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Browsing the Ontology
In AmiGO, the ontology is presented as a tree of terms. An example of part of a tree is displayed below:
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.