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 (plant), SGD (yeast) and GOA (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 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 |
|
GOA and whole proteome analysis
Developed by N. Mulder, M. Pruess |
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 of PIR |
OBO format |
|
Schizosaccharomyces pombe slim
Developed by Val Wood |
OBO format |
|
Yeast slim
Developed by Saccharomyces Genome Database |
OBO format |
MGI have also produced a GO slim but it is not in standard format so is not integrated into the GO flat file.
Archived GO Slims
There is also an archive of deprecated GO slims that are no longer maintained or updated.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.
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Users should note that the majority of these GO slims are no longer maintained by the authors, and they may contain GO terms which are now obsolete.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. [PubMed Abstract]
Apr 2002 |
old GO format |
| Drosophila |
M. Adams, M. Ashburner, G.M. Rubin, S.E. Lewis et al.; Adams et al. [PubMed Abstract]
Feb 2000 |
old GO format |
| Glossina ESTs |
M. Berriman
Sep 2002 |
old GO format |
| GOA |
N. Mulder, M. Pruess [PubMed Abstract]
Nov 2002 |
old GO format |
| Mouse |
The RIKEN Genome Exploration Group Phase II Team and the FANTOM Consortium [PubMed Abstract]
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]
Apr 2002 |
old GO format |
| Rice (Syngenta) |
J. Yu et al. [PubMed Abstract]
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. 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 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).
