DQD reports on SOURCE_TO_CONCEPT_MAP but table is deprecated

OHDSI / DataQualityDashboard

A tool to help improve data quality standards in observational data science.

https://ohdsi.github.io/DataQualityDashboard

Apache License 2.0

145 stars 96 forks source link

DQD reports on SOURCE_TO_CONCEPT_MAP but table is deprecated #520

Closed jam560 closed 10 months ago

jam560 commented 10 months ago

I don't see any previous issues on this topic. We just ran DQD for the first time. It still contains 24 checks on the SOURCE_TO_CONCEPT_MAP table. This page says the table is no longer part of the CDM standard: https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:source_to_concept_map.

clairblacketer commented 10 months ago

Hi @jam560 the SOURCE_TO_CONCEPT_MAP table is part of the cdm but is considered a vocabulary table. It is very much in use by many collaborators usually to house manually curated mappings. http://ohdsi.github.io/CommonDataModel/cdm54.html#Vocabulary_Tables

jam560 commented 10 months ago

Fair enough. But if you google “omop source_to_concept_map” the first two hits tell you it is obsolete.

clairblacketer commented 10 months ago

All they say is that the table is no longer used as it was in v4, not that it was removed. If you don’t want to use it or populate it, leave it empty. The dqd will not check tables that are empty.