Merge branch 'master' into patch-3

Author: FernandaFarinelli

_config.yml

@@ -385,6 +385,36 @@ ontologies:
       structure
     type: owl_import
     user: http://obofoundry.org
+- activity_status: active
+  browsers:
+  - label: BioPortal
+    title: BioPortal Ontology Browser
+    url: https://bioportal.bioontology.org/ontologies/BMONT
+  contact:
+    email: alpha.tom.kodamullil@scai.fraunhofer.de
+    github: akodamullil
+    label: Alpha Tom Kodamullil
+    orcid: 0000-0001-9896-3531
+  description: An application ontology that represents comprehensive knowledge involving
+    a variety of fields of medical and biological aspects.
+  domain: health
+  homepage: https://github.com/SCAI-BIO/BiomarkerOntology
+  id: bmont
+  layout: ontology_detail
+  license:
+    label: CC BY 4.0
+    logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
+    url: http://creativecommons.org/licenses/by/4.0/
+  ontology_purl: http://purl.obolibrary.org/obo/bmont.owl
+  preferredPrefix: BMONT
+  products:
+  - description: Includes axioms linking to other ontologies, but no imports of those
+      ontologies
+    id: BMONT.owl
+    ontology_purl: http://purl.obolibrary.org/obo/BMONT.owl
+  repository: https://github.com/SCAI-BIO/BiomarkerOntology
+  title: Biomarker Ontology
+  tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues
 - activity_status: active
   build:
     checkout: git clone https://github.com/obophenotype/biological-spatial-ontology.git
@@ -458,34 +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
@@ -572,7 +574,7 @@ ontologies:
     github: amalik01
     label: Adnan Malik
     orcid: 0000-0001-8123-5351
-  depicted_by: https://www.ebi.ac.uk/chebi/images/ChEBI_logo.png
+  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
@@ -1051,8 +1053,8 @@ ontologies:
     path: .
     system: git
   contact:
-    email: lucas.leclere@obs-vlfr.fr
-    github: L-Leclere
+    email: lucas.leclere@obs-banyuls.fr
+    github: Leclere-L
     label: Lucas Leclere
     orcid: 0000-0002-7440-0467
   dependencies:
@@ -1426,9 +1428,9 @@ ontologies:
   browsers:
   - label: DO
     title: DO Browser
-    url: http://www.disease-ontology.org/
+    url: https://disease-ontology.org/
   build:
-    source_url: https://github.com/DiseaseOntology/DiseaseDriversOntology/tree/main/src/ontology/disdriv.owl
+    source_url: https://raw.githubusercontent.com/DiseaseOntology/DiseaseDriversOntology/refs/heads/main/src/ontology/disdriv.owl
   contact:
     email: lynn.schriml@gmail.com
     github: lschriml
@@ -1438,7 +1440,7 @@ ontologies:
     ExO ontology exposure stressors. An application ontology. Built in collaboration
     with EnvO, ExO, ECTO and ChEBI.
   domain: health
-  homepage: http://www.disease-ontology.org
+  homepage: https://disease-ontology.org/
   id: disdriv
   layout: ontology_detail
   license:
@@ -1463,13 +1465,13 @@ ontologies:
   - description: Human Disease Ontology
     examples:
     - description: fetal alcohol syndrome, has exposure stressor some alcohol
-      url: https://www.disease-ontology.org/?id=DOID:0050665
-    user: https://www.disease-ontology.org
+      url: https://disease-ontology.org/?id=DOID:0050665
+    user: https://disease-ontology.org/
 - activity_status: active
   browsers:
   - label: DO
     title: DO Browser
-    url: http://www.disease-ontology.org/do
+    url: https://disease-ontology.org/do
   build:
     infallible: 1
     method: obo2owl
@@ -1479,11 +1481,11 @@ ontologies:
     github: lschriml
     label: Lynn Schriml
     orcid: 0000-0001-8910-9851
-  depicted_by: http://www.disease-ontology.org/media/images/DO_logo.jpg
+  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: http://www.disease-ontology.org
+  homepage: https://disease-ontology.org
   id: doid
   in_foundry_order: 1
   layout: ontology_detail
@@ -1529,8 +1531,8 @@ ontologies:
   - description: MGI disease model annotations use DO
     examples:
     - description: physical disorder
-      url: http://www.informatics.jax.org/disease/DOID:0080015
-    user: http://www.informatics.jax.org/disease
+      url: https://www.informatics.jax.org/disease/DOID:0080015
+    user: https://www.informatics.jax.org/disease
   - description: Immune Epitope Database
     examples:
     - description: Antibody and T cell epitopes associated with human diseases
@@ -2032,6 +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
@@ -3203,9 +3233,9 @@ ontologies:
   id: ico
   layout: ontology_detail
   license:
-    label: CC BY 3.0
