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.

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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.

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 the NCBO Extraction tool.

    NCBO_Extraction Tool 1._Users_Guide_1-1 Users Guide     Users Guide for version 1.1 of the NCBO Extraction tool

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Release

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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