obophenotype / obophenotype/uberon

Uberon should make use of xrefs in other ontologies

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#2,801 8 comments 1 reaction 1 assignee View on GitHub

@gouttegd is already working on this.

Since Feb 14, 2023.

composite mapping Stale
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Description

Historically uberon was the only SOT for mappings, but we have not kept the mapping pipelines up to date and there are now sometimes mappings curated in external AOs (e.g. XAO #2796).

We should add a step to include these. I suggest a periodic slurp into the edit file where they will be visible to editors rather than just at release time.

Before doing we should make sure there are checks in place to avoid introducing non 1-1 mappings. The SOP is that if on running a slurp the editor finds these, to raise an issue on either this tracker (if uberon mapping is questionable) or external AO tracker.

This could be done as part of a boomer-like workflow but this is probably overkill.

perhaps the script that generates bridge files for CL can be adapted (in contrast to Uberon, CL treats many upstreams as SOT).

Or it might be easiest to do in OAK. Basically just query the upstream for X-to-Uberon and flip that into

id: UBERON:...
xref: X:....

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