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This figure is a structure diagram for FPO as it is expressed in OWL and RDFS.
As is typical for diagrams of this kind, the boxes represent classes of objects in FPO, and the lines between them indicate semantic connections. There are two quite different kinds of connections shown.
The structure might appear quite complex to a viewer who is seeing it for the first time, but it is useful to notice that it divides into several different areas, representing conceptually related parts, described below.