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Use of Python in OHDSI projects


(Ildong Lee) #21

i’ve been interested in using python for my research as well. plz keep me in the loop!

(Alexander Sivura) #22

Hi @MaximMoinat May you share an ETL example in Python with me too? I’m working on ETL for EHR data now and use Python as a main language.

(Bell Eapen) #23

I started pyomop before I saw @jbadger3 's inspectomop. pyomop is similar but may be easier to extend for ETL and machine learning. https://github.com/dermatologist/pyomop (I have not tested it much yet).

(Hung Do) #24

Hi all and @jbadger3 ,
Thank you a lot for suggesting different packages. I spent sometime studying both pyomop and inspectomop.
I am currently more inclined to the idea of inspectomop, which uses SQLAlchemy to connect to all database back-ends. Our database may not grow over 500GB very soon, however, we might need to move to Redshift in order to allow connections from multiple users. (Another reason is that I am not an expert in SQL anyway, so I would rather learn SQLAlchemy)

In contrast, I think pyomop is still using the raw SQL queries which are stored in the file sqldict.py. I am wondering how this package is easier to extend for machine learning? I guess that after each query, we just convert the result to a dataframe (which both packages offer) and then use the dataframe for data exploration/machine learning?

By the way, @jbadger3, thank you for your long insightful reply. Are you still updating the package on your personal repos, or have you completely migrated to OHDSI’s repos?
(I downloaded it from your personal link 1 or 2 weeks ago)

Cheers and have a nice weekend to all,

(Maxim Moinat) #25

Great to see developments in Python packages for OHDSI.

Sure, a lot of what we develop at The Hyve is open source: https://github.com/thehyve/ohdsi-etl-caliber