i2b2-on-OMOP With ENACT-OMOP Ontology v4.1

[Vincent Lee]

Hi all,

We are looking to implement this at our institution.  We have recently tried out our first i2b2 with out-of-the-box sample data for testing purposes. We are looking to leverage the I2b2 API on our institutional OMOP (V5.3) via this approach:  

https://community.i2b2.org/wiki/display/getstarted/i2b2-on-OMOP+With+ENACT-OMOP+Ontology+v4.1

Has anyone successfully implemented the i2b2 system using this type of setup? If so, will you be willing to share your experience with us?

Thanks

-Vincent

 

[mabaj...@mac.com]

Hello, Vincent,

My name is Mark Abajian, and I am more of a facilitator for i2b2/SHRINE users, not a direct user myself. I recently was assisting a hospital group on the East Coast to configure and deploy their i2b2 on OMOP setup.

Here are some caveats:

• You mention OMOP 5.3 for your institutional database, but the i2b2-on-OMOP documentation references OMOP 5.4. I'm not certain if that discrepancy is important or not.
  
• The i2b2-on-OMOP system for i2b2 version 1.8.1a is built on the ACT-on-OMOP ontology v4.1, which is based on the OMOP vocabulary (concept codes) from May 2023. Either your institutional OMOP needs to reflect that same vocabulary, or you should create a new copy of your OMOP database that utilizes that May 2023 vocabulary. You must use the same vocabulary in your OMOP database as is being used in the ACT-on-OMOP ontology.
  
• Going from the default "demo data" setup to an i2b2-on-OMOP setup is kind of like learning to drive a Ferrari after only having ridden a Vespa... lots more "moving parts".
  
• In the next couple of weeks, version 1.8.2 of i2b2 will be released, and my understanding is that the ACT-on-OMOP ontology will be updated to version 4.2. This will almost certainly be using a different version of the OMOP vocabulary, so you may want to wait until that is released before you commit to any new vocabulary for your OMOP database.
  

I hope this information proves useful. Visit abajian-consulting.com if you are interested in learning more about our services.

Kind regards,

Mark Abajian

Abajian Consulting, LLC
P.O. Box 8017, Glendale, CA  91224
Email  in...@abajian-consulting.com   |   Mobile  +1 (818) 726–0372