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OHDSI / Themis

Repository for OMOP CDM conventions as defined by THEMIS. These can be reference lists of concepts, pieces of standardized code for data generation or quality certification, and debates.
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Proposal: Clinical trial data conventions for OMOP CDM #196

Open soniaarau opened 4 years ago

soniaarau commented 4 years ago

The Clinical Trials Working Group proposes conventions for the OMOP CDM and Standardized Vocabularies to capture clinical trial specific data.

Our use case is the conversion of clinical trial data in CDISC SDTM format to OMOP, with a view to allowing trial planning optimization. SDTM was chosen as it is a clinical trials’ submission standard that is “required” by the FDA and PMDA, “preferred” by the China NMPA, and “accepted” by the EMA.

We advocate minimum changes to the OMOP CDM and Standardized Vocabularies to minimize impact on OHDSI tools like Atlas, whilst providing a value-add SDTM-to-OMOP conversion with minimum data loss.

Our proposals cover eight main topics for which there is currently insufficient support in the OMOP CDM and Standardized Vocabularies. They include introducing new concepts and modifiers, but no new CDM tables. Furthermore, we provide guidance for ETL developers where appropriate.

The attached document details our proposals for each of those eight topics, built on OMOP CDM v6 and the Oncology extension, with v5.3.1 backward compatibility.

We, the Clinical Trials Working Group would be delighted to join a CDM meeting to walk through these proposals.

OMOP clinical trial data conventions v1.0 July 2020.pdf

vojtechhuser commented 4 years ago

Very important proposal. Hopefully this will get discussed by the CDM group soon.

davedorr9 commented 4 years ago

I enjoyed reading this. I think you covered a number of important domains. The HL7 definitions for a research study are in process, and they may be very useful to compare against your suggestions here. https://www.hl7.org/fhir/researchstudy.html

clairblacketer commented 3 years ago

This looks great @soniaarau! I definitely want to get you on the schedule for 2021. We have an aggressive plan for Q1/Q2 to create a v6.1 but since your suggestions don't include any real changes to the model we can implement them at any time. How about joining our meeting to present on 2/16 at 1pm eastern?

labouz commented 3 years ago

@clairblacketer is there a way for others to join this upcoming meeting? I too work with clinical trial data and am trying to integrate the CDM with some difficulty. I would like to see @soniaarau and work group's modifications discussed.

vagarwal77 commented 3 years ago

@clairblacketer - we are currently working on transforming CDISC SDTM -> CDM -> CDM OMOP. I would also love to attend this meeting. Please share the details to join.

Daniel-Olson commented 3 years ago

@clairblacketer I too would like to join this working group if possible. We are mapping data from SDTM to OMOP and would like to contribute to the discussion. Thank you.

priagopal commented 2 years ago

I am trying to implement AE using OMOP. Please include me to the group as well.

tevariou commented 2 years ago

@clairblacketer Is there a follow-up to this proposal ? Will this be included with OMOP v6.1 ? Is OMOP v6.1 planed to be released in 2022 ?

priyame commented 1 year ago

@soniaarau do you have any updates on the proposal for the community ? I am working to map trial data to OMOP and would really appreciate any leads on the project. Thanks

clairblacketer commented 1 year ago

The necessary fields as listed in the proposal have been added in v5.4 and the oncology extension is now in v5.4 as well. These conventions should be added to the documentation.

katy-sadowski commented 1 year ago

I can bring this up for discussion in the next Clinical Trials Data WG meeting. I'm guessing to add to documentation we'd just put up a PR here to add a page to the Conventions tab on the CDM website?