I’ve been watching the OHDSI-tutorials on the OMOP vocabulary (https://www.ohdsi.org/past-events/2018-tutorials-omop-common-data-model-and-standardized-vocabularies/), and have a few questions on how to proceed. We are working on an R-package that is supposed to run some scripts on longitudinal OMOP-data, and return aggregated data for a long list (~1000) of drug-reaction-combination-pairs (coded in ATC and MedDRA). What we would like is an automated procedure to translate each of these terms, into some vocabulary we can use in OMOP-databases, i.e. standard concepts.
Drugs are coded in whodrug at source, which we translate to ATC with an in-house dictionary. As an example, I try “Influenza pandemic vaccine”, which has an ATC of J07BB. I query the concept table for the concept_id of this ATC, and find 21601333. Following the tutorial, I would now try to find the “Maps to” in the concept-relationship-table. Even though I find 40 000 matches, I only find relations of the relationship_id “ATC - RxNorm”. Is this what I want?
If I take the mappings from “ATC-RxNorm” and ask for them in the concepts-table, I find around 17 000 standard concepts. Is this the (/at least one reasonable?) way to translate the ATC of “influenza pandemic vaccine” into OMOP vocabulary, or should I include the children of these 17 000 standard concepts as well, if I want to capture all pandemic influenza vaccines?
Second part of my question relates to MedDRA. From reading other forum posts, I understand that MedDRA is “on top” of SNOMED in some way, but I don’t understand what this means in practice. Can I proceed with some possibly defect mapping or is mapping not possible at current state? I found a thread (Relation between MedDRA and SNOMED) that claims that only 39 % of the PT-terms in MedDRA are mapped to SNOMED.
When I try with a medDRA-PT-term, I don’t find “Maps to”, instead I sometimes find “MedDRA - SNOMED eq”, but also “Is a”/“Subsumes”. Which one should I use?
For the (if still accurate) 61 % of the PT:s which don’t have a mapping to a standard concept, what is recommended, should I for instance move upwards in the medDRA-hierarchy before searching for a standard concept for the non-mapped PT:s?
And if all/any part of this is documented somewhere, I’d be happy to read up on it, it’s just that I don’t know where to look for it.