Rename OMIM axiom annotation properties

[joeflack4]

Warning

These should be merged at the same time:

• Rename OMIM axiom annotation properties #698
• MONDO:omim_included rename omim#167

Overview

Update OMIM properties in properties.txt to the correct spelling / casing.

Context

This is a follow-up from our tech meeting today. We discussed:

• MONDO:omim_formerly mondo#8235

I tried to show that the casing (snake vs camel) wasn't consistent between repos but I couldn't find an example.

Basically in mondo-ingest and omim repos, it's snake case. But now in mondo, it's camel case (monarch-initiative/mondo#8235, axiom annotation docs).

Pre-merge checklist

Documentation

Was the documentation added/updated under docs/?

• Yes
• No, updates to the docs were not necessary after careful consideration

QC

Was the full pipeline run before submitting this PR using sh run.sh make build-mondo-ingest on this branch (after
docker pull obolibrary/odkfull:dev), and no errors occurred?

• Yes
• No, there are no functional (code-related) changes to the pipeline in the PR, so no re-run is necessary

New Packages

Were any new Python packages added?

• Yes, requirements.txt.full was updated and an ODK issue submitted
• No

Were any other non-Python packages added?

• Yes, Dockerfile updated and an ODK issue submitted
• No

PR Review and Conversations Resolved

Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?

• Yes

[joeflack4]

Don't these need to actually appear in properties.txt?

During the tech meeting today, @matentzn was surprised I was calling them properties. But I feel like they belong here, alongside http://purl.obolibrary.org/obo/mondo#GENERATED which I think was disappearing if we didn't have it showing in this file.

I could do a before/after test to check this myself but for now I'll just pose the question.

[matentzn]

I dont think this needs to be here. Most of the things you see here, like "GENERATED" are synonym type properties.. That is very different from the MONDO:includedEntryInOMIM source annotations (see Mondo file)

[joeflack4]

Aren't the also supposed to be synonym type properties? Is there anything about the nature of MONDO:GENERATED that makes it more appropriate to say that it is a property of the synonym's type than the OMIM ones?

I remember that we have been discussing making object property declarations (I believe for these) in omim.ttl, but have not yet.

[twhetzel]

At some point things were failing without these being added, but this may not be the location that fixed things.

[matentzn]

Look at how includedInOMIM is used in Mondo:

xref: OMIM:184850 {source="MONDO:includedEntryInOMIM"}

As a oboInOwl:source annotation. This is not at all like:

synonym: "undetermined early-onset epileptic encephalopathy" EXACT GENERATED []

Which is how the GENERATED synonym type was used.

The confusion of why includedEntryInOMIM isn't used the same way, i.e.

synonym: "undetermined early-onset epileptic encephalopathy" EXACT includedEntryInOMIM []

That question is valid! I don't know the exact answer, but lets say for the sake of rapid progress now that the reason is historical.

[joeflack4]

Ahh I see, right.

Well I have to look at this more tomorrow to double check unless someone else wants to, but I think the way that MONDO:omimFormerly is being used might be different than MONDO:includedEntryInOMIM. I think it is being added directly onto the synonyms.

And shucks... I think maybe MONDO:includedEntryInOMIM might be now as well in:

• "Alternative symbol" synonyms & "Formerly" - props rename omim#168

I'll have to look into it tomorrow.

But for 'included', I think there were two things we were doing. One was a general thing on the OMIM class to say "this thing has included entries" (perhaps that's what MONDO:includedEntryInOMIM is supposed to be...), and then there are things directly added onto synonyms. Perhaps the latter was MONDO:omim_included and I was simply conflating the two.

[matentzn]

Yea maybe.. I dont think you really need the synonym type "omim included", but you may need the synonym type "omim formerly". Right now I think we should do whatever can be done right now and open issues to revise the decision if need be..

[twhetzel]

@joeflack4 have you looked further into this? Also, I set this to merge into develop since it was set incorrectly.

[joeflack4]

I had this on our recent 1:1 agenda, section titled "MONDO: omimFormerly & includedEntryInOMIM".

Can wait until our next meeting if you like.