Merge branch 'master' into fix/2832-fix-lint-fail

Author: jsstevenson

_config.yml

@@ -1171,6 +1171,16 @@ ontologies:
   repository: https://github.com/OBOFoundry/COB
   title: Core Ontology for Biology and Biomedicine
   tracker: https://github.com/OBOFoundry/COB/issues
+  usages:
+  - description: Ontologies using COB terms
+    examples:
+    - description: List of ontologies using at least one COB term (See section entitled
+        "Which ontologies use it?")
+      url: http://dashboard.obofoundry.org/dashboard/cob/dashboard.html
+    - description: List of ontologies using the term 'organism' (See section entitled
+        "Ontologies that use the Class")
+      url: https://ontobee.org/ontology/COB?iri=http://purl.obolibrary.org/obo/COB_0000022
+    user: (multiple)
 - activity_status: active
   contact:
     email: entiminae@gmail.com
@@ -1902,12 +1912,12 @@ ontologies:
   - id: https://doi.org/10.1016/B978-0-12-800043-4.00023-3
     title: 'Textual Anatomics: the Mouse Developmental Anatomy Ontology and the Gene
       Expression Database for Mouse Development (GXD)'
-  repository: https://github.com/obophenotype/mouse-anatomy-ontology
+  repository: https://github.com/obophenotype/developmental-mouse-anatomy-ontology
   taxon:
     id: NCBITaxon:10088
     label: Mus
   title: Mouse Developmental Anatomy Ontology
-  tracker: https://github.com/obophenotype/mouse-anatomy-ontology/issues
+  tracker: https://github.com/obophenotype/developmental-mouse-anatomy-ontology/issues
   usages:
   - description: GXD
     seeAlso: https://doi.org/10.25504/FAIRsharing.q9neh8
@@ -2588,10 +2598,6 @@ ontologies:
   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
@@ -7068,6 +7074,8 @@ ontologies:
     ontology_purl: http://purl.obolibrary.org/obo/uo.owl
   - id: uo.obo
     ontology_purl: http://purl.obolibrary.org/obo/uo.obo
+  - id: uo.json
+    ontology_purl: http://purl.obolibrary.org/obo/uo.json
   publications:
   - id: https://www.ncbi.nlm.nih.gov/pubmed/23060432
     title: 'The Units Ontology: a tool for integrating units of measurement in science'

ontology/cob.md

@@ -33,6 +33,14 @@ products:
   status: alpha
 repository: https://github.com/OBOFoundry/COB
 tracker: https://github.com/OBOFoundry/COB/issues
+usages:
+- description: Ontologies using COB terms
+  examples:
+  - description: List of ontologies using at least one COB term (See section entitled "Which ontologies use it?")
+    url: http://dashboard.obofoundry.org/dashboard/cob/dashboard.html
+  - description: List of ontologies using the term 'organism' (See section entitled "Ontologies that use the Class")
+    url: https://ontobee.org/ontology/COB?iri=http://purl.obolibrary.org/obo/COB_0000022
+  user: (multiple)
 activity_status: active
 ---
 

ontology/emapa.md

@@ -30,11 +30,11 @@ publications:
   title: 'Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating Biomedical Data'
 - id: https://doi.org/10.1016/B978-0-12-800043-4.00023-3
   title: 'Textual Anatomics: the Mouse Developmental Anatomy Ontology and the Gene Expression Database for Mouse Development (GXD)'
-repository: https://github.com/obophenotype/mouse-anatomy-ontology
+repository: https://github.com/obophenotype/developmental-mouse-anatomy-ontology
 taxon:
   id: NCBITaxon:10088
   label: Mus
-tracker: https://github.com/obophenotype/mouse-anatomy-ontology/issues
+tracker: https://github.com/obophenotype/developmental-mouse-anatomy-ontology/issues
 usages:
 - description: GXD
   seeAlso: https://doi.org/10.25504/FAIRsharing.q9neh8

ontology/gaz.md

@@ -2,10 +2,6 @@
 layout: ontology_detail
 id: gaz
 title: Gazetteer
-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

ontology/uo.md

@@ -21,6 +21,7 @@ preferredPrefix: UO
 products:
 - id: uo.owl
 - id: uo.obo
+- id: uo.json
 publications:
 - id: https://www.ncbi.nlm.nih.gov/pubmed/23060432
   title: 'The Units Ontology: a tool for integrating units of measurement in science'

principles/fp-001-open.md

@@ -61,8 +61,7 @@ The attribution method for individual terms reused in another ontology (e.g., by
 1. **In OWL** - Any ontology re-using individual terms from another ontology should:
 
