OBOMapper

Synopsis

Maps names and synonyms of terms defined in OBO files.

Description

OBOMapper maps names and synonyms of terms described in oboFiles on target .

Snippet

📋

<obomapper class="OBOMapper">
    <form></form>
    <oboFiles></oboFiles>
    <target></target>
</obomapper>

Mandatory parameters

form

Expression evaluated as a string with the target element as context that specifies the target key.

oboFiles

Paths to the OBO files to map.

target

Expression evaluated as a list of elements with the corpus as context that specify the elements to be mapped.

Optional parameters

altPathFeatures

UNDOCUMENTED

ancestorsFeature

Name of the feature where to store the term ancestors ids.

childrenFeature

Name of the feature where to store the term children ids.

idFeature

Name of the feature where to store the term id.

nameFeature

Name of the feature where to store the term name.

parentsFeature

Name of the feature where to store the term parents ids.

pathFeature

Name of the feature where to store the term id path from the root.

synonymsFeature

Name of the feature where to store the term synonyms.

versionFeature

Name of the feature where to store the ontology version.

idKeys

Map the term keys instead of name and synonyms

ignoreCase

Either to match ignoring the case.

keepDBXref

Either to store term dbxrefs. Dbxrefs are stored in features that match the database name.

operator

Matching operator: either exact (default) or prefix.

Deprecated parameters