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Vaccine concept mapping improvement

I definitely would like to be involved with this group. I manage the CIEL dictionary for OpenMRS and have published an open source concept dictionary (mapped to SNOMED, ICD-10, CVX, RxNORM) for COVID including vaccination concepts (including global vaccines) here: https://app.openconceptlab.org/#/orgs/CIEL/collections/COVID-19-Starter-Set/

There are also other vaccine concepts (unrelated to COVID) which are included in the core CIEL concept database: https://app.openconceptlab.org/#/orgs/CIEL/sources/CIEL/

Someone should update the CIEL load in Athena.

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April 21 meeting summary

  • Adam presented the decomposition of four pneumo CVX codes.
  • Why are we decomposing? We want a use case driven hierarchy and decomposition will help us identify the important attributes that should be considered when building a hierarchy.
  • In past work on vaccines vocab team did not infer attributes that were not explicitly stated in CVX concept name. Possibly better to decompose branded drug rather than CVX code.
  • In the case where CVX codes have only one branded drug form the decomposition is simple. For “unspecified” case the decomposition is less clear.
  • Application – (1st, 2nd, 3rd dose) should be handled from the cohort building perspective and not encoded in the vocabulary.
  • Ingredient, brand, and vaccine type are important attributes for use cases
  • RxNorm separates dose of each individual ingredient. Is the dose of each individual ingredient important for vaccine use cases?
  • A lot of vaccine records are recorded in source data as procedures with very limited attribute information.
  • Ideas for improvements could be made in the near future
  • How much vaccine content is not represented as CVX?
  • CVX ‘maps to’ RxNorm in a small number of cases: when there is an exact equivalent

April 28 meeting agenda

  • Decomposition update: Denys will present decomposition of Merck branded drugs
  • Review use cases and attributes required by use cases
  • Roadmap update and discussion:
    • Fix incorrect vaccine mappings identified by Denys
    • Introduce CVX Vaccine Group
    • ATC-RxNorm (CVX) hierarchy improvements – where to start
    • Review CVX “maps to” RxNorm relationships
    • Refresh CVX descriptions

Hi @Adam_Black ,

I’ve been following this thread and the vocabulary work from afar. The 6am MT meeting time is just too early for me. Here in Colorado, and other Epic data I’ve seen, have most vaccine data coming across as string text and not coded. Is providing guidance on mapping these data to standard concept_ids part of this WGs role? I define “guidance” as the process on mapping a string text. Something along the lines, map a drug based on the following attributes with #1 being the most important:

  1. active ingredient
  2. disease prevented
  3. amount of ingredient
  4. dose form
  5. route
  6. preservative or preservative free
  7. live or attenuated
  8. etc
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@MPhilofsky:

Short answer: Yes.

Right now, we are building the grand truth table with all codes and all their attributes, so we can create a target structure. It’s a mess.

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Hi everyone,

Given that we have a significant amount of decomposition work to complete I would like to adjust this meeting to every two weeks instead of weekly. This will give us more time to make progress on the decomposition work before we check in again. Our next meeting will be 5/19. Denys Kaduk and I will continue our work decomposing branded vaccine products. If anyone else wants to coordinate with us on this work please reach out to me or Denys directly.

Thanks again for your participation in this group! I’ll post the agenda for the 5/19 meeting here a few days before we meet again.

t