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OBO Metadata Ontology
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Request for adding property "has database cross reference" to OMO #123

Closed matentzn closed 5 months ago

matentzn commented 1 year ago

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

matentzn commented 1 year ago

Note that:

  1. The property should not be used to map across OBO Foundry ontologies.
  2. The design decision of having the range be xsd:string has been extensively discussed in #59

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.

matentzn commented 1 year ago

@anitacaron can you take care of this?

gouttegd commented 8 months ago

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:

cmungall commented 7 months ago

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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