Gene Page: Gene Ontology

PomBase uses the Gene Ontology (GO) to describe the biological context of genes.

GO consists of three distinct ontologies (or sets of vocabularies) that describe a gene’s:

  1. Molecular Function (MF) — single-step activities such as kinase activity or transporter activity
  2. Biological Process (BP) — a series of functions with a common goal such as MAPK cascade or cytokinesis
  3. Cellular component (CC) — the location where the gene product can be found, and what complexes it is part of, for instance nucleus or fatty acid synthase complex

A gene product may be annotated to several GO terms from each of the three ontologies; cyr1, for instance, is annotated to adenylate cyclase activity, magnesium ion binding and protein binding (MFs), it acts in cAMP biosynthesis and positively regulates protein import into nucleus (BPs), and is found in the plasma membrane (CC).

The GO annotation display on PomBase gene pages includes ontology term details and supporting data. The Summary view shows just the essentials; each unique combination of gene, GO term, and extension(s) is shown once:

summary gene page GO annotations


  1. The GO term name, which links to a page with additional information, including the term definition, any synonyms, relationships to other GO terms, and a list of genes annotated to the term.
  2. Link to a page with term details and a list of genes annotated to the term and its is_a and part_of descendants (see the GO documentation on Ontology Structure and Ontology Relations for more information).
  3. GO annotations may have extensions to capture any of several types of additional detail. S. pombe genes link to PomBase gene pages.
  4. GO Slim terms applicable to the gene.

The Full view shows more details, including separate entries for repeat determinations of a given gene/term/extension combination (if supported by more than one line of evidence and/or reported in more than one paper):

full gene page GO annotations


  1. The unique ID and name for a GO term. The ID links to a page with additional information, including the term definition, any synonyms, relationships to other GO terms, and a list of genes annotated to the term.
  2. An abbreviation (code) for the type of evidence that supports the annotation. The evidence categories come from the set of evidence codes defined by the GO Consortium.
  3. An additional identifier that provides supporting details for annotations using certain evidence codes (see below and GO documentation).
  4. The paper from which the annotation comes.
  5. Link to a page with term details and a list of genes annotated to the term and its is_a and part_of descendants (see the GO documentation on Ontology Structure and Ontology Relations for more information).
  6. GO annotations may have extensions to capture any of several types of additional detail. S. pombe genes link to PomBase gene pages.
  7. GO Slim terms applicable to the gene.

Term ID and name

Annotations are made to the definition of a term, not the term name itself, so we recommend users always read the term definition. The definition of a term can be found by clicking the term ID. This page will also supply a list of all genes annotated to the specific term.

GO Structure

GO is structured in a hierarchal order with less specific terms being parents of more specific child terms. A child term may have multiple parents and multiple children; the BP mitosis, for instance, has child terms representing each phase of mitosis, as well as parent terms connecting it to both a cell cycle phase and nuclear division. Crucially, whenever an annotation is made to a term, the gene product is automatically annotated to all the parent terms. The ancestry of a term can be viewed on the page linked to the term ID. For more information, see the GO Ontology Structure documentation.

Multiple relationships exist to describe the links within the ontologies. A child term can have an is_a relation to the parent term, where the child is a more specific type of the parent, or a part_of relationship where the child makes up a part of the parent. For instance, the mitochondrion is_a intracellular organelle and is part_of a cell. Additionally, GO also include regulatory relationships. For more information on relationships in GO, see the GO Ontology Relations documentation.

Evidence codes

In PomBase, every annotation is supported by a reference that states where the annotation comes from, and an evidence code that describes the type of data that supports the annotation. An annotation may be inferred from experimental ‘wet lab’ data, backed by a literature reference and citing experimental evidence such as IDA (Inferred from Direct Assay) or IMP (Inferred from Mutant Phenotype). Further information on evidence codes is available in the GO Evidence Codes documentation.

Another source of annotations come from computational methods. Please note that all computational annotations are based on predictions. In cases where a sequence model has been used to annotate genes, but the genes annotated based on the model have not been manually checked, the IEA (Inferred from Electronic Annotation) evidence code is assigned. If the annotations have been manually checked other evidence codes may be used, for instance ISO (Inferred from Sequence Orthology) or ISM (Inferred from Sequence Model). PomBase uses ISO to cross-reference to the roles of known S. cerevisiae genes, and uses ISM when domains present in a gene product can give clues to its biological role.

For some types of evidence, such as sequence comparisons or interaction data, it is important to note what gene or gene product was used in the comparison or detected in the interaction. In these cases the With/From column provides more information regarding the source of the information.

Annotation extensions

Where available, annotation extensions are displayed underneath the GO term name. The extensions provide additional specificity to the annotation by linking the term to another ontology term or a gene product via a relationship. Examples include specifying substrates of molecular functions or specifying the cellular localization during a process (for instance, pka1 has protein serine/threonine kinase activity and has the substrates mei3 and rst2. It is a cellular component of the nucleus during nitrogen starvation, but part of the cytoplasm during glucose starvation).

The GO Consortium provides further information on annotation extensions in its annotation documentation, including the file format guide, on a wiki page, and in a publication. PomBase converts many extension names to more human-friendly text, as described here.

If an extension mentions another S. pombe gene, the extension data will also be displayed as an annotation in the "Target Of" section of the page for that gene.

Finding other genes annotated to a specific GO term

From a gene page, all S. pombegenes annotated to a term (or its children) can be found by clicking on a term ID.

Additionally, the advanced search (or ‘query builder’) can be used to search for all genes annotated to a particular GO term (see the advanced search documentation for more information). To find annotations to specific GO terms in organisms other than S. pombe we recommend using AmiGO or QuickGO.