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monarch-initiative / mondo-ingest

Coordinating the mondo-ingest with external sources
https://monarch-initiative.github.io/mondo-ingest/
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Links to MedGen #193

Open PabloBotas opened 1 year ago

PabloBotas commented 1 year ago

Hi, According to https://mondo.monarchinitiative.org/pages/sources/, MedGen terms should be linked from Mondo terms, yet I don't see a lot of terms are linked to it in the obo file. I do see links to Mondo in MedGen, but not viceversa. Is this intended? Do you know of a resource establishing this mapping?

Thanks!

matentzn commented 1 year ago

Thank you @PabloBotas for the push, we have had the medgen sync on our agenda for a long long time, and we should probably just prioritise it now.

@joeflack4 Lets talk about this at our next call - I would like to at least fold in the mappings provided by Medgen asap.

kanems commented 1 year ago

MedGen has a report on our FTP Site (https://ftp.ncbi.nlm.nih.gov/pub/medgen/) of all the ID Mappings including MedGen's mapping of Mondo IDs to a CUI, or if no suitable CUI is available from UMLS (C#) Our own supplemental "CUI-like" code (CN#). This is freely available should be machine readable. MedGenIDMappings.txt.gz

nicolevasilevsky commented 1 year ago

Thanks all! I'll move this ticket to the Mondo ingest tracker. Nevermind - it is already here!

PabloBotas commented 1 year ago

Thank you all for picking this up so quickly!!

joeflack4 commented 2 months ago

@matentzn @twhetzel What are the remaining sub-tasks that would render this completed?

I'm currently seeing MedGen refs in mondo-edit.obo, but not mondo.sssom.tsv.

matentzn commented 2 months ago

MedGen xrefs are not mappings in the strict sense - they dont have to be in the sssom. As soon as your latest batch (updated xrefs) is updated in mondo-edit.obo we can can close this issue.