Merge branch 'master' into nataled-patch-50

Author: nataled

.github/ISSUE_TEMPLATE/new-ontology.yml

@@ -115,7 +115,7 @@ body:
     attributes:
       label: Ontology Download Link
       description: What URL can be used to download your Ontology?
-      placeholder: e.g. https://github.com/obophenotype/uberon/raw/master/uberon.owl
+      placeholder: e.g. https://github.com/obophenotype/uberon/blob/master/uberon.obo
     validations:
       required: true
 
@@ -208,7 +208,7 @@ body:
       render: yaml
       description: |
         Please provide a list of current uses for your ontology in YAML format as a list of objects with `user`, `description`, and `example` keys like in the following example:
-        
+
         ```yaml
         - user: https://www.rhea-db.org/
           description: Rhea uses CHEBI to annotate reaction participants
@@ -228,7 +228,7 @@ body:
     attributes:
       value: |
         # Finishing Up
-        
+
         This final section asks you to introspect on your ontology request.
   - type: textarea
     id: scenarios
@@ -266,7 +266,7 @@ body:
           required: false
         - label: My identifiers (classes and properties IRIs) are formatted according to the [OBO Foundry Identifier Policy](http://obofoundry.org/id-policy)
           required: false
-        - label: My term labels are in English and conform to the OBO Foundry [Naming Conventions](http://obofoundry.org/http://obofoundry.org/principles/fp-012-naming-conventions.html)
+        - label: My term labels are in English and conform to the OBO Foundry [Naming Conventions](http://obofoundry.org/principles/fp-012-naming-conventions.html)
           required: false
         - label: I understand that term definitions are key to understanding the intentions of a term, especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology--and all top level terms--have definitions, in English, using the [IAO:0000115](https://ontobee.org/ontology/IAO?iri=http://purl.obolibrary.org/obo/IAO_0000115) property.
           required: false

_config.yml

@@ -10,6 +10,9 @@ author:
   name: OBO Technical WG
 plugins:
   - jekyll-sitemap
+  - jekyll-feed
+feed:
+  disable_in_development: true
 ## --Anything above this line can be edited in _config_header.yml --
 ## --Everything below this line automatically generated in _config.yml --
 ontologies:
@@ -796,9 +799,9 @@ ontologies:
     label: Alexander Diehl
     orcid: 0000-0001-9990-8331
   dependencies:
-  - id: chebi
   - id: go
   - id: ncbitaxon
+  - id: omo
   - id: pato
   - id: pr
   - id: ro
@@ -826,29 +829,57 @@ ontologies:
     ontology_purl: http://purl.obolibrary.org/obo/cl.owl
     title: Main CL OWL edition
     uses:
-    - uberon
-    - chebi
     - go
-    - pr
-    - pato
     - ncbitaxon
+    - omo
+    - pato
+    - pr
     - ro
+    - uberon
   - derived_from: cl.owl
     description: Complete ontology, plus inter-ontology axioms, and imports modules
       merged in
     format: obo
     id: cl.obo
     ontology_purl: http://purl.obolibrary.org/obo/cl.obo
     title: CL obo format edition
+  - derived_from: cl.owl
+    description: Complete ontology, plus inter-ontology axioms, and imports modules
+      merged in
+    format: json
+    id: cl.json
+    ontology_purl: http://purl.obolibrary.org/obo/cl.json
+    title: CL OBOGraph-JSON format edition
+  - description: Basic version, no inter-ontology axioms
+    format: owl-rdf/xml
+    id: cl/cl-basic.owl
+    ontology_purl: http://purl.obolibrary.org/obo/cl/cl-basic.owl
+    title: Basic CL
   - description: Basic version, no inter-ontology axioms
     format: obo
     id: cl/cl-basic.obo
     ontology_purl: http://purl.obolibrary.org/obo/cl/cl-basic.obo
-    title: Basic CL
+    title: Basic CL (OBO version)
+  - description: Basic version, no inter-ontology axioms
+    format: json
+    id: cl/cl-basic.json
+    ontology_purl: http://purl.obolibrary.org/obo/cl/cl-basic.json
+    title: Basic CL (OBOGraph-JSON version)
   - description: complete CL but with no imports or external axioms
+    format: owl-rdf/xml
     id: cl/cl-base.owl
     ontology_purl: http://purl.obolibrary.org/obo/cl/cl-base.owl
     title: CL base module
+  - description: complete CL but with no imports or external axioms
+    format: obo
+    id: cl/cl-base.obo
+    ontology_purl: http://purl.obolibrary.org/obo/cl/cl-base.obo
+    title: CL base module (OBO version)
+  - description: complete CL but with no imports or external axioms
+    format: json
+    id: cl/cl-base.json
+    ontology_purl: http://purl.obolibrary.org/obo/cl/cl-base.json
+    title: CL base module (OBOGraph-JSON version)
   publications:
   - id: https://www.ncbi.nlm.nih.gov/pubmed/27377652
     title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
@@ -894,6 +925,20 @@ ontologies:
         Program.'
