feat: hackathon/create a knowledge graph using mock OMOP data (Team Sanofi US)

[PrithviPKamath]

For authors

Description

Created a jupyter notebook as a first attempt at inserting data from csv files in OMOP format into a knowledge graph (networkx). csv files are uploaded into a folder called 'DataFiles'
This notebook will have to be enhanced to either update PrimeKG or use both knowledge graphs together. (We tried an attempt at am creating an LLM, but it fails for now)
There are no changes to the front end or any other aspect of the application.

Type of change

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• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

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[lilijap]

Hi @PrithviPKamath, 👋

Thanks for your PR and creating a graph from the patient health record data! 🥳
How did you create these OMOP-standardized files from the initial spreadsheet, did you do it manually or used some scripts to do so?

I suggest considering an alternative path for these files/notebook. However, I'll defer to @awmulyadi to determine the most suitable location.

Thank you for your contributions!

[PrithviPKamath]

Hi @PrithviPKamath, 👋

Thanks for your PR and creating a graph from the patient health record data! 🥳 How did you create these OMOP-standardized files from the initial spreadsheet, did you do it manually or used some scripts to do so?

I suggest considering an alternative path for these files/notebook. However, I'll defer to @awmulyadi to determine the most suitable location.

Thank you for your contributions!

Hi @lilijap. Yes, the files were created manually since this was mock data. Converting real world databases to OMOP format would be a complete project in itself and my team does so in about 12 weeks time and make it available to downstream projects like this one. These files and location are temporary for the hackathon. Our databases are currently in Snowflake and with the right level of approvals you should be able to access them.

[lilijap]

Hi @PrithviPKamath, 👋
Thanks for your PR and creating a graph from the patient health record data! 🥳 How did you create these OMOP-standardized files from the initial spreadsheet, did you do it manually or used some scripts to do so?
I suggest considering an alternative path for these files/notebook. However, I'll defer to @awmulyadi to determine the most suitable location.
Thank you for your contributions!

Hi @lilijap. Yes, the files were created manually since this was mock data. Converting real world databases to OMOP format would be a complete project in itself and my team does so in about 12 weeks time and make it available to downstream projects like this one. These files and location are temporary for the hackathon. Our databases are currently in Snowflake and with the right level of approvals you should be able to access them.

Thank you for this update. I look forward to hearing from you and your team regarding the conversion!