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I’m trying to define a new cohort and am puzzled by the different messages that are displayed by Atlas. For example, I built a new concept set and then tried to use that concept set as an inclusion rule for the cohort definition. In the messages tab, this informational message is displayed:
It’s not specified what type of records to look for in condition occurrence at inclusion rule
I do not understand what the message means and I do not know how to resolve this. Any suggestions?
That was a message to encourage condition type concept ID in your condition occurrence criteria. If you specify the condition type concept ID in your criteria, the message should go away. It is debatable if this is something that should be raised as a warning, so if anyone from CDM group or others have opinions on if criteria should specify the {domain}_type_concept_id in criteria, I’d like to hear about it.
Hi~did you figure out it?
I encountered the same problem.
No - I never was able to figure out how to resolve it. The warning does not seem to affect anything. I made sure that the Concept Set used by the Cohort had only concepts that were from the “Condition” domain, but that did not seem to change anything. I believe this is what Chris_Knoll was suggesting, but the warning persists.
The message is defined here, and the check is done here.
The conditionType is null when you don’t specify a attribute of ‘Condition Type’ in your condition occurrence. This field is described here. Most domain tables will have the ‘{domain}_type_concept_id’, which the checker referenced above will look for null.
Documentation on the Condition Occurrence table is here.
I’m not sure how concerned you should be about this warning, at one point it was a CDM suggestion to specify the condition type in your criteria so that you can specify which ‘provenance’ the source data came from, but in my experience, this isn’t really necessary to specify (shouldn’t all data base treated equal?)
If you want to get rid of this warning, you have to check each of your criteria and ensure you have the ‘type’ attribute specified and filled with the concepts representing the provenance you are interested in. Again, I’m not sure this is really a necessary step, but that’s what the warning message is displaying.
Hope that helps.