Stream: OMOP + FHIR Terminologies
Topic: Loading OHDSI Athena extracts to FHIR
Craig McClendon (Mar 10 2022 at 00:28):
OHDSI/Athena allows you download ~60 different terminologies in a common model (as CSVs) - including many commonly used in FHIR (CPT, DRG, various flavors of ICD, SNOMED, LOINC, NDC, RxNorm, etc.)
The HAPI cli tool can process the direct extracts from SNOMED, LOINC, and ICD10 into a HAPI JPA server. I am curious if anyone's looked into extending the HAPI CLI too to process the Athena extracts - or to load them via some other means.
@Michael Lawley
Davera Gabriel (Mar 10 2022 at 13:08):
Craig McClendon said:
OHDSI/Athena allows you download ~60 different terminologies in a common model (as CSVs) - including many commonly used in FHIR (CPT, DRG, various flavors of ICD, SNOMED, LOINC, NDC, RxNorm, etc.)
The HAPI cli tool can process the direct extracts from SNOMED, LOINC, and ICD10 into a HAPI JPA server. I am curious if anyone's looked into extending the HAPI CLI too to process the Athena extracts - or to load them via some other means.
Michael Lawley
great question @Craig McClendon ... @Joe Flack @Shahim Essaid @Sigfried Gold let's follow!
Michael Lawley (Mar 10 2022 at 23:55):
I have no idea how complete these extracts are, but I would very much doubt that a SNOMED extract would contain sufficient detail to support a FHIR terminology server providing sufficient support for it.
In general we prefer to transform from the publisher's original distribution format otherwise there's ample opportunity for loss of information going from, for example, LOINC -> format "X" -> FHIR CodeSystem.
I'll also go a step further with SNOMED by noting that the Athena ingest process that combines International, US and UK does things that are not guaranteed to maintain the integrity of the relationships.
Craig McClendon (Mar 11 2022 at 19:14):
The model is pretty generic and captures rich detail.
https://github.com/OHDSI/CommonDataModel/blob/v5.4.0/inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_ddl.sql
There are tables for:
VOCABULARY
CONCEPT
DOMAIN
CONCEPT_CLASS
CONCEPT_RELATIONSHIP
RELATIONSHIP
CONCEPT_SYNONYM
CONCEPT_ANCESTOR
SOURCE_TO_CONCEPT_MAP
DRUG_STRENGTH
I can say that the SNOMED hierarchies and attributes appear to be represented.
But I'm not a SNOMED nor terminology expert, so I don't know what I don't know.
The idea of being able to pull all of these in from one source is compelling though:
https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:sidebar
Joe Flack (Mar 14 2022 at 20:49):
@Davera Gabriel thanks for sharing. I guess it's not a huge deal for me if HAPI doesn't support natively. I'm not necessarily against the QC mentality here. The transformations necessary to get from this format into FHIR JSON are not too bad, but it'd certainly save time on the implementer end if they were supported.
Last updated: Apr 12 2022 at 19:14 UTC
