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Update fp-009-users.md to emphasize requirements for links (OBOFoundry#2363)
* Update fp-009-users.md to emphasize requirements for links
Revised the document to draw attention to the need for links in usages declarations (this requirement was already present, but was spelled out in the examples). The examples as they were prior to revision were general and contained important information, so these were moved to the R & R section, while the Examples section was revised to give concrete examples.
* Update fp-009-users.md to use highlighted code
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@@ -17,15 +17,39 @@ scientific area and does so in a usable and sustainable fashion.
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## Recommendations and Requirements
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It is important to be able to illustrate usage outside of the immediate circle of ontology developers and stakeholders. Note that the ontology can still be listed on
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the OBO Foundry website while publicising your resource in appropriate channels and searching for users with needs you can meet.
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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:
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- 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.
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- 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_.
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- 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.
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- Use of terms from the ontology to provide structure to or annotation of experimental or derived data. Indicators of this type MUST provide a link to a URL that shows the annotation or demonstrates the structure.
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- Terms imported into external ontologies. Indicators of this type MUST link to direct evidence of import, such as the OntoBee page for the term (which includes a section indicating which ontologies have imported it), OR to the OBO Dashboard page for the target ontology (which includes a section "Which ontologies use it?"), OR to any other source of direct evidence. A link to the importing ontology as a whole does not constitute appropriate evidence, as this is too indirect (that is, it requires extra steps to verify).
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- Inclusion of the target ontology on a documentation page that lists which resources are used for the project. Indicators of this type MUST include a link to the appropriate documentation page.
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Other indicators are currently possible as well:
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- Use in semantic web projects (e.g., Open PHACTS usage).
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- Use in software applications, including text mining or analysis pipelines.
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- Citations to the ontology publication(s); Note that such citations are only
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relevant if the authors indicate actual use of the cited ontology
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within some community (mere mention of the existence is not enough
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to warrant inclusion).
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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.
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## Implementation
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The ontology developers should provide links/citations to evidence of
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use (publication, external ontology; see examples below for additional types) within your ontology [metadata file](https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology) (replacing with the correct group name, link, and description):
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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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```
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```yaml
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usages:
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- user: http://www.informatics.jax.org/disease (link to group)
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description: MGI disease model annotations use DO (description of group)
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## Examples
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- Use of the target ontology's term IRIs in other ontologies. This can
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be evidenced by linking to the other ontology that uses an ontology
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term IRI from this ontology
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- Imports in other ontologies, again, evidenced through a link to the
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importing ontology
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- A documentation page with links to databases using the ontology for
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annotation
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- Use in semantic web projects (e.g., Open PHACTS usage)
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- Use in diverse software applications, including text mining or
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analysis pipelines
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- Publications showing the ontology being used in research (evidenced
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by citation details for the publications; if behind paywall it may
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be necessary to provide a PDF for the paper)
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- Citations to the ontology publication(s); such citations are only
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relevant if the authors indicate actual use of the cited ontology
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within some community (mere mention of the existence is not enough
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to warrant inclusion)
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- Documentation of requests from multiple users, e.g., via an issue
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tracker (provide a link to the issue tracker online)
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- Use of the terms from the ontology to structure or annotate
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experimental or derived data (e.g. GOA; provide details of how to
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review the annotations)
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Use of PSI-MOD term IRI (in the form of a CURIE) in the PR ontology:
description: List of issues tagged with 'Term Request' to PRO
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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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- user: https://pubmed.ncbi.nlm.nih.gov/36860337/
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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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- url: 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..."
description: List of ontologies using the term 'ABI 377 automated sequencer' (See section entitled "Ontologies that use the Class")
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```
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## Counter-Examples
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Mere mention of the existence of an ontology in a publication is not
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- Mere mention of the existence of an ontology in a publication is not
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enough to count as evidence of usage
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- Reference to any evidence that cannot be viewed publicly
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## Criteria for Review
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Ontology developers must demonstrate at least three external users specified within the metadata file. External users are defined either as researchers not
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