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Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Thrombocythemia, X linked MONDO:0010301[Merge] #3172

Closed kanems closed 3 years ago

kanems commented 3 years ago

Mondo term (ID and Label) Thrombocythemia, X linked MONDO:0010301

Reason for deprecation OMIM has merged 300331 with 187950 "Thrombocythemia 1" and the UMLS CUI X-ref on this term has been retired.

Term to be merged with Thrombocythemia 1 MONDO:0008554

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kanems commented 3 years ago

Actually, even though OMIM directs users to the 187950 term, there is no "X linked" locus on the thrombocythemia 1 page Phenotype-gene relationships table . Perhaps this entry should be deleted? @ahamosh Any input here? This page (https://www.omim.org/entry/187950) still points folks back to the 300331 entry for the "possible X-linked form," creating a bit of a loop for anyone looking for info on X-linked thrombocythemia.

ahamosh commented 3 years ago

Bad link. Will be corrected by morning. Sorry.

sabrinatoro commented 3 years ago

Hello @kanems I'm Sabrina, a new curator who recently joined the Mondo team. We will address your issue as soon as possible. Thank you for your patience. If this is a high priority, please let me know and we can prioritize it. Thank you!

kanems commented 3 years ago

Upon closer review, MedGen has decided to delete the term with the old MIM number and "x-linked" term, as other CUIs and MIM numbers already represent the concepts. Since UMLS has deleted the CUI and the merged MIM term doesn't include "x-linked" in the alternate names, I think this might be a term to obsolete in the Mondo dictionary.

sabrinatoro commented 3 years ago

@nicolevasilevsky I think this issue should be : obsolete 'thrombocythemia, X-linked' (MONDO:0010301) Do you agree? (Maybe a good first issue?)

nicolevasilevsky commented 3 years ago

yes, I agree it should be obsoleted (not merged).

I think you and I should do the obsoletions, so let's not label it as a good first issue.

galyea-gard commented 3 years ago

Hi! X-linked thrombocythemia links to https://omim.org/entry/313900 (it is considered a synonym of X-linked thrombocytopenia (THC1) as well as other websites such as MedlinePlus: https://medlineplus.gov/genetics/condition/x-linked-thrombocytopenia/ Orphanet: https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=852 (added normal platelets) We have a page at GARD.
In this case it may be better to merge it . Thank you! Gioconda

nicolevasilevsky commented 3 years ago

@galyea-gard I don't see a mention of X-linked thrombocythemia on the OMIM page (https://omim.org/entry/313900), I only see X-linked thrombocytopenia.

@sabrinatoro I think we should obsolete Thrombocythemia, X linked MONDO:0010301 and add a consider: Thrombocythemia 1 MONDO:0008554, since that is what OMIM points to, but it does not seem like they are the same terms.

@galyea-gard please let us know if you have any objections. Thanks!

galyea-gard commented 3 years ago

Hi! I apologize I made a mistake here: I meant to say that "Thrombocytopenia 1 is a synonym of X-linked thrombocytopenia". Regarding the questions you have here in this ticket:

Thank you! Gioconda