GO subsets

What are GO subsets?

GO subsets (also known as GO slims) are simplified versions of the GO containing a reduced number of terms. There are several types of subsets:

  • Binning: Binning subsets are intended to be used to summarize the molecular function/biological processes/cellular components for sets of genes, including entire genomes/proteomes.
  • Ribbon: Ribbons are used to give a quick overview of the broad classes of terms annotated for a gene. Ribbon subsets are usually smaller than binning subsets.
  • Exclusion List: Exclusion lists are terms that should not be used for annotations, either because the term is too broad to be informative (for example, “GO:0008152 metabolic process”), and/or because a more specific term should be used (for example, more specific children of “GO:0048856 anatomical structure development” should be used that describe the actual structure formed).

GO subsets are part of the ontology, under the tag subset. For example:

  • [Term]
  • id: GO:0048856
  • name: anatomical structure development
  • namespace: biological_process
  • subset: goslim_generic

How are GO subsets used?

  • GO subsets can be used to provide an overview of the range of functions and processes found in an organism’s genome or a group of organisms.
  • GO subsets are also useful for addressing specific research needs in particular areas of biology. For instance, if for researchers specifically interested in the process of development or in the nuclear proteome, specific subsets allow them to focus solely on the terms under that section of the ontology.
  • GO subsets can also be useful for simplifying searches or annotation operations, by reducing the number of choices a user is presented with.

Who creates and maintains GO subset?

  • The GO consortium provides a generic subset which, like the GO itself, is species-agnostic, and which should be suitable for most purposes. In addition, many model organism-specific subsets have been created by GO consortium members and are available for download as listed below.
  • Users and user communities can create their own GO subsets. Please contact the GO helpdesk for more information about creating and submitting your GO subsets.
  • Groups who have created a GO subset are responsible for keeping it up to date as the ontology changes.

Download GO subsets

  • The files available below for download are generated by script from that file.
  • GO subsets are available in OBO, OWL as as well as JSON formats.
Subset name Maintainer File name OBO format OWL format json format tsv format
Alliance of Genome Resources subset Developed by GO Consortium for the Alliance of Genomes Resources goslim_agr obo owl json tsv
Generic GO subset GO Consortium goslim_generic obo owl json tsv
Aspergillus subset Aspergillus Genome Data goslim_aspergillus obo owl json tsv
Candida albicans subset Candida Genome Database goslim_candida obo owl json tsv
Drosophila subset FlyBase goslim_drosophila obo owl json tsv
Chembl Drug Target subset ChEMBL goslim_chembl obo owl json tsv
Metagenomics subset InterPro group goslim_metagenomic obo owl json tsv
Mouse GO subset Mouse Genome Informatics goslim_mouse obo owl json tsv
Plant subset The Arabidopsis Information Resource goslim_plant obo owl json tsv
Prokaryote subset GO Consortium goslim_prokaryote obo owl json tsv
Protein Information Resource subset PIR goslim_pir obo owl json tsv
Schizosaccharomyces pombe subset PomBase goslim_pombe obo owl json tsv
Yeast subset Saccharomyces Genome Database goslim_yeast obo owl json tsv

GO Exclusion Lists

For internal checking purposes, GO maintains two “anti-slims”, terms to which annotations should not be made. “Anti-slim” terms should never be used when creating a subset, and terms that are obsoleted are removed from subsets.

Subset name Usage File name OBO format OWL format json format tsv format*
Do not annotate The set of high level terms that are useful for grouping, but should have no direct annotations gocheck_do_not_annotate obo owl json tsv
Obsoletion candidate GO terms planned for obsoletion. This subsets serves as an early warning system both for users and curators gocheck_obsoletion_candidate  obo owl json tsv

Related tools

  • Map2Slim option in OWLTools: Given a GO subset, a current ontology, and specific gene product associations to precise terms from this current ontology, the Map2Slim script will map these term associations up to their respective broader terms from the GO subset. This script is an option of OWLTools, and it can be used to either create a new gene associations file, which contains the same annotations but made to the subset terms; or in count-mode, in which case it will give distinct gene product counts for each subset 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.

  • On the web: Similarly, there are online tools that may be of use including the Princeton slimming tool. It should be noted that online tools do often contain limitations and timeouts.