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'Maps to value' in source_to_concept_map export from Usagi

A quick question: the “maps_to_value” flag is lost in the ‘source_to_concept_map export’ from Usagi, but they are correctly saved in the ‘export codes for review’. Does this mean that only direct lookup tables are supposed to be used in this cases instead of including them in the source_to_concept_map table?

The OMOP source_to_concept_map table does not have a column for the mapping relationship. So we cannot include that information in the export. If you wish to work with the other mapping relationships, please consider using the regular usagi save format in your mapping scripts.

There is a proposal on a new source to concept map table, but we are still discussing the format. See Wide MAPPING table (in vocabulary) (problems with relationship)


If you want to map source values to standard concept_ids using other relationship_ids, you will need to create custom concept_ids, the 2 billionaires, in the Concept table. And then map them to standard concept_ids in the Concept Relationship table.

I am wondering what the best way is to create those new concepts and relationships. As I created the mapping in USAGI, is it possible to export the mapping in a way that already fits the needed format or only needs little adaptations? Is there some documentation that I missed supporting this use case?

Unfortunately, Usagi does not support export to concept_relationship-formatted records at the moment. Would be a good addition though. For now, the regular ‘Usagi-save’ format will be best to use.