diff --git a/.github/ISSUE_TEMPLATE/new-ontology.yml b/.github/ISSUE_TEMPLATE/new-ontology.yml index 8479f2dd8..260eb5c8f 100644 --- 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 index 2257c018c..e7c192ac8 100644 --- 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: meghan.balk@gmail.com @@ -3881,7 +3902,7 @@ 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 diff --git a/_includes/header.html b/_includes/header.html index 20d62b6df..96fee970d 100644 --- a/_includes/header.html +++ b/_includes/header.html @@ -169,13 +169,6 @@ FAQ -
diff --git a/docs/roles/RoleNORManager.md b/docs/roles/RoleNORManager.md index a804179c5..b4816dc43 100644 --- 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 index 09b42c225..2a7b412b8 100644 --- 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 index 36e62fc86..5bd0d701d 100644 --- a/ontology/mp.md +++ b/ontology/mp.md @@ -13,7 +13,7 @@ browsers: label: Monarch 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 diff --git a/registry/ontologies.jsonld b/registry/ontologies.jsonld index e3680681b..67ad36ff4 100644 --- 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": "drsbello@gmail.com", + "email": "pheno@jax.org", "github": "sbello", "label": "Sue Bello", "orcid": "0000-0003-4606-0597" diff --git a/registry/ontologies.nt b/registry/ontologies.nt index 677119049..15cf51cc3 100644 --- a/registry/ontologies.nt +++ b/registry/ontologies.nt @@ -7,7 +7,7 @@