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README.md

JCoRe BioNLP 09 Event Reader

Reader that converts BioNLP Shared Task formatted files to CAS objects.

Descriptor Path:

de.julielab.jcore.reader.bionlp09event.desc.jcore-bionlp09event-reader

Objective

This reader takes as input a folder with txt,a1 & a2 files - format of the BioNLP Shared Task - and creates CAS annotations as described in Capabilities. Therefore it serves e.g. as reader in relation extraction pipelines.

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/reader/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
inDirectory String yes no Path to an input folder
bioEventServiceMode Boolean no no desc here
abstractFile String no no desc here
proteinFile String no no desc here

2. Predefined Settings

Parameter Name Parameter Syntax Example
inDirectory valid Path to an input directory data/BioNLPinData
bioEventServiceMode boolean Variable false
abstractFile desc none
proteinFile desc none

3. Capabilities

Type Input Output
de.julielab.jcore.CorefExpression +
de.julielab.jcore.types.AbstractText +
de.julielab.jcore.types.Annotation +
de.julielab.jcore.types.ArgumentMention +
de.julielab.jcore.types.CorefRelation +
de.julielab.jcore.types.Entity +
de.julielab.jcore.types.EntityMention +
de.julielab.jcore.types.EventMention +
de.julielab.jcore.types.EventTrigger +
de.julielab.jcore.types.Gene +
de.julielab.jcore.types.Title +
de.julielab.jcore.types.pubmed.Header +

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.