What is a GO slim?
GO slims are cut-down versions of the GO ontologies containing a subset of the terms in the whole GO. They give a broad overview of the ontology content without the detail of the specific fine grained terms.
GO slims are particularly useful for giving a summary of the results of GO annotation of a genome, microarray, or cDNA collection when broad classification of gene product function is required. See the Map2Slim section below for a description on implementing the Map2Slim option in OWLTools.
GO slims are created by users according to their needs, and may be specific to species or to particular areas of the ontologies. GO provides a generic GO slim which, like the GO itself, is not species specific, and which should be suitable for most purposes. Alternatively, users can create their own GO slims or use one of the model organism-specific slims integrated into the GO flat file. Please email the GO helpdesk for more information about creating and submitting your GO slim.
GO slims available
Maintained GO slims
The GO slims in this list are maintained as part of the GO flat file. The files available below for download are generated by script from that file.
|Organism or Usage||Download|
|Generic GO slim Developed by GO Consortium||OBO format|
|Plant slim Developed by The Arabidopsis Information Resource||OBO format|
|Candida albicans Developed by Candida Genome Database||OBO format|
|Protein Information Resource slim Developed by Darren Natale, PIR||OBO format|
|Schizosaccharomyces pombe slim Developed by Val Wood, PomBase||OBO format|
|Yeast slim Developed by Saccharomyces Genome Database||OBO format|
|Aspergillus slim Developed by Aspergillus Genome Data||OBO format|
|Metagenomics slim Developed by Jane Lomax and the InterPro group||OBO format|
|Virus slim Developed by Jane Lomax and Rebecca Foulger.||OBO format|
|Chembl Drug Target slim developed by Prudence Mutowo and Jane Lomax||OBO format|
Archived GO Slims
There is also an archive of deprecated GO slims that are no longer maintained or updated. These files have been deposited for two reasons; the first is to give easy access to the GO slim used in a particular publication or analysis; the second is for reuse by others in the community.
All archival GO slims are in the deprecated GO flat file format, which can be converted into OBO format using the the obo2flat script, part of the OBO-Edit package; instructions on usage are provided in the OBO-Edit User Guide.
Users should note that the majority of these GO slims are no longer maintained by the authors, and they may contain GO terms which are now obsolete.
|Topic / Usage||Information||Download|
|Generic GO slim||Suparna Mundodi and Amelia Ireland Aug 2002||old GO format|
|Honey bee ESTs||C.W. Whitfield, M.R. Band, M.F. Bonaldo, C.G. Kumar, L. Liu, J.R. Pardinas, H.M. Robertson, M.B. Soares, G.E. Robinson, PMID:11923340 Apr 2002||old GO format|
|Drosophila||M. Adams, M. Ashburner, G.M. Rubin, S.E. Lewis et al.; Adams et al., PMID:10731132 Mar 2000||old GO format|
|Glossina ESTs||M. Berriman Sep 2002||old GO format|
|UniProtKB-GOA||N. Mulder, M. Pruess PMID:12230037 Nov 2002||old GO format|
|Mouse||The RIKEN Genome Exploration Group Phase II Team and the FANTOM Consortium PMID:11217851 Feb 2001||old GO format|
|P. falciparum||M. Berriman July 2002||old GO format|
|Plant||Suparna Mundodi Dec 2002||old GO format|
|Rice (Beijing)||J. Yu et al. PMID:11935017 Apr 2002||old GO format|
|Rice (Syngenta)||J. Yu et al.PMID:11935018 Apr 2002||old GO format|
|Yeast||SGD curators Aug 2003||old GO format|
Map2Slim option in OWLTools
Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim. This script is an option of OWLTools, and it can be used to either create a new gene association file, which contains the most pertinent GO slim accessions, or in count-mode, in which case it will give distinct gene product counts for each slim term.
Background information and details on how to download, install, and implement OWLTools, as well as instructions on how to run the Map2Slim script are available from the OWLTools Wiki at https://github.com/owlcollab/owltools/wiki/Map2Slim.
On the web
Similarly, there are a couple of online tools that may be of use. The first is the Princeton slimming tool, the second is the legacy amigo slimmer. It should be noted that online tools do often contain limitations and timeouts.
In addition to GO slims, GO also provides a prokaryote-specific subset of GO terms. This subset contains only terms that are applicable to prokaryotes, so for example, the terms nucleus and mitochondrion are excluded from the subset while the terms membrane and cytoplasm are included. At approximately 7000 terms, the set is much larger than the GO slims and it is intended to be used as a viewing tool for reducing the complexity of the ontologies for those users not interested in viewing eukaryotic terms, rather than to get a high-level view of an annotation set in the way that GO slims are used.
Unlike GO slims, the prokaryotic subset is not generated as a separate file, but is stored as a category in the GO ontology file. It is possible to view the terms in this subset using a filter in OBO-Edit (see the OBO-Edit user guide for instructions).