What, exactly are mapped terms? What does this mean if I include mapped terms in a concept set?
@mmmckillop: Can you give some context? Who said “Mapped terms”?
@Christian_Reich my apologies for not being clearer - I am still getting used to the appropriate format for questions on this forum. Specifically, I am creating a concept set using Atlas. If I go to the concept set expression tab, there is an option to check mapped for a particular concept. I am not clear what checking this box will mean for the concept set I create.
@mmmckillop: I believe that this option will include concepts from non-standard vocabularies that are synonymous with the standard concept for which that flag is applied. For example, if your concept set includes an RxNorm code (the “standard” vocabulary for representing drugs) representing a drug, clicking Mapped will include concepts from other vocabularies such as Multum or NDC (“non-standard” vocabularies for representing drugs) that are synonymous with that RxNorm code. @Christian_Reich, please let me know if this is incorrect.
@aperotte has it right: selecting ‘mapped’ in a concept set expression means to return the concepts that have a ‘Mapped To’ relationship to the concept (or any of the descendants if ‘descendants’ is also selected).
You’d use this if you wanted to make a concept set for use in the ‘source concept’ filters of CIRCE/Calypso. But, most of the time, you’d just want to use the standard concepts in your concept set and find events based on the primary concept_id field. (drug_concept_id or condition_cocnept_id for example)
-Chris
@Chris_Knoll, @aperotte, thank you very much this is helpful. I am defining a cohort and trying to see how many patients fit this cohort in my local institution. I then want to have others use the same cohort definition and see how many patients meet the criteria for that cohort. It sounds like I do not want to use mapped terms. Please correct me if I am wrong, Thank you again.
That’s right, because only standard concepts are mapped into the CDM tables (if the ETL is done properly), you won’t need to use the ‘mapped’ option in concept sets. You’ll just create a concept set that selects descendants of standard concepts or classifications.
Have you installed ‘Achilles’? Here is a link to the demo:
http://www.ohdsi.org/web/achilles/#
This is a demo based on synthetic data, but it does demonstrate the idea: it gives a nice overview of the data in your database, and also lets you drill down into some pretty specific details (such as after selecting a condition, what is the prevalence month-over-month of the condition in the database).
If you like this, it’s pretty straight forward to set up on your local CDM (provided you are familiar with R to execute the analysis, and setting up a web application to render the results). The repo is at:
You don’t even have to do a “git pull” on the repo, there are R commands to that lets you install packages (Achilles is an R package) from github.
-Chris