Extraction Tool 2.0

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. This version of the Extraction tool was updated to work with the NCBO BioPortal v4.0 REST services API

New Features

This version of the Extraction tool was updated to work with the NCBO BioPortal v4.0 REST services API

Tutorials

NCBO_Extraction_Overview  Step by step example of how metadata trees are created and configured using the NCBO Extraction tool.

NCBO_Extraction_Users_Guide_2-0 Users Guide for version 2.0 of the NCBO Extraction tool

Software

NCBO Extraction Tool 2.0 package Software package for version 2.0 of the command-line based NCBO metadata extraction tool