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We need to work out how to transform MIMIC-IV to the `OMOP` person table. We could base our initial transform on the approach at: https://github.com/OHDSI/MIMIC/blob/master/etl/etl/cdm_person.sql
T…
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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](https://github.co…
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Our ambition is for Carrot to support mapping the complete OMOP CDM, but this is a journey that will be delivered over time. We may need to update the Carrot CDM tool to support these as well.
This i…
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The CCDA and OMOP sides don't line up perfectly WRT No matching concept, Null and Unknown.
There's little enough data we should be able to count these and see what should be there.
Tagging folks fo…
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It would be nice to have a single entrypoint for the meds command line tools. e.g.
```
meds convert --from omop --to meds [OMOP_PATH] [MEDS_PATH]
meds convert --from meds --to omop [MEDS_PATH] [O…
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i.e. OMOP domains (Patient, Encounter, MedicationRequest) and tables and how they relate to the in scope FHIR resources
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[Achilles](https://github.com/OHDSI/Achilles)
This would be helpful when we have data in OMOP format.
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In the Download screen (where you select to download entire vocabularies), some of the OMOP-generated vocabularies are available (e.g. Gender) but others are missing (e.g. Condition Status and Type Co…
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Maybe these should be combined, but will start with them being separate.
- [x] Drug exposure
- [ ] Device exposure
- [ ] Environmental exposure (no OMOP example to follow, will hold off on this f…
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Establish a overall pipeline infrastructure for transforming and mapping FHIR resource data into appropriate OMOP CDM domains.
-generate code_map_walk to translate code/code system to OMOP concept id…