    1. re-use the original term IRI (which for OBO Foundry ontologies is generally in the form of an OBO Foundry PURL)
-   2. use an IAO:imported from annotation <http://purl.obolibrary.org/obo/IAO_0000412> on each imported term to link back to the group (i.e. ontology) maintaining it, where more information would be available about the license
-   3. include any annotations for term or definition editors from the original ontology
+   2. include any annotations for term or definition editors from the original ontology
 
 2. **In OBO** - Any ontology re-using individual terms from another ontology should:
    1. re-use the original term ID (of the form <GO:0000001>)
@@ -124,31 +123,6 @@ The first course of action should be to reuse the external term as is, by import
 
 Please see the discussion tab for additional discussion of how to use different annotation properties to credit external ontologies or definition sources.
 
-#### Example 3A: IAO:imported from
-
-The Ontology for Biomedical Investigation (OBI) imports the class "environmental material" from the Environment Ontology (ENVO), using OntoFox. The imported from axiom is automatically generated by Ontofox and added to "environmental material" in OBI:
-
-```
-<!-- <http://purl.obolibrary.org/obo/ENVO_00010483> -->
-
-<owl:Class rdf:about="&obo;ENVO_00010483">
-
-<rdfs:label rdf:datatype="&xsd;string">environmental
-material</rdfs:label>
-
-<rdfs:subClassOf rdf:resource="&obo;BFO_0000040"/>
-
-<obo:IAO_0000115 rdf:datatype="&xsd;string">Material in or on which
-organisms may live.</obo:IAO_0000115>
-
-<obo:IAO_0000111 rdf:datatype="&xsd;string">environmental
-material</obo:IAO_0000111>
-
-<obo:IAO_0000412 rdf:resource="&obo;envo.owl"/>
-
-</owl:Class>
-```
-
 ## Counter-Examples
 
 - An ontology with no license statement is by default subject to the most restrictive copyright laws for those parts of the ontology that are copyrightable, and therefore is not useful within the OBO Foundry.

principles/fp-002-format.md

@@ -15,7 +15,7 @@ A common format allows the maximum number of people to access and reuse an ontol
 
 ## Recommendations and Requirements
 
-All ontologies MUST have at least one OWL product whose name corresponds to the registered prefix (e.g., 'GO' --> go.owl, 'OBI' --> obi.owl). Thus the ontology whose IRI is http://purl.obolibrary.org/obo/ro.owl (known to the OBO Foundry as 'RO'), must have at least the product ro.owl. Developers are free to use whatever combination of technologies and formats is appropriate for development. However, the official OWL PURL (see [Principle 3](https://obofoundry.org/principles/fp-003-uris.html)) for the ontology MUST resolve to a syntactically valid OWL file using the [RDF-XML](https://www.w3.org/TR/rdf-syntax-grammar/) syntax.
+All ontologies MUST have at least one OWL product whose name corresponds to the registered prefix (e.g., 'GO' --> go.owl, 'OBI' --> obi.owl). Thus the ontology whose IRI is http://purl.obolibrary.org/obo/ro.owl (known to the OBO Foundry as 'RO'), MUST have at least the product ro.owl which MUST be a syntactically valid OWL file using the [RDF-XML](https://www.w3.org/TR/rdf-syntax-grammar/) syntax. Developers are free to use whatever combination of technologies and formats is appropriate for development.
 
 Developers can OPTIONALLY produce ontologies in other formats. These are conventionally the same IRI as the owl, but with .owl changed to the relevant extension (e.g., '.obo', '.json'). Note that such products are not listed by default. If you produce an additional format product, you should register it under the 'products' field in the appropriate metadata file found in this [folder](https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology).
 

principles/fp-003-uris.md

@@ -17,6 +17,8 @@ A unique namespace within the OBO Foundry Library allows the source of an elemen
 
 Each ontology MUST have a unique IRI in the form of an OBO Foundry permanent URL (PURL). The PURL must include the ontology namespace, which is a short string of letters (usually 2-5) that represents the ontology. Namespaces MUST be approved by the OBO Foundry Operations Committee. Every element (class, property, etc.) created by the ontology MUST use the namespace in the identifier of each element, as specified in the OBO Foundry [ID policy](http://www.obofoundry.org/id-policy).
 
