diff --git a/principles/fp-009-users.md b/principles/fp-009-users.md index cfe0c5e5b..ff6d58cf6 100644 --- a/principles/fp-009-users.md +++ b/principles/fp-009-users.md @@ -47,15 +47,15 @@ Note that the ontology can still be listed on the OBO Foundry website while publ ## 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: -- description: MGI disease model annotations use DO (description of group) +- description: MGI disease model annotations use DO (description of usage) examples: - - description: Human genes and mouse homology associated with nail diseases (description of specific example) - url: "http://www.informatics.jax.org/disease/DOID:4123" # link to specific example) - user: "http://www.informatics.jax.org/disease" # link to group + - 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 multiple users under the `usages` tag. @@ -67,41 +67,41 @@ Use of PSI-MOD term IRI (in the form of a CURIE) in the PR ontology: - description: Protein Ontology examples: - description: OBO Format stanza showing use of PSI-MOD term in logical definition - url: "https://proconsortium.org/app/export/obo/PR:000027653/" - user: "http://purl.obolibrary.org/obo/pr" + url: https://proconsortium.org/app/export/obo/PR:000027653/ + user: http://purl.obolibrary.org/obo/pr ``` Term requests to PR from multiple users: ```yaml - description: Term requests made via the Protein Ontology GitHub tracker examples: - - 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" + - 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 - description: Machine learning-based prediction of candidate gene biomarkers correlated with immune infiltration in patients with idiopathic pulmonary fibrosis examples: - - 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/" + - 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 - description: UniProt examples: - description: Functional annotation using GO (see subsection entitled "GO annotations") - url: "https://www.uniprot.org/uniprotkb/Q15796/entry#function" - user: "https://www.uniprot.org" + url: https://www.uniprot.org/uniprotkb/Q15796/entry#function + user: https://www.uniprot.org ``` OBI terms imported into external ontologies ```yaml - description: Ontologies using OBI terms examples: - - 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" + - 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) ```