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FHIR Vocabulary

(prasanth n.) #1

Hello, what is the process for requesting vocabularies to be added as part of the standard OMOP vocabulary?

In particular, we have a colleague at Northwestern that is very interested in doing this for FHIR.

I have searched the forums and closest thing related to FHIR I have come across is about a working group. Are there any plans in the near future to get FHIR added to the standard vocabulary table?


(Clark C. Evans) #2

What do you mean by FHIR Vocabulary? FHIR profiles could use all sorts of terminologies, such as ICD10, SNOMED, and such. Mapping FHIR resources to/from OMOP data elements be seen more as an ETL activity. However, I’m not sure exactly what challenges your colleague is facing. Could you be more specific?

(prasanth n.) #4

Apologize for not being too familiar with how FHIR works prior to posting the question.

Quick background on why I was asked the original question: my colleague was looking for languages spoken that weren’t part of the OMOP vocabulary, but found them in the FHIR US Core Profile. She wanted to know how to get the languages found in FHIR into OMOP.

(Christian Reich) #5


Those languages should all be in OMOP already. Like SNOMED CT, LOINC, RxNorm, ICD family, etc. Is there anything she wants we don’t have yet?

(Alona) #6

I wonder which of standard concepts one should go for while mapping following languages:
Acoli, Hupa, Valencian?

Somehow failed to fins in available vocabularies.
Thank you a lot for your time.

(Kristin Kostka, MPH) #7

If I’m reading your post correctly (which may be a big assumption): you are asking how to translate from specific languages into OMOP concepts? Yes?

If <500k terms, you could use Google Translate APIs to batch up unsupported languages and translate to a string in a supported language. Maybe someone from @nigam’s team could give you some insight on this approach. If you’re very ambitious, you could be the first to pioneer an OMOP vocabulary amendment to create concepts from each mother tongue into the common tongue. @Dymshyts @Christian_Reich @aostropolets could give you guidance. I would imagine our colleagues in Spain may have some concepts you could leverage for Valencian. @Rijnbeek could help connect you.

But more intriguingly, what kind of data is this? A Ugandan dialect, an Athabaskan dialect and A Catalan dialect. What do you map from? :smile:

(Alona) #8

Dear, Kristin,
you are right in your assumptions.
Examples I used are languages available in both PCORI and FHIR. In fact, Hupa are a Native American people in northwestern California. I expected to see standard OMOP concepts available at least for local to USA languages.

The hope was to get some of FHIR standards as part of standard OMOP consepts. At least for things not available in OMOP yet.
An example of language coding could be seeing from https://www.hl7.org/fhir/v3/AmericanIndianAlaskaNativeLanguages/cs.html

(Kristin Kostka, MPH) #9

Hi Alona,

I’m curious, are you aware of examples when a medical provider is logging a clinical encounter in one of these dialects? Or is the intent here to capture the native language of the patient?

We certainly care about what language patients speak but, in the data, we generally only see what the provider is communicating about the patient. If a provider isn’t logging health encounters in these dialects, we wouldn’t have OMOP concepts for these languages. OMOP concepts have to be used in practice to exist. We don’t translate OMOP concepts so a patient can see their clinical condition in their mother tongue. Does that make sense?

(Alona) #10

You are right. This is for specifying language spoken by patient.
Thank you for your time.