     type: annotation
     user: https://hubmapconsortium.org/
+  - description: The single-cell transcriptomics platform CZ CELLxGENE uses CL to
+      annotate all cell types. All datasets on CellXGene are annotated according to
+      a standard schema that specifies the use of CL to record Cell Type.
+    examples:
+    - description: A CELLxGENE Cell Guide entry for 'luminal adaptive secretory precursor
+        cell of mammary gland', which includes the CL ID (CL:4033057), CL definition
+        and a visualizer of CL hierarchy
+      url: https://cellxgene.cziscience.com/cellguide/CL:4033057
+    publications:
+    - id: https://doi.org/10.1101/2021.04.05.438318
+      title: 'CELLxGENE: a performant, scalable exploration platform for high dimensional
+        sparse matrices'
+    type: annotation
+    user: https://cellxgene.cziscience.com/
   - description: The Human Cell Atlas (HCA) is an international group of researchers
       using a combination of these new technologies to create cellular reference maps.
       The HCA use CL to annotate cells in their reference maps.
@@ -2334,9 +2379,9 @@ ontologies:
   id: foodon
   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/foodon.owl
   preferredPrefix: FOODON
   products:
@@ -2357,6 +2402,27 @@ ontologies:
   - food
   title: Food Ontology
   tracker: https://github.com/FoodOntology/foodon/issues/
+  usages:
+  - description: FoodData Central nutrition database web portal provided by USDA Agricultural
+      Research Service.
+    examples:
+    - description: An entry for 'Apples, fuji, with skin, raw' from the FoodData Central
+        nutrition database which is annotated with the term FOODON:00002862.
+      url: https://fdc.nal.usda.gov/fdc-app.html#/food-details/1750340/attributes
+    user: https://fdc.nal.usda.gov/
+  - description: FDA GenomeTrackr surveillance program for reporting foodborne pathogen
+      biosamples.
+    examples:
+    - description: An entry from NCBI Biosample that describes a *Samonella enterica*
+        sample extracted from Chicken and annotated with the term FOODON:03411457.
+      url: https://www.ncbi.nlm.nih.gov/biosample/SAMN03455272
+    user: https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network
+  - description: Wiki database consolidating over 30 global food composition databases.
+    examples:
+    - description: An entry from WikiFCD that describes Walnuts and is annotated with
+        the term FOODON:03301364.
+      url: https://wikifcd.wikibase.cloud/wiki/Item:Q568877
+    user: https://wikifcd.wikibase.cloud/wiki/Main_Page
 - activity_status: active
   contact:
     email: meghan.balk@gmail.com
@@ -3765,32 +3831,36 @@ ontologies:
   ontology_purl: http://purl.obolibrary.org/obo/mondo.owl
   preferredPrefix: MONDO
   products:
-  - description: Complete ontology. Uses MONDO IDs. Imports merged. The original mondo.owl
-      without merged imports and with equivalence axioms can now be obtained from
-      the release pages and is called mondo-with-equivalents.
+  - description: Complete ontology with merged imports.
     format: owl-rdf/xml
     id: mondo.owl
     is_canonical: true
     ontology_purl: http://purl.obolibrary.org/obo/mondo.owl
-    title: Main OWL edition
+    title: Mondo OWL edition
   - derived_from: mondo.owl
-    description: As OWL. xrefs can be used as proxy for equivalence. Uses Mondo IDs.
+    description: OBO serialization of mondo.owl.
     format: obo
     id: mondo.obo
     ontology_purl: http://purl.obolibrary.org/obo/mondo.obo
-    title: obo-format edition
+    title: Mondo OBO Format edition
   - derived_from: mondo.owl
-    description: Equivalent to the OWL edition.
