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Pancreatic Cancer OMOP compatible database

Dear OHDSI community,

I am a graduating oncology fellow at Stanford, soon to be a GI Oncologist at Northwell Health specializing in pancreatic cancer. I aim to build a large curated database of patients with pancreatic cancer, and then explore whether differences in survival exist among centers, and whether those differences relate to several clinical and molecular covariates. To facilitate analyses across centers I was thinking of building the database with a OMOP CDM. Much of the data input data I will be using lie in the hospital’s EMR, but these data need to be curated (to be accurate/reliable), added to new data that arise when I see patients, and then stored somewhere (to be aggregated/analyzed) to be analyzed with other institutions.

I would appreciate advice from the community for how to accomplish the above, i.e. to build an OMOP-compatible database from an existing EMR to analyze data across centers.

I did a PhD in genomics and comfortable in perl/R, am a novice in mysql. I learned about OMOP last week at Stanford’s clinical informatics conferences, thank you to those who presented there.

Dan King MD PhD


We are working on an extension to OMOP to help it better support oncology data. See here:

We have a couple of sub-workgroups. Sounds like it would be great for you to participate. Maybe you could start by attending the Development Workgroup to discuss you plans to ETL to the OMOP CDM.

1 Like

Hello @Dan_King,

Some links to start:

I join @mgurley in inviting you to participate in Oncology WG. Oncology extension is under active development and would benefit from your input. It would also make OMOP CDM better tailored to oncology research, including your use-case.


Excellent. The Oncology Tutorial course is just what I was looking for! https://github.com/OHDSI/OncologyWG/wiki/Oncology-Tutorial

Great, look fwd to joining you in a subsequent meeting. -Dan

Hello @Dan_King, Below are link to the various Oncology WG calls that you may find interesting and also please feel free to bring your questions to the WG discussions as we have SMEs from various organizations attending these discussions that can share their experience on the Oncology OMOP.

OMOP CDM Oncology WG – Genomic Subgroup Meeting: Every Tuesday at 9 am ET (Meeting Link)

OMOP CDM Oncology WG – Development Subgroup Meeting: Every other Wednesday, 10 am ET. Next meeting is on May 12th : (Meeting Link)

OMOP CDM Oncology WG – CDM/Vocabulary Subgroup Meeting: Every Thursday at 1 pm ET: (Meeting Link)

hi @Dan_King,

While you are still at Stanford you can request access to our STARR-OMOP database.


We also have youtube videos to guide you through so you get more familiar

Those videos are not a replacement of the wonderful EHDEN academy but it will be helpful to guide you for our setup at Stanford.

Welcome to the journey!