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i2b2 Sponsored Project - NCBO Ontology Tools

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.


  i2b2 Ontology Tutorial  Step by step example of how metadata trees are created and configured using both Edit View and Extraction tool

 NCBO_Extraction_Overview   Similar to tutorial above but concentrates on what is needed to work with the NCBO Extraction tool.

 NCBO_Extraction_Users_Guide_1-0 User's Guide for the command line based NCBO Extraction tool


NCBO Extraction tool 1.0 package        Software package for the command-line based NCBO metadata extraction tool

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