+    description: Obographs serialization of mondo.owl.
     format: obo
     id: mondo.json
     ontology_purl: http://purl.obolibrary.org/obo/mondo.json
-    title: json edition
+    title: Mondo JSON edition
   - description: The main ontology plus axioms connecting to select external ontologies,
       excluding the external ontologies themselves
     format: owl
     id: mondo/mondo-base.owl
     ontology_purl: http://purl.obolibrary.org/obo/mondo/mondo-base.owl
-    title: Mondo Base Module
+    title: Mondo Base Release
+  - description: The main ontology classes and their hierarchies, without references
+      to external terms.
+    format: owl
+    id: mondo/mondo-simple.owl
+    ontology_purl: http://purl.obolibrary.org/obo/mondo/mondo-simple.owl
+    title: Mondo Simple Release
   publications:
   - id: https://www.medrxiv.org/content/10.1101/2022.04.13.22273750
     title: 'Mondo: Unifying diseases for the world, by the world'
@@ -3802,7 +3872,6 @@ ontologies:
     label: Metazoa
   title: Mondo Disease Ontology
   tracker: https://github.com/monarch-initiative/mondo/issues
-  twitter: MonarchInit
   usages:
   - description: Mondo is used by the Monarch Initiative for disease annotations.
     examples:
@@ -3881,7 +3950,7 @@ ontologies:
     title: Monarch Phenotype Page
     url: http://monarchinitiative.org/phenotype/MP:0000001
   contact:
-    email: drsbello@gmail.com
+    email: pheno@jax.org
     github: sbello
     label: Sue Bello
     orcid: 0000-0003-4606-0597
@@ -5582,7 +5651,7 @@ ontologies:
     github: jaiswalp
     label: Pankaj Jaiswal
     orcid: 0000-0002-1005-8383
-  depicted_by: https://github.com/Planteome/plant-ontology/blob/master/Planteome_profile.jpg
+  depicted_by: https://raw.githubusercontent.com/Planteome/plant-ontology/refs/heads/master/Planteome_profile.jpg
   description: The Plant Ontology is a structured vocabulary and database resource
     that links plant anatomy, morphology and growth and development to plant genomics
     data.
@@ -5737,14 +5806,22 @@ ontologies:
   ontology_purl: http://purl.obolibrary.org/obo/pr.owl
   preferredPrefix: PR
   products:
-  - description: PRO after reasoning has been applied, OWL format.
+  - description: PRO after reasoning has been applied, OWL format. Add '.gz' for compressed.
     id: pr.owl
     ontology_purl: http://purl.obolibrary.org/obo/pr.owl
     title: pro_reasoned.owl
   - description: PRO after reasoning has been applied, OBO format.
     id: pr.obo
     ontology_purl: http://purl.obolibrary.org/obo/pr.obo
     title: pro_reasoned.obo
+  - description: PRO without reasoning applied, OWL format. Add '.gz' for compressed.
+    id: pr-asserted.owl
+    ontology_purl: http://purl.obolibrary.org/obo/pr-asserted.owl
+    title: pro_nonreasoned.owl
+  - description: PRO without reasoning applied, OBO format.
