1.8.1a - OMOP - has anyone implemented this yet?

[RobSchuff]

Hi All,

We at OCHIN are looking to implement the i2b2 on OMOP feature. Has anyone deployed this yet? If so, any gotchas with install process or performance we should be aware of?

Thanks!

Rob

[diane...@transmartfoundation.org]

Hi Rob,

 

So far we know of the following sites that are running i2b2 on OMOP:

 

University of Virginia

Boston Medical Center

UC Irvine

UC San Diego

Yale

Rochester NY

 

I hope this helps!

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[mabaj...@mac.com]

Hello, Rob and Diane!

When I was at USC (University of Southern California) in 2022, we ran i2b2 v1.7.12a on OMOP, but we used a copy of our OMOP database using ACT ontology codes, not the ACT-on-OMOP ontology codes. (We had beta-tested the ACT-on-OMOP ontology back in 2020-2021, and we had issues, so we used the ACT ontology instead.) (I do not know what USC is currently running.)

Kind regards,

Mark Abajian

Mark Abajian, Independent Software Consultant
P.O. Box 8017, Glendale, CA  91224
Email  maba...@mac.com   |   Mobile  +1 (818) 726–0372

[mabaj...@mac.com]

Hello, Rob,

I see that you mentioned "gotchas". It's been a while since I implemented this, but one thing to remember is to set the multi-fact-table parameter in the Hive parameters. I'm sure that's mentioned in the instructions for i2b2-on-OMOP, and this is just a reminder.

Naturally, using "views" in your database/schema, you'll need to make sure that the names of your views are reflected correctly in your ontology tables. I believe that if you are using the bundled ACT-on-OMOP implementation from i2b2 v1.8.1a, you will find that the names of the views match with the settings inside the ontology tables. 

However, if you are building your own i2b2-on-OMOP setup with your own ontology tables, you will need to make sure that you are referencing your CRC views/tables correctly in your ontology tables. (This is true for any multi-fact-table implementation, not only for OMOP implementations.)

I hope you find this helpful. 

Kind regards,

Mark Abajian

Mark Abajian, Independent Software Consultant
P.O. Box 8017, Glendale, CA  91224
Email  maba...@mac.com   |   Mobile  +1 (818) 726–0372

[Sebi Metzler]

Hello all,

I'm a newcomer in the scene so forgive me if my questions are naive. I've been expirementing i2b2 with the end goal to enable cohort building against our intern OMOP data using the lovely i2b2 webclient.

I've first wanted to get a grip of using i2b2 "normally" and used the i2b2-docker images to get a working 1.81 server/db/webclient. This part worked great. The install guide to use the ENACT ontology seems to necessitate a different method of setting up the postgres database than the one which is probably used in the i2b2-docker images. I've been searching the internet whether somebody has already made a docker image of a postgres db suitable for use with act-omop into which I can just import the pre-existing OMOP data into. Does anyone if such a project exists out there?

If that is not the case, could I create an postgres database with the instructions provided myself and use that as a stand-in for the pg-db used in the docker image? Maybe my lack of experience and expertise shows and I'm totally missing something so I would appreciate if someone could jump in and tell me whether I'm even remotely on the right track.

Kind regards and all the best

Sebastian

[Jeff Klann]

Sebastian,

It looks like no one ever responded to this! Are you still trying to get this working? Yes, you can either install the OMOP database components inside the existing postgres Docker container to turn it into an i2b2-OMOP container or you can install postgres locally, load i2b2-data for OMOP on it, and tell the Docker container to use that. It's not a supported configuration yet, but I've gotten it working and Kavi & team are working on making it part of the release. If you'd like me to help you with either approach, send me a reply - I'll try to check the group more regularly.

Thanks,

Jeff