parcel out OMIM ", Included" entries in OMIM ingest

nicolevasilevsky commented 1 year ago

OMIM has 'included' entries in their records, which are properly distinct diseases and should be added separately to Mondo. Per our conversation on the technical call on 11/18/22:

we should parcel out OMIM Included entries, add a string included and use this convention to integrate the links on the Mondo site
Create these terms as new classes in the OMIM ingest
the dbxref should be OMIM:XXXXXX with source: MONDO:includedEntryInOMIM

For example: https://omim.org/entry/607665 TUBULOINTERSTITIAL NEPHRITIS WITH UVEITIS should be a MONDO class with source: 'MONDO:equivalentTo' ACUTE TUBULOINTERSTITIAL NEPHRITIS should be a separate Mondo class with source: MONDO:includedEntryInOMIM

ACUTE TUBULOINTERSTITIAL NEPHRITIS should not be a synonym of TUBULOINTERSTITIAL NEPHRITIS WITH UVEITIS

I can't assign @joeflack4

cc @matentzn @sabrinatoro

joeflack4 commented 1 year ago

@nicolevasilevsky I just added you to the repo! You should be able to assign me in the future now.

Thanks~. Most of this will be easy to do, but I think there is some additional nuance I'll run into. I think Nico said I should not have it be a top priority for right now.

nicolevasilevsky commented 1 year ago

thanks @joeflack4! I'm taking next week off too. Happy TG! 🦃

matentzn commented 1 year ago

I thought a bit more about this, and I would like to be involved in the design of this feature. Essentially, we want:

The first step in the process is to

[ ] Add OMIM ids in the OMIM ingest with the above ids, and the labels from the included term
[ ] Making them subclass of their non-included variants

nicolevasilevsky commented 1 year ago

when we split out the included terms, we'll need to review the parents manually

monarch-initiative / omim

parcel out OMIM ", Included" entries in OMIM ingest #84