UserGuide:Gene Ontology

Gene Ontology Search

Gene Ontology (GO) is a controlled vocabulary aimed at capturing three different aspects of a gene product in a living organism: its biological process or processes (essentially, the reason why a given gene product benefits the organism whose genome encodes them); its biochemical function or functions (i.e., what the gene products do at a basic biochemical level); and its cellular location or locations (i.e., where in a cell the gene product will normally be).

Gene Ontology is extensively documented at the official Web page of the GO Consortium: http://www.geneontology.org and has also been described in the following papers:

Ashburner et al. (2000). Gene ontology: tool for the unification of biology. Nat. Genet. vol. 25, pp. 25-29.

The Gene Ontology Consortium (2001). Creating the gene ontology resource: design and implementation. Genome Res. vol 11, pp. 1425-1433.

At the moment, the Gene Ontology search page for Wormbase allows the following search:

• 1. Pick a term for a biological process, biochemical function, or cellular localization that is of interest. Enter the term as text in the "Search text or GO accession number:" window.
• 2. Press "Search" button to run a search.
• 3. The result will display GO terms, and clicking on them will link to the summary reports.

An Example Search:

Searching for 'chitinase' returns two objects: the term names 'chitinase' and 'endochitinase' along with the corresponding seven digit GO ID within parentheses.

Clicking on 'chitinase' links to the summary report page for 'chitinase'.

The summary page for the GO term 'chitinase' displays the definition for this term and the position of this term in the directed acylic graph (DAG) format so that the entire ontology structure showing the parent and children terms for 'chitinase' are displayed. Each term in this structure can be clicked on to access its summary report.

Below this, is displayed a list of all the Sequence and Motif objects in WormBase associated with the GO term 'chitinase'. Click on them to access the specific sequence and motif reports.