module__BioNLPSTReader

#org.bibliome.alvisnlp.modules.bionlpst.BioNLPSTReader

Synopsis

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

Description

org.bibliome.alvisnlp.modules.bionlpst.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.

Parameters

textDir

Optional

Type: InputDirectory

Path to the directory containing .a2 files.

a1Dir

Optional

Type: InputDirectory

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

a2Dir

Optional

Type: InputDirectory

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

constantAnnotationFeatures

Optional

Type: Mapping

Constant features to add to each annotation created by this module

constantDocumentFeatures

Optional

Type: Mapping

Constant features to add to each document created by this module

constantRelationFeatures

Optional

Type: Mapping

Constant features to add to each relation created by this module

constantSectionFeatures

Optional

Type: Mapping

Constant features to add to each section created by this module

constantTupleFeatures

Optional

Type: Mapping

Constant features to add to each tuple created by this module

schema

Optional

Type: DocumentSchema

Annotation schema against which the annotations are checked. org.bibliome.alvisnlp.modules.bionlpst.BioNLPSTReader aborts if the annotations do not check. If not set, the annotations are not checked.

charset

Default value: UTF-8

Type: String

Character encoding of all imported files.

equivalenceItemPrefix

Default value: item

Type: String

Prefix of the role of arguments that represent group elements.

equivalenceRelationName

Default value: equiv

Type: String

Name of the relation whose tuples represent equivalences.

eventKind

Default value: event

Type: String

Kind value for event annotations.

fragmentCountFeatureName

Default value: fragments

Type: String

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

idFeatureName

Default value: id

Type: String

Feature where to store the annotation identifier.

kindFeatureName

Default value: kind

Type: String

Feature of relations contatining the annotation kind.

relationKind

Default value: relation

Type: String

Kind value for relation annotations.

sectionName

Default value: text

Type: String

Name of the unique section contating all the text.

textBoundAsAnnotations

Default value: false

Type: Boolean

If true, org.bibliome.alvisnlp.modules.bionlpst.BioNLPSTReader imports text-bound annotations as annotations instead of tuples. Multiple fragments text-bound annotations are merged.

textBoundFragmentRolePrefix

Default value: frag

Type: String

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

textKind

Default value: text

Type: String

Kind value for text annotations.

triggerRole

Default value: trigger

Type: String

Role of the argument that represent an event trigger.

typeFeatureName

Default value: type

Type: String

Feature where to store the type of the annotation.