+The official PURL for the ontology, after redirection, MUST resolve to the ontology OWL file (see [Principle 2](https://obofoundry.org/principles/fp-002-format.html) for format requirements). Furthermore, PURLs for individual terms, after redirection, MUST resolve to a dedicated _term-centric_ destination page containing the appropriate content.
+
 ## Implementation
 
 ### Ontology Namespace:

principles/fp-009-users.md

@@ -20,7 +20,7 @@ scientific area and does so in a usable and sustainable fashion.
 It is important to be able to illustrate usage outside of the immediate circle of ontology developers and stakeholders. Demonstrations of usage MUST be publicly available. Preferred indicators of usage are those that directly demonstrate such, including:
 
 - Use of the target ontology's term IRIs in an external ontology. Indicators of this type MUST include one or more IRIs for a term _within the external ontology_ that uses a term from the target ontology.
-  
+
 - Documentation of requests from multiple users. Indicators of this type MUST link to specific requests in the issue tracker, OR link to an issue tracker search (for example, showing new term requests), OR link to an email thread or other mechanism _if publicly viewable_.
 
 - Publications showing the ontology being used in research by external users. Indicators of this type MUST provide citation details for the publications (link to PubMed or full text) and MUST include a sentence demonstrating the use (preferably taken from the title, abstract, or full text of the cited reference). Note that if citing full text that is behind a paywall, it may be necessary to provide a PDF for the paper.
@@ -42,67 +42,67 @@ Other indicators are currently possible as well:
   within some community (mere mention of the existence is not enough
   to warrant inclusion).
 
-Note that the ontology can still be listed on the OBO Foundry website while publicising your resource in appropriate channels and searching for users with needs you can meet. 
+Note that the ontology can still be listed on the OBO Foundry website while publicising your resource in appropriate channels and searching for users with needs you can meet.
 
 ## Implementation
 
 The ontology developers MUST provide links/citations to publicly available evidence of
-use within your ontology [metadata file](https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology) as given below (replacing with the correct group name, link, and description):
+use within your ontology [metadata file](https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology) as given below (after replacing with the correct description of usage, description of example, link to example, and link to user group):
 
 ```yaml
 usages:
-- user: http://www.informatics.jax.org/disease (link to group)
-  description: MGI disease model annotations use DO (description of group)
+- description: MGI disease model annotations use DO (description of usage)
   examples:
-   - url: http://www.informatics.jax.org/disease/DOID:4123 (link to specific example)
-     description: Human genes and mouse homology associated with nail diseases (description of specific example)
+    - description: Human genes and mouse homology associated with nail diseases (description of example)
+      url: http://www.informatics.jax.org/disease/DOID:4123 (link to example)
+  user: http://www.informatics.jax.org/disease (link to user group)
 ```
 
-You may have multiple examples for each user, and mulitple users under the `usages` tag.
+You may have multiple examples for each user, and multiple users under the `usages` tag.
 
