AmiGO Manual: GraphViz
From GO Public
In addition to a text representation of the ontology structure, AmiGO provides a graphical view of the ontology. This option is available when viewing the details of GO term and when browsing the ontology, and can be accessed by clicking on the Graphical View hyperlink in the blue box to the right of the tree.
The more granular GO terms, the terms that describes a more specific aspect of biology, are drawn at the top of the display. Arrows point to the GO terms that are direct parents with the relationship between the GO terms (is_a, part_of, etc.) written next to the arrow.
The layout, box color, and text color can be customized in the graphical view by selecting the appropriate option in the pull-down menus at the top of the page. In addition, a dot text file can be generated of the graph by selecting Dot Text from the Format menu. This file can be imported into drawing tools such as ZRGViewer or OmniGraffle.