Rename OMIM axiom annotation properties

[joeflack4]

Warning

These should be merged at the same time:

• Rename OMIM axiom annotation properties #698
• included / formerly refactor 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.

[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.

[twhetzel]

@joeflack4 can you sort out if this change is needed, try to run relevant make goals with and without the change to check and any other ways you may think of to test this.

[joeflack4]

@twhetzel May want to just move this to our meeting, that might be easier. This is basically a sub issue of:

• Grouping: omimFormerly, omimIncluded, & includedEntryInOMIM #715

And the answers to those questions / decisions will impact whether this is needed or not. If they will become synonym types as Nico seems to suggest might be appropriate, these will definitely be needed.If you / we decide that they should not be changed to that, then I can go ahead and run such an examination now.

[joeflack4]

Spoke with Nico today: conclusions.

• @joeflack4 Keep includedEntryInOMIM
• @joeflack4 Also keep omimIncluded

[matentzn]

No, includedEntryInOMIM has nothing to do here; it is not a property. It is a source code value. Yes. It should be kept in mondo. No, it should not be kept in this list.

[joeflack4]

Yes you're right. Not sure why I put that checkbox on this particular PR. But it does also need:

• @joeflack4 omimFormerly