -documentation: https://proconsortium.org/download/current/pro_readme.txt domain: chemistry and biochemistry homepage: http://proconsortium.org in_foundry_order: 1 diff --git a/ontology/ro.md b/ontology/ro.md index d53e921af..406de1062 100644 --- a/ontology/ro.md +++ b/ontology/ro.md @@ -2,14 +2,12 @@ layout: ontology_detail id: ro title: Relation Ontology -canonical: ro.owl contact: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 description: Relationship types shared across multiple ontologies -documentation: https://oborel.github.io/obo-relations/ domain: upper homepage: https://oborel.github.io/ license: diff --git a/ontology/uberon.md b/ontology/uberon.md index 51d7c1f51..06800140a 100644 --- a/ontology/uberon.md +++ b/ontology/uberon.md @@ -18,7 +18,6 @@ browsers: - title: INCF KnowledgeSpace Portal label: KnowledgeSpace url: https://knowledge-space.org/index.php/pages/view/UBERON:0000061 -canonical: uberon.owl contact: email: cjmungall@lbl.gov github: cmungall @@ -50,7 +49,6 @@ funded_by: - id: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0956049 title: NSF DEB-0956049 homepage: http://uberon.org -label: Uberon license: label: CC BY 3.0 url: http://creativecommons.org/licenses/by/3.0/ @@ -103,9 +101,7 @@ publications: title: Uberon, an integrative multi-species anatomy ontology - id: https://www.ncbi.nlm.nih.gov/pubmed/25009735 title: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon -releases: http://purl.obolibrary.org/obo/uberon/releases/ repository: https://github.com/obophenotype/uberon -slack: https://obo-communitygroup.slack.com/archives/C01CR698CF2 taxon: id: NCBITaxon:33208 label: Metazoa @@ -161,7 +157,6 @@ usages: title: 'ChEMBL: towards direct deposition of bioassay data' type: Database user: https://www.ebi.ac.uk/chembl/ -wikidata_template: https://en.wikipedia.org/wiki/Template:Uberon activity_status: active --- diff --git a/ontology/xlmod.md b/ontology/xlmod.md index b45108fc6..a1bde69f7 100644 --- a/ontology/xlmod.md +++ b/ontology/xlmod.md @@ -10,7 +10,6 @@ contact: description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. domain: chemistry and biochemistry homepage: http://www.psidev.info/groups/controlled-vocabularies -label: xlmod license: label: CC BY 3.0 url: https://creativecommons.org/licenses/by/3.0/ diff --git a/registry/ontologies.jsonld b/registry/ontologies.jsonld index f74260a5d..42d77ac3f 100644 --- a/registry/ontologies.jsonld +++ b/registry/ontologies.jsonld @@ -1047,7 +1047,6 @@ }, { "activity_status": "active", - "canonical": "cl.owl", "contact": { "email": "do12@sanger.ac.uk", "github": "dosumis", @@ -1082,7 +1081,6 @@ "domain": "anatomy and development", "homepage": "https://obophenotype.github.io/cell-ontology/", "id": "cl", - "label": "Cell Ontology", "layout": "ontology_detail", "license": { "label": "CC BY 4.0", @@ -2728,7 +2726,6 @@ "domain": "health", "homepage": "https://github.com/SCAI-BIO/EpilepsyOntology", "id": "epio", - "label": "Epilepsy Ontology", "layout": "ontology_detail", "license": { "label": "CC BY 4.0", @@ -3961,8 +3958,6 @@ "homepage": "http://geneontology.org/", "id": "go", "in_foundry_order": 1, - "integration_server": "http://build.berkeleybop.org/view/GO", - "label": "GO", "layout": "ontology_detail", "license": { "label": "CC BY 4.0", @@ -4673,7 +4668,6 @@ "title": "LABO: An Ontology for Laboratory Test Prescription and Reporting" } ], - "releases": "https://github.com/OpenLHS/LABO/releases/", "repository": "https://github.com/OpenLHS/LABO", "tags": [ "clinical documentation" @@ -5201,7 +5195,6 @@ "title": "Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)" } ], - "releases": "https://github.com/evoinfo/miapa/releases", "repository": "https://github.com/evoinfo/miapa", "title": "MIAPA Ontology", "tracker": "https://github.com/evoinfo/miapa/issues" @@ -5352,7 +5345,6 @@ "url": "https://monarchinitiative.org/disease/MONDO:0019609" } ], - "canonical": "mondo.owl", "contact": { "email": "Sabrina@tislab.org", "github": "sabrinatoro", @@ -5364,7 +5356,6 @@ "domain": "health", "homepage": "https://monarch-initiative.github.io/mondo", "id": "mondo", - "label": "Mondo", "layout": "ontology_detail", "license": { "label": "CC BY 4.0", @@ -5784,8 +5775,6 @@ "domain": "investigations", "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 3.0", @@ -5939,8 +5928,7 @@ ], "user": "https://www.iedb.org" } - ], - "wasDerivedFrom": "ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat" + ] }, { "activity_status": "active", @@ -6045,7 +6033,6 @@ }, { "activity_status": "active", - "canonical": "nomen.owl", "contact": { "email": "diapriid@gmail.com", "github": "mjy", @@ -6062,7 +6049,6 @@ ], "homepage": "https://github.com/SpeciesFileGroup/nomen", "id": "nomen", - "label": "NOMEN", "layout": "ontology_detail", "license": { "label": "CC0 1.0", @@ -6342,7 +6328,6 @@ "homepage": "http://obi-ontology.org", "id": "obi", "in_foundry_order": 1, - "integration_server": "http://build.berkeleybop.org/job/build-obi/", "layout": "ontology_detail", "license": { "label": "CC BY 4.0", @@ -6926,7 +6911,6 @@ "domain": "diet, metabolomics, and nutrition", "homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies", "id": "one", - "label": "Ontology for Nutritional Epidemiology", "layout": "ontology_detail", "license": { "label": "CC BY 4.0", @@ -6989,7 +6973,6 @@ "domain": "diet, metabolomics, and nutrition", "homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies", "id": "ons", - "label": "Ontology for Nutritional Studies", "layout": "ontology_detail", "license": { "label": "CC BY 4.0", @@ -8125,7 +8108,6 @@ }, "depicted_by": "https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png", "description": "An ontological representation of protein-related entities", - "documentation": "https://proconsortium.org/download/current/pro_readme.txt", "domain": "chemistry and biochemistry", "homepage": "http://proconsortium.org", "id": "pr", @@ -8486,7 +8468,6 @@ }, { "activity_status": "active", - "canonical": "ro.owl", "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", @@ -8494,7 +8475,6 @@ "orcid": "0000-0002-6601-2165" }, "description": "Relationship types shared across multiple ontologies", - "documentation": "https://oborel.github.io/obo-relations/", "domain": "upper", "homepage": "https://oborel.github.io/", "id": "ro", @@ -9424,7 +9404,6 @@ "url": "https://knowledge-space.org/index.php/pages/view/UBERON:0000061" } ], - "canonical": "uberon.owl", "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", @@ -9492,7 +9471,6 @@ ], "homepage": "http://uberon.org", "id": "uberon", - "label": "Uberon", "layout": "ontology_detail", "license": { "label": "CC BY 3.0", @@ -9574,9 +9552,7 @@ "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon" } ], - "releases": "http://purl.obolibrary.org/obo/uberon/releases/", "repository": "https://github.com/obophenotype/uberon", - "slack": "https://obo-communitygroup.slack.com/archives/C01CR698CF2", "taxon": { "id": "NCBITaxon:33208", "label": "Metazoa" @@ -9672,8 +9648,7 @@ "type": "Database", "user": "https://www.ebi.ac.uk/chembl/" } - ], - "wikidata_template": "https://en.wikipedia.org/wiki/Template:Uberon" + ] }, { "activity_status": "active", @@ -10430,7 +10405,6 @@ "domain": "chemistry and biochemistry", "homepage": "http://www.psidev.info/groups/controlled-vocabularies", "id": "xlmod", - "label": "xlmod", "layout": "ontology_detail", "license": { "label": "CC BY 3.0", @@ -11049,7 +11023,6 @@ "title": "Controlled vocabularies and semantics in systems biology" } ], - "releases": "https://github.com/SED-ML/KiSAO/releases", "repository": "https://github.com/SED-ML/KiSAO", "tags": [ "systems biology", @@ -12434,7 +12407,6 @@ "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", "domain": "information", "homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology", "id": "ero", diff --git