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changes.mady.by.user Reeta Metta

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Top New Features

Description

Data Exporter extension for i2b2

Using the webclient breakdownsRun Query breakdown dialog, patient data can be exported as flat files to be loaded into SAS, R and other data analytic tools for further analysis.

ACT Ontology Version 4.1

Version 4.1 provides 19 ontologies supporting i2b2 and OMOP CDM architectures on ORACLE, SQLServer and Postgres databases.

i2b2 on OMOP for Postgres database

The core i2b2 platform now supports the OMOP data model on Postgres database (adding to existing Oracle and SQLServer OMOP support), which is queryable through the comprehensive ENACT-OMOP Ontology. 

Bug fixes


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Contribution

Contributor

Description

ACT-Ontology Version V4.1

Michele Morris (University of Pittsburgh)

The ACT V4.1 Ontology supporting i2b2 and OMOP CDMs enables queries to be run in i2b2 query tool against ORACLE, SQLServer and Postgres databases. 

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i2b2 can now export patient data for a patient set. The workflow involves breakdowns in the webclient, which allow users to request exports and data managers to generate exports. The export types and options are fully configurable in the database. Detailed documentation on set up can be at found here: Data Exporter Set-up

Below The below steps describe the overall process:

  • User logs into i2b2 webclient and runs a regular i2b2 query, checking the desired Data request breakdown option when running the query.
  • E-mail is sent to the data manager and the User on , informing them that the user's data request has been made.
  • The manager logs in and reruns the user query with the Data Export breakdown selection to generate the export flat files.
  • The generated export flat file is stored in a configurable location specified in the HIVE_CELL_Params setting.Email on the i2b2 server.
  • An e-mail is sent to the manager confirming the file extract and how to access the files (which can be shared with the requester).

Steps to upgrade:

First, install the new war file. Next, upgrade the database. Because the upgrade requires loading some new content from the NewInstall, we have created an ant target to upgrade the data tables: upgrade_tables_release_1-8-0 This should be run from Upgrade/CrcData, e.g., ant f data_build.xml upgrade_tables_1 8-0 

Detailed upgrade instructions can be found here: Upgrade to version 1.8.1 release candidate

ACT - V4.1 Ontology

The V4.1 Ontology includes total of includes  19 ontologies- 3 new and 11 updated and 5 unchanged

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The CPT4 ontology table is not included with i2b2 due to AMA restrictions on redistribution of CPT code information. Contact the ACT ENACT team to get a copy if your institution is an AMA member.

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