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1.7.13 Release Notes

i2b2 1.7.13 offers support for SAML federated login, enhanced security due to improvements found via an internal Veracode scan, a client-based user registration tool, support for Synthea synthetic data for testing, and a variety of other bugfixes and performance improvements.


Insert_Concept_FROMTableAccess  is designed to populate concept_dimenison table using the ontologies listed in table_access table records.
The stored procedure loops through the table_access  and inserts values from each metadata table (specified in the c_table_name column), when
c_dimtablename is set to 'concept_dimension'
Example usage: exec Insert_Concept_FROMTableAccess

I2b2-Synthea data Load

Synthetic patient data generated by Synthea can be loaded into i2b2. The Synthea SyntheticMass sample files have been converted to i2b2-ACT format, and scripts to load Synthea data from scratch are available here:

Synthea Load Process

  1. Set up an i2b2 project with the ACT ontology.
  2. Either download the SyntheticMass 63k sample in i2b2 format from, or follow the instructions below to load any Synthea dataset from scratch. This information can also be found on the Synthea-i2b2 Community Project page.
Loading Synthea data from scratch
  1. Download SyntheticMass Data, Version 2 (24 May, 2017) 
    • All data sets (1k, COVID 10k, COVID 100k) have been verified to work EXCEPT the 100k patients in the large SyntheticMass Version 2 download. 
    • The 100k patients in the large SyntheticMass Version 2 download needs an extra step to delete invalid records before import. In this case, download to your disk, and then run "synthea_cleanup <directory-for-synthea-csv-files>" The fixed csv files will be in <directory-for-synthea-csv-files>/fixcsv.
  2. Set up an i2b2 project with the ACT ontology.
  3. Download the scripts from
  4. Run create_synthea_table_<your dbServertype>.sql in your project to create the Synthea tables.
  5. Import the Synthea data you downloaded in step one into the Synthea tables in your project.
  6. Load the i2b2-to-SNOMED table in this repository into your project.
  7. Click on the "Download SNOMED-CT to ICD-10-CM Mapping Resources" link to download. (You will need a UMLS account.)
  8. Unzip the file
  9. Import the TSV file into a table called SNOMED_to_ICD10 in your database.
  10. In Postgres and Oracle, follow the additional instructions in the comments at the top of synthea_to_i2b2_<your dbServerType>.sql to clean up the date formatting.
  11. Run synthea_to_i2b2_<your dbServertype>.sql to convert Synthea data into i2b2 tables (this will truncate your existing fact and dimension tables!)
  12. Replace references to i2b2metadata.dbo in the script. Use the database and schema where your ACT ontology tables are.


Previously, i2b2 db upgrade was a multi-step process of running upgrade SQL scripts and stored procedures individually on the db instance. This release simplifies the process of running the table upgrade SQL scripts  scripts and stored procedures from data_build.xml files. Details are on the i2b2 Upgrade Page here.


Supported Operating Systems

CentOS versions 6 (deprecated) or 7 (highly recommended) 

Windows 7-2019

Unofficially, MacOS and other flavors of Linux are likely to work.

i2b2 Server and Client Changes


Webclient Core-server

WEBCLIENT-351 Obfuscated User Not Showing Graph

WEBCLIENT-342 switch response status check from "OK" to 200 to handle lab value pop up in http/2 protocols

WEBCLIENT-335 temporal query in webclient with no anchoring events not running

WEBCLIENT-350  Unable to drag items in workplace 

WEBCLIENT-294 Webclient Reports "QUERY CANCELLED" While Query Is Still Running 

WEBCLIENT-354 Removed broken context menu in Find Previous Queries

CORE-418 Local timestamps in sessions on Oracle - appserver /db server in diff time zones 

CORE-282 Error returned when obfuscated user is locked out 

CORE-281 Query continues to run after user receives lockout message 

CORE-399 use alias for index hint  

Notes for Developers

For Java 11 install, if you change the xsd (REST API message definitions), then you will need to regenerate gensrc via JAXB in Java 8. In the i2b2-core cell directory for which you're regenerating the XSD-Java, run the ant target target "jaxb_gen" on Java 8 and then build as usual using Java 11.