New OHDSI github repository

Developers
1

Hi,

We are developing a new algorithm/tool to query OMOP data. The tool may benefit the broader OHDSI community.
Is that possible to host the code under OHDSI github (Observational Health Data Sciences and Informatics · GitHub)?
What is the process to do it?

Thanks!

Yupeng

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2

There’s no formal procedure for this, but I can create a repo for you if you provide the requested repo name and your github user name. I guess there are two requirements for the software

  1. Open source
  2. Runs against the OMOP CDM (when applicable)

What language does the tool use? R? Python?

3

I bet on R… It’s my guess

4

Thank you! @schuemie

Merck and Amazon are working together to develop a tool that can translate user’s question to SQL query and directly retrieve the result from OMOP data.

It has a similar concept with Criteria2Query Criteria2Query, but it is a deep learning model with higher accuracy and flexibility. The workflow does not depend on Atlas.

We also have a set of training data (user-generated questions and corresponding SQL queries) we can include in the github repository. The training data can be used for more general Text-to-SQL purpose.

Can we call it “NL2SQL-OMOP”? (Changing it to NOSTOS, “navigate omop-structured data via text-to-sql" based on suggestion from Chris)
The github users are: miguelrc1, liyupeng111, Weilin37.

cc @gregk

5

Mostly python

6

I wonder if ‘NL2SQL-OMOP’ is too generic? Do you think you could come up with a project name for this? Examples are CIRCE, ACHILLES, HADES, CAPER, etc.

7

How about “navigate omop-structured data via text-to-sql (NOSTOS)”?

8

That works for me (not that I have any say in this :slight_smile: ) and if there are other implemenattions/efforts to create a simiilar function, the other impl can come up with their own name.

9

I’ve created the Nostos repo and have made miguelrc1, liyupeng111, Weilin37 repo admins.

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