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OHDSI / DataQualityDashboard

A tool to help improve data quality standards in observational data science.
https://ohdsi.github.io/DataQualityDashboard
Apache License 2.0
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plausibleGenderUseDescendants not checking ancestor and all domains of descendants #556

Open lore-edencehealth opened 3 weeks ago

lore-edencehealth commented 3 weeks ago

the plausible gender use descendants check does not seem to check the ancestor itself. suggested update: JOIN @vocabDatabaseSchema.concept_ancestor ca ON ca.descendant_concept_id = cdmTable.@cdmFieldName *OR ca.ancestor_concept_id =cdmTable.@cdmFieldName**

OMOP_CDMv5.4_Concept_Level.csv has checks on condition_occurrence but some of them or its descendants are observations. OMOP_CDMv5.4_Concept_Level.csv has checks on procedure_occurrence but some of the descendants are observations or measurements. Should a copy of the rows be made for these extra cdmTables?

katy-sadowski commented 3 weeks ago

Every concept is its own descendant, so we do not need to add this additional SQL logic. (see https://ohdsi.github.io/TheBookOfOhdsi/StandardizedVocabularies.html#conceptAncestor)

Regarding cross-domain checks, I think this is out of scope for this check. We'd probably want to add specific checks on gender-specific observations and measurements in order to capture these additional concepts. I'm actually surprised that the hierarchy contains a mix of domains - @dimshitc is this expected?