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.
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.
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.
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.
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
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:
Introduction
Review previous efforts
Share ongoing efforts and brainstorm new ideas and solutions
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
Improve the hierarchy among vaccine concepts
Check the mappings from source concepts to standard concepts to ensure the mappings are correct without losing useful information.
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.
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.
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!
