thehyve/trait_odm_to_i2b2

Name: trait_odm_to_i2b2

Owner: The Hyve

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

Forked from: CTMM-TraIT/trait_odm_to_i2b2

Created: 2016-03-01 08:34:34.0

Updated: 2016-03-01 08:34:35.0

Pushed: 2016-03-01 08:40:29.0

Homepage: null

Size: 14930

Language: Java

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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 (June 12th 2015): 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 (Harvard Medical School, Boston)
• Freek de Bruijn (NKI, Amsterdam)