module__org.bibliome.alvisnlp.modules.OBOReader

#org.bibliome.alvisnlp.modules.OBOReader

Synopsis

Reads terms in OBO files as documents.

Description

org.bibliome.alvisnlp.modules.OBOReader reads files specified by oboFiles in OBO format. Each term is loaded as a distinct document with the term identifier as the document identifier. Each document contains a section (nameSectionName) containing the term name, and one section for each term synonym (synonymSectionName). Optionally org.bibliome.alvisnlp.modules.OBOReader also sets features on the document with the term path from the root (pathFeature), the identifier of the parent term (parentFeature), the identifiers of each ancestor (ancestorsFeature), of the identifiers of each child term (childrenFeature).

Parameters

oboFiles

Optional

Type: String[]]

OBO files to read.

ancestorsFeature

Optional

Type: String

Name of the feature that contains the term ancestors ids.

childrenFeature

Optional

Type: String

Name of the feature that contains the term children ids.

constantDocumentFeatures

Optional

Type: Mapping

Constant features to add to each document created by this module

constantSectionFeatures

Optional

Type: Mapping

Constant features to add to each section created by this module

excludeOBOBuiltins

Default value: true

Type: Boolean

Either to exclude builtin OBO terms.

idPrefix

Default value: ``

Type: String

Prefix to prepend to each Term identifier.

nameSectionName

Default value: name

Type: String

Name of the section that contains the term name.

parentFeature

Default value: is_a

Type: String

Name of the feature that contains the term parents.

pathFeature

Default value: path

Type: String

Name of the feature that contains the term paths.

synonymSectionName

Default value: synonym

Type: String

Name of the sections that contains the term synonyms.