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ICD11 ingest: grouping issue #16
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See relevant PR: https://github.com/monarch-initiative/mondo-ingest-private/pull/1 |
FYI @joeflack4 updated the description above with a quote from Orphanet:
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Oh, thanks. I forgot about those mappings. Right now I'm focused on 1. ICD11 source rather than 2. ICD11::ORDO mappings. If you want, I can kinda do them in parallel too. Right now I'm not sure where to get that ORDO release. Maybe here?: https://www.orphadata.com/orphanet-nomenclature-for-coding/ Sounds like she's saying right now they only have ICD11 MMS(Morbidity and Mortality) terms, but they'll soon also have (the rest of the) foundation terms, as well as a list of Orphanet diseases not mapped to ICD11. |
I think ICD11:ORDO can be done as a second PR - just to keep things as small as possible, but it should be done (1) before this ticket is closed, and (2) before someone starts with the manual curation process. |
Think about what exactly? |
@matentzn Sorry I meant think about "to evaluate this" (issue). As in where these are in the priorities, as well as expanding on (2). Actually, let's just leave this to the next meeting; we'll have a better idea then after I've made progress on other issues. |
Complete! |
Overview
Ingest ICD11 into Mondo.
Sub-task list
1. Ingest ICD11 source
Add ICD 11 foundation as a regular sync source in ODK /
mondo-ingest.Makefile
.How to get data via REST API (defunct)
Defunct because we now have an `.owl` to work with.
From Can Celik (WHO):
And:
2. ICD11::ORDO mappings
Get ahold of all ICD11 - ORDO mappings from a respectable source and derive an initial set of Mondo - ICD11 mappings from that (with the mapping set id as the source)
From Julie at Orphanet:
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