Merge branch 'master' into nlharris-patch-13

Author: jsstevenson

_config.yml

@@ -2585,6 +2585,41 @@ ontologies:
   repository: https://github.com/adeans/gallont
   title: Plant Gall Ontology
   tracker: https://github.com/adeans/gallont/issues
+- activity_status: active
+  build:
+    method: archive
+    path: archive
+    source_url: http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/*zip*/archive.zip
+  contact:
+    email: lschriml@som.umaryland.edu
+    github: lschriml
+    label: Lynn Schriml
+    orcid: 0000-0001-8910-9851
+  description: A gazetteer constructed on ontological principles. The countries are
+    actively maintained.
+  domain: environment
+  homepage: http://environmentontology.github.io/gaz/
+  id: gaz
+  layout: ontology_detail
+  license:
+    label: CC0 1.0
+    logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
+    url: https://creativecommons.org/publicdomain/zero/1.0/
+  mailing_list: https://groups.google.com/forum/#!forum/obo-gazetteer
+  ontology_purl: http://purl.obolibrary.org/obo/gaz.owl
+  preferredPrefix: GAZ
+  products:
+  - id: gaz.owl
+    ontology_purl: http://purl.obolibrary.org/obo/gaz.owl
+  - id: gaz.obo
+    ontology_purl: http://purl.obolibrary.org/obo/gaz.obo
+  - description: A country specific subset of the GAZ.
+    id: gaz/gaz-countries.owl
+    ontology_purl: http://purl.obolibrary.org/obo/gaz/gaz-countries.owl
+    title: GAZ countries
+  repository: https://github.com/EnvironmentOntology/gaz
+  title: Gazetteer
+  tracker: https://github.com/EnvironmentOntology/gaz/issues
 - activity_status: active
   contact:
     email: rbca.jackson@gmail.com
@@ -3841,10 +3876,10 @@ ontologies:
     url: https://monarchinitiative.org/disease/MONDO:0019609
   canonical: mondo.owl
   contact:
-    email: nicole@tislab.org
-    github: nicolevasilevsky
-    label: Nicole Vasilevsky
-    orcid: 0000-0001-5208-3432
+    email: Sabrina@tislab.org
+    github: sabrinatoro
+    label: Sabrina Toro
+    orcid: 0000-0002-4142-7153
   depicted_by: https://raw.githubusercontent.com/monarch-initiative/mondo/master/docs/images/mondo_logo_black-stacked-small.png
   description: A global community effort to harmonize multiple disease resources to
     yield a coherent merged ontology.
@@ -3892,6 +3927,8 @@ ontologies:
     ontology_purl: http://purl.obolibrary.org/obo/mondo/mondo-simple.owl
     title: Mondo Simple Release
   publications:
+  - id: https://doi.org/10.1093/genetics/iyaf215
+    title: 'Mondo: Integrating Disease Terminology Across Communities'
   - id: https://www.medrxiv.org/content/10.1101/2022.04.13.22273750
     title: 'Mondo: Unifying diseases for the world, by the world'
   repository: https://github.com/monarch-initiative/mondo
@@ -4022,9 +4059,16 @@ ontologies:
     page: https://github.com/mgijax/mammalian-phenotype-ontology/releases/tag/current
     title: MP Base Module
   publications:
+  - id: https://www.ncbi.nlm.nih.gov/pubmed/40963406
+    title: Expanding and refining the Mammalian Phenotype Ontology to enhance disease
+      model discovery
   - id: https://www.ncbi.nlm.nih.gov/pubmed/22961259
     title: The Mammalian Phenotype Ontology as a unifying standard for experimental
       and high-throughput phenotyping data
+  - id: https://www.ncbi.nlm.nih.gov/pubmed/25825651
