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Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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[NTR] ClinGen Retina GCEP new terms #4937

Closed nicolevasilevsky closed 5 months ago

nicolevasilevsky commented 2 years ago

See spreadsheet

nicolevasilevsky commented 2 years ago

related to https://github.com/monarch-initiative/mondo/issues/3898

nicolevasilevsky commented 2 years ago

@jennygoldstein

I have a question about this term: NYX-related congenital stationary night blindness

From what I can see, there is nothing different about this from the existing Mondo class MONDO:0010690 'congenital stationary night blindness 1A'. I added this as an exact synonym and updated the def to match your definition, and added the parent class to that term: 'inherited retinal dystrophy'.

Thanks!

jennygoldstein commented 2 years ago

Hi Nicole,

That sounds fine. Thank you for checking.

Jenny

jennygoldstein commented 2 years ago

Hi Nicole, I am so sorry - I misunderstood your last question. Is it possible to make the label "NYX-related congenital stationary night blindness" and have 'congenital stationary night blindness 1A' as a synonym? MONDO:0010690

Thank you, and many apologies for any confusion.

Jenny

nicolevasilevsky commented 2 years ago

Hi @jennygoldstein Our team discussed this on the Mondo curation call and for a disease that is part of an OMIM phenotypic series, we want to use the OMIM names for consistency. In this case, congenital stationary night blindness 1A is part of the OMIM phenotypic series MONDO:0044749 'X-linked congenital stationary night blindness'.

Thanks for understanding!

nicolevasilevsky commented 2 years ago

@jennygoldstein please let me know if you'd like to discuss further, I can reopen the ticket.

jennygoldstein commented 2 years ago

Hi @nicolevasilevsky, Thanks very much for following up on the disease entity for NYX. In discussing this with the Retina GCEP, we totally understand that this is part of a phenotypic series in OMIM and not wanting to change the disease entity for that reason. However, we wondered if we could please discuss further. The dyadic (gene-disease) naming approach is being supported by the ClinGen Disease Naming Advisory Committee. Dr. Hamosh is a member of that group. However, I do not know if or when OMIM may adopt the dyadic disease-naming approach. Perhaps we could talk with Dr. Hamosh and other DNAC members? I would be happy to coordinate any discussion that could be helpful in this regard. Please let me know what you think. Thanks again, Nicole, for all of your help in dealing with our many requests.

nicolevasilevsky commented 2 years ago

Hi @jennygoldstein - let me discuss with our team and I will get back to you. :)

nicolevasilevsky commented 2 years ago

Hi @jennygoldstein - We are open to having a conversation with your developers to figure out ways to have the ClinGen preferred label show up, or another possible solution is having a particular release file for you that displays the labels that are preferred by ClinGen. Do you think those solutions could work? We are happy to meet on a call to discuss further as well. Thank you!

nicolevasilevsky commented 2 years ago

emailed Jenny on 08/17/22 to inquire about having a call

nicolevasilevsky commented 7 months ago

@sabrinatoro I think this can be closed