Ontology Tools
Space shortcuts
Space Tools
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 17 Next »

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.

Extraction tool

 NCBO hosts a repository of biomedical ontologies.  These ontologies are stored in formats that are not understood by i2b2.  A command line 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.

Mapping tools

 A set of mapping tools have been created for the workbench.  These tools were designed to assist users in assigning, editing and verifying mappings between ontologies.  These tools consist of a set of workbench plugins and a new Mapper cell (MAP). In version 1.1 of the mapping tools we add the ability to automate mappings to UMLS ontologies. 

Integration tool

A command line integration tool has been developed that integrates a source ontology into the hierarchy of a target ontology as dictated by the mappings between the two. The feature has been absorbed into the mapping tool.


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

i2b2/NCBO Ontology tools overview  -  Overview of the extraction, mapping and integration tools and how they work together.

Navigate space
  • No labels