+    title: Expanding the mammalian phenotype ontology to support automated exchange
+      of high throughput mouse phenotyping data generated by large-scale mouse knockout
+      screens
   repository: https://github.com/mgijax/mammalian-phenotype-ontology
   taxon:
     id: NCBITaxon:40674
@@ -5178,8 +5222,11 @@ ontologies:
   - label: BioPortal
     title: BioPortal Browser
     url: https://bioportal.bioontology.org/ontologies/ONTONEO
+  - label: OntoBee
+    title: OntoBee Browser
+    url: https://ontobee.org/ontology/ONTONEO
   build:
-    source_url: http://purl.obolibrary.org/obo/ontoneo/ontoneo.owl
+    source_url: https://raw.githubusercontent.com/ontoneo-project/Ontoneo/master/ontoneo.owl
   contact:
     email: fernanda.farinelli@gmail.com
     github: FernandaFarinelli
@@ -5189,24 +5236,49 @@ ontologies:
     to provide a representation of the data from electronic health records (EHRs)
     involved in the care of the pregnant woman, and of her baby.
   domain: health
-  homepage: ontoneo.com
+  homepage: https://ontoneo.com/
   id: ontoneo
   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: https://creativecommons.org/licenses/by/4.0/
   mailing_list: http://groups.google.com/group/ontoneo-discuss
   ontology_purl: http://purl.obolibrary.org/obo/ontoneo.owl
   preferredPrefix: ONTONEO
   products:
-  - id: ontoneo.owl
+  - description: The full version of ONTONEO in OWL format
+    id: ontoneo.owl
     ontology_purl: http://purl.obolibrary.org/obo/ontoneo.owl
+    title: ONTONEO
+  publications:
+  - id: https://doi.org/10.5281/zenodo.17429771
+    title: 'OntONeo: The Obstetric and Neonatal Ontology'
+  - id: https://doi.org/10.5281/zenodo.17508651
+    title: Formal Ontologies in Knowledge Organization within the Obstetric and Neonatal
+      Domain
   repository: https://github.com/ontoneo-project/Ontoneo
-  tags:
-  - biomedical
   title: Obstetric and Neonatal Ontology
   tracker: https://github.com/ontoneo-project/Ontoneo/issues
+  usages:
+  - description: The ReCOL research group uses OntONeo to model and structure biomedical
+      information, particularly in obstetrics and neonatology.
+    examples:
+    - description: The ontology has been applied in studies on data interoperability
+        and semantic integration, improving access to structured medical information
+        and enabling knowledge sharing between systems.
+      url: https://mba.eci.ufmg.br/wp-content/uploads/Anais_CBIS_2018_FarinelliAlmeidaLouize.pdf
+    user: http://recol.eci.ufmg.br/
+  - description: OntONeo serves as a knowledge representation framework to support
+      clinical decision-making and data interoperability in healthcare. It is used
+      in information retrieval applications, enabling structured queries over medical
+      databases and facilitating access to critical obstetric and neonatal health
+      information.
+    examples:
+    - description: Demonstrates OntONeo’s application for enabling structured data
+        access and semantic reasoning in clinical contexts.
+      url: https://doi.org/10.56238/devopinterscie-267
+    user: http://hdl.handle.net/1843/38044
 - activity_status: active
   contact:
     email: mbrochhausen@gmail.com
@@ -7078,6 +7150,7 @@ ontologies:
     orcid: 0000-0002-4142-7153
   dependencies:
   - id: ncbitaxon
