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

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nicolevasilevsky opened this issue Nov 18, 2022 · 5 comments
Open

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

nicolevasilevsky opened this issue Nov 18, 2022 · 5 comments
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@nicolevasilevsky
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nicolevasilevsky commented Nov 18, 2022

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

Related to monarch-initiative/mondo#5507

I can't assign @joeflack4

cc @matentzn @sabrinatoro

@joeflack4 joeflack4 self-assigned this Nov 18, 2022
@joeflack4 joeflack4 changed the title parcel out OMIM Included entries in OMIM ingest parcel out OMIM ", Included" entries in OMIM ingest Nov 18, 2022
@joeflack4
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joeflack4 commented Nov 18, 2022

@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.

@joeflack4 joeflack4 added the bug Something isn't working label Nov 18, 2022
@nicolevasilevsky
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thanks @joeflack4!
I'm taking next week off too. Happy TG! 🦃

@matentzn
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matentzn commented Nov 19, 2022

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

@joeflack4
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@twhetzel Wondering if this has effectively been addressed. #132 seems to address what remained here on the automation side of things, I think.

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