 ## Examples
 
 Use of PSI-MOD term IRI (in the form of a CURIE) in the PR ontology:
 ```yaml
-- user: http://purl.obolibrary.org/obo/pr
-  description: Protein Ontology
+- description: Protein Ontology
   examples:
-   - url: https://proconsortium.org/app/export/obo/PR:000027653/
-     description: OBO Format stanza showing use of PSI-MOD term in logical definition
+    - description: OBO Format stanza showing use of PSI-MOD term in logical definition
+      url: https://proconsortium.org/cgi-bin/entry_pro?stanza_id=PR:000027653
+  user: http://purl.obolibrary.org/obo/pr
 ```
 Term requests to PR from multiple users:
 ```yaml
-- user: (multiple)
-  description: Term requests made via the Protein Ontology GitHub tracker
+- description: Term requests made via the Protein Ontology GitHub tracker
   examples:
-   - url: https://github.com/PROconsortium/PRoteinOntology/issues?q=is%3Aissue+label%3A%22Term+Request%22
-     description: List of issues tagged with 'Term Request' to PRO
+    - description: List of issues tagged with 'Term Request' to PRO
+      url: https://github.com/PROconsortium/PRoteinOntology/issues?q=is%3Aissue+label%3A%22Term+Request%22
+  user: (multiple)
 ```
 Publication showing the Disease Ontology being used in research by external users
 ```yaml
-- user: https://pubmed.ncbi.nlm.nih.gov/36860337/
-  description: Machine learning-based prediction of candidate gene biomarkers correlated with immune infiltration in patients with idiopathic pulmonary fibrosis
+- description: Machine learning-based prediction of candidate gene biomarkers correlated with immune infiltration in patients with idiopathic pulmonary fibrosis
   examples:
-   - url: https://pubmed.ncbi.nlm.nih.gov/36860337/
-     description: In abstract, "Functional annotation, pathway enrichment, Disease Ontology and gene set enrichment analyses revealed..."
+    - description: In abstract, "Functional annotation, pathway enrichment, Disease Ontology and gene set enrichment analyses revealed..."
+      url: https://pubmed.ncbi.nlm.nih.gov/36860337/
+  user: https://pubmed.ncbi.nlm.nih.gov/36860337/
 ```
 Use of terms from GO for annotation:
 ```yaml
-- user: https://www.uniprot.org
-  description: UniProt
+- description: UniProt
   examples:
-   - url: https://www.uniprot.org/uniprotkb/Q15796/entry#function
-     description: Functional annotation using GO (see subsection entitled "GO annotations")
+    - description: Functional annotation using GO (see subsection entitled "GO annotations")
+      url: https://www.uniprot.org/uniprotkb/Q15796/entry#function
+  user: https://www.uniprot.org
 ```
 OBI terms imported into external ontologies
 ```yaml
-- user: (multiple)
-  description: Ontologies using OBI terms
+- description: Ontologies using OBI terms
   examples:
-   - url: http://dashboard.obofoundry.org/dashboard/obi/dashboard.html
-     description: List of ontologies using at least one OBI term (See section entitled "Info: Which ontologies use it?")
-   - url: https://ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0000691
-     description: List of ontologies using the term 'ABI 377 automated sequencer' (See section entitled "Ontologies that use the Class")
+    - description: List of ontologies using at least one OBI term (See section entitled "Info: Which ontologies use it?")
+      url: http://dashboard.obofoundry.org/dashboard/obi/dashboard.html
+    - description: List of ontologies using the term "ABI 377 automated sequencer" (See section entitled "Ontologies that use the Class")
+      url: https://ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0000691
+  user: (multiple)
 ```
 
 ## Counter-Examples

registry/ontologies.jsonld

@@ -1602,7 +1602,23 @@
             ],
             "repository": "https://github.com/OBOFoundry/COB",
             "title": "Core Ontology for Biology and Biomedicine",
-            "tracker": "https://github.com/OBOFoundry/COB/issues"
+            "tracker": "https://github.com/OBOFoundry/COB/issues",
+            "usages": [
+                {
+                    "description": "Ontologies using COB terms",
+                    "examples": [
+                        {
+                            "description": "List of ontologies using at least one COB term (See section entitled \"Which ontologies use it?\")",
+                            "url": "http://dashboard.obofoundry.org/dashboard/cob/dashboard.html"
+                        },
+                        {
+                            "description": "List of ontologies using the term 'organism' (See section entitled \"Ontologies that use the Class\")",
+                            "url": "https://ontobee.org/ontology/COB?iri=http://purl.obolibrary.org/obo/COB_0000022"
+                        }
+                    ],
+                    "user": "(multiple)"
+                }
+            ]
         },
         {
             "activity_status": "active",
@@ -2636,13 +2652,13 @@
                     "title": "Textual Anatomics: the Mouse Developmental Anatomy Ontology and the Gene Expression Database for Mouse Development (GXD)"
                 }
             ],
-            "repository": "https://github.com/obophenotype/mouse-anatomy-ontology",
+            "repository": "https://github.com/obophenotype/developmental-mouse-anatomy-ontology",
             "taxon": {
                 "id": "NCBITaxon:10088",
                 "label": "Mus"
             },
             "title": "Mouse Developmental Anatomy Ontology",
-            "tracker": "https://github.com/obophenotype/mouse-anatomy-ontology/issues",
+            "tracker": "https://github.com/obophenotype/developmental-mouse-anatomy-ontology/issues",
             "usages": [
                 {
                     "description": "GXD",
@@ -3648,11 +3664,6 @@
         },
         {
             "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",
@@ -9865,6 +9876,10 @@
                 {
                     "id": "uo.obo",
                     "ontology_purl": "http://purl.obolibrary.org/obo/uo.obo"
+                },
+                {
+                    "id": "uo.json",
+                    "ontology_purl": "http://purl.obolibrary.org/obo/uo.json"
                 }
             ],
             "publications": [