Merge branch 'master' into 2747-remove-docs-completed-reviews

Author: nlharris

_config.yml

@@ -488,34 +488,6 @@ ontologies:
   repository: https://github.com/BRENDA-Enzymes/BTO
   title: BRENDA tissue / enzyme source
   tracker: https://github.com/BRENDA-Enzymes/BTO/issues
-- activity_status: active
-  build:
-    method: obo2owl
-    notes: moving to owl soon
-    source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo
-  contact:
-    email: haendel@ohsu.edu
-    github: mellybelly
-    label: Melissa Haendel
-    orcid: 0000-0001-9114-8737
-  description: An upper level ontology to facilitate interoperability between existing
-    anatomy ontologies for different species
-  domain: anatomy and development
-  homepage: https://github.com/obophenotype/caro/
-  id: caro
-  layout: ontology_detail
-  license:
-    label: CC BY 4.0
-    logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
-    url: https://creativecommons.org/licenses/by/4.0/
-  ontology_purl: http://purl.obolibrary.org/obo/caro.owl
-  preferredPrefix: CARO
-  products:
-  - id: caro.owl
-    ontology_purl: http://purl.obolibrary.org/obo/caro.owl
-  repository: https://github.com/obophenotype/caro
-  title: Common Anatomy Reference Ontology
-  tracker: https://github.com/obophenotype/caro/issues
 - activity_status: active
   build:
     method: owl2obo
@@ -2062,6 +2034,34 @@ ontologies:
   - disease
   title: Epilepsy Ontology
   tracker: https://github.com/SCAI-BIO/EpilepsyOntology/issues
+- activity_status: active
+  contact:
+    email: xyz19940216@163.com
+    github: DarkKnight0-0
+    label: Xingyun Liu
+    orcid: 0000-0002-9295-2767
+  description: A core reference ontology built upon BFO about exercise medicine and
+    it contains the related terms for healthy people, people with chronic conditions
+    and people living with diability to exercise.
+  domain: health
+  homepage: https://github.com/Exercise-Medicine-Ontology/EXMO
+  id: exmo
+  layout: ontology_detail
+  license:
+    label: CC BY 4.0
+    logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
+    url: https://creativecommons.org/licenses/by/4.0/
+  ontology_purl: http://purl.obolibrary.org/obo/exmo.owl
+  preferredPrefix: EXMO
+  products:
+  - id: exmo.owl
+    ontology_purl: http://purl.obolibrary.org/obo/exmo.owl
+  publications:
+  - id: https://www.ncbi.nlm.nih.gov/pubmed/39695140
+    title: Core reference ontology for individualized exercise prescription
+  repository: https://github.com/Exercise-Medicine-Ontology/EXMO
+  title: Exercise Medicine Ontology
+  tracker: https://github.com/Exercise-Medicine-Ontology/EXMO/issues
 - activity_status: active
   contact:
     email: annethessen@gmail.com
@@ -4289,7 +4289,7 @@ ontologies:
     abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with
     OBO Library ontologies. NCIt OBO Edition releases should be considered experimental.
   domain: health
-  homepage: https://github.com/NCI-Thesaurus/thesaurus-obo-edition
+  homepage: https://github.com/ncit-obo-org/ncit-obo-edition
   id: ncit
   layout: ontology_detail
   license:
@@ -4307,25 +4307,9 @@ ontologies:
   - id: ncit.obo
     ontology_purl: http://purl.obolibrary.org/obo/ncit.obo
     title: NCIt OBO Edition OBO format
-  - description: This version replaces NCIt terms with direct references to terms
-      from other domain-specific OBO Library ontologies (e.g. cell types, cellular
-      components, anatomy), supporting cross-ontology reasoning. The current release
-      incorporates CL (cell types) and Uberon (anatomy).
-    id: ncit/ncit-plus.owl
-    mireots_from:
-    - cl
-    - uberon
-    ontology_purl: http://purl.obolibrary.org/obo/ncit/ncit-plus.owl
-    title: NCIt Plus
-  - description: This is a subset extracted from NCIt Plus, based on the [NCIt Neoplasm
-      Core value set](https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/Neoplasm/About_Core.html)
-      as a starting point.
-    id: ncit/neoplasm-core.owl
-    ontology_purl: http://purl.obolibrary.org/obo/ncit/neoplasm-core.owl
-    title: NCIt Plus Neoplasm Core
-  repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition
+  repository: https://github.com/ncit-obo-org/ncit-obo-edition
   title: NCI Thesaurus OBO Edition
-  tracker: https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues
+  tracker: https://github.com/ncit-obo-org/ncit-obo-edition/issues
 - activity_status: active
   build:
     method: owl2obo
@@ -8900,6 +8884,34 @@ ontologies:
   layout: ontology_detail
   replaced_by: molecular_function
   title: Gene Regulation Ontology
+- activity_status: inactive
+  build:
+    method: obo2owl
+    notes: moving to owl soon
+    source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo
+  contact:
+    email: haendel@ohsu.edu
+    github: mellybelly
+    label: Melissa Haendel
+    orcid: 0000-0001-9114-8737
+  description: An upper level ontology to facilitate interoperability between existing
+    anatomy ontologies for different species
+  domain: anatomy and development
+  homepage: https://github.com/obophenotype/caro/
+  id: caro
+  is_obsolete: true
+  layout: ontology_detail
+  license:
+    label: CC BY 4.0
+    logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
+    url: https://creativecommons.org/licenses/by/4.0/
+  preferredPrefix: CARO
+  products:
+  - id: caro.owl
+    ontology_purl: http://purl.obolibrary.org/obo/caro.owl
+  repository: https://github.com/obophenotype/caro
+  title: Common Anatomy Reference Ontology
+  tracker: https://github.com/obophenotype/caro/issues
 - activity_status: inactive
   contact:
     email: engelsta@ohsu.edu