+    id: pr-asserted.obo
+    ontology_purl: http://purl.obolibrary.org/obo/pr-asserted.obo
+    title: pro_nonreasoned.obo
   publications:
   - id: https://www.ncbi.nlm.nih.gov/pubmed/27899649
     title: 'Protein Ontology (PRO): enhancing and scaling up the representation of
@@ -6261,10 +6338,10 @@ ontologies:
   tracker: https://github.com/obophenotype/spider-ontology/issues
 - activity_status: active
   contact:
-    email: alejandra.gonzalez.beltran@gmail.com
-    github: agbeltran
-    label: Alejandra Gonzalez-Beltran
-    orcid: 0000-0003-3499-8262
+    email: proccaserra@gmail.com
+    github: proccaserra
+    label: Philippe Rocca-Serra
+    orcid: 0000-0001-9853-5668
   depicted_by: https://raw.githubusercontent.com/ISA-tools/stato/dev/images/stato-logo-3.png
   description: STATO is a general-purpose STATistics Ontology. Its aim is to provide
     coverage for processes such as statistical tests, their conditions of application,
@@ -6287,11 +6364,43 @@ ontologies:
   products:
   - id: stato.owl
     ontology_purl: http://purl.obolibrary.org/obo/stato.owl
+  publications:
+  - id: https://www.ncbi.nlm.nih.gov/pubmed/31831744
+    title: Experiment design driven FAIRification of omics data matrices, an exemplar
+  - id: https://www.ncbi.nlm.nih.gov/pubmed/32109232
+    title: Semantic concept schema of the linear mixed model of experimental observations
   repository: https://github.com/ISA-tools/stato
   tags:
   - statistics
   title: The Statistical Methods Ontology
   tracker: https://github.com/ISA-tools/stato/issues
+  usages:
+  - description: struct (Statistics in R using Class-based Templates), Struct integrates
+      with the STATistics Ontology to ensure consistent reporting and maximizes semantic
+      interoperability
+    publications:
+    - id: https://www.ncbi.nlm.nih.gov/pubmed/33325493
+      title: 'struct: an R/Bioconductor-based framework for standardized metabolomics
+        data analysis and beyond'
+    type: annotation
+    user: https://bioconductor.org/packages/release/bioc/html/struct.html
+  - description: Scientific Evidence Code System (SEVCO) on the FEvIR platform. The
+      FEvIR Platform includes many Builder Tools to create FHIR Resources without
+      requiring expertise in FHIR or JSON, and Converter Tools to convert structured
+      data to FHIR Resources
+    publications:
+    - id: https://www.ncbi.nlm.nih.gov/pubmed/33486066
+      title: 'Making science computable: Developing code systems for statistics, study
+        design, and risk of bias'
+    type: annotation
+    user: https://fevir.net/resources/CodeSystem/27270#STATO:0000039
+  - description: OBCS
+    publications:
+    - id: https://www.ncbi.nlm.nih.gov/pubmed/27627881
+      title: The Ontology of Biological and Clinical Statistics (OBCS) for standardized
+        and reproducible statistical analysis
+    type: annotation
+    user: https://github.com/obcs/obcs
 - activity_status: active
   contact:
     email: allyson.lister@oerc.ox.ac.uk
@@ -6865,10 +6974,10 @@ ontologies:
     path: archive/ontology
     source_url: http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip
   contact:
-    email: vasilevs@ohsu.edu
-    github: nicolevasilevsky
-    label: Nicole Vasilevsky
-    orcid: 0000-0001-5208-3432
+    email: jmcl@ebi.ac.uk
+    github: jamesamcl
+    label: James McLaughlin
+    orcid: 0000-0002-8361-2795
   description: The uPheno ontology integrates multiple phenotype ontologies into a
     unified cross-species phenotype ontology.
   domain: phenotype
@@ -6895,22 +7004,25 @@ ontologies:
     page: https://github.com/obophenotype/upheno/tree/master/hp-mp
     title: uPheno MP-HP equivalence axioms
   - description: The new version of uPheno, along with species independent phenotypes
-      amd additional phenotype relations. The ontology is still in Beta status, but
+      and additional phenotype relations. The ontology is still in Beta status, but
       we recommend users to migrate their infrastructures to uPheno 2 as uPheno 1
       is no longer actively maintained.
     id: upheno/v2/upheno.owl
     ontology_purl: http://purl.obolibrary.org/obo/upheno/v2/upheno.owl
     page: https://github.com/obophenotype/upheno-dev
     title: uPheno 2
   publications:
+  - id: https://doi.org/10.1101/2024.09.18.613276
+    title: 'The Unified Phenotype Ontology (uPheno): A framework for cross-species
+      integrative phenomics'
   - id: https://zenodo.org/record/2382757
     title: Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims
       to reconcile logical definitions across species
   - id: https://zenodo.org/record/3352149
     title: 'Phenotype Ontologies Traversing All The Organisms (POTATO) workshop: 2nd
       edition'
   repository: https://github.com/obophenotype/upheno
-  title: Unified phenotype ontology (uPheno)
+  title: Unified Phenotype Ontology (uPheno)
   tracker: https://github.com/obophenotype/upheno/issues
   usages:
   - description: uPheno is used by the Monarch Initiative for cross-species inference.

_config_header.yml

@@ -10,5 +10,8 @@ author:
   name: OBO Technical WG
 plugins:
   - jekyll-sitemap
+  - jekyll-feed
+feed:
+  disable_in_development: true
 ## --Anything above this line can be edited in _config_header.yml --
 ## --Everything below this line automatically generated in _config.yml --