OMOP Documentation suggestion for source_to_concept_map

[heschmidt04]

Hi Folks, Andrew mentioned I should open an issue here for this. If this is not the place for this suggestion - let me know. Thanks!

The link here source_to_concept_map does not have any references to Usagi being a tool to help create a look up table for Athena Vocab concept codes per domain used in the ELT to get source data into OMOP tables.

It is mentioned deeper into the FAQ

This came up in CHoRUS Bridge2AI Standards Office Hours demonstration on Usagi 11/9/2023 and is a recorded session if you want to reach out to Tufts contact Marta Alvarez for access to the GDrive.

Polina had more context that isn't mentioned in Usagi docs about DDL to help stage the codes for review. I'll follow up with that question to add that use case in their repo and tie back to this issue for reference.

Thanks for creating the shared framework. Best regards, Heidi
hschmidt@mgb.org

[heschmidt04]

At the Usagi repo I opened an enhancement to tie back here. https://github.com/OHDSI/Usagi/issues/158

[MaximMoinat]

Thanks for raising this. I agree it would be beneficial to have a reference to Usagi (or other ETL tooling) in the STCM table description. How do you feel about this updated description?

The source to concept map table is ~a legacy data structure within the OMOP Common Data Model,~ recommended for use in ETL processes to maintain local source codes which are not available as Concepts in the Standardized Vocabularies, and to establish mappings for each source code into a Standard Concept as target_concept_ids that can be used to populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table is no longer populated with content within the Standardized Vocabularies published to the OMOP community. There are OHDSI tools to help you populate this table; Usagi and Perseus. You can read more about OMOP vocabulary mapping in The Book of OHDSI Chapter 6.3.

[heschmidt04]

Thanks Maxim for tying Usagi as the tool to help generate the reference lookup table for use in ETL. Much appreciated! Heidi

[heschmidt04]

I like it. Do you think it is feasible to have folks who'd be willing to give example of how they set up their stcm (source to concept map(s))? I figure they could provide it without their local to them codes.

I think we'd find folks using it in unique ways. What I notice is that there isn't a way to group by domain in stcm and so we appropriate one of the established columns to make it clear what codes are associated with measurement, observation, drug routes, unit values, etc.

Not sure where to officially raise that so we could make it reflect in the field use.

Warm regards Heidi

On Mon, Nov 13, 2023, 07:02 Maxim Moinat @.***> wrote:

Thanks for raising this. I agree it would be beneficial to have a reference to Usagi (or other ETL tooling) in the STCM table description. How do you feel about this updated description?

The source to concept map table is a legacy data structure within the OMOP Common Data Model, recommended for use in ETL processes to maintain local source codes which are not available as Concepts in the Standardized Vocabularies, and to establish mappings for each source code into a Standard Concept as target_concept_ids that can be used to populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table is no longer populated with content within the Standardized Vocabularies published to the OMOP community. There are OHDSI tools to help you populate this table; Usagi https://github.com/OHDSI/Usagi and Perseus https://github.com/ohdsi/Perseus. You can read more about OMOP vocabulary mapping in The Book of OHDSI Chapter 6.3 https://ohdsi.github.io/TheBookOfOhdsi/ExtractTransformLoad.html#step-2-create-the-code-mappings .

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