ontology/caro.md

@@ -14,6 +14,7 @@ contact:
 description: An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species
 domain: anatomy and development
 homepage: https://github.com/obophenotype/caro/
+is_obsolete: true
 license:
   label: CC BY 4.0
   url: https://creativecommons.org/licenses/by/4.0/
@@ -22,7 +23,10 @@ products:
 - id: caro.owl
 repository: https://github.com/obophenotype/caro
 tracker: https://github.com/obophenotype/caro/issues
-activity_status: active
+activity_status: inactive
 ---
 
-The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO will be described in Anatomy Ontologies for Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and Richard Baldock (Editors)
+The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO will be described in Anatomy Ontologies for Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and Richard Baldock (Editors).
+
+**Important note**: CARO has been _obsoleted_ in favour of Uberon.
+However, not all CARO terms have been migrated to Uberon; please request any terms you were using from CARO and are missing from Uberon on the Uberon issue tracker: https://github.com/obophenotype/uberon/issues.

ontology/exmo.md

@@ -0,0 +1,25 @@
+---
+layout: ontology_detail
+id: exmo
+title: Exercise Medicine Ontology
+contact:
+  email: xyz19940216@163.com
+  github: DarkKnight0-0
+  label: Xingyun Liu
+  orcid: 0000-0002-9295-2767
+description: A core reference ontology built upon BFO about exercise medicine and it contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise.
+domain: health
+homepage: https://github.com/Exercise-Medicine-Ontology/EXMO
+license:
+  label: CC BY 4.0
+  url: https://creativecommons.org/licenses/by/4.0/
+preferredPrefix: EXMO
+products:
+- id: exmo.owl
+publications:
+- id: https://www.ncbi.nlm.nih.gov/pubmed/39695140
+  title: Core reference ontology for individualized exercise prescription
+repository: https://github.com/Exercise-Medicine-Ontology/EXMO
+tracker: https://github.com/Exercise-Medicine-Ontology/EXMO/issues
+activity_status: active
+---