+  depicted_by: https://github.com/tis-lab/closed-illustrations/blob/15058315cba1018e09572b28ebeee262a458b1c6/logos/vbo-logo/VBO-black-logo-stackedv2.png
   description: Vertebrate Breed Ontology is an ontology created to serve as a single
     computable resource for vertebrate breed names.
   domain: organisms
@@ -7088,6 +7161,7 @@ ontologies:
     label: CC BY 4.0
     logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
     url: https://creativecommons.org/licenses/by/4.0/
+  mailing_list: https://groups.google.com/group/VBO-users
   ontology_purl: http://purl.obolibrary.org/obo/vbo.owl
   preferredPrefix: VBO
   products:
@@ -7109,6 +7183,9 @@ ontologies:
   - id: vbo/vbo-base.json
     name: Vertebrate Breed Ontology additional release in OBOJSon format
     ontology_purl: http://purl.obolibrary.org/obo/vbo/vbo-base.json
+  publications:
+  - id: https://doi.org/10.1111/jvim.70133
+    title: 'The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization'
   repository: https://github.com/monarch-initiative/vertebrate-breed-ontology
   title: Vertebrate Breed Ontology
   tracker: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues
@@ -7120,6 +7197,14 @@ ontologies:
       url: https://www.omia.org/OMIA001289/9685/
     type: annotation
     user: https://omia.org/home/
+  - description: VBO is used in Cellosaurus for breed/subspecies of origin of cell
+      lines.
+    examples:
+    - description: The cell line AG07906 derived from the Thoroughbred (VBO:0001083)
+        breed of Equuus caballus (Horse).
+      url: https://www.cellosaurus.org/CVCL_2L83
+    type: annotation
+    user: https://www.cellosaurus.org/index.html
 - activity_status: active
   build:
     source_url: https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl
@@ -8590,40 +8675,6 @@ ontologies:
     label: Homo sapiens
   title: Foundational Model of Anatomy Ontology (subset)
   tracker: https://bitbucket.org/uwsig/fma/issues
-- activity_status: inactive
-  build:
-    method: archive
-    path: archive
-    source_url: http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/*zip*/archive.zip
-  contact:
-    email: lschriml@som.umaryland.edu
-    github: lschriml
-    label: Lynn Schriml
-    orcid: 0000-0001-8910-9851
-  description: A gazetteer constructed on ontological principles. The countries are
-    actively maintained.
-  domain: environment
-  homepage: http://environmentontology.github.io/gaz/
-  id: gaz
-  layout: ontology_detail
-  license:
-    label: CC0 1.0
-    logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png
-    url: https://creativecommons.org/publicdomain/zero/1.0/
-  mailing_list: https://groups.google.com/forum/#!forum/obo-gazetteer
-  ontology_purl: http://purl.obolibrary.org/obo/gaz.owl
-  products:
-  - id: gaz.owl
-    ontology_purl: http://purl.obolibrary.org/obo/gaz.owl
-  - id: gaz.obo
-    ontology_purl: http://purl.obolibrary.org/obo/gaz.obo
-  - description: A country specific subset of the GAZ.
-    id: gaz/gaz-countries.owl
-    ontology_purl: http://purl.obolibrary.org/obo/gaz/gaz-countries.owl
-    title: GAZ countries
-  repository: https://github.com/EnvironmentOntology/gaz
-  title: Gazetteer
-  tracker: https://github.com/EnvironmentOntology/gaz/issues
 - activity_status: inactive
   contact:
     email: topalis@imbb.forth.gr

