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Update fp-009-users.md (#2814)
Revised wording in Implementation section to ensure that the sentence referring to parts of the example--and those parts--use the same string. Also removed superfluous quote marks in Examples section (these aren't found in real .md file examples).
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principles/fp-009-users.md

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@@ -47,15 +47,15 @@ Note that the ontology can still be listed on the OBO Foundry website while publ
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## Implementation
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The ontology developers MUST provide links/citations to publicly available evidence of
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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):
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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):
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```yaml
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usages:
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- description: MGI disease model annotations use DO (description of group)
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- description: MGI disease model annotations use DO (description of usage)
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examples:
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- description: Human genes and mouse homology associated with nail diseases (description of specific example)
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url: "http://www.informatics.jax.org/disease/DOID:4123" # link to specific example)
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user: "http://www.informatics.jax.org/disease" # link to group
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- description: Human genes and mouse homology associated with nail diseases (description of example)
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url: http://www.informatics.jax.org/disease/DOID:4123 (link to example)
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user: http://www.informatics.jax.org/disease (link to user group)
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```
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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:
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- description: Protein Ontology
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examples:
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- description: OBO Format stanza showing use of PSI-MOD term in logical definition
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url: "https://proconsortium.org/app/export/obo/PR:000027653/"
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user: "http://purl.obolibrary.org/obo/pr"
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url: https://proconsortium.org/app/export/obo/PR:000027653/
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user: http://purl.obolibrary.org/obo/pr
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```
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Term requests to PR from multiple users:
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```yaml
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- description: Term requests made via the Protein Ontology GitHub tracker
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examples:
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- description: "List of issues tagged with 'Term Request' to PRO"
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url: "https://github.com/PROconsortium/PRoteinOntology/issues?q=is%3Aissue+label%3A%22Term+Request%22"
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- description: List of issues tagged with 'Term Request' to PRO
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url: https://github.com/PROconsortium/PRoteinOntology/issues?q=is%3Aissue+label%3A%22Term+Request%22
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user: (multiple)
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```
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Publication showing the Disease Ontology being used in research by external users
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```yaml
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- description: Machine learning-based prediction of candidate gene biomarkers correlated with immune infiltration in patients with idiopathic pulmonary fibrosis
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examples:
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- description: 'In abstract, "Functional annotation, pathway enrichment, Disease Ontology and gene set enrichment analyses revealed..."'
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url: "https://pubmed.ncbi.nlm.nih.gov/36860337/"
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user: "https://pubmed.ncbi.nlm.nih.gov/36860337/"
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- description: In abstract, "Functional annotation, pathway enrichment, Disease Ontology and gene set enrichment analyses revealed..."
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url: https://pubmed.ncbi.nlm.nih.gov/36860337/
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user: https://pubmed.ncbi.nlm.nih.gov/36860337/
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```
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Use of terms from GO for annotation:
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```yaml
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- description: UniProt
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examples:
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- description: Functional annotation using GO (see subsection entitled "GO annotations")
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url: "https://www.uniprot.org/uniprotkb/Q15796/entry#function"
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user: "https://www.uniprot.org"
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url: https://www.uniprot.org/uniprotkb/Q15796/entry#function
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user: https://www.uniprot.org
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```
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OBI terms imported into external ontologies
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```yaml
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- description: Ontologies using OBI terms
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examples:
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- description: 'List of ontologies using at least one OBI term (See section entitled "Info: Which ontologies use it?")'
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url: "http://dashboard.obofoundry.org/dashboard/obi/dashboard.html"
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- description: 'List of ontologies using the term "ABI 377 automated sequencer" (See section entitled "Ontologies that use the Class")'
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url: "https://ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0000691"
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- description: List of ontologies using at least one OBI term (See section entitled "Info: Which ontologies use it?")
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url: http://dashboard.obofoundry.org/dashboard/obi/dashboard.html
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- description: List of ontologies using the term "ABI 377 automated sequencer" (See section entitled "Ontologies that use the Class")
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url: https://ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0000691
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user: (multiple)
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```
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