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TuftsCTSI / CVB

CVB, or Custom Vocabulary Builder, is designed to interface with SSSOM-based mappings hosted in GoogleSheets together with self-hosted runners in the Tufts Azure environment to create custom representations of semantic concepts with ID assignments in OMOP CDM format.
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Add MIMIC Custom Terminology in support of the MIMIC IV - OMOP ETL #10

Open jshoughtaling opened 1 week ago

jshoughtaling commented 1 week ago

In addition to GIS, we would like to incorporate terms needed to capture the MIMIC IV data in OMOP CDM format. Currently, these terms are built and handled by the MIMIC -> OMOP ETL, but @p-talapova has made updates to the terminology that should be represented here as well.

jshoughtaling commented 5 days ago

@p-talapova - the availability of your latest MIMIC vocabulary work in this repo is key for updating the MIMIC IV to OMOP ETL. Can you please link that work and or put together a GoogleSheet with mappings in SSSOM format that I can use to integrate into this repo. Thanks in advance!

p-talapova commented 3 days ago

hi @jshoughtaling, thank you for reaching out. Here is the link to the latest version of the SSSOM-formatted MIMIC IV mappings to OMOP (Google Sheet "MIMIC4-to-OMOP-SSSOM-custom-mapping"): https://docs.google.com/spreadsheets/d/1LgNSwxx7uDjc6hAJb4m6o_6WvVmuBgH5QYzAqeS3aD0/edit?gid=853181322#gid=853181322