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Mappings from NPU codes to standard vocabulary?


(Benjamin Skov Kaas Hansen) #1

HI guys,

We’re building an OMOP CDM with drug administrations (ATC), diagnoses and procedures (Danish ICD10 dialect) and biochemical measurements (NPU). I was wondering if NPU codes have been mapped to an OMOP standard vocabulary already. From what I can see in Athena, no such mapping scheme exists. If this is correct, we’ll make our own mappings, but I just wanted to ask the community first to avoid duplicative work.

Cheers,
Ben


(Dmytry Dymshyts) #2

Hi @benskov
There’s no NPU in OHDSI Vocabularies.

Do you want to contribute and share the mappings and some high level explanations how the source vocabulary (NPU) is organized?
It has some advantages:

  • people might look and check whether you did them right
  • we include them into official Athena package, so it would be easier to maintain.

BTW, why are you using ATC for drug administration?
ATC are non-standard concepts, so according to CDM rules, you can’t use them.
Please let me know if you are interested in improving this.


(Benjamin Skov Kaas Hansen) #3

Hi @Dymshyts,

Thanks for your swift reply. Unfortunately, you confirmed my suspicion — but I believe we’d be happy to share the mappings once done. At least, they’d be helpful for other Danish datasets that need OMOPing.

ATC is the source vocabulary for our drug data. I meant to mention the source vocabularies, so of course we’ll map them to the standard vocabularies. The Danish dialect of ICD-10 has some quirks that we also must work out, but it’s a minor thing and idiosyncratic to Danish data.

Cheers,
Ben


(Anna Ostropolets) #4

Just as a remainder, Danish ICD10 can be added to vocabularies so that additional codes are stored in the system with proper concept_ids and relationships. The same was done, for example, for Korean version(Adding KCD7 code (Korean ICD-10 ) to the OMOP vocabulary). The only thing is that a good translation of Danish ICD10 is needed.


(Anna Ostropolets) #5

Also, although we’re building a system to reliably connect ATC to RxNorm, it’s highly suggested to convert the source drug vocabulary (which as far as I’m concerned you have) and map it to RxNorm/RxE. In this way, you’ll be able to capture much more granular information about drug exposures.


(Benjamin Skov Kaas Hansen) #6

Great. This would be useful. When we get to it, I’ll raise my hand to understand the practicalities of that.

Regarding ATC->RxNorm/RxE, I’m not sure I follow. Our data dump with prescriptions and administrations uses ATC to encode ingredients. We also have free-text descriptions with brand names and other stuff; this is not of immediate use for us at the moment, so we’d probably defer mapping these components for now. Strengths are given as (fairly) structured data with units, and that we will definitely map. Does this make sense?

Cheers,
Ben


(Anna Ostropolets) #7

Totally does. So, if you want all this additional info, you need to map your source prescription/administration records with ingredients, doses, forms etc to a standard vocabulary (which is RxNorm or RxNorm Extension). ATC will only give you the ingredients.


(Vojtech Huser) #8

It is interesting to see NPU used for lab. Can you share how many distinct codes the data has (the granularity of it) (are we talking 300 codes or 30 000 codes). Also, are units implied by (subsumed within) the NPU code?


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