Hi everyone!
I recently managed to set up the “default” OMOP CDM schema on a PostgreSQL database, thanks to the .sql scripts available in the OMOP Github repository and a Python script aiding the insertion of Athena vocabularies.
I used the word “default” above, because I’m trying to set up a OMOP compliant database for a project in which also biomedical images will be collected. In fact, I’d like to implement a OMOP schema extension as the one that was conceived by the Bioimages WG (https://www.ohdsi.org/wp-content/uploads/2023/10/6-Park-BriefReport.pdf), but given that the linked paper provides only some structure for the implementation, I’d like to discuss about the actual PostgreSQL implementation with someone that possibly had my same necessity.
Also, once the database will be set up with the proper schema extension, I’ll need to interface it with a Python project. I’d like to know if someone had previously worked with Python to interact with the database, to discuss about the best modules to use in order to create an Object-Relational Mapping of the tables (SQLAcodegen?), and to actually query the database with Python code (SQLAlchemy?).
Thank you for your time, any type of help is appreciated!