ontology/ncit.md

@@ -9,7 +9,7 @@ contact:
   orcid: 0000-0000-0000-0000
 description: NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental.
 domain: health
-homepage: https://github.com/NCI-Thesaurus/thesaurus-obo-edition
+homepage: https://github.com/ncit-obo-org/ncit-obo-edition
 license:
   label: CC BY 4.0
   url: https://creativecommons.org/licenses/by/4.0/
@@ -20,17 +20,8 @@ products:
   description: A direct transformation of the standard NCIt content using OBO-style term and ontology IRIs and annotation properties.
 - id: ncit.obo
   title: NCIt OBO Edition OBO format
-- id: ncit/ncit-plus.owl
-  title: NCIt Plus
-  description: This version replaces NCIt terms with direct references to terms from other domain-specific OBO Library ontologies (e.g. cell types, cellular components, anatomy), supporting cross-ontology reasoning. The current release incorporates CL (cell types) and Uberon (anatomy).
-  mireots_from:
-  - cl
-  - uberon
-- id: ncit/neoplasm-core.owl
-  title: NCIt Plus Neoplasm Core
-  description: This is a subset extracted from NCIt Plus, based on the [NCIt Neoplasm Core value set](https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/Neoplasm/About_Core.html) as a starting point.
-repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition
-tracker: https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues
+repository: https://github.com/ncit-obo-org/ncit-obo-edition
+tracker: https://github.com/ncit-obo-org/ncit-obo-edition/issues
 activity_status: active
 ---
 

registry/obo_context.jsonld

@@ -272,6 +272,10 @@
             "@id": "http://purl.obolibrary.org/obo/EV_",
             "@prefix": true
         },
+        "EXMO": {
+            "@id": "http://purl.obolibrary.org/obo/EXMO_",
+            "@prefix": true
+        },
         "ExO": {
             "@id": "http://purl.obolibrary.org/obo/ExO_",
             "@prefix": true

registry/obo_prefixes.ttl

@@ -15,7 +15,6 @@
 ,[ sh:prefix "BMONT" ; sh:namespace "http://purl.obolibrary.org/obo/BMONT_"]
 ,[ sh:prefix "BSPO" ; sh:namespace "http://purl.obolibrary.org/obo/BSPO_"]
 ,[ sh:prefix "BTO" ; sh:namespace "http://purl.obolibrary.org/obo/BTO_"]
-,[ sh:prefix "CARO" ; sh:namespace "http://purl.obolibrary.org/obo/CARO_"]
 ,[ sh:prefix "CDAO" ; sh:namespace "http://purl.obolibrary.org/obo/CDAO_"]
 ,[ sh:prefix "CDNO" ; sh:namespace "http://purl.obolibrary.org/obo/CDNO_"]
 ,[ sh:prefix "CHEBI" ; sh:namespace "http://purl.obolibrary.org/obo/CHEBI_"]
@@ -50,6 +49,7 @@
 ,[ sh:prefix "EMAPA" ; sh:namespace "http://purl.obolibrary.org/obo/EMAPA_"]
 ,[ sh:prefix "ENVO" ; sh:namespace "http://purl.obolibrary.org/obo/ENVO_"]
 ,[ sh:prefix "EPIO" ; sh:namespace "http://purl.obolibrary.org/obo/EPIO_"]
+,[ sh:prefix "EXMO" ; sh:namespace "http://purl.obolibrary.org/obo/EXMO_"]
 ,[ sh:prefix "ExO" ; sh:namespace "http://purl.obolibrary.org/obo/ExO_"]
 ,[ sh:prefix "FAO" ; sh:namespace "http://purl.obolibrary.org/obo/FAO_"]
 ,[ sh:prefix "FBbt" ; sh:namespace "http://purl.obolibrary.org/obo/FBbt_"]
@@ -217,6 +217,7 @@
 ,[ sh:prefix "BCGO" ; sh:namespace "http://purl.obolibrary.org/obo/BCGO_"]
 ,[ sh:prefix "BILA" ; sh:namespace "http://purl.obolibrary.org/obo/BILA_"]
 ,[ sh:prefix "BOOTSTREP" ; sh:namespace "http://purl.obolibrary.org/obo/BOOTSTREP_"]
+,[ sh:prefix "CARO" ; sh:namespace "http://purl.obolibrary.org/obo/CARO_"]
 ,[ sh:prefix "CMF" ; sh:namespace "http://purl.obolibrary.org/obo/CMF_"]
 ,[ sh:prefix "DC_CL" ; sh:namespace "http://purl.obolibrary.org/obo/DC_CL_"]
 ,[ sh:prefix "DINTO" ; sh:namespace "http://purl.obolibrary.org/obo/DINTO_"]