ontoget reads ontology terms matching a query. Optionally, the parents or children of the term, related to the term by 'is_a' (class/subclass) relationships, may also be returned. The information may be written to an output file in various formats.
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The default behaviour is to report the entire OBO term statement from the ontology. Optionally, then only the the term id, name and namespace, or just the term id will be reported.
The output file by default is in OBO plain text format as used by the ontologies in the EMBOSS data directory and explained at http://www.geneontology.org/GO.format.obo-1_2.shtml.
Optionally, the output can be in HTML, OBO-XML or JSON format.
OBO-format ontologies must be installed in the EMBOSS data directory and indexed. This is done automatically for typical installations.
The default behaviour is to report a single term with the specified id. Optionally, it will also return the parent(s) or children of that term, i.e. terms which are related to the specified term id via an is_a (class/subclass) relationship.
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