ontology/gaz.md

@@ -18,6 +18,7 @@ license:
   label: CC0 1.0
   url: https://creativecommons.org/publicdomain/zero/1.0/
 mailing_list: https://groups.google.com/forum/#!forum/obo-gazetteer
+preferredPrefix: GAZ
 products:
 - id: gaz.owl
 - id: gaz.obo
@@ -26,5 +27,5 @@ products:
   description: A country specific subset of the GAZ.
 repository: https://github.com/EnvironmentOntology/gaz
 tracker: https://github.com/EnvironmentOntology/gaz/issues
-activity_status: inactive
+activity_status: active
 ---

ontology/mondo.md

@@ -8,10 +8,10 @@ browsers:
   url: https://monarchinitiative.org/disease/MONDO:0019609
 canonical: mondo.owl
 contact:
-  email: nicole@tislab.org
-  github: nicolevasilevsky
-  label: Nicole Vasilevsky
-  orcid: 0000-0001-5208-3432
+  email: Sabrina@tislab.org
+  github: sabrinatoro
+  label: Sabrina Toro
+  orcid: 0000-0002-4142-7153
 depicted_by: https://raw.githubusercontent.com/monarch-initiative/mondo/master/docs/images/mondo_logo_black-stacked-small.png
 description: A global community effort to harmonize multiple disease resources to yield a coherent merged ontology.
 domain: health
@@ -47,6 +47,8 @@ products:
   description: The main ontology classes and their hierarchies, without references to external terms.
   format: owl
 publications:
+- id: https://doi.org/10.1093/genetics/iyaf215
+  title: 'Mondo: Integrating Disease Terminology Across Communities'
 - id: https://www.medrxiv.org/content/10.1101/2022.04.13.22273750
   title: 'Mondo: Unifying diseases for the world, by the world'
 repository: https://github.com/monarch-initiative/mondo

ontology/mp.md

@@ -45,8 +45,12 @@ products:
   description: The main ontology plus axioms connecting to select external ontologies, excluding axioms from the the external ontologies themselves.
   page: https://github.com/mgijax/mammalian-phenotype-ontology/releases/tag/current
 publications:
+- id: https://www.ncbi.nlm.nih.gov/pubmed/40963406
+  title: Expanding and refining the Mammalian Phenotype Ontology to enhance disease model discovery
 - id: https://www.ncbi.nlm.nih.gov/pubmed/22961259
   title: The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data
+- id: https://www.ncbi.nlm.nih.gov/pubmed/25825651
+  title: Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens
 repository: https://github.com/mgijax/mammalian-phenotype-ontology
 taxon:
   id: NCBITaxon:40674

ontology/ontoneo.md

@@ -6,28 +6,45 @@ browsers:
 - title: BioPortal Browser
   label: BioPortal
   url: https://bioportal.bioontology.org/ontologies/ONTONEO
+- title: OntoBee Browser
+  label: OntoBee
+  url: https://ontobee.org/ontology/ONTONEO
 build:
-  source_url: http://purl.obolibrary.org/obo/ontoneo/ontoneo.owl
+  source_url: https://raw.githubusercontent.com/ontoneo-project/Ontoneo/master/ontoneo.owl
 contact:
   email: fernanda.farinelli@gmail.com
   github: FernandaFarinelli
   label: Fernanda Farinelli
   orcid: 0000-0003-2338-8872
 description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.
 domain: health
-homepage: ontoneo.com
+homepage: https://ontoneo.com/
 license:
-  label: CC BY 3.0
-  url: http://creativecommons.org/licenses/by/3.0/
+  label: CC BY 4.0
+  url: https://creativecommons.org/licenses/by/4.0/
 mailing_list: http://groups.google.com/group/ontoneo-discuss
 preferredPrefix: ONTONEO
 products:
 - id: ontoneo.owl
+  title: ONTONEO
+  description: The full version of ONTONEO in OWL format
+publications:
+- id: https://doi.org/10.5281/zenodo.17429771
+  title: 'OntONeo: The Obstetric and Neonatal Ontology'
+- id: https://doi.org/10.5281/zenodo.17508651
+  title: Formal Ontologies in Knowledge Organization within the Obstetric and Neonatal Domain
 repository: https://github.com/ontoneo-project/Ontoneo
-tags:
-- biomedical
 tracker: https://github.com/ontoneo-project/Ontoneo/issues
+usages:
+- description: The ReCOL research group uses OntONeo to model and structure biomedical information, particularly in obstetrics and neonatology.
+  examples:
+  - description: The ontology has been applied in studies on data interoperability and semantic integration, improving access to structured medical information and enabling knowledge sharing between systems.
+    url: https://mba.eci.ufmg.br/wp-content/uploads/Anais_CBIS_2018_FarinelliAlmeidaLouize.pdf
+  user: http://recol.eci.ufmg.br/
+- description: OntONeo serves as a knowledge representation framework to support clinical decision-making and data interoperability in healthcare. It is used in information retrieval applications, enabling structured queries over medical databases and facilitating access to critical obstetric and neonatal health information.
+  examples:
+  - description: Demonstrates OntONeo’s application for enabling structured data access and semantic reasoning in clinical contexts.
+    url: https://doi.org/10.56238/devopinterscie-267
+  user: http://hdl.handle.net/1843/38044
 activity_status: active
 ---
-
-The OntONeo suite is a collection of open ontologies available about Obstetric and Neonatal domain, currently designed to be composed by three complementary sub-ontologies covering several data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.

