CTMM-TraIT/trait_odm_to_i2b2

Name: trait_odm_to_i2b2

Owner: CTMM TraIT

Description: TraIT ODM to i2b2 (OpenClinica to transMART converter)

Created: 2014-02-06 11:07:51.0

Updated: 2017-06-05 06:54:57.0

Pushed: 2016-03-02 16:52:27.0

Homepage: null

Size: 14932

Language: Java

GitHub Committers

User	Most Recent Commit	# Commits
Freek de Bruijn	2015-09-16 13:31:39.0	88
Jacob Rousseau	2018-03-05 15:28:01.0	3
Ward Blondé	2016-03-02 16:52:27.0	179

Other Committers

User	Email	Most Recent Commit	# Commits
Ward Blonde	w.blonde@vumc.nl	2014-08-21 13:05:05.0	1

README

ODM-to-i2b2

A presentation of the project, users information and developers information are all included in this repository.

The ODM-to-i2b2 project is a forked version of the REDCap-to-i2b2 project with added functionality: community.i2b2.org/wiki/display/ODM2i2b2.

This tools allows you to convert an ODM file to tabular data files that are ready to be imported in an i2b2-like system like tranSMART. The 'OpenClinica to tranSMART' conversion, which exports tabular text files, builds on the same automatically generated Java sources as the 'REDCap to i2b2' conversion, which exports to a database:

Status at release 3.0 (2015 June 12th): 3 tabular files are produced for each study:

• a clinical data file (with the data),
• a columns file (with metadata about each column in the clinical data file) and
• a wordmap file (with the full word values that come in place of the numerical codes that can be used in the clinical data file)

This conversion runs without errors for a wide variety of tested ODM exports from OpenClinica. It also deals appropriately with repeating elements, like events and item groups.

Main developers:

• Ward Blondé
• Freek de Bruijn