Remove in_foundry annotations

cthoyt · cthoyt · commit 029f12426e02 · 2026-04-20T19:19:45.000+02:00
diff --git a/_config.yml b/_config.yml
@@ -317,7 +317,6 @@ ontologies:
   domain: organisms
   homepage: https://github.com/BiodiversityOntologies/bco
   id: bco
-  in_foundry: false
   layout: ontology_detail
   license:
     label: CC0 1.0
@@ -352,7 +351,6 @@ ontologies:
   domain: upper
   homepage: http://ifomis.org/bfo/
   id: bfo
-  in_foundry_order: 1
   layout: ontology_detail
   license:
     label: CC BY 4.0
@@ -548,7 +546,6 @@ ontologies:
   domain: chemistry and biochemistry
   homepage: http://www.ebi.ac.uk/chebi
   id: chebi
-  in_foundry_order: 1
   layout: ontology_detail
   license:
     label: CC BY 4.0
@@ -1429,7 +1426,6 @@ ontologies:
   domain: health
   homepage: https://disease-ontology.org
   id: doid
-  in_foundry_order: 1
   layout: ontology_detail
   license:
     label: CC0 1.0
@@ -2781,7 +2777,6 @@ ontologies:
   domain: biological systems
   homepage: http://geneontology.org/
   id: go
-  in_foundry_order: 1
   layout: ontology_detail
   license:
     label: CC BY 4.0
@@ -4460,7 +4455,6 @@ ontologies:
   domain: information technology
   homepage: https://github.com/obcs/obcs
   id: obcs
-  in_foundry: false
   layout: ontology_detail
   license:
     label: CC BY 4.0
@@ -4500,7 +4494,6 @@ ontologies:
   domain: investigations
   homepage: http://obi-ontology.org
   id: obi
-  in_foundry_order: 1
   layout: ontology_detail
   license:
     label: CC BY 4.0
@@ -4806,7 +4799,6 @@ ontologies:
   domain: chemistry and biochemistry
   homepage: http://omit.cis.usouthal.edu/
   id: omit
-  in_foundry: false
   layout: ontology_detail
   license:
     label: CC BY 3.0
@@ -5291,7 +5283,6 @@ ontologies:
   domain: phenotype
   homepage: https://github.com/pato-ontology/pato/
   id: pato
-  in_foundry_order: 1
   layout: ontology_detail
   license:
     label: CC BY 3.0
@@ -5344,7 +5335,6 @@ ontologies:
   domain: chemistry and biochemistry
   homepage: https://github.com/InSilicoVida-Research-Lab/pbpko
   id: pbpko
-  in_foundry_order: 1
   layout: ontology_detail
   license:
     label: CC BY 3.0
@@ -5645,7 +5635,6 @@ ontologies:
   domain: anatomy and development
   homepage: http://browser.planteome.org/amigo
   id: po
-  in_foundry_order: 1
   layout: ontology_detail
   license:
     label: CC BY 4.0
@@ -5778,7 +5767,6 @@ ontologies:
   domain: chemistry and biochemistry
   homepage: http://proconsortium.org
   id: pr
-  in_foundry_order: 1
   layout: ontology_detail
   license:
     label: CC BY 4.0
@@ -6308,7 +6296,6 @@ ontologies:
   domain: information technology
   homepage: http://stato-ontology.org/
   id: stato
-  in_foundry: false
   layout: ontology_detail
   license:
     label: CC BY 3.0
@@ -6883,7 +6870,6 @@ ontologies:
   domain: phenotype
   homepage: https://github.com/bio-ontology-research-group/unit-ontology
   id: uo
-  in_foundry: false
   layout: ontology_detail
   license:
     label: CC BY 3.0
@@ -7325,7 +7311,6 @@ ontologies:
   domain: anatomy and development
   homepage: http://www.xenbase.org/anatomy/xao.do?method=display
   id: xao
-  in_foundry_order: 1
   layout: ontology_detail
   license:
     label: CC BY 3.0
@@ -7510,7 +7495,6 @@ ontologies:
   domain: anatomy and development
   homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
   id: zfa
-  in_foundry_order: 1
   layout: ontology_detail
   license:
     label: CC BY 3.0
@@ -7550,7 +7534,6 @@ ontologies:
   domain: anatomy and development
   homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
   id: zfs
-  in_foundry: false
   layout: ontology_detail
   license:
     label: CC BY 3.0
@@ -7988,7 +7971,6 @@ ontologies:
   domain: chemistry and biochemistry
   homepage: http://www.ebi.ac.uk/chebi
   id: fix
-  in_foundry: false
   layout: ontology_detail
   ontology_purl: http://purl.obolibrary.org/obo/fix.owl
   products:
@@ -8604,7 +8586,6 @@ ontologies:
   domain: anatomy and development
   homepage: https://github.com/obi-bcgo/bcgo
   id: bcgo
-  in_foundry: false
   is_obsolete: true
   layout: ontology_detail
   license:
@@ -8819,7 +8800,6 @@ ontologies:
   domain: health
   homepage: https://code.google.com/p/epidemiology-ontology/
   id: epo
-  in_foundry: false
   is_obsolete: true
   layout: ontology_detail
   products:
@@ -8885,7 +8865,6 @@ ontologies:
   domain: health
   homepage: http://purl.obolibrary.org/obo/flu/
   id: flu
-  in_foundry: false
   is_obsolete: true
   layout: ontology_detail
   products:
@@ -8949,7 +8928,6 @@ ontologies:
   description: An ontology representation of the LIPIDMAPS nomenclature classification.
   domain: chemistry and biochemistry
   id: lipro
-  in_foundry: false
   is_obsolete: true
   layout: ontology_detail
   tags:
diff --git a/_includes/ontology_table.html b/_includes/ontology_table.html
@@ -5,21 +5,8 @@
 <a href="/registry/ontologies.ttl">RDF/Turtle</a> ]
 <table class="table">
   <tbody>
-    {% for ont in site.ontologies %} {% if ont.in_foundry_order %}
+    {% for ont in site.ontologies %}
     <tr>
-      {% elsif ont.is_obsolete %}
-    </tr>
-
-    <tr class="obsolete">
-      {% elsif ont.activity_status == "orphaned" %}
-    </tr>
-
-    <tr class="obsolete">
-      {% elsif ont.activity_status == "inactive" %}
-    </tr>
-
-    <tr class="obsolete">
-      {% endif %}
       <td>
         <a href="ontology/{{ ont.id }}.html">
           {% if ont.is_obsolete %}
diff --git a/faq/where-is-the-obo-file.md b/faq/where-is-the-obo-file.md
@@ -23,7 +23,6 @@ The different products are listed as objects under the `product` key, for exampl
 ---
 layout: ontology_detail
 id: go
-in_foundry_order: 1
 label: GO
 description: An ontology for describing the function of genes and gene products
 title: Gene Ontology
diff --git a/ontology/bcgo.md b/ontology/bcgo.md
@@ -10,7 +10,6 @@ contact:
 description: An application ontology built for beta cell genomics studies.
 domain: anatomy and development
 homepage: https://github.com/obi-bcgo/bcgo
-in_foundry: false
 is_obsolete: true
 license:
   label: CC BY 3.0
diff --git a/ontology/bco.md b/ontology/bco.md
@@ -10,7 +10,6 @@ contact:
 description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.
 domain: organisms
 homepage: https://github.com/BiodiversityOntologies/bco
-in_foundry: false
 license:
   label: CC0 1.0
   url: https://creativecommons.org/publicdomain/zero/1.0/
diff --git a/ontology/bfo.md b/ontology/bfo.md
@@ -15,7 +15,6 @@ depicted_by: https://avatars2.githubusercontent.com/u/12972134?v=3&s=200
 description: The upper level ontology upon which OBO Foundry ontologies are built.
