scope of processing from OMIM

[maglott]

Submitters to ClinVar and GTR often provide the name of a disorder according to the value they see in genemap2.txt.
In some cases, these names do not match any preferred , alternate, or included term in a record from OMIM itself.
Are there any plans to integrate the unique terms from genemap into Mondo?
NCBI often retains those terms as distinct entities, e.g.
https://www.ncbi.nlm.nih.gov/medgen/CN301185

vs.
https://www.omim.org/entry/135400 /MONDO:0007610/C1851120

Any opinion about whether or not that is appropriate?
Thanks

[kanems]

@ahamosh @nicolevasilevsky Would be very interested to hear your thoughts this topic.

[nicolevasilevsky]

@ahamosh said that genmap2 comes from OMIM and the disease names should map. @maglott could you please share the cases where you see mismatches with OMIM?

[maglott]

I am not saying there is a mismatch; I am saying there are terms unique to genemap2 and not in Mondo. Let me do some analyses and return a list. Is genemap2 included in the slurps that Mondo does? (My first use of slurp). And please remind me of the path to the documentation.

[maglott]

I think I've worked out query that provides some signal. I'll send a list next, with the following caveats:

• NCBI has not processed the March release yet

• NCBI needs to understand the use of 'has_narrow_synonym' because at present we are not exacting these terms for evaluation. Thus this file over-reports
  gene_map_names.xlsx

• {} and ? were stripped from the values in the genemap2.txt
  This is a report of Mondo IDs with skos exact matches to a MIM number, for which the name in genemap2.txt does not have an exact string match to any name we extract from Mondo (case insensitive).

[maglott]

Megan and I have been reviewing some of the terms unique to genemap2.
One example is in https://www.omim.org/entry/158350. MONDO:0019002.
genemap2.txt uses 'Lhermitte-Duclos syndrome' not Lhermitte-Duclos disease. It would be great if Mondo provided the answer whether or not Lhermitte-Duclos syndrome = Lhermitte-Duclos disease. Right now MedGen has them as distinct, not having raised this specific question yet.

[maglott]

Or, for https://www.omim.org/entry/613703, is 'Microphthalmia with coloboma 6' to be considered equivalent to MICROPHTHALMIA, ISOLATED, WITH COLOBOMA 6? Submitters to the NIH Genetic Testing Registry have used the value from genemap2.txt. Last specific example. Hoping for a policy.

[nicolevasilevsky]

Thanks @maglott. I'll review this with @matentzn asap.

[nicolevasilevsky]

@ahamosh - could you clarify why there are different names in the genemap2 file which are not included the usual OMIM metadata on the website (the file we pull from is called mimtitles.txt) ? We'd like to use the authoritative source for pulling in OMIM synonyms.

@maglott we can add the synonyms for you from the genemap2 file that you shared.

[nicolevasilevsky]

Note to self, this is the ROBOT template:
https://docs.google.com/spreadsheets/d/1GMXDtq2vOLjOVyFYSrquFpxVOu6dJfBCyHzQRGcD6YM/edit#gid=688099271

[nicolevasilevsky]

see related ticket: #4939

[yasmeen-pg]

I noticed a case where an OMIM disease that is broadly considered rare does not have the "rare" designation in its subset, nor does it have the rare MONDO term as an ancestor. I'm now concerned that filtering for rare diseases in MONDO will result in an incomplete list. Any ideas as to why this is happening? Am I looking in the wrong place for "rare" designation?

The disease in question is APOL1-mediated kidney disease or AMKD (in MONDO, "focal segmental glomerulosclerosis 4, susceptibility to", MONDO:0012931)

[sabrinatoro]

Hi @yasmeen-pg, thank you for your question.
You are correct: MONDO:0012931 is currently not in the Mondo rare subset.

Diseases are added to the rare disease subset when they are considered rare according to rare disease authoritative sources (these are currently Orphanet, NORD, GARD). Since OMIM is not considered an authoritative source for rare diseases, this disease was not added to the rare disease subset.
We also have the possibility to manually annotate that a disease is considered "rare" (though we must have evidence, ie we need a reference).
Therefore, all rare diseases should be in the rare disease subset, EXCEPT if they are not reported by an rare disease authoritative source, or have not yet been manually curated.

In the specific case of "focal segmental glomerulosclerosis 4, susceptibility to" (MONDO:0012931):

• If they are evidence that this disease is rare, we can add it to the rare disease subset.
• Most importantly, this term refers to a susceptibility to disease (and not to a disease). We currently do not mark susceptibilities as "rare".
  If you think that MONDO:0012931 should be considered a disease and/or annotated as "rare", please let us know (preferably in a separate issue).
  Thank you