Remove several fields used less than five times (#2899)

* Update scripts

* Remove several fields

* Remove slack

* Format code

* Define script requirements inline

* Make outputs

* Update obo-test.yml

* Update build.yml

Author: cthoyt

.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

.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'

_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

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/

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/

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

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/

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

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

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