i2b2 Sponsored Project - Extraction Tool 1.1

The i2b2 Hive software is composed of core modules called 'cells' that create a system to allow the use of patient data for research. These cells communicate through web services and use i2b2 standard XML messages to transfer ontology-related metadata.  To date, a subset of ICD-9 has been provided with the i2b2 demo software package.  There has been a need in the community for access to a complete ICD-9 ontology as well as other clinical-based ontologies.

NCBO hosts a repository of biomedical ontologies.  These ontologies are stored in formats that are not understood by i2b2.  A tool has been developed to not only extract these ontologies via bioportal REST services, but to transform them into a format that is understood by the i2b2 ONT cell.

New Features

Users can specify an optional time-out parameter in the Extraction step.

The default NCBO REST timeout is set to 300 seconds.  Users may now set the timeout to a setting of their choice.

Users can specify a single root node in the Process step.

Often the data extracted from NCBO will have several root nodes.  If desired, users can specify a single root node name for the final table.

Tooltip generation has been redesigned and now allows multi-line tooltips.

Tutorials

  NCBO_Extraction_Overview  Step by step example of how metadata trees are created and configured using both Edit View and the NCBO Extraction tool   Similar to tutorial above but concentrates on what is needed to work with .

  NCBO_Extraction_Users_Guide_1-1 Users Guide for version 1.1 of the NCBO Extraction tool.

...

Release

...

1.1 Software

coming soon...NCBO Extraction Tool 1.1 package   Software package for version 1.1 of the command-line based NCBO metadata extraction tool