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README.md

JCoRe IEXML Consumer

Consumer that generates stand-off IEXML files as used in the mantra project/challenge

Descriptor Path:

de.julielab.jcore.consumer.iexml.desc.jcore-iexml-consumer

Objective

This consumer takes the annotations specified in Capabilities and outputs IEXML files for each document to a specified outputFile.

Requirements 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.

Using the CC - 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/iexml/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
outputFile String yes no Path to an output file
author String no no The author of the document
description String no no The description of the document

2. Predefined Settings

Parameter Name Parameter Syntax Example
outputFile valid Path to an output file data/IEXMLOutputData

3. Capabilities

Type Input Output
de.julielab.jcore.types.mantra.Corpus +
de.julielab.jcore.types.mantra.Document +
de.julielab.jcore.types.mantra.Unit +
de.julielab.jcore.types.mantra.Entity +

Reference

Rebholz-Schuhmann, Dietrich, Harald Kirsch, and Goran Nenadic. "IeXML: towards an annotation framework for biomedical semantic types enabling interoperability of text processing modules." SIG BioLink, ISMB (2006).

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