BioNLPSTReader

Synopsis

Reads documents and annotations in the BioNLP-ST 2013 a1/a2 format .

Description

BioNLPSTReader reads text files in the directory specified by textDir as documents, then imports annotations in the corresponding files in the directories specified by a1Dir and a2Dir .

Snippet

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<bionlpstreader class="BioNLPSTReader">
    <textDir></textDir>
</bionlpstreader>

Mandatory parameters

textDir

Path to the directory containing .txt files.

Optional parameters

a1Dir

Path to the directory containing .a1 files. If this parameter is not set, then BioNLPSTReader does not read a1 files. This directory must contain one .a1 file for each .txt file found in textDir .

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<a1Dir>/path/to/a1/</a1Dir>

a2Dir

Path to the directory containing .a2 files. If this parameter is not set, then BioNLPSTReader does not read a2 files. This directory must contain one .a2 file for each .txt file found in textDir .

constantAnnotationFeatures

Constant features to add to each annotation created by this module.

constantDocumentFeatures

Constant features to add to each document created by this module.

constantRelationFeatures

Constant features to add to each relation created by this module.

constantSectionFeatures

Constant features to add to each section created by this module.

constantTupleFeatures

Constant features to add to each tuple created by this module.

schema

Annotation schema against which the annotations are checked. BioNLPSTReader aborts if the annotations do not check. If not set, the annotations are not checked.

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<schema>
			<text-bound type="Title"/>
			<text-bound type="Paragraph"/>
			<text-bound type="Microorganism"/>
			<text-bound type="Habitat"/>
			<text-bound type="Phenotype"/>
			<text-bound type="Geographical"/>
			<relation type="Lives_In">
				<roles>Microorganism,Location</roles>
				<mandatory-arguments>Microorganism,Location</mandatory-arguments>
				<argument-types role="Microorganism">Microorganism</argument-types>
				<argument-types role="Location">Habitat,Geographical,Microorganism</argument-types>
			</relation>
			<relation type="Exhibits">
				<roles>Microorganism,Property</roles>
				<mandatory-arguments>Microorganism,Property</mandatory-arguments>
				<argument-types role="Microorganism">Microorganism</argument-types>
				<argument-types role="Property">Phenotype </argument-types>
			</relation>
        </schema>

charset

Character encoding of all imported files.

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<charset>UTF-8</charset>

equivalenceItemPrefix

Prefix of the role of arguments that represent group elements.

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<equivalenceItemPrefix>item</equivalenceItemPrefix>

equivalenceRelation

Name of the relation whose tuples represent equivalences.

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<equivalenceRelation>equiv</equivalenceRelation>

eventKind

Kind value for event annotations.

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<eventKind>event</eventKind>

fragmentCountFeature

Feature where to store the number of merged fragments. This feature is only set if textBoundAsAnnotations is true .

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<fragmentCountFeature>fragments</fragmentCountFeature>

idFeature

Feature where to store the annotation identifier.

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<idFeature>id</idFeature>

kindFeature

Feature of relations contatining the annotation kind.

kind<h3 id="relationKind" class="param">relationKind</h3>

Kind value for relation annotations.

relation<h3 id="section" class="param">section</h3>

Name of the unique section contating all the text.

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<section>text</section>

textBoundAsAnnotations

If true , BioNLPSTReader imports text-bound annotations as annotations instead of tuples. Multiple fragments text-bound annotations are merged.

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<textBoundAsAnnotations/>

textBoundFragmentRolePrefix

Prefix of the role of arguments that represent text-bound fragments.

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<textBoundFragmentRolePrefix>frag</textBoundFragmentRolePrefix>

textKind

Kind value for text annotations.

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<textKind>text-bound</textKind>

triggerRole

Role of the argument that represent an event trigger.

typeFeature

Feature where to store the type of the annotation.

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<typeFeature>type</typeFeature>

Deprecated parameters

equivalenceRelationName

Deprecated alias for equivalenceRelation .

fragmentCountFeatureName

Deprecated alias for fragmentCountFeature .

idFeatureName

Deprecated alias for idFeature .

kindFeatureName

Deprecated alias for kindFeature .

sectionName

Deprecated alias for section .

typeFeatureName

Deprecated alias for typeFeature .