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monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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MedGen obsoletion requests (Spring 2024) #7700

Open kanems opened 2 months ago

kanems commented 2 months ago

What: A list of Mondo terms that MedGen is suggesting may be candidates for obsoletion. Why: Some Mondo terms have x-refs to only obsolete terms in another ontology (OrphaNet, DOID, GARD) or no X-refs at all; they do not match any string/concept in UMLS that we can find. We are not certain that these are active/true disease concepts. (Some may represent historic terms that are no longer used in the community; is it worth the effort to find and link PubMed IDs as sources for the case reports for these? TBD.)

Details: The attached Excel workbook contains 3 sheets: MedGen_OBS_to_mondo_050124.xlsx

1- all (all the candidates, regardless of source details/issues)
2-GARD (cases where either the GARD link from Mondo does not exist or the page is “under development” and presumably GARD is considering whether or not to maintain; review of these likely require coordination with GARD team) 3-orpha (Cases where Mondo on OLS still shows the Orphanet ID an x-ref (obsolete) but no other sources)

This analysis has taken us a couple of months to complete, our final cross-checking is based on the X-refs and data available from the April 2024 release, so apologies if some of these have been addressed in the interim, or if independent tickets were opened and we forgot to remove from this batch request.

We will respect the Mondo community’s decision if some of these still warrant display in Mondo because of references from other projects to the Mondo term or specific requests to retain/create them in the first place (I hope we have not grabbed any ClinGen or DO terms, for example). Based on the UMLS data and Mondo data at time of review, any of these that will be maintained will get a MedGen ‘CN’ identifier. Note: This list may significantly overlap with the inherited disease branch, which I think I have read is on the docket for a comprehensive review, but there are probably some outside of that branch as well.

sabrinatoro commented 2 months ago

Thank you @kanems for this issue and for the reporting all these obsoletion candidates. We will review this list and proceed accordingly. Please note that we have a lot of ongoing work, and therefore this will take some time. Thank you for your patience!

sabrinatoro commented 1 month ago

First we should see if these terms are in used by other groups, or are in subsets indicating that they are in used by other groups. Also, we need to make sure that these terms have not been updated recently (ie since this file was created). For each of these terms, we need to review:

Sparql query is here Updated spreadsheet is here Note: we should re-run this after we updated all subsets again.

To do: review this spreadsheet and determine whether 1) we agree with the obsoletion based on the information above 2) we should reach out to other groups for specific terms

sabrinatoro commented 1 month ago

I added "obsoletion candidate" tags to all these terms, so we will be ready to obsolete by the time the review is finished.