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Request for adding property "has database cross reference" to OMO #123
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Note that:
Without any further discussion, the specification above reflects current practice and I advice against re-hashing the discussion now. If anything, someone should offer advice on the definition, which I just sucked out of my nose but may not be ideal. |
@anitacaron can you take care of this? |
Replying here to your request for comments on Slack (“What is the ideal label (and definition) for oboInOwl:hasDbXref?”): Should the label and definition reflects how the property is supposed to be used, or how it is used effectively? If it’s supposed to reflect how the property is effectively used in the wild, then I’d suggest to drop the “database“ part, because the property is certainly not used exclusively to point to database entries (in particular, and contrary to what the note says, it is intensively used to “map across OBO Foundry ontologies“). I’d suggest:
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This looks good, but I would add more gloss to the definition, first
explaining how it’s used for entities, then axioms
Bear in mind this is also the correct AP to use when translating databases
to OWL and in fact the obo format adoption of this merely continued
semantics that existed back in the early 90s
I know it’s common to assume that an xref has zero semantics but this would
be wrong. Xrefs have consistent semantics it just varies based on subject
prefix object prefix tuple (or sometime subtype of subject and object).
…On Mon, Mar 25, 2024 at 1:48 AM Damien Goutte-Gattat < ***@***.***> wrote:
Replying here to your request for comments on Slack (“What is the ideal
label (and definition) for oboInOwl:hasDbXref?”):
Should the label and definition reflects how the property is *supposed*
to be used, or how it is used effectively?
If it’s supposed to reflect how the property is effectively used in the
wild, then I’d suggest to drop the “database“ part, because the property is
certainly not used exclusively to point to database entries (in particular,
and contrary to what the note says, it *is* intensively used to “map
across OBO Foundry ontologies“).
I’d suggest:
- label: “has cross-reference“
- definition: “An annotation property that points to an identifier of
some sort.”
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IRI
http://www.geneontology.org/formats/oboInOwl#hasDbXref
Label
has database cross reference
Definition of the property
An annotation property that links an ontology entity to a database identifier.
Parent property
No response
What is the range of the property in question?
xsd:string
Examples of use
MONDO:0021125 http://www.geneontology.org/formats/oboInOwl#hasDbXref "NCIT:C41009"^^xsd:string
Motivation to add
oboInOwl:hasDbXref is one of the most widely used annotation properties across OBO Foundry ontologies.
ORCID, ROR or Wikidata identifier of the contributor
https://orcid.org/0000-0002-7356-1779
OMO Checklist
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