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cladteam / CCDA_OMOP_by_Python

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Proactive Value Sets (for JHU?) #89

Open chrisroederucdenver opened 1 month ago

chrisroederucdenver commented 1 month ago

Looking at the HL7 Spec.s I can see value sets used for the codes in different subsections. It's not clear where to find the contents, or how useful these are, but here's a start at a list of them, by (structure type, those names you see in the doc.s or the comments in the XML. They are often the values of component or entry).

chrisroederucdenver commented 1 month ago

These are in the VSAC and need OIDs to be found https://vsac.nlm.nih.gov/valueset/2.16.840.1.113883.1.11.12839/expansion/Latest The OIDs are in the doc.s where I found these names.

AdamLeeIT commented 1 month ago

@chrisroederucdenver Did you get to peek at the oid_lookup.py in branch 88? I think it will be a fun conversation (like legit fun) OID 2.16.840.1.113883.1.11.12839 leads to UCUM and codeSystem 2.16.840.1.113883.6.8, and for contents (parsable) viola https://phinvads.cdc.gov/baseStu3/CodeSystem/2.16.840.1.113883.6.8

stephanieshong commented 1 month ago

ucum unit mappings should be already present in our valueset mapping table, we can transfer for CCDA use.

stephanieshong commented 1 month ago

which encounterType are you using? You need to let us know the encounter type data element values you are using or the codeSystem. For the following items please let us know the respective codeSystem, if not actual values you are extracting along with the meaning.
ProblemType value set Problem value set HealthStatusObservation HealthStatus value set

chrisroederucdenver commented 1 month ago

Adding OIDs to this list is on my ToDo. I'll comment and tag when I do.

This isn't urgent, but was meant as a conversation starter.

chrisroederucdenver commented 1 month ago

@stephanieshong @tannerzhang Links to HL7 docs and VSAC valueset pages added.

stephanieshong commented 1 month ago

@chrisroederucdenver - There are three different mapping tables we are currently managi7g:

  1. Vocabulary id mapping between HL7 and OHDSI ( i.e. OIDS to vocabulary_ids)
  2. Externally defined and managed terminology codes that OHDSI OMOP CDM harmonize into OMOP concept_ids
  3. valueset mapping data element entries that falls out of the externally managed terminology codes and falls somewhere in the area that the source data uses like custom defined terms, or like unit of measure UCUM codes, discharge status codes, race, ethnicity, and gender

If you are asking something else we should meet and make sure we are on the same page.

chrisroederucdenver commented 1 month ago

@stephanieshong this is about #3 valueset mapping, but not an immediate need. Closing for now.

stephanieshong commented 1 month ago

ok. Sound good.

chrisroederucdenver commented 2 weeks ago

Re-opening for Tanner's request to list value sets as in this FHIR document. https://docs.google.com/spreadsheets/d/1mBCswpIahjJMrGAz7dKNaChfGAbbgJDEpOZNT3wCFk4/edit?gid=736610689#gid=736610689