+    label: CC BY 4.0
     logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
-    url: http://creativecommons.org/licenses/by/3.0/
+    url: http://creativecommons.org/licenses/by/4.0/
   ontology_purl: http://purl.obolibrary.org/obo/ico.owl
   preferredPrefix: ICO
   products:
@@ -4259,7 +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:
@@ -4277,25 +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
@@ -4486,11 +4500,12 @@ ontologies:
   - description: OBA terms are used by the NHGRI-EBI GWAS Catalog for phenotypic trait
       annotation.
     examples:
-    - description: age of onset of depressive disorder
-      url: https://www.ebi.ac.uk/gwas/efotraits/OBA_2040166
+    - description: hip circumference
+      url: https://www.ebi.ac.uk/gwas/efotraits/OBA_1000032
     publications:
-    - id: https://doi.org/10.1093/nar/gkac1010
-      title: 'The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource'
+    - id: https://doi.org/10.1093/nar/gkae1070
+      title: 'The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability
+        and diversity'
     type: annotation
     user: https://www.ebi.ac.uk/gwas/
   - description: OBA trait terms facilitate computational drug target identification
@@ -5216,6 +5231,23 @@ ontologies:
   repository: https://github.com/OOSTT/OOSTT
   title: Ontology of Organizational Structures of Trauma centers and Trauma systems
   tracker: https://github.com/OOSTT/OOSTT/issues
+  usages:
+  - description: OOSTT terms, such as OOSTT_00000017 'trauma program' and OOSTT_00000021
+      'trauma medical director role,' are used in the CAFE questionnaire to assess
+      trauma centers and systems.
+    type: application
+    user: https://cafe-trauma.com/
+  - description: OOSTT terms, such as OOSTT_00000002 'trauma center' and OOSTT_00000066
+      'emergency medicine liaison role,' are used in the TIPTOE questionnaire to relate
+      trauma center/system structure to patient outcomes.
+    type: application
+    user: https://tiptoe.apps.dbmi.cloud/tiptoe
+  - description: Terms from OOSTT are imported and used by OMRSE.
+    examples:
+    - description: academic degree
+      url: http://purl.obolibrary.org/obo/OOSTT_00000074
+    type: owl:Ontology
+    user: https://github.com/mcwdsi/OMRSE
 - activity_status: active
   contact:
     email: zhengj2007@gmail.com
@@ -6439,7 +6471,7 @@ ontologies:
   build:
     infallible: 1
     method: obo2owl
-    source_url: https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/symp.obo
+    source_url: https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/src/ontology/symp.obo
   contact:
     email: lynn.schriml@gmail.com
     github: lschriml
@@ -6449,7 +6481,7 @@ ontologies:
     changes in function, sensations or appearance reported by a patient indicative
     of a disease.
   domain: health
-  homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page
+  homepage: https://github.com/DiseaseOntology/SymptomOntology
   id: symp
   layout: ontology_detail
   license:
@@ -6481,8 +6513,8 @@ ontologies:
   - description: Symptoms of human diseases in the DO
     examples:
     - description: symptoms of human diseases
-      url: http://www.disease-ontology.org/?id=DOID:0060164
-    user: http://www.disease-ontology.org
+      url: https://disease-ontology.org/?id=DOID:0060164
+    user: https://disease-ontology.org/
 - activity_status: active
   contact:
     email: allyson.lister@oerc.ox.ac.uk
@@ -6664,11 +6696,11 @@ ontologies:
   title: Pathogen Transmission Ontology
   tracker: https://github.com/DiseaseOntology/PathogenTransmissionOntology/issues
   usages:
-  - description: Methods of trnasmission of human diseases in the DO
+  - description: Methods of transmission of human diseases in the DO
     examples:
     - description: methods of transmission of human diseases
-      url: http://www.disease-ontology.org/?id=DOID:12365
-    user: http://www.disease-ontology.org
+      url: https://disease-ontology.org/?id=DOID:12365
+    user: https://disease-ontology.org/
 - activity_status: active
   contact:
     email: balhoff@renci.org
@@ -8869,6 +8901,34 @@ 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
@@ -9675,6 +9735,9 @@ principles:
 - id: fp-016-maintenance
   layout: principle
   title: Maintenance (principle 16)
+- id: fp-019-term-stability
+  layout: principle
+  title: Stability of Term Meaning (principle 19)
 - id: fp-020-responsiveness
   layout: principle
   title: Responsiveness (principle 20)