Searching and visualising data from GO

QuickGO browser

QuickGO is a web-based browser developed by the UniProt-GOA project (see Figure 5).

When viewing an individual GO term, all of the information associated with that particular term is displayed. This includes the definition, synonyms, child terms, etc. You can also view the GO term in the context of its related terms by using the ancestor chart view.

For more information on using QuickGO for browsing terms, annotations, and the filtering options to search for custom sets of annotations, see the UniProt-GOA quick tour.

Figure 5 The QuickGO web browser. For searching Gene Ontology terms and annotations from UniProtKB.

AmiGO search tool: Term Information

Several browsers are available that allow you to explore the GO ontologies and annotations.

Browsing GO using AmiGO

AmiGO is a web-based tool developed by the GO project, which allows you to search and browse GO terms and GO annotations, or perform more complex queries including GO enrichment analysis, or analysis using GO slims.

AmiGO features a search bar at the top of the page, which allows you to search for GO terms. When viewing an individual GO term, all of the information associated with that particular term is displayed (Figure 6). This includes the definition, synonyms, child terms, mappings, etc.

The tabs at the bottom of the page allow you to view the placement of the GO term in either graphical or text formats.

AmiGO display for 'rubidium ion transmembrane transporter activity
AmiGO display for 'rubidium ion transmembrane transporter activity
Figure 6 AmiGO display for 'rubidium ion transmembrane transporter activity (GO:0035827)'

OBO-Edit for visualising ontologies

Viewing GO using OBO-Edit

OBO-Edit is a downloadable java-based tool that allows you to visualise GO and other ontologies (see Figure 7). It is also one of the tools that the GO editors use to build and maintain the ontologies.

The Graphviz viewer for 'rubidium ion transmembrane transporter activity

Figure 7 The Graphviz viewer for 'rubidium ion transmembrane transporter activity (GO:0035827)', part of the OBO-Edit display of this term. The OBO-Edit display also provides an ontology tree editor, text editor and search panel.

  • You can download OBO-Edit for free from SourceForge.
  • To visualise GO in OBO-Edit, you need to load an ontology file into the tool. The Gene ontology file in OBO format can be downloaded from the GO downloads web page.
  • The OBO-Edit display is configurable, to suit your individual needs.
  • When viewing GO terms, all of the information associated with that particular term is displayed. This includes the definition, synonyms, parent and child terms, mappings, etc.
  • OBO-Edit does not display annotation data; it is used only to visualise the ontologies.