I2B2Reader

Synopsis

I2B2Reader reads files in the format of the I2B2 challenge.

Description

I2B2Reader reads documents in I2B2 challenge including the text of documents, tokenization as annotations, concepts as annotations, assertions as annotation features and relations as tuples.

Snippet

📋

<i2b2reader class="I2B2Reader">
    <textDir></textDir>
</i2b2reader>

Mandatory parameters

textDir

Path to the directory containing I2B2 text files.

Optional parameters

assertionsDir

Path to the directory where assertion files can be found.

conceptsDir

Path to the directory that contains concept annotations.

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.

relationsDir

Path to the directory where relation files can be found.

assertionFeature

conceptTypeFeature

Feature where to store the concept type.

conceptsLayer

Name of the layer where to store concepts annotations.

leftRole

Name of the left argument of relations.

linenoFeature

Name of the feature where to store the line number.

linesLayer

Name of the layer where to store lines.

rightRole

section

Name of the unique section of each document.

tokenNumberFeature

Feature where to store the token index.

tokensLayer

Name of the layer where to store tokens.

Deprecated parameters

conceptsLayerName

Deprecated alias for conceptsLayer .

linesLayerName

Deprecated alias for linesLayer .

sectionName

Deprecated alias for section .

tokensLayerName

Deprecated alias for tokensLayer .