ontology/vbo.md

@@ -9,12 +9,14 @@ contact:
   orcid: 0000-0002-4142-7153
 dependencies:
 - id: ncbitaxon
+depicted_by: https://github.com/tis-lab/closed-illustrations/blob/15058315cba1018e09572b28ebeee262a458b1c6/logos/vbo-logo/VBO-black-logo-stackedv2.png
 description: Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.
 domain: organisms
 homepage: https://github.com/monarch-initiative/vertebrate-breed-ontology
 license:
   label: CC BY 4.0
   url: https://creativecommons.org/licenses/by/4.0/
+mailing_list: https://groups.google.com/group/VBO-users
 preferredPrefix: VBO
 products:
 - id: vbo.owl
@@ -29,6 +31,9 @@ products:
   name: Vertebrate Breed Ontology additional release in OBO format
 - id: vbo/vbo-base.json
   name: Vertebrate Breed Ontology additional release in OBOJSon format
+publications:
+- id: https://doi.org/10.1111/jvim.70133
+  title: 'The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization'
 repository: https://github.com/monarch-initiative/vertebrate-breed-ontology
 tracker: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues
 usages:
@@ -38,5 +43,11 @@ usages:
     url: https://www.omia.org/OMIA001289/9685/
   type: annotation
   user: https://omia.org/home/
+- description: VBO is used in Cellosaurus for breed/subspecies of origin of cell lines.
+  examples:
+  - description: The cell line AG07906 derived from the Thoroughbred (VBO:0001083) breed of Equuus caballus (Horse).
+    url: https://www.cellosaurus.org/CVCL_2L83
+  type: annotation
+  user: https://www.cellosaurus.org/index.html
 activity_status: active
 ---

registry/obo_prefixes.ttl

@@ -62,6 +62,7 @@
 ,[ sh:prefix "FOVT" ; sh:namespace "http://purl.obolibrary.org/obo/FOVT_"]
 ,[ sh:prefix "FYPO" ; sh:namespace "http://purl.obolibrary.org/obo/FYPO_"]
 ,[ sh:prefix "GALLONT" ; sh:namespace "http://purl.obolibrary.org/obo/GALLONT_"]
+,[ sh:prefix "GAZ" ; sh:namespace "http://purl.obolibrary.org/obo/GAZ_"]
 ,[ sh:prefix "GECKO" ; sh:namespace "http://purl.obolibrary.org/obo/GECKO_"]
 ,[ sh:prefix "GENEPIO" ; sh:namespace "http://purl.obolibrary.org/obo/GENEPIO_"]
 ,[ sh:prefix "GENO" ; sh:namespace "http://purl.obolibrary.org/obo/GENO_"]
@@ -203,7 +204,6 @@
 ,[ sh:prefix "CEPH" ; sh:namespace "http://purl.obolibrary.org/obo/CEPH_"]
 ,[ sh:prefix "EHDAA2" ; sh:namespace "http://purl.obolibrary.org/obo/EHDAA2_"]
 ,[ sh:prefix "FMA" ; sh:namespace "http://purl.obolibrary.org/obo/FMA_"]
-,[ sh:prefix "GAZ" ; sh:namespace "http://purl.obolibrary.org/obo/GAZ_"]
 ,[ sh:prefix "IDOMAL" ; sh:namespace "http://purl.obolibrary.org/obo/IDOMAL_"]
 ,[ sh:prefix "MIRO" ; sh:namespace "http://purl.obolibrary.org/obo/MIRO_"]
 ,[ sh:prefix "RNAO" ; sh:namespace "http://purl.obolibrary.org/obo/RNAO_"]