UserGuide:Gene Ontology Page
Gene Ontology Page
The Gene Ontology (GO) project (www.geneontology.org) has a central goal of building a controlled vocabulary that captures three different aspects of a gene product in a living organism: Biological Process or Processes (which is essentially, the reason why a gene product benefits the organism whose genome encodes it); Molecular Function or Functions (which is what the gene product does at a basic biochemical level) and Cellular Component (which is where in a cell the gene product is normally expressed).
The Gene Ontology project is extensively documented at the official web page of the GO consortium: http://www.geneontology.org
It 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.
Currently GO terms for a given gene product can be found in the Gene Ontology Classification section on the Gene Summary page.
GO terms are grouped under the three different Ontology Types of Biological Process, Cellular Component and Molecular Function. The annotation of a gene product to a GO term includes the following:
Term name: This is the primary name of the GO term assigned by the GO consortium to which the gene product is annotated. Clicking on the GO term links to the GO browser page view which displays the summary for the GO term. See below for section on 'Gene Ontology browser'.
Evidence: To the right of the GO term is the evidence on which this annotation is based, essentially the source to which the annotation is attributed. In most cases, especially in curator-performed annotations this will be a literature reference, this may also be another database or a method in computational analysis. Sometimes the annotation is based on homology to a known protein in which case it is known as 'protein_id evidence' and includes the GenBank id for the cited protein. Both curator-performed, literature-based annotations and those obtained from computational analysis-'IEA annotations' are displayed by WormBase. Clicking on the reference links to the citation display page.
Evidence code: To the immediate right of the GO term is the 'evidence code' which is the type of evidence found in the cited source to support the association of the gene product with the GO term, eg. Inferred from mutant phenotype (IMP), Inferred from direct assay (IDA), Inferred from genetic interaction (IGI), etc. Clicking on the evidence code links to the Gene ontology consortium's documentation on evidence codes and their usuage.
The annotations in each Ontology Type are displayed according to the following priority of order:
* IDA=Inferred from Direct Assay * IMP=Inferred from Mutant Phenotype * IGI=Inferred from Genetic Interaction * IPI=Inferrred from Physical Interaction * IEP=Inferred from Expression Pattern
* IEA=Inferred from Electronic Annotation
* TAS=Traceable author statement * IC=Inferred by curator * NAS=Non-traceable author statement * ND=No biological data available