[Merge] IDDM1 and type 1 diabetes mellitus

[maglott]

Mondo term (ID and Label)
MONDO:0005147/type 1 diabetes mellitus
MONDO:0009100/IDDM 1

Reason for deprecation
I don't see any definition to justify treating IDDM1 as a subtype of type 1 diabetes mellitus. I know that OMIM treats IDDM1 as an included title for T1D, but I am not certain of the distinction. There are papers that seem to treat these as the same entity.
https://pubmed.ncbi.nlm.nih.gov/15505007/. Should these be lumped?

Term to be merged with

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[maglott]

I should have done one more lookup i guess. I see that IDDM1 is the subset based on the MHC.
https://www.nature.com/articles/6363875; maybe that could be added to the definition, and the xrefs/synonyms be cleaned up accordingly.

[nicolevasilevsky]

@sabrinatoro could you review this ticket?

I think these are the action items, let me know if you agree:

It seems like this class is equiv to OMIM:222100 and I think this Mondo class is referring to an included entry in OMIM:222100:
name: DIABETES MELLITUS, INSULIN-DEPENDENT, 1, INCLUDED
synonym: IDDM1

• I think that 'insulin-dependent diabetes mellitus 1' is a separate class (it is currently a synonym in Mondo, it is an 'included' entry in OMIM) and should be a new class in Mondo
• 'type 1 diabetes mellitus' should be a broad synonym
• 'diabetes mellitus, insulin-dependent' should be a narrow synonym
• 'diabetes mellitus, type 1' should be a narrow synonym
• 'IDDM' should be a narrow synonym
• 'IDDM1' should be an exact synonym
• 'juvenile-onset diabetes' should be a narrow synonym
• Proposed definition of IDDM1: Any type 1 diabetes mellitus that is caused by variation in genes located in the MHC complex on chromosome 6p21.3. [dbxref: PMID:12140742]

[sabrinatoro]

@nicolevasilevsky
I agree with the definition and with "insulin-dependent diabetes mellitus 1" being a separate class. I am not sure to which terms the synonyms above refer.

I think the ontology should be:

• type 1 diabetes mellitus (MONDO:0005147)

  • Mondo:EquivalentTo : OMIM:222100
  • 'diabetes mellitus, insulin-dependent' should be exact synonym
  • 'IDDM' should be exact synonym
  • 'IDDM1' should be narrow synonym

• IDDM 1 (MONDO:0009100)

  • is a more specific type 1 diabetes, and should be a child of type 1 diabetes mellitus
  • 'diabetes mellitus, insulin-dependent' should be broad synonym
  • 'IDDM' should be broad synonym
  • OMIM:222100 should/could probably also be Mondo:EquivalentTo (since the omim term seems to include both the "broad" type 1 diabetes, and the more specific IDDM1), however we might have issue of proxi-merge (or reverse proxi-merge).

[nicolevasilevsky]

@sabrinatoro I merged the PR b/c I was having trouble viewing your changes on your branch for some reason.

I agree with your suggestions above. Currently OMIM:222100 is equiv to IDDM 1 (MONDO:0009100), I am going to make it relatedTo and make OMIM:222100 equiv to type 1 diabetes mellitus (MONDO:0005147)