Source_concept_ids

[boverdui]

Hello,

I performed mapping and transformation for some (fake) test date to come to grips with the Carrot system.

In the output files for OMOP the various _source_concept_id fields are filled with the same values as the _concept_id_fields. This doesn't seem right to me. As far as I understand the _source_concept_id fields are to store the concept_ids of the source data, if available, not the OMOP concept-ids.

Cheers,
Bert

[DrUrwin]

Hi Bert,

Yes the source_concept_id fields are there to represent the source data attributes. If you could please send an example output.json file to the development team that would be useful to check what is happening, thanks.

Regards,

     Esmond

[boverdui]

Hello Esmond,

This is the JSON output file:

Rules - carrot_test_scan_report - 7 - 2025-03-10 08_06_23.002429.json

Cheers,
Bert

[prquinlan]

Hi @boverdui, great observation.

The source_concept_id is there to capture concept ids from OMOP that best represent the source data, but could be non-standard. So it can be used for someone to indicate this is the closest OMOP term to the source value (_source_concept_id) vs the most correct, i.e. standard and valid, term for the source value (_concept_id). Carrot just defaults to adding to both. Something worth us looking at though, thanks for raising.