AmiGO Manual: Term Details

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Overview

The term details page displays information associated with the GO term. The GO term is shown in large font at the top of the term details page.

Below the term, links are provided for direct access to the three subsections of the term details page: Term information, Term lineage and External references. The Term associations is a hyperlink to a page listing all the genes and gene products that are associated with the GO term.

Term Information

Term Information displays a list of the fields associated with the GO term.

Accession

The accession is the unique identifier for the GO term in the GO database. This is always in the format GO: followed by a seven digit number, e.g. GO:0003684.

Ontology

Ontology indicates which of the three GO ontologies (biological process, cellular component or molecular function) the term is in.

Synonyms

The synonym section lists phrases with the same or similar meaning to the GO term. Synonyms are prefixed by a type (exact, broader, narrower or related) that indicates the degree of equivalence in meaning to the GO term. The GO synonym documentation contains more information about the different synonym types.

Definition

The definition is an explanation of what the term means. The origin of the definition is indicated in square brackets after 'source:'. Some GO terms do not have definitions at present; missing definitions will be added gradually as part of the ongoing development of GO.

Comment

A wide variety of additional information relating to the term is added in the 'comment' section. This may include noteworthy biological information relating to the term, advice for database curators to help them choose the most appropriate term or historical information on the term.

Subset

A list of the subsets that this term belongs to. For more information about GO subsets, please see the guide.

Community

A count of the number of community annotations that have been provided for this term by the users through the GONUTS wiki. If there annotations, it will indicate the number that have been added in the past year. Clicking on the N comments link will take the user to the "Notes" section of the GONUTS wiki page for this term. Clicking on the GONUTS page link will take the user to the GONUTS wiki page for this term.

Term Lineage

This section shows the term in relation to other terms in the ontology. The term can be viewed in the context of either Term Ancestors or Term Siblings by clicking the preferred radio button and change view. Viewing the Term Ancestors is the default view.

Further details are available about browsing the ontology.

Viewing Options

  • Graphical View
  • View in tree browser

The links box gives users to view the tree they have created. Graphical view shows the tree as a graph using the GraphViz plug in, and users can then download a GraphViz dot file; View in tree browser links back out to the main term browser for further browsing.

External References

This section shows cross references between the GO term and external databases. The number of external database entries mapping to the GO term is shown in brackets after the database abbreviation. A list of database identifiers can be viewed by clicking on the Icon-plus.png icon; where direct links to the database entries are provided (if available).

Typical examples are links to databases of protein domains such as InterPro and Pfam. Conserved protein domains are often associated with particular biological processes, molecular functions or cellular components that can be described using GO terms.

The relationship between GO terms and biochemical pathways is also captured in cross references to the databases such as Reactome, MetaCyc and the Enzyme Commission.