search

monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
Creative Commons Attribution 4.0 International
223 stars 51 forks source link

ensure ClinVar submissions from UDN are in mondo #7773

Open mellybelly opened 1 month ago

mellybelly commented 1 month ago

See the list here: https://www.ncbi.nlm.nih.gov/clinvar/submitters/505999/ This may require coordination with UDP/UDN and/or medGen.

twhetzel commented 3 weeks ago

I can take a first pass at checking whether all Conditions in the table at https://www.ncbi.nlm.nih.gov/clinvar/submitters/505999/ are in Mondo.

kanems commented 3 weeks ago

@twhetzel - FYI if the condition name in that table has no hyperlink, it's not assigned a CUI in MedGen so it's highly unlikely it's in Mondo already (our logic being that nearly all Mondo human disease records are in scope for MedGen display, not including injury or poisoning terms that are not clearly associated with genetic conditions)

twhetzel commented 3 weeks ago

Thanks @kanems - that is very helpful!

I looked at the list of Conditions from link originally posted and eventually used the MedGenIDMappings.txt from https://ftp.ncbi.nlm.nih.gov/pub/medgen/ and from those sources there are 143 Conditions listed on https://www.ncbi.nlm.nih.gov/clinvar/submitters/505999/ that do not have a corresponding Mondo ID.

clinvar_udn_submissions-no_mondo-disease_name_only.txt

@mellybelly is there a timeline for reviewing and adding these Conditions into Mondo?

twhetzel commented 2 weeks ago

A first pass review is at: https://github.com/monarch-initiative/mondo/tree/master/src/scripts/notebooks/clinvar-udn-submission-analysis from this PR. Please note, this first pass review was only intended to scope the issue by identifying easily confirmed diseases in the list that also exist in Mondo knowing that further curation efforts and plan would be needed to move forward for those diseases not initially found to be in Mondo in this first pass review.

twhetzel commented 1 week ago

I have not heard of any next steps so I am removing myself from this ticket.