Vocabulary mapping for Covid vaccination given

Vocabulary Users
1

Hello !
We are wondering how to map the Covid vaccination status of a patient admitted to the hospital. Here is the information we have for patients:

  • no vaccination date
  • vaccinated / not vaccinated / ongoing vaccination
    for some patients :
  • number of doses
  • the brand of vaccine
  • a multi-brand vaccination scheme

We came up with the following concept for flu vaccination:

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But we haven’t found a concept to use for the Covid vaccination?
Any help would be appreciated,

The team of the CHU of Montpellier (France)

2

Hi, @Dominique. Currently in most cases in OMOP we use CVX codes for vaccination or their mapping to RxNorm/RxNormExt, when relevant CVX codes are non-standard and with “maps to” links. For example, in case of “COVID vaccination” using any SARS-CoV-2 vaccine it’s possible to use CVX 213 SARS-COV-2 (COVID-19) vaccine, UNSPECIFIED (Athena)

3

Hello, @Dominique

A small addition to the previous answer: all the COVID ETL instructions could be found on github. Vaccines are well covered.

If you are uncertain about dates, you can map vaccination as historical content. Use Maps to + Maps to value links to populate observation_concept_id (historical concepts) and value_as_concept_id (vaccine itself).

4

Thanks a lot for this clarification. This is very helpful.

5

Thank you for this precision !