Merge branch 'master' into patch-2

OBOFoundry · Aug 21, 2024 · 9578e73 · 9578e73
2 parents 7a4ea68 + 8d779fc
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diff --git a/.github/ISSUE_TEMPLATE/new-ontology.yml b/.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

diff --git a/_config.yml b/_config.yml
@@ -2334,9 +2334,9 @@ 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 +2357,27 @@ 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: [email protected]
@@ -3881,7 +3902,7 @@ ontologies:
     title: Monarch Phenotype Page
     url: http://monarchinitiative.org/phenotype/MP:0000001
   contact:
-    email: [email protected]
+    email: [email protected]
     github: sbello
     label: Sue Bello
     orcid: 0000-0003-4606-0597

diff --git a/_includes/header.html b/_includes/header.html
@@ -169,13 +169,6 @@
                     <a class="nav-link" href="/faq/index.html">FAQ</a>
                 </li>
             </ul>
-            <form class="d-flex" role="search" action="https://ontobee.org/search" method="get">
-                <!-- while the ontology input doesn't do anything, the Ontobee site is broken and doesn't work if it's missing -->
-                <input name="ontology" type="hidden" value=""/>
-                <input class="form-control me-2" type="search" placeholder="Search Ontobee" aria-label="Search"
-                       name="keywords">
-                <button class="btn btn-outline-success" type="submit">Search</button>
-            </form>
         </div>
     </div>
 </nav>
diff --git a/docs/roles/RoleNORManager.md b/docs/roles/RoleNORManager.md
@@ -11,6 +11,7 @@ The New Ontology Request (NOR) Manager has these basic duties:
 3. Supporting the New Ontology requestor to pass the OBO Dashboard
 4. Assigning a provisional reviewer from the OBO Operations Committee
 5. Removing the accepted ontology from the NOR Dashboard upon acceptance
+6. Maintaining the OBO Duty Rotation Table
 
 ### Receiving `new ontology` requests on OBO and acknowledging the receipt
 
@@ -78,7 +79,6 @@ In addition, some checks need to be carried out manually by the NOR manager unti
 
 - URIs: check if it includes "https"  and if it [conforms with the overall format](http://obofoundry.org/id-policy) "http://purl.obolibrary.org/obo/ONTOLOGY_"
 
-
 - Release artefact: check if release artefacts are identified as such and ensure that, alongside a "main release", a base release is provided which **does not include imported terms**.
 
 - Imports: Ensure that there is a mechanism in place to update imported terms (classes and properties).
@@ -98,3 +98,10 @@ If and only if the requested ontology passes the dashboard, i.e. no more "red" e
 When the ontology is accepted, the OBO NOR reviewer needs to make sure that the accepted ontology is removed from the OBO NOR Dashboard.
 
 Note 29.11.2022: There is a [work in progress](https://github.com/OBOFoundry/obo-nor.github.io/pull/23) which can deal with this step automatically, but the responsibility still stays with the OBO NOR Manager.
+
+### Maintaining the OBO Duty Rotation Table
+
+The OBO Duty Rotation Table is a Google spreadsheet available [here](https://docs.google.com/spreadsheets/d/19GrEWVnpxjnrig0iYUOiUvsZ0JDbprMh1USnRb-SXtg/edit).
+When a new member is added to the OBO Operations Committee, the OBO NOR reviewer should add the new member's name to this table. Similarly, former members should be removed from the table. The list of current OBO Operations members is maintained in the file [operations.yml](https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/_data/operations.yml).
+
+In addition, when a new ontology has been submitted, it should be added to the ['Ontology Reviewers' tab](https://docs.google.com/spreadsheets/d/19GrEWVnpxjnrig0iYUOiUvsZ0JDbprMh1USnRb-SXtg/edit?gid=1683009411#gid=1683009411) in the OBO Duty Rotation spreadsheet.
diff --git a/ontology/foodon.md b/ontology/foodon.md
@@ -20,8 +20,8 @@ description: A broadly scoped ontology representing entities which bear a “foo
 domain: diet, metabolomics, and nutrition
 homepage: https://foodon.org/
 license:
-  label: CC BY 3.0
-  url: http://creativecommons.org/licenses/by/3.0/
+  label: CC BY 4.0
+  url: http://creativecommons.org/licenses/by/4.0/
 preferredPrefix: FOODON
 products:
 - id: foodon.owl
@@ -37,6 +37,22 @@ repository: https://github.com/FoodOntology/foodon
 tags:
 - food
 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
 ---
 

diff --git a/ontology/mp.md b/ontology/mp.md
@@ -13,7 +13,7 @@ browsers:
   label: Monarch
   url: http://monarchinitiative.org/phenotype/MP:0000001
 contact:
-  email: [email protected]
+  email: [email protected]
   github: sbello
   label: Sue Bello
   orcid: 0000-0003-4606-0597

diff --git a/registry/ontologies.jsonld b/registry/ontologies.jsonld
@@ -3283,9 +3283,9 @@
             "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",
@@ -3314,7 +3314,39 @@
                 "food"
             ],
             "title": "Food Ontology",
-            "tracker": "https://github.com/FoodOntology/foodon/issues/"
+            "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",
@@ -5464,7 +5496,7 @@
                 }
             ],
             "contact": {
-                "email": "[email protected]",
+                "email": "[email protected]",
                 "github": "sbello",
                 "label": "Sue Bello",
                 "orcid": "0000-0003-4606-0597"