Converting vocabulary search to concept set

[chantekhani89]

Hello,
I am one of the project leads on an OHDSI investigation of antibiotic use for acne (collaborators: Lisa Schilling, Robert Dellavalle). I have a technical question regarding the atlas database. When I search for a vocabulary term, I would like to limit my search to "drug" and "standard." I am able to do this with the left hand column in the vocabulary tab. I then would like to select all of the results after limiting to "drug" and "standard." If I click on the shopping cart icon, it selects all the vocab results, completely disregarding the limitation to "drug and "standard." How can I avoid doing this? Thank you.

[Chris_Knoll]

I'd recommend you do not create a concept set based on a text-based search of the vocabulary and then add everything that is a 'drug' and 'standard' to it. This will not perform, and it will be hard to understand how the concept set was constructed.

Is there any reason why you couldn't find a parent concept in the vocabulary, select it, and then in the concept set 'include descendants'? You can do this for a variety of hierarchies in the CDM: by ATC class, ingredient, dose form, etc. If you want to describe the specific concept set you are working on, maybe we can help you construct it here...

[chantekhani89]

I appreciate your help and suggestions very much. Here is a concept set that I am currently working on: all standard drugs listed under "phenytoin." How do you suggest I go about doing this?

[Chris_Knoll]

There seems to be an issue woth ohdsi.org's ATLAS install, so I can't link you a ConceptSet expression, but I am able to create cohorts, so I will create a concept set inside that for your review:

I created the cohort, and then added a new concept set to the cohort.
I did a vocabulary search for 'phenytoin'. I located the row that says the class is 'Ingredient', a Standard concept from RxNorm. I clicked the shopping cart to add it to my concept set.

Then i went back to my concept set view, and clicked the 'descendents' checkbox so that all the drugs found under phenytoin will be used.

Here's the cohort definition: http://www.ohdsi.org/web/atlas/#/cohortdefinition/1729468

You can go into the Concept Sets tab, chose the concept set 'phenytoin', and then look at the included concepts. You will see you will find all the branded and clinical drug forms that are under the ingredient (there are over 1000!). This is a much better approach to selecting your drugs of interest than manually clicking on 1000 items in a text search.

[chantekhani89]

This is so helpful, thank you so much! For some reason, I am not able to create concept sets in Atlas. Whenever I try to save a concept set, I get an error screen that says "An error occurred while attempting to find a concept set with the name you provided." Do you think that this is just a malfunction of the OHDSI software?

[Chris_Knoll]

Yes, I believe there's a problem with concept set creation, I'm seeing errors on on the public site: http://ohdsi.org/web/atlas, and if you are running the same version in your own local environment, you probably will get the error there too. I am not seeing this error running on our internal environments, so not sure what is causing it.

[chantekhani89]

Do you know who can I contact to find out about this issue? It's been going on for 48 hours at least.

[Chris_Knoll]

Submitting an issue on the atlas repo: https://github.com/ohdsi/atlas/issues is probably the best way to get an issue addressed.

[chantekhani89]

Awesome, thank you so much!