OHDSI Home | Forums | Wiki | Github

Error Executing "Characterizations" in OHDSI Atlas with Broadsea Deployment

Implementers
#1

Hello everyone,

I’m reaching for some assistance with an issue we’re facing in our OHDSI Atlas setup that’s deployed using Broadsea. Our environment is structured with three PostgreSQL schemas (omop_diseaseArea1 to omop_diseaseArea3), each dedicated to a distinct disease area, and a fourth schema where our vocabulary is stored.

We’re encountering an error when attempting to execute “characterizations” in Atlas. The error message in WebAPI is:

ERROR: relation "omop_diseaseAreaX.concept" does not exist

This suggests that Atlas is trying to access a ‘concept’ table within a schema that doesn’t seem to be correctly specified.

It appears that during the “characterization” process, the system is either misinterpreting the schema names or not properly directing the query to the right schema where the ‘concept’ table resides.

Other features of Atlas, however, are working properly.

Has anyone else encountered a similar issue, or does anyone have suggestions on where else we might look to resolve this?

Thanks in advance for your help!

Best regards,

Felix

#2

The concept table should be in your CDM schema…there are some places where the code attempts to look for a ‘centralized’ schema, but I don’t think FeatureExtraction (which is the core functionality that handles characterization) allows you to specify a ‘vocaularySchema’ (@anthonysena could you confirm?).

If you are in a situation where you have an external vocabulary schema from your CDM schema, i would create VIEWs in your cdm schema that points out to the shared vocabulary schema (ie: create a view for concept that does select * from vocabSchema.concept).

If that isn’t it, then you should confirm your records in the SOURCE_DAIMON table to ensure that you have the correct values as ‘tableQualifier’ for the given source. The question is if you can explain why you got the cdmSchema of ‘omop_diseaseAreaX’ and that should help you locate where to make the necessary update.

Update:

@Ajit_Londhe : do you have any thoughts on this? I remember that you wanted the ability to have external vocabulary schemas, but i’m not sure all tools support that…and so I’m not sure if this is something you should handle in the BroadSea deployment.

-Chris

#3

but I don’t think FeatureExtraction (which is the core functionality that handles characterization) allows you to specify a ‘vocaularySchema’ (@anthonysena could you confirm?).

Correct - FeatureExtraction and our other analytic methods assume the vocabulary tables are in the same schema as your patient-level data converted to the OMOP CDM. @Chris_Knoll provides a good option if you’d like to attempt to use VIEWs to accomplish this.

#4

Thank you very much for your answers.
We implemented the idea of creating a view which seems to solve our problem.

Kind regards,

Felix

t