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GOSlimmer (version 1.0.1)

Full Gene Ontology File:

Full Gene Ontology file in OBO or OWL format (see http://geneontology.org/docs/download-ontology)

GOSlim File:

Slim Gene Ontology file in OBO or OWL format (see http://geneontology.org/docs/download-ontology)

Gene Product Annotation File:

Tabular file containing annotations from gene products to GO terms (in GAF or BLAST2GO format, or a simple two-column table)

GOSlimmer is a Java application that converts a set of annotations from the full GO version to a given GOSlim version.

It requires:

A full Gene Ontology file in either OBO or OWL format (see http://geneontology.org/docs/download-ontology).
A slim Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/go-subset-guide).
A tabular annotation file in GAF (http://geneontology.org/docs/download-go-annotations) format, BLAST2GO format, or a simple two-column table (e.g. from BioMart) with gene product ids in the first column and GO terms in the second one.

GOSlimmer can also be applied to other pairs of OWL/OBO ontologies where one is a subset of the other and you want to convert annotations from the larger to the smaller one.