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OMOP etl module #52

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tiadams opened this issue Nov 27, 2024 · 0 comments

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tiadams commented Nov 27, 2024

Feature

Input: A Dataframe (csv/excel) + [optionally] DataDictionarySource

Map each column to the closest (OMOP) concept based on the data dictionary descriptions (if applicable) or column names (if not)
Create a etl pipeline (as part of a new module, e.g. etl.py) to convert input to OMOP

TBD

Which terminologies/concepts are required to map to OMOP?
Concept Identifers from OMOP / OHDSI source terminologies?
Get OMOP IDs from Athena API call? (to be implemented)
Extend DB schema to support OMOP?

tiadams added the enhancement label

tiadams assigned mehmetcanay

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