GO Slim and Subset Guide
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.pl section for a perl implementation of this.
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; TAIR [external website] (plant), SGD [external website] (yeast) and GOA [external website] (generic) have submitted GO slims which have been 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 OBO format GO flat file. The files available below for download are generated by script from the flat file.
| Topic / Usage | Author(s) | Download | |
|---|---|---|---|
| Generic GO slim | Suparna Mundodi and Amelia Ireland | OBO format | old GO format |
| GOA and whole proteome analysis | N. Mulder, M. Pruess | OBO format | old GO format |
| Plant GO slim | Suparna Mundodi | OBO format | old GO format |
| Yeast GO slim | SGD curators | OBO format | old GO format |
MGI [external website] have also produced a GO slim [external website] but it is not in standard format so is not integrated into the GO flat file.
Archived GO Slims
The GO FTP site also holds archival copies of GO slims which are no longer maintained or updated. These files have be 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.
Users should note that the majority of these GO slims are no longer maintained by the authors, and they may contain GO terms which are now obsolete.
All archival GO slims are in the old GO flat file format.
| 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. [PubMed Abstract [external website]] Apr 2002 |
old GO format |
| Drosophila |
M. Adams, M. Ashburner, G.M. Rubin, S.E. Lewis et al.; Adams et al. [PubMed Abstract [external website]] Feb 2000 |
old GO format |
| Glossina ESTs |
M. Berriman Sep 2002 |
old GO format |
| GOA |
N. Mulder, M. Pruess [PubMed Abstract [external website]] Nov 2002 |
old GO format |
| Mouse |
The RIKEN Genome Exploration Group Phase II Team and the FANTOM Consortium [PubMed Abstract [external website]] 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. [PubMed Abstract [external website]] Apr 2002 |
old GO format |
| Rice (Syngenta) |
J. Yu et al. [PubMed Abstract [external website]] Apr 2002 |
old GO format |
| Yeast |
SGD curators Aug 2003 |
old GO format |
map2slim.pl
The map2slim.pl script, distributed as part of the go-perl package, maps a set of annotations up to their parent GO slim terms. Further documentation, installation help and instructions on running the script are available from the go-perl page at CPAN [external website]. A web version is available from AmiGO.
Prokaryotic subset
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 OBO format GO 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).
