Join GitHub today
GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.Sign up
Specify the mapped/equivalent terms #31
Most commonly used approach is using annotationProperty: database_cross_reference (example: http://purl.obolibrary.org/obo/DOID_9351). When multiple mapped terms need to be listed, what is the correct format we should use to separate these mapped terms? Is this approach applied to both OBO Foundry ontologies and other ontologies/terminologies, like SNOMED, ICD-9?
Some used class equivalent, like GO:cell = CL:cell, when should we take this approach? Does it only apply to OBO Foundry ontologies?
Some used rdfs:seeAlso annotationProperty, see example: http://purl.obolibrary.org/obo/VO_0000609, (Note: it may not the correct annotationProperty to use.)
Some used self-defined annotationProperty, see example: http://purl.obolibrary.org/obo/DRON_00016163
Related issue: #24
Comments from Chris M:
We should discourage db-specific prefixes
xref has no semantics. It's not that it isn't useful, it's just weaker than equivalence. If you know it's equivalent, use an equivalence axiom. If you don't know then don't. In some cases we shadow an equivalence axiom with an xref, for applications that want xrefs. See notes for obo version of obofoundry.org/ontology/mondo.html. Also I believe OxO expects xrefs, cc @simonjupp
I would say seeAlso is even weaker. It is also typically used with a URL not a CURIE. E.g. it may link a class to a page about that class.
Glad to see the discussion here.
We will share a document soon that groups the results per ontology and show the number of unresolvable targets.
I agree with @cmungall point before and included in original post. If we could encourage a bit more the community to adopt standard mapping properties that would be very good.
As a recall the OBO spec provide headers for XREFS:
So how can we do to improve /curate the XREFS?