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README.md

JCoRe BioSEM Analysis Engine

Wrapper for the BioSEM Event Extraction System

Objective

Requirement and Dependencies

The input and output of an AE is done via annotation objects. The classes corresponding to these objects are part of the JCoRe Type System. Furthermore this AE is only a wrapper, so the BioSEM Event Extraction System is needed, too. Without a model this AE is not really of any use, therefore we encourage you to use one of the JCoRe projects if you want to use this AE in your pipeline.

Using the AE - Descriptor Configuration

In UIMA, each component is configured by a descriptor in XML. Such a preconfigured descriptor is available under src/main/resources/de/julielab/jcore/ but it can be further edited if so desired; see UIMA SDK User's Guide for further information.

1. Capabilities

Type Input Output
de.julielab.jcore.types.Gene +
de.julielab.jcore.types.EventTrigger +
de.julielab.jcore.types.EventMention +
de.julielab.jcore.types.ArgumentMention +

Reference

Quoc C. Bui and Peter M. A. Sloot. 2012. A robust approach to extract biomedical events from literature. In Bioinformatics (Oxford, England), 28(20), pages 2654–2661.

Original Code

http://dl.dropbox.com/u/10256952/BioEvent.zip