I am new to OMOP CDM and try to implement a custom drug database into the CDM.
Basically, the data contains all austrian drug registrations with an own unique pharma_number, a description and the corresponding ATC-Code.
Here is an example of some data.
Whats the best way to implement this data into the CDM? Is the source_to_concept_map necessary? Or just create a new vocabulary “pharma_numbers” and add all these entries into the concept table. I have read, that you should not add data into the concept table since its standardized.
Maybe work with the Ancestor table to get the connection between pharma number and atc-code?
What you are doing is very laudable, but unfortunately not easy. We are currently doing exactly this for drug registries in Canada, UK, France and Germany. There is a process you may want to follow described [here][1]. But before you do that I strongly recommend touching base with the team who are working on it (@gregk, @Dymshyts) and getting some insight. They also have done the mappings for German drug forms (like such beautiful things like “Alveoleneinlagen”), brand names and manufacturers.
[1]: http://www.ohdsi.org/web/wiki/doku.php?id=documentation:international_drugs
@Deniz_Gezgin - I propose we have a quick session where we can introduce you to the OHDSI vocabularies, walk you through the process and show your some similar work that was done? Then we can discuss options on how to get your need addressed. Please shoot me a quick email at gregory.klebanov@odysseusinc.com and we can schedule a session with you
Whats the best way to implement this data into the CDM?
Map each source_value code to a standard concept. In this case DRUG_EXPOSURE expects RxNorm or RxNorm Extension concepts.
ATC mapping that you currently have (shown above) is good to have but ATC is (as far as I know) not a “targeted vocabulary” for leaf-data-events.
A “lazy workaround” would be to only implement DRUG_ERA table only (that works on the ingredient level) and utilize the ATC mapping you have (when transformed to RxNorm+RxNormExt ingredient codes). (but ignore my last sentence (I never said that) (just protecting myself here…)