 domain: upper
 homepage: http://ifomis.org/bfo/
-in_foundry_order: 1
 license:
   label: CC BY 4.0
   url: http://creativecommons.org/licenses/by/4.0/
diff --git a/ontology/chebi.md b/ontology/chebi.md
@@ -15,7 +15,6 @@ depicted_by: https://www.ebi.ac.uk/chebi/chebi_logo.svg
 description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.
 domain: chemistry and biochemistry
 homepage: http://www.ebi.ac.uk/chebi
-in_foundry_order: 1
 license:
   label: CC BY 4.0
   url: https://creativecommons.org/licenses/by/4.0/
diff --git a/ontology/doid.md b/ontology/doid.md
@@ -15,7 +15,6 @@ depicted_by: https://disease-ontology.org/media/images/DO_logo_teal.png
 description: An ontology for describing the classification of human diseases organized by etiology.
 domain: health
 homepage: https://disease-ontology.org
-in_foundry_order: 1
 license:
   label: CC0 1.0
   url: https://creativecommons.org/publicdomain/zero/1.0/
diff --git a/ontology/epo.md b/ontology/epo.md
@@ -5,7 +5,6 @@ title: Epidemiology Ontology
 description: An ontology designed to support the semantic annotation of epidemiology resources
 domain: health
 homepage: https://code.google.com/p/epidemiology-ontology/
-in_foundry: false
 is_obsolete: true
 products:
 - id: epo.owl
diff --git a/ontology/fix.md b/ontology/fix.md
@@ -8,7 +8,6 @@ contact:
 description: An ontology of physico-chemical methods and properties.
 domain: chemistry and biochemistry
 homepage: http://www.ebi.ac.uk/chebi
-in_foundry: false
 products:
 - id: fix.owl
 - id: fix.obo
diff --git a/ontology/flu.md b/ontology/flu.md
@@ -7,7 +7,6 @@ contact:
   label: Burke Squires
 domain: health
 homepage: http://purl.obolibrary.org/obo/flu/
-in_foundry: false
 is_obsolete: true
 products:
 - id: flu.owl
diff --git a/ontology/go.md b/ontology/go.md
@@ -34,7 +34,6 @@ depicted_by: /images/go_logo.png
 description: An ontology for describing the function of genes and gene products
 domain: biological systems
 homepage: http://geneontology.org/
-in_foundry_order: 1
 license:
   label: CC BY 4.0
   url: https://creativecommons.org/licenses/by/4.0/
diff --git a/ontology/lipro.md b/ontology/lipro.md
@@ -8,7 +8,6 @@ contact:
   orcid: 0000-0003-4004-6479
 description: An ontology representation of the LIPIDMAPS nomenclature classification.
 domain: chemistry and biochemistry
-in_foundry: false
 is_obsolete: true
 tags:
 - lipids
diff --git a/ontology/obcs.md b/ontology/obcs.md
@@ -10,7 +10,6 @@ contact:
 description: A biomedical ontology in the domain of biological and clinical statistics.
 domain: information technology
 homepage: https://github.com/obcs/obcs
-in_foundry: false
 license:
   label: CC BY 4.0
   url: http://creativecommons.org/licenses/by/4.0/
diff --git a/ontology/obi.md b/ontology/obi.md
@@ -15,7 +15,6 @@ depicted_by: https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lote
 description: An integrated ontology for the description of life-science and clinical investigations
 domain: investigations
 homepage: http://obi-ontology.org
-in_foundry_order: 1
 license:
   label: CC BY 4.0
   url: https://creativecommons.org/licenses/by/4.0/
diff --git a/ontology/omit.md b/ontology/omit.md
@@ -10,7 +10,6 @@ contact:
 description: Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain
 domain: chemistry and biochemistry
 homepage: http://omit.cis.usouthal.edu/
-in_foundry: false
 license:
   label: CC BY 3.0
   url: https://creativecommons.org/licenses/by/3.0/
diff --git a/ontology/pato.md b/ontology/pato.md
@@ -14,7 +14,6 @@ contact:
 description: An ontology of phenotypic qualities (properties, attributes or characteristics)
 domain: phenotype
 homepage: https://github.com/pato-ontology/pato/
-in_foundry_order: 1
 license:
   label: CC BY 3.0
   url: http://creativecommons.org/licenses/by/3.0/
diff --git a/ontology/pbpko.md b/ontology/pbpko.md
@@ -14,7 +14,6 @@ contact:
 description: An ontology for modeling and understanding of pharmacokinetics in biological systems.
