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Standard vocabulary asthma drugs


(Aniek Markus) #1

Hi!

I’m looking to find standard concepts in OMOP CDM for all asthma drugs. I have a list of medications with ATC 7 codes that I’m interested in (approx. 120), but the existing mapping to standard concepts seems to be incomplete (especially for combination medicines). I might be able to go back to the ingredient level and build it up from there, but I was wondering if anyone here has any experience with using asthma medications in OMOP CDM (or other experience) that could be of help.

Thanks in advance!


(Katy Sadowski) #2

Hi there,

On my team we use ingredients to build our medication concept sets. However, things get tricky when you need to restrict to inhaled formulations & combination drugs for asthma; I don’t think this is possible to do within the ATLAS UI. For such scenarios we write a SQL query to get the concept_ids and then import them into ATLAS on the Search>Import tab.

We’ve created the following table to make it easier to write such queries:

CREATE TABLE medications_categorized AS (

SELECT DISTINCT
    all_concepts.concept_id,
    all_concepts.concept_name,
    standard_concepts.concept_id as standard_concept_id,
    standard_concepts.concept_name as standard_concept_name,
    ancestor_concepts.concept_id as ingred_id,
    ancestor_concepts.concept_name as ingred,
    dose_form_concept.concept_id as dose_form_id,
    dose_form_concept.concept_name as dose_form
FROM omop.concept all_concepts
    JOIN omop.concept_relationship ON concept_relationship.concept_id_1 = all_concepts.concept_id
        AND concept_relationship.relationship_id = 'Maps to'
    JOIN omop.concept standard_concepts ON standard_concepts.concept_id = concept_relationship.concept_id_2
    JOIN omop.concept_ancestor ON concept_ancestor.descendant_concept_id = concept_relationship.concept_id_2
    JOIN omop.concept ancestor_concepts ON ancestor_concepts.concept_id = concept_ancestor.ancestor_concept_id
    	AND ancestor_concepts.concept_class_id = 'Ingredient' 
    JOIN omop.concept_ancestor dose_form_ancestor ON dose_form_ancestor.descendant_concept_id = concept_relationship.concept_id_2
    JOIN omop.concept dose_form_concept ON dose_form_concept.concept_id = dose_form_ancestor.ancestor_concept_id
		AND dose_form_concept.concept_class_id = 'Dose Form Group');

You can write queries on this table to find concepts which represent combinations of different ingredients; inhaled formulations; etc.

Hope that’s helpful. I’d also be curious to see how others approach creation of custom concept sets outside the ATLAS UI :slight_smile:

Katy


(Anna Ostropolets) #3

We have a group in Erasmus @mdewilde who does studies with asthma drugs.
In the meanwhile, we know that ATC isn’t complete and are actively working on it. The release with comprehensive coverage including asthma drugs is coming shortly.
If you’re interested, you can shoot me an email and I’ll give you the lists before the release.


(Aniek Markus) #4

@katy-sadowski I agree, thanks for sharing your approach to this problem! I will check it out.


(Christian Reich) #5

I agree the UI needs work, @katy-sadowski, but you could define those inhalant asthma medications by picking Clinical Drug Forms (e.g. Budesonide / formoterol Inhalation Solution). You can select descendants, and you will get all products in the various markets. It would not be such a long list.


(Katy Sadowski) #6

@Christian_Reich thanks for this suggestion! I didn’t realize Clinical Drug Forms could be used in this way. I will try this out - definitely prefer to reserve imported custom sets for the last resort.


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