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_Users_Guide   User's Guide for the command line based NCBO Extraction tool

Software

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