2.1 Term information
Term data are split into two types: details of the term itself and information on the gene products annotated to that term or its children. Clicking on a term name in AmiGO will bring up the term details page, which displays ontology information, including the term accession, synonyms, definition, comments and mappings to similar or equivalent terms in other databases. The term lineage is displayed in a tree browser, allowing users to view and explore the areas of the ontology graph surrounding the term.
The term annotations page, which can be accessed via the associations link next to a term name, lists gene products annotated to (i.e. associated with) the GO term and its children in the ontology. Each annotation includes the evidence used to make the assertion, commonly a paper reference and a code representing the evidence type (e.g. IMP, Inferred from Mutant Phenotype; TAS, Traceable Author Statement; IC, Inferred by Curator). Annotations can be filtered by the properties of the gene products, such as species, source database or gene product type (e.g. protein, gene, transcript); by evidence code; and by whether the gene products are annotated directly to the term or to a child of the term. Links are provided to download the data in RDF-XML or the GO Consortium's gene association file format. Gene products can be selected and used for other operations, such as retrieval of annotation data, or as input for the Term Enrichment or GO Slimmer tools.
2.2 Gene product information
As with term-related data, AmiGO provides gene product information and a list of the terms to which a gene product is annotated. Gene product details are supplied by the source database and include the symbol, full name, synonyms and database ID; if a sequence is available, this will be displayed along with information parsed from the FASTA headers. The terms to which the gene product is annotated are shown on a separate page; these data can be filtered to display only annotations with certain evidence codes and/or terms from chosen ontologies. Download links are provided and terms can be selected for further actions, such as viewing in the context of the GO tree or for use with the GO Slimmer.
Every page in AmiGO offers a simple search box through which users can query the GO database for GO terms or gene products. AmiGO returns search results ordered by how closely the result matches the original query; results can also be sorted by other parameters, such as accession in term searches, or gene symbol when querying for gene products. Users can fine-tune their results by setting term- or gene product-related filters, or confine the search to certain parameters of the term or gene product. Each search result has links to both the details and annotations of the term or gene product.
An alternative to searching for terms and gene products is to explore the GO ontology using the browse option. Starting at the top of the ontology tree, users can expand term nodes to view their children and navigate down through the hierarchy. If a term appears in multiple locations in the tree, all occurrences are displayed, thus giving users an idea of how terms are related. The display shows the number of gene products annotated to each term, including annotations to its descendants; filters can be used to generate the number for selected databases or species. There are several options for viewing and saving tree information. Users can visualize the ontology as rendered by GraphViz (http://www.graphviz.org
), or download it as a GraphViz dot file, as RDF-XML, or in OBO (http://www.geneontology.org/GO.format.obo-1_2.shtml
) format. Additionally, AmiGO shows the distribution of annotations to a term and its children in both graphical and tabular formats via the bar chart viewer.