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 a single root node.

   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.

Users can specify if summary basecodes should be included in the final output.

   Often the data extracted from NCBO contains summary basecodes. Summary basecodes are defined as those containing a '-'.  If desired, users can       specify if they want the summary basecodes in 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 Tool 1.1 Users Guide    Users Guide for version 1.1 of the NCBO Extraction tool.

Preliminary Release Candidate Software

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