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README.md

JCoRe BioNLP 09 Event Consumer

Consumer that writes CAS annotations into the BioNLP Shared Task format.

Descriptor Path:

de.julielab.jcore.consumer.bionlp09event.desc.jcore-bionlp09event-consumer

Objective

This consumer takes the annotations specified in Capabilities and outputs three seperate text files for each document to outDirectory. The text files follow the format of the BioNLP Shared Task and are therefore applicable for being evaluated by their eval tool or the online evaluation of the test files.

Using the Consumer - 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/consumer/bionlp09event/desc but it can be further edited if so desired; see UIMA SDK User's Guide for further information.

1. Parameters

Parameter Name Parameter Type Mandatory Multivalued Description
outDirectory String yes no Path to an output folder
bioEventServiceMode Boolean no no desc here
a2FileString String no no desc here

2. Predefined Settings

Parameter Name Parameter Syntax Example
outDirectory valid Path to an output directory data/BioNLPoutData
bioEventServiceMode boolean Variable false
a2FileString desc none

3. Capabilities

Type Input Output
de.julielab.jcore.types.Gene +
de.julielab.jcore.types.EventTrigger +
de.julielab.jcore.types.EntityMention +

Reference

Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, and Jun’ichi Tsujii. 2009. Overview of BioNLP’09 Shared Task on Event Extraction. In BioNLP 2009 - Proceedings of the Companion Volume: Shared Task on Event Extraction. Boulder, CO, USA, June 5, 2009, pages 1–9.