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Vaccine concept mapping improvement

Vocabulary Users
#5

Hi,

I work with Lixia and Yupeng at Merck and would like to help with this effort as well.

Adam

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#6

We are going to set up a regular meeting to discuss the issues and work on solutions. Please send me a message if any one is interested. Thanks!

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#7

Hi Yupeng, some members of the Vocabulary team are currently working on improvements in the vaccine hierarchy. We would be very interested in learning about your use cases. Would you like to let us know when you are going to meet?
Thanks ~ Mik

#8

The first meeting is schedule at 8-9am March 17th (US Eastern Time). If you are interested, please send me your email address via message. I can forward the meeting invite.

Tentative agenda:

  1. Introduction
  2. Review previous efforts
  3. Share ongoing efforts and brainstorm new ideas and solutions
  4. Extend to regular meeting?
  5. Next steps
#9

We had a good meeting this week and will continue the discussion in following weeks at the same time (Wednesday 8-9 am US Eastern Time).

During this week meeting we presented some quality issues:

  • ambiguity of domain assignment
  • lacking and imprecise mapping from non-standard to standard concepts
  • using retired CVX codes
  • missing ATC relationships

The vocabulary team also shared some ongoing efforts to improve the hierarchy of vaccine concepts, e.g. integrating CVX into ATC hierarchy.

For next step, we will collect a list of requirements from data scientists’ perspective, discuss them, and brainstorm solutions in next week meeting.

Thank you to the people who joined. Please add or correct anything I missed.

Everyone is welcome to join. Thanks!

Yupeng

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#10

March 24 Meeting summary

This week we reviewed the problems associated with integration of CVX with the drug hierarchy. A draft document is in preparation.

The OHDSI vocab team uses a “top down/high level” approach to integrate CVX with ATC, RxNorm and other vaccine related vocabularies. The Merck team adopted a bottom up data driven approach by specifying the vaccine concepts, relationships and their issues occurred in real world databases. These two approaches complement each other and allow us to have a thorough investigation in vaccine vocabularies in OMOP CDM.

Yupeng highlighted three major opportunities for vaccine concept improvement

  1. Improve the hierarchy among vaccine concepts
  2. Check the mappings from source concepts to standard concepts to ensure the mappings are correct without losing useful information.
  3. Map all vaccine exposures to the drug domain.

Meeting agenda for next week 3/31

  • Denys will present findings from the manual review of “maps to” relationships
  • Mik will present slides explaining current thinking about integration of CVX with RxNorm and ATC

Reply to this forum post or email Yupeng or Adam if you would like to join this meeting.

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Vaccine Mapping - Current State and QA
#11

@yupengli @Adam_Black

I would like to attend this meeting. Please send me the meeting information to qi.yang@us.imshealth.com

Thanks,

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#12

Hi Adam, I would also like to join this meeting, many thanks!

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#13

Dear all, thank you very much for joining the meeting today. We will skip the next week meeting and continue on April 14th.

#14

Hi Adam,

This is Licong Cui from UTHealth. I would like to join this meeting. Please send me (licong.cui@gmail.com) the meeting information.

Thanks,
Licong

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#15

Hi Adam,

My name is Rashmie Abeysinghe. I’m also from UTHealth. Please send me (rashmie0045@gmail.com) meeting information as well.

Best,
Rashmie

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IMPORTANT: Use caution when using Covid-19 vaccine ingredient concepts
#16

Hi Adam,

This is Fengbo Zheng from UTHealth. I would also like to join the meeting. Please send me (fzh229@gmail.com) the meeting information.

Best,
Fengbo

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#17

Hi everyone,

Our next meeting will be Wednesday April 14 at 8 am Eastern Daylight Time (UTC-4). The link to the meeting is available on theOHDSI workgroup website next to Vaccine Vocabulary WG.

Agenda

  • Introductions
  • Adam will present
    • Recap of work done so far
    • User stories to motivate an improved vaccine hierarchy
    • A first draft proposal for CVX/ATC integration
  • Discussion

After 4/14 we will move future meetings and collaboration to the OHDSI Teams environment which will allow us to share documents more easily.

See you Wednesday!

Adam

#18

Welcome, Licong!

#19

The file I’ve mentioned at the meeting we’d started working on. It’s Branded product-based.
@Adam_Black I hope it will help.

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#20

April 14 meeting summary

Adam presented use cases/user stories that we would like an improved vaccine hierarchy to support including

  • Ability to build vaccine concept sets using descendent relationships in ATC, CVX, and RxNorm
  • Ability to target strains, brands, and vaccine type using the hierarchy

Adam introduced a rough draft of a complete integration between CVX and ATC vaccine concepts which is available in the vaccine vocabulary OHDSI Teams environment.

The presentation was followed by a discussion about how to build the hierarchy. Christian suggested decomposing vaccine concepts into component parts or attributes.
Attributes included ingredient/ingredient class, dose, form, brand, application (1st, 2nd, 3rd, etc), NDC codes, live-attenuate/inactive, recombinant, child/adult.

Adam and Denys will perform the decomposition for some pneumococcal and HPV vaccines and present the results at the next meeting on April 21.

Note that there will be a new meeting link for next week and document sharing will occur in the Vaccine Vocabulary Workgroup OHDSI Team. All future meetings will be recorded and made available in the OHDSI Teams environment. Joining the Teams environment is not required to attend meetings but is required to share documents. To join follow the links under “Collaborate in MSTeams” on https://www.ohdsi.org/
image

April 21 meeting agenda

  • Open feedback on vaccine hierarchy use cases/user stories
  • Adam and Denys will present example vaccine decomposition
  • Discussion about challenges and next steps

Thanks for sharing the branded product decomposition @Alexdavv! Thanks to everyone for your participation!

Adam

#21

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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#22

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
#23

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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#24

@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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