a/registry/ontologies.yml b/registry/ontologies.yml index 6a84804ac..86be33142 100644 --- a/registry/ontologies.yml +++ b/registry/ontologies.yml @@ -746,7 +746,6 @@ ontologies: title: Confidence Information Ontology tracker: https://github.com/BgeeDB/confidence-information-ontology - activity_status: active - canonical: cl.owl contact: email: do12@sanger.ac.uk github: dosumis @@ -766,7 +765,6 @@ ontologies: domain: anatomy and development homepage: https://obophenotype.github.io/cell-ontology/ id: cl - label: Cell Ontology layout: ontology_detail license: label: CC BY 4.0 @@ -1928,7 +1926,6 @@ ontologies: domain: health homepage: https://github.com/SCAI-BIO/EpilepsyOntology id: epio - label: Epilepsy Ontology layout: ontology_detail license: label: CC BY 4.0 @@ -2768,8 +2765,6 @@ ontologies: homepage: http://geneontology.org/ id: go in_foundry_order: 1 - integration_server: http://build.berkeleybop.org/view/GO - label: GO layout: ontology_detail license: label: CC BY 4.0 @@ -3293,7 +3288,6 @@ ontologies: publications: - id: https://doi.org/10.5281/zenodo.6522019 title: 'LABO: An Ontology for Laboratory Test Prescription and Reporting' - releases: https://github.com/OpenLHS/LABO/releases/ repository: https://github.com/OpenLHS/LABO tags: - clinical documentation @@ -3650,7 +3644,6 @@ ontologies: - id: https://doi.org/10.1089/omi.2006.10.231 title: 'Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)' - releases: https://github.com/evoinfo/miapa/releases repository: https://github.com/evoinfo/miapa title: MIAPA Ontology tracker: https://github.com/evoinfo/miapa/issues @@ -3760,7 +3753,6 @@ ontologies: - label: Monarch title: Monarch Initiative Disease Browser url: https://monarchinitiative.org/disease/MONDO:0019609 - canonical: mondo.owl contact: email: Sabrina@tislab.org github: sabrinatoro @@ -3772,7 +3764,6 @@ ontologies: domain: health homepage: https://monarch-initiative.github.io/mondo id: mondo - label: Mondo layout: ontology_detail license: label: CC BY 4.0 @@ -4082,8 +4073,6 @@ ontologies: domain: investigations 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 3.0 @@ -4194,7 +4183,6 @@ ontologies: pertussis as the source organism. url: http://www.iedb.org/assay/1505273 user: https://www.iedb.org - wasDerivedFrom: ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat - activity_status: active contact: email: noreply@example.com @@ -4282,7 +4270,6 @@ ontologies: title: Next Generation Biobanking Ontology tracker: https://github.com/Dalalghamdi/NGBO/issues - activity_status: active - canonical: nomen.owl contact: email: diapriid@gmail.com github: mjy @@ -4296,7 +4283,6 @@ ontologies: title: NSF ABI-1356381 homepage: https://github.com/SpeciesFileGroup/nomen id: nomen - label: NOMEN layout: ontology_detail license: label: CC0 1.0 @@ -4498,7 +4484,6 @@ ontologies: homepage: http://obi-ontology.org id: obi in_foundry_order: 1 - integration_server: http://build.berkeleybop.org/job/build-obi/ layout: ontology_detail license: label: CC BY 4.0 @@ -4948,7 +4933,6 @@ ontologies: domain: diet, metabolomics, and nutrition homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies id: one - label: Ontology for Nutritional Epidemiology layout: ontology_detail license: label: CC BY 4.0 @@ -4987,7 +4971,6 @@ ontologies: domain: diet, metabolomics, and nutrition homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies id: ons - label: Ontology for Nutritional Studies layout: ontology_detail license: label: CC BY 4.0 @@ -5775,7 +5758,6 @@ ontologies: orcid: 0000-0001-5809-9523 depicted_by: https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png description: An ontological representation of protein-related entities - documentation: https://proconsortium.org/download/current/pro_readme.txt domain: chemistry and biochemistry homepage: http://proconsortium.org id: pr @@ -6013,14 +5995,12 @@ ontologies: title: Radiation Biology Ontology tracker: https://github.com/Radiobiology-Informatics-Consortium/RBO/issues - activity_status: active - canonical: ro.owl contact: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 description: Relationship types shared across multiple ontologies - documentation: https://oborel.github.io/obo-relations/ domain: upper homepage: https://oborel.github.io/ id: ro @@ -6707,7 +6687,6 @@ ontologies: - label: KnowledgeSpace title: INCF KnowledgeSpace Portal url: https://knowledge-space.org/index.php/pages/view/UBERON:0000061 - canonical: uberon.owl contact: email: cjmungall@lbl.gov github: cmungall @@ -6741,7 +6720,6 @@ ontologies: title: NSF DEB-0956049 homepage: http://uberon.org id: uberon - label: Uberon layout: ontology_detail license: label: CC BY 3.0 @@ -6806,9 +6784,7 @@ ontologies: - id: https://www.ncbi.nlm.nih.gov/pubmed/25009735 title: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon - releases: http://purl.obolibrary.org/obo/uberon/releases/ repository: https://github.com/obophenotype/uberon - slack: https://obo-communitygroup.slack.com/archives/C01CR698CF2 taxon: id: NCBITaxon:33208 label: Metazoa @@ -6880,7 +6856,6 @@ ontologies: title: 'ChEMBL: towards direct deposition of bioassay data' type: Database user: https://www.ebi.ac.uk/chembl/ - wikidata_template: https://en.wikipedia.org/wiki/Template:Uberon - activity_status: active contact: email: g.gkoutos@gmail.com @@ -7415,7 +7390,6 @@ ontologies: domain: chemistry and biochemistry homepage: http://www.psidev.info/groups/controlled-vocabularies id: xlmod - label: xlmod layout: ontology_detail license: label: CC BY 3.0 @@ -7860,7 +7834,6 @@ ontologies: publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22027554 title: Controlled vocabularies and semantics in systems biology - releases: https://github.com/SED-ML/KiSAO/releases repository: https://github.com/SED-ML/KiSAO tags: - systems biology @@ -8842,7 +8815,6 @@ ontologies: 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 domain: information homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology id: ero diff --git a/src/obofoundry/remove_field.py b/src/obofoundry/remove_field.py index 333d46ca0..317797456 100644 --- a/src/obofoundry/remove_field.py +++ b/src/obofoundry/remove_field.py @@ -1,12 +1,13 @@ """A workflow for removing a field from all ontology markdown files' metadata.""" +import json from io import StringIO from pathlib import Path import click import yaml -from obofoundry.constants import ONTOLOGY_DIRECTORY +from obofoundry.constants import ONTOLOGY_DIRECTORY, ROOT from obofoundry.standardize_metadata import ModifiedDumper @@ -15,6 +16,12 @@ def remove_field(name: str) -> None: for path in ONTOLOGY_DIRECTORY.glob("*.md"): remove_field_from_file(path, name) + schema_path = ROOT.joinpath("util", "schema", "registry_schema.json") + schema = json.loads(schema_path.read_text()) + if name in schema["properties"]: + del schema["properties"][name] + schema_path.write_text(json.dumps(schema, indent=2) + "\n") + def remove_field_from_file(path: Path, name: str) -> None: """Update the given markdown file.""" @@ -41,10 +48,11 @@ def remove_field_from_file(path: Path, name: str) -> None: @click.command() -@click.argument("name") -def main(name: str) -> None: +@click.argument("names", nargs=-1) +def main(names: list[str]) -> None: """Remove the metadata key from all ontologies' metadata.""" - remove_field(name) + for name in names: + remove_field(name) if __name__ == "__main__": diff --git a/util/check_schema.py b/util/check_schema.py index 7ddf56210..60321845b 100644 --- a/util/check_schema.py +++ b/util/check_schema.py @@ -21,14 +21,14 @@ @click.command() -@click.option("--max-cutoff", type=int, default=3, show_default=True) +@click.option("--max-cutoff", type=int, default=20, show_default=True) @click.option("--links", is_flag=True) def main(max_cutoff: int, links: bool): """Check schema usage.""" _check_schema(max_cutoff=max_cutoff, links=links) -def _check_schema(max_cutoff: int = 3, links: bool = True): +def _check_schema(max_cutoff: int, links: bool = True): ontologies = get_data() property_usage = Counter() @@ -44,27 +44,31 @@ def _check_schema(max_cutoff: int = 3, links: bool = True): if key in data: r[key].add(prefix) - print(f"Fields used at most {max_cutoff} times:") - print( - tabulate( - [ - ( - k, - ", ".join( - ( - f"[{prefix}](https://obofoundry.org/ontologies/{prefix})" - if links - else prefix - ) - for prefix in prefixes - ), - ) - for k, prefixes in r.items() - ], - tablefmt="github", - headers=["key", "ontologies"], + if r: + print(f"Fields used at most {max_cutoff} times:") + print( + tabulate( + [ + ( + k, + len(prefixes), + ", ".join( + ( + f"[{prefix}](https://obofoundry.org/ontologies/{prefix})" + if links + else prefix + ) + for prefix in prefixes + ), + ) + for k, prefixes in r.items() + ], + tablefmt="github", + headers=["key", "count", "ontologies"], + ) ) - ) + else: + print(f"No fields used less than {max_cutoff} times!") with SCHEMA_PATH.open() as file: schema = json.load(file) @@ -73,8 +77,11 @@ def _check_schema(max_cutoff: int = 3, links: bool = True): for prop in schema["properties"] if prop not in property_usage and prop not in SKIP_KEYS } - print("Unused properties:") - print(*sorted(unused), sep="\n") + if unused: + print("Unused properties:") + print(*sorted(unused), sep="\n") + else: + print("No unused properties!") if __name__ == "__main__": diff --git a/util/extract-metadata.py b/util/extract-metadata.py index 4527d15e0..8656d4d97 100755 --- a/util/extract-metadata.py +++ b/util/extract-metadata.py @@ -1,4 +1,14 @@ -#!/usr/bin/env python3 +#!/usr/bin/env -S uv run --script + +# /// script +# requires-python = ">=3.10" +# dependencies = [ +# "python-frontmatter==0.5.0", +# "pyyaml", +# "ruamel-yaml==0.16.12", +# "yamllint==1.25.0", +# ] +# /// import argparse import sys diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json index 8a24ff039..ca2acaf07 100644 --- a/util/schema/registry_schema.json +++ b/util/schema/registry_schema.json @@ -46,9 +46,6 @@ ] } }, - "canonical": { - "suggest": false - }, "contact": { "level": "error", "principle": "http://obofoundry.org/principles/fp-011-locus-of-authority.html", @@ -91,9 +88,6 @@ "depicted_by": { "suggest": false }, - "documentation": { - "suggest": false - }, "domain": { "level": "error", "description": "'domain' is a mandatory field. The value is the scientific topic area addressed by the ontology.", @@ -167,9 +161,6 @@ "in_foundry_order": { "suggest": false }, - "integration_server": { - "suggest": false - }, "is_obsolete": { "suggest": false, "level": "info", @@ -177,9 +168,6 @@ "type": "boolean", "default": false }, - "label": { - "suggest": false - }, "layout": { "level": "error", "description": "'layout' is a required field. It manages the display of the ontology record on the OBO Foundry website. The value should be 'ontology_detail'. ", @@ -381,9 +369,6 @@ "type": "integer", "description": "This encodes the number of the pull request on the OBO Foundry GitHub repository that was originally used to add this ontology. You can curate additional ones by going to the ontology page (e.g., https://github.com/OBOFoundry/OBOFoundry.github.io/commits/master/ontology/clyh.md) and looking the whole way down the list for the first commit. Click on the title for the commit then you will see if there's a PR associated with it." }, - "releases": { - "suggest": false - }, "replaced_by": { "suggest": false }, @@ -393,9 +378,6 @@ "type": "string", "format": "uri" }, - "slack": { - "suggest": false - }, "taxon": { "level": "info", "description": "'taxon' is an informative field. The value is the taxonomic identifier of the organism that is the subject of the ontology.", @@ -498,12 +480,6 @@ "description" ] } - }, - "wasDerivedFrom": { - "suggest": false - }, - "wikidata_template": { - "suggest": false } }, "required": [