OBOReader

Synopsis

Reads terms in OBO files as documents.

Description

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 ( nameSection ) containing the term name, and one section for each term synonym ( synonymSection ). Optionally 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 ).

Snippet

📋

<oboreader class="OBOReader">
    <oboFiles></oboFiles>
</oboreader>

Mandatory parameters

oboFiles

OBO files to read.

Optional parameters

ancestorsFeature

Name of the feature that contains the term ancestors ids.

childrenFeature

Name of the feature that contains the term children ids.

constantDocumentFeatures

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

constantSectionFeatures

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

excludeOBOBuiltins

Either to exclude builtin OBO terms.

idPrefix

Prefix to prepend to each Term identifier.

nameSection

Name of the section that contains the term name.

parentFeature

Name of the feature that contains the term parents.

pathFeature

Name of the feature that contains the term paths.

synonymSection

Name of the sections that contains the term synonyms.

Deprecated parameters

nameSectionName

Deprecated alias for nameSection .

synonymSectionName

Deprecated alias for synonymSection .