Page History
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Contribution | Contributor | |||
ACT V41- OMOP Ontology | Michelle Morris (University of Pittsburgh) Mike Mendis, Jeff Klann, Reeta Metta (Mass General Brigham) | With i2b2 interface, using ACT-OMOP Ontology, queries can be run against OMOP data with OMOP table view structure. For information on installing and running queries using ACT-OMOP Data model | ||
| ACT v4 Postgres bugfixes | Ambreen Zaver | Bugfixes in time interval calculation (for age and age-at-visit) in ACT v4 ontology for Postgres. New Webclient User Interface | Nick Benik (Harvard Medical School) | The new web client version eliminates usage of YUI, uses the latest versions of JQuery, Bootstrap 5 and Golden-Layout libraries |
Detailed Documentation on New Features
User Registration Tool
There is a new user registration tool that can be enabled in the webclient. It allows users to request an i2b2 account that can then be activated by an administrator. It supports manual entry of user information through the form shown below, or automatic population of user information through SAML.
Documentation on this new feature is here: 6.5a i2b2 Webclient User Registration
SAML Authentication
i2b2 now includes support for SAML-based enterprise authentication via an institutional Identity Provider.
Detailed setup instructions are in Chapter 8 of the Installation Guide.
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ACT Version-4.1 OMOP Ontology data load
ACT V41OMOP metadata and CRC scripts along with OMOP views are now available for load into i2b2 db schema.
The CPT4 ontology table is not included with i2b2 due to AMA restrictions on redistribution of CPT code information. Contact the ACT team to get a copy if your institution is an AMA member.
Ontology tables load process.
- Download and extract the new install zip package from "Download Binary Distribution" section of https://www.i2b2.org/software
- Edit the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\db.properties file to update the project properties to 'ACT-OMOP'; example: db.project=ACT-OMOP
- From the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata folder, run the ant command: ant -f data_build.xml db_metadata_load_data
- This will execute the SQL scripts from the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act\scripts\<db type> folder and will create and load ACT-OMOP Ontology metadata tables
- You can now verify the new Ontology by logging into the web client.
OMOP views and Concept dimension load process
- From the edu.harvard.i2b2.data\Release_1-7\NewInstall\Crcdata folder, run the ant command: ant -f data_build.xml db_demodata_load_data
- This will execute the BUILD_ACT_OMOP_Views _<dbtpye> script from the edu.harvard.i2b2.data\Release_1-7\NewInstall\crcdata\act-omop\scripts\<db type> folder and will create the OMOP views under the Views section in the database.
- In addition, the corresponding ACT-OMOP concept_dimension data is populated by executing the scripts form the crcdata.zip folders.
2. You can now run queries against the OMOP data from the webclient
| Note |
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Delete your Patient_dimension and Visit_dimension tables before executing the crc scripts. The OMOP views will build these as Views |
Totalnum counts execution
Load and execute file totalnum_usp/sqlserver/totalnum_fast_prep_OMOP.sql and run the following command:
exec totalnum_fast_prep_OMOP 'observation_fact','dbo','@
When finished, verify by checking that c_totalnum columns in your ontology tables contain numbers. These total counts will be visible in the ontology browser in the web client for 2b2 users with DATA_AGG user permission.
| Info |
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Ontologies derived from visit_dimension or patient_dimension top folders will not have counts because of the way these terms are defined and cannot be rolled up. |
SAML Authentication
Improved Totalnum Scripts
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