Make XRefs Clickable, when possible

[matthewhorridge]

When I'm browsing class definitions I would like to be able to jump to classes other ontology that are mentioned in XRefs (or really, any annotation).

See here, in MonDO, where I'm looking at Sickle Cell Anemia. I'll like to jump to the class in the Disease Onotology (DOID).

There's some exact matches further down, but clicking on these takes me out of BioPortal.

[jonquet]

This feature request is totally justified. I fully support it, although it does not belongs directly to BioPortal.

Several complex issues hide behind :

• OBO Xrefs do not use a standard "short acronyms", often those are the OBO Foundry ones but not always. For sure, aligning this "system" to BioPortal acronym-IDs is not trivial.
• What to do when a target is not in BioPortal?
• What to do when a target is not even an ontology class but an author or a paper ?
• Shall we transform the short ids into the corresponding URIs (what should be done if the XRef were finally abandoned) or directly by a BioPortal link?
• What to do when short IDs cannot be resolved (many many cases...)

An interesting resource to check before starting working on Xrefs: https://hal-lirmm.ccsd.cnrs.fr/lirmm-02945170/

@amirlad and I had in mind to extend the previous study to the whole OBO foundry set but we have not done it yet. We have discussed to involved @matentzn @cmungall and others from the Foundry onto this extended study...

Ultimately, an XREF curation campaign should be launch to remove them definitively from ontologies and replace them by relevant qualified URI/URL links.

See also discussion here : https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1276#issuecomment-770089954

[matentzn]

The key to enabling this request is prefix resolution; as there is no way to guarantee that the xref value DO:001 in one ontology refers to the same concept as DOID:001 in another, there needs to be a coordinated effort to standardise prefixes across the board. Relevant efforts are projects like:

• Bioregistry - (I am using, for one of my tools, for example, this map)
• Biocontext of prefixcommons
• prefix.cc

and a dozen other such efforts, and a commitment for large organisations like OBO and Bioportal to one of these, and systematically filter out everything that is not in there.

Then Bioportal, and OLS, can start self redirecting these qualified names reliably as they wish (so rather than "leaving" OLS when clicking on DOID:001, you redirect to wherever you store which ontology this resolved to).

I am also slightly against xrefs between OBO ontologies - xrefs should be between ontologies and biological databases, which makes their "clickability" a bit less relevant perhaps - but maybe not. Xrefs between ontologies should be migrated to skos:has*Match vocabulary.