A UIMA wrapper for the NCBO annotator

Roeder C, Jonquet C, Shah NH, Baumgartner WA Jr, Verspoor K, Hunter L (2010)

Bioinformatics (26):1800-1801 doi:10.1093/bioinformatics/btq250

 

Summary

The Unstructured Information Mangement Architecture (UIMA) framwork and web services are emerging as useful tools for integrating biomedical text mining tools. This note describes our work, which warps the National Center for Biomedical Ontology (NCBO) Annotator - an ontology-based annotation service - to make it available as a component in UIMA workflows.

 

Availibility

The wrapper is freely available on the web at http://bionlp-uima.sourceforge.net/ as part of the UMIA tools distribution from the Center for Computational Pharmacology (CCP) at the University of Colorado School of Medicine. It has been implemented in Java for support on Mac OS X, Linux and MS Windows.