FuGE provides