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.

Tutorials

  - 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 tool version 1._Extraction_Users_Guide_1-0 User's Guide for the command line based NCBO Extraction tool

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