AmiGO help Term Details

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Term Details Page

The term (e.g. damaged DNA binding) is shown in large font across 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.

'Term associations' provides a link to a page listing all the genes and gene products that are associated with the GO term.

The 'XML' link displays the term report page in XML format.

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

Synonyms lists expressions with the same or similar meaning to the GO term

e.g. exact: glucose biosynthesis

Synomyms 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 guide http://www.geneontology.org/GO.usage.shtml#synonyms 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:'. Sources include research papers, books and enzyme commission (EC) definitions. Relevant identifiers are provided e.g. ISBN for books and where possible these link to external databases (e.g. to PubMed from PMIDs).

'Source' may also include the initials of the GO consortium (GOC) member that supplied the definition.

e.g. [source: GOC:mcc, PMID:10873824, PMID:11389764]

Note that 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.

For example comments sometimes highlight similar sounding terms that are easily confused such as for 'pseudouridylate synthase activity' (GO:0004730) which contains the comment:

comment: Note that this term should not be confused with 'pseudouridine synthase activity ; GO:0009982', which refers to the intramolecular isomerization of uridine to pseudouridine.

Ontologies are constantly under development and occasionally this process involves making a term obsolete (see obsoleting terms http://www.geneontology.org/GO.usage.shtml#obsoletions for more about this process). Comments are used to explain why a term has become obsolete and to suggest alternative related GO terms.

Comments also record noteworthy biological information relating to the term and provide advice for database curators to help them choose the most appropriate 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 (default setting) by clicking the preferred radio button and change view.

!! copy Jane's image here!!

The level of a term is represented by its indentation within the tree, with general terms being less indented than more specific terms. In the above image, you can see that "extracellular organelle" is a child (less specific) term of "organelle", and a sibling term of "intracellular organelle". Each term name is preceded by its GO identifier (e.g. GO:0012345).

Clicking the term name will take you to more detailed information about that term.

The relationship of a term to its parent is represented by the icon immediately preceding the term identifier; the relationship types are "part_of" (represented by the pink 'P' icon) and "is_a" (represented by a green 'I' icon). So in the above case we can see relationships like: "organelle lumen part_of organelle" or "intracellular organelle is_a organelle".

Preceeding each term is either a '+', '-', or '.' icon. A '+' icon means that the term has children which are not shown in the current treeview; the node can be expanded by clicking the icon. A '-' icon means that the term has been selected and all of its children are shown in the tree (as is "organelle" in the above image). The node can be collapsed by clicking the '-' icon. Finally, a '.' icon means that the term does not have children.

Near the end of each term line is a number in brackets. This number represents the number of genes and proteins that are associated with that GO term. This number can change based on the search filters the user selects. For instance, if a user opts to only look at genes that have been annotated by FlyBase, the number will be lower. For certain filters, the numbers of genes associated to a term cannot be easily computed, in which case the number in the brackets will not be shown.

Clicking the number will take you to a full list of the gene associations.

At the end of some term lines is a pie icon, clicking on this will take you to a pie-chart showing the distribution of genes associated for that term and its children.


External References

This section shows cross references between the GO term and external databases.

Typical examples are links to databases of protein domains such as InterPro, PRINTS, Pfam, ProDom and SMART. Conserved protein domains are often associated with particular biological processes, molecular functions or cellular components that can be described using GO terms. GOC try to ensure that mappings between protein domains and GO terms are accurate; you can help us by reporting any suspect mappings to GO. !!should the database abbreviations link-out to the relevant db??

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

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; where possible direct links to the database entries are provided.