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Custom concepts do not appear in ATLAS search results

(Ayo A.) #1


I mapped a dataset of observational / survey data to standard concepts as well as several custom concepts ( with IDs > 2B) due to missing coverage with standard concepts.

When I look up the dataset in a local ATLAS instance, in the Data Sources tab, all standard and custom records show up in the tables / treemaps, and the total # of observational entities matches the number in the source dataset.

However, when I search for a concept ID in the Search tab, only the standard concepts can be located, whereas custom concepts when searched produce a “NO RESULTS FOUND FOR …” message. This in turn impedes the creation of concept sets with custom concepts for cohort generation etc.

Does anyone have an idea how to resolve this (i.e. ATLAS recognizing custom concepts in some context but not others)?


(Anna Ostropolets) #2

A short answer will be: if you add custom concepts through SOURCE_TO_CONCEPT_MAP, these concepts won’t show up in Atlas. What you would have to do it add them to CONCEPT table (and mappings to CONCEPT_RELATIONSHIP table if you want to see mappings in Atlas).
The process may be tricky as you have to pick a vocabulary name, assign domains and classes and handle constraints. This is, actually, one of the reasons why we advocate for adding custom vocabularies to the official OMOP vocabs.

(Ayo A.) #3

Thanks for the reply! I was able to pinpoint and resolve the issue following the steps in your answer (there was an error in how the custom concepts were mapped to the CONCEPT_RELATIONSHIP table).