 domain: chemistry and biochemistry
 homepage: https://github.com/InSilicoVida-Research-Lab/pbpko
-in_foundry_order: 1
 license:
   label: CC BY 3.0
   url: http://creativecommons.org/licenses/by/3.0/
diff --git a/ontology/po.md b/ontology/po.md
@@ -15,7 +15,6 @@ depicted_by: https://raw.githubusercontent.com/Planteome/plant-ontology/refs/hea
 description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
 domain: anatomy and development
 homepage: http://browser.planteome.org/amigo
-in_foundry_order: 1
 license:
   label: CC BY 4.0
   url: https://creativecommons.org/licenses/by/4.0/
diff --git a/ontology/pr.md b/ontology/pr.md
@@ -18,7 +18,6 @@ depicted_by: https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo
 description: An ontological representation of protein-related entities
 domain: chemistry and biochemistry
 homepage: http://proconsortium.org
-in_foundry_order: 1
 license:
   label: CC BY 4.0
   url: http://creativecommons.org/licenses/by/4.0/
diff --git a/ontology/stato.md b/ontology/stato.md
@@ -11,7 +11,6 @@ depicted_by: https://raw.githubusercontent.com/ISA-tools/stato/dev/images/stato-
 description: STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of application, and information needed or resulting from statistical methods, such as probability distributions, variables, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results.
 domain: information technology
 homepage: http://stato-ontology.org/
-in_foundry: false
 license:
   label: CC BY 3.0
   url: http://creativecommons.org/licenses/by/3.0/
diff --git a/ontology/uo.md b/ontology/uo.md
@@ -10,7 +10,6 @@ contact:
 description: Metrical units for use in conjunction with PATO
 domain: phenotype
 homepage: https://github.com/bio-ontology-research-group/unit-ontology
-in_foundry: false
 license:
   label: CC BY 3.0
   url: http://creativecommons.org/licenses/by/3.0/
diff --git a/ontology/xao.md b/ontology/xao.md
@@ -10,7 +10,6 @@ contact:
 description: XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.
 domain: anatomy and development
 homepage: http://www.xenbase.org/anatomy/xao.do?method=display
-in_foundry_order: 1
 license:
   label: CC BY 3.0
   url: http://creativecommons.org/licenses/by/3.0/
diff --git a/ontology/zfa.md b/ontology/zfa.md
@@ -10,7 +10,6 @@ contact:
 description: A structured controlled vocabulary of the anatomy and development of the Zebrafish
 domain: anatomy and development
 homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
-in_foundry_order: 1
 license:
   label: CC BY 3.0
   url: http://creativecommons.org/licenses/by/3.0/
diff --git a/ontology/zfs.md b/ontology/zfs.md
@@ -10,7 +10,6 @@ contact:
 description: Developmental stages of the Zebrafish
 domain: anatomy and development
 homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
-in_foundry: false
 license:
   label: CC BY 3.0
   url: http://creativecommons.org/licenses/by/3.0/
diff --git a/registry/ontologies.jsonld b/registry/ontologies.jsonld
diff --git a/registry/ontologies.yml b/registry/ontologies.yml
diff --git a/tests/test_integrity.py b/tests/test_integrity.py
diff --git a/util/auto-foundry-check.py b/util/auto-foundry-check.py
diff --git a/util/extract-metadata.py b/util/extract-metadata.py
diff --git a/util/make-shacl-prefixes.py b/util/make-shacl-prefixes.py
diff --git a/util/processor.py b/util/processor.py
diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json
diff --git a/util/sort-ontologies.py b/util/sort-ontologies.py
diff --git a/util/validate-metadata.py b/util/validate-metadata.py
diff --git a/util/yaml2json.py b/util/yaml2json.py
