The i2b2 Import Tool is intended to facilitate import of structured clinical data into an i2b2 instance. It is a Java Eclipse application, tested on Windows and Ubuntu Linux.
Currently, we support the following extractors:
- CDISC ODM/XML
- German § 21 KHEntgG dataset
- STARLIMS Biobank
Additionally, you can use a limited number of third party tools:
- TMF PID generator for pseudoymization
- Medical terminologies
The IDRT Import and Mapping Tool (IMT) serves two purposes:
The IMT is Java client application. It is expected to run locally and requires a network connection to the i2b2 database.
We describe the general architecture in detail, but you first may want to download and install the application. In case you find a bug, want to request additional features or are willing to contribute own code, please send a request.
The IMT provides extractors for importing data from certain generic formats like character-separated files (CSV), database scripts (SQL), or XML-files in CDISC ODM.
Additionally, a number of special dataset specifications can be imported, too:
Editing the i2b2 ontology
The IMT furthermore provides a means to rearrange the i2b2 ontology by creating, renaming, moving and mapping source concepts as well as folders with the help of a graphical user interface.