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Vaccine concept mapping improvement

(Yupeng Li) #1


This is Yupeng Li from Merck. I am relatively new to real-world evidence and OMOP CDM.
When doing vaccine related outcomes research, I found a few obstacles and later listed some of them in the OHDSI symposium poster, “Quality assessment of vaccine concepts in OMOP common data model” https://www.ohdsi.org/2020-global-symposium-showcase-26/. @Christian_Reich have provided many good comments and suggestions during the Symposium.

Given the pandemic, upcoming covid-19 vaccines, and vaccine outcomes research needs, it becomes more and more urgent to have better hierarchy and mappings for all vaccine concepts. I’d like to follow up with the community to see if anyone is interested to improve the mappings and seek guidance on how to do it.



(Alexander Davydov) #2


Great job, very impressive!
We’re trying to build a hierarchy out of the Standard RxNorm, CVX and ATC: link1, link2. Cpt4/hcpcs is somehow out of the scope now.
The problem is that they provide the granularity of the different axes and to get the real standardization a new vocabulary would be a choice.

The source vocabulary mappings definitely need a big clean-up, but we started pay additional attention when adding/refreshing them.

Does it sound as a new working group? :smile:

Preparing for COVID vaccine codes in the vocabulary and modeling in the OMOP CDM
(Xintong Li) #3

Hi Yupeng,

Thanks for sharing the great work.
I am now working on the influenza vaccine concept with Read code in the UK and found a similar issue with the mapping. I’m interested in further work with the community to improve the mappings.


(Lixia Yao) #4

Alexander and Xintong,

My name is Lixia and I am Yupeng’s colleague at Merck. Thank you very much for you to share the same interests! We look forward to an opportunity to discuss with you further on this timely and important topic.

(Adam Black) #5


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


(Yupeng Li) #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!

(Michael Kallfelz) #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

(Yupeng Li) #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

(Yupeng Li) #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!


(Adam Black) #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.

Vaccine Mapping - Current State and QA
(Qi Yang) #11

@yupengli @Adam_Black

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


(Dermot Doyle) #12

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

(Lixia Yao) #13

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

(Licong Cui) #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.


(Rashmie Abeysinghe) #15

Hi Adam,

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


(Fengbo Zheng) #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.


(Adam Black) #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.


  • 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!


(Lixia Yao) #18

Welcome, Licong!

(Alexander Davydov) #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.

(Adam Black) #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/

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!