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Need help and guidance to implement CDM

Implementers
#1

Hello,

I have introduced myself before, but still quite new to OHDSI. I have been watching activities and reading materials to understand CDM and OMOP. I have acquired SEER-Medicare data and now is the time to practice and implement OHDSI approach and tools as a RWD infrastructure for my company. I appreciate any help and advice. I’d really appreciate if someone accepts to show me how to start and guide me through different steps.

I have MD and PhD of epidemiology. I have been involved in number crunching and data analysis at academy and industry. I use R and Stata and I am familiar with python, database structure and sql commands somehow. I have a good IT and database support at my company for IT technical aspects.

Thanks,
Mehrdad

#2

Hi Mehrdad!

Welcome, welcome! As they say, “A journey of a thousand miles begins with a single step.”

To start, what does your technical stack look like? Are you using AWS by any chance? @JamesSWiggins has an incredible reference architecture available and can point you to his CloudFormation templates.

If you’re not on AWS, tell us a bit more about your environment. What kind of database layer are you using? What kind of analytics layer do you have? @Chris_Knoll, @anthonysena, @Ajit_Londhe, and @Frank are friendly folks who can direct you to the right documentation for your architecture.

Best,
Kristin

#3

Hi Kristen,

Thanks for the reply. I never used AWS (any web server). We are planning to save the data on a local server/database. I don’t know the answer to your questions but I would be happy to followup with my IT colleagues. Would you or other colleagues send me some materials to study?

Thanks,
Mehrdad

#4

The SEER Medicare data can’t be placed on any cloud server according to the data use agreement. Just FYI. Part of the application asks for the location of the data.

1 Like
#5

You should also talk to people in the oncology workgroup (@rimma @mgurley). They are wrestling with some issues specific to oncology data. For example, one challenge is mapping the SEER location, histology, and behavior information into a single standard concept (i.e., lung = location, 9050, 9051 and 9052 might indicate “mesothelioma”, and “/3” would be used to indicate malignant). These 3 ideas don’t fit neatly into one standard concept yet, as far as I am aware. I believe people are working on that and there may be something available for use or testing. LOINC codes can be used to map other oncology features like grade, stage, etc.

1 Like
#6

Thanks to @Dymshyts and his team, precoordinated standard concepts corresponding to the SEER combinations of histology/topography/behavior are in the OMOP vocabulary, ready for testing. Please use these documents for the background information and ETL instructions:

http://www.ohdsi.org/web/wiki/lib/exe/fetch.php?media=documentation:oncology:etl_instructions_for_icd-o_code_mappings.docx

Don’s hesitate to reach out.

#7

Thanks!
Mehrdad

#8

Hi Mehrdad,

The CDMBuilder tool (link below) has ETL for SEER → CDM v5.2. It is windows application and it supports MS SQL and Amazon Redshift databases. If you need help with CDMBuilder just let me know.

Thanks,
Anton

#9

Thanks!
Mehrdad

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