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Preparing for COVID vaccine codes in the vocabulary and modeling in the OMOP CDM

Vocabulary Users
#7

Friends:

There are Standard RxNorm concepts:

37003436 “SARS-CoV-2 (COVID-19) vaccine, mRNA-BNT162b2 0.1 MG/ML Injectable Suspension” (Pfizer BioNTech)
37003518 “SARS-CoV-2 (COVID-19) vaccine, mRNA-1273 0.2 MG/ML Injectable Suspension” (Moderna)

They are not mapped yet. In particular, NDC 42796198 “MODERNA COVID-19 VACCINE - cx-024414 injection” and 42797616 “rna ingredient bnt-162b2 .23g/1.8mL INTRAMUSCULAR INJECTION, SUSPENSION” are not. There are no other NDCs in the system, yet. We will hunt that down and fix it up.

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#8

@Christian_Reich any idea of when the mapping between NDC and RxNorm might come into the vocabulary :slight_smile: I’m waiting for it before we do an update of the vocabulary in our network.

#9

Hi @cukarthik,
we are currently composing a hopefully comprehensive package that is supposed to cover SARS-CoV2 vaccines and monoclonal antibodies. See also this github issue.
We aim to include CVX, CPT4, HCPCS, NDC, RxNorm and maybe also early ATC codes (meant to be released in 2022).
This all means we also need to make sure the dependencies work out and go through anyway necessary refreshes besides only the vaccine codes. The bulk of the work will probably happen during February and we hope that by beginning / mid of March we can release most of the vocabularies involved.
~ Mik

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#10

Well, generic coding at the source is an issue. Would @Christian_Reich, @mik, or @Dymshyts please provide some mapping guidance? In our source data, we have COVID-19 vaccine data coming across in free text string. Which concept_ids should I map the following:

  • Pfizer, SARS-COV2 (COVID-19) VACCINE

  • Moderna, SARS-COV2 (COVID-19) VACCINE

#11

Pfizer:
37003436 SARS-CoV-2 (COVID-19) vaccine, mRNA-BNT162b2 0.1 MG/ML Injectable Suspension

Moderna:
37003518 SARS-CoV-2 (COVID-19) vaccine, mRNA-1273 0.2 MG/ML Injectable Suspension

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#12

Only now I’ve realized why I don’t really like this mapping:

It’s valid while the only formulation exists. Let them introduce a lower dosage or something else, we are screwed up. For sure, official mappings will be fixed, but it’s an additional work and a big pain to constantly review the custom mappings done here and there.

But the problem is that we don’t have any better option - CVX is very specific too (or very general).

So this is another reason to build a homemade vocabulary for vaccines.

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#13

Hi Alexander,

What would be better - using the official mappings if they could be more easily maintained, or building a homemade vocabulary?

I might be able to maintain the official mappings automatically. I have the technology to remap automatically (it’s new).

Also, out of curiosity, why would a custom vocabulary not also require updating if dosages were changing?

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#14

Probably if they introduce, let’s say, child dose, the vaccine will have different concentration. So we will be able to reflect it using RxNorm.
On the other making a homemade vocabulary is tempting idea as we can fully control it.
But it also requires more maintanance and effort.
For now I would stick to RxNorm, so users would be able to map their records to standard concepts.

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#15

Thank you for the concept_ids, @Dymshyts!

I have watched the source coding for data elements related to Covid evolve over time. When COVID-19 was first identified as a disease in our EHR source data, it was an internal custom text string mapped via an internal mapping table to multiple SNOMED codes. The EHR now maps to the ICD10CM codes for COVID-19 disease. We also had lab Measurement data coded to custom, internal identifiers that are now all mapped to appropriate LOINC codes. I hope the drug coding will also evolve into standard coding. If not, I will post new source values as they appear in our data :slight_smile:

#16

Well, there’s already a standard coding:
CVX is already in OMOP Vocabulary.
CPT4 is going to be available in Athena tomorrow
what about NDC @Alexdavv?

And RxNorm and CVX makes a standard vocabulary for vaccines.

#17

I was talking the source data being coded with a national terminology versus the internal custom coding the EHR is using now :slight_smile: I searched for the CVX, CPT4, NDC and RxNorm codes at our source. None were found. I only found the text strings

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#18

Actually both. RxNorm provides specific drug products, CVX works on a high level, while homemade vocabulary can help join everything into one system. So the mappings is not the key problem.

Sounds very interesting. Want to show it?

We’d not map to the specific dosages unless the source explicitly states it.
Moderna would be mapped to “COVID-19 mRNA-1273 spike protein vaccine” without indication of the entire formulation/dosage.

Righ, it will work for official vocabularies where every other code is the entire drug product.
As for custom mapping, “Pfizer, SARS-COV2 (COVID-19) VACCINE” may change the meaning over time. So once it happened, we need to get back to all the ETL done and review it.

It was released with new codes/mappings.

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#19

@Alexdavv

Yes, sure - you can see the description on www.dynaccurate.com. We’re currently leaving the funding research program in three weeks and then we can distribute the technology. I’d be very happy to set up a test for OHDSI.

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#20

Hi @mik, I just wanted to check if you are on track for the bulk of the work in Feb and March. Unfortunately, 2022 is too late for us. Is there a way to move up the time line b/c COVID vaccines are being coded as CVX, CPT, and RxNorm in EHR systems in the US and without these mappings it makes it difficult on the analytics side. Thanks!

#21

Karthik, can you elaborate on the CPT codes you mention. This page (Find your COVID-19 Vaccine CPT® Codes | American Medical Association) shows codes 0001A and 0011A. But are those modifiers (those only have two characters) in addition to CPT codes 91300 to 91303.

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#22

are already in OMOP vocabulary

Vocabulary refresh with SNOMED domain adjustments
#23

Oh, great to hear! The last version I downloaded didn’t have it or had missing relationships. Now the only piece is the CVX to RxNorm mappings, so we can use one vocabulary for drug analyses.

#24

@Alexdavv or @Dymshyts

I found another custom source value which lacks a code, "JOHNSON & JOHNSON, SARS-COV2 (COVID-19) VACCINE ". What’s the appropriate concept_id for it?

#25

Here you are:
https://athena.ohdsi.org/search-terms/terms/739906

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#26

Thanks, @Alexdavv!

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