CODEWITHSUNDEEP
hl7-fhirohdsi-omop
John
John

Reputation: 3996

Are FHIR code systems available in OMOP from Athena?

FHIR seems to have implemented their own coding systems. For example, this was found in a Synthea patient:

          "valueCoding": {
            "code": "2106-3",
            "system": "urn:oid:2.16.840.1.113883.6.238",
            "display": "White"
          }

Which seems to be from: https://www.hl7.org/fhir/us/core/CodeSystem-cdcrec.html

I'm not seeing anything on the Athena terminology download page for this (login required).
https://athena.ohdsi.org/vocabulary/list

The code '2106-3' does appear in the standard download of terminology from Athena but as a LOINC code for a Choriogonadotropin test (so, not the same thing).

Are these FHIR terminologies available for OMOP in Athena (or elsewhere)?

Is there a place to download all of these FHIR terminologies in csv (or other bulk uploadable format)?

Upvotes: 0

Views: 171

Answers (1)

Lloyd McKenzie
Lloyd McKenzie

Reputation: 6803

The FHIR terminologies can be downloaded as XML or JSON. Some have hierarchy and relationships, so flat CSV files are harder, though I believe there's a proposal to add that to FHIR IG publication tooling in the future. Note that FHIR is a data exchange standard and the terminologies themselves are defined in a variety of places - some on http://terminology.hl7.org, some in the core FHIR specification and some in different FHIR implementation guides (which can be defined by anyone). As such, there won't be a single place to download content, though there are registries you can use to search and download large sets of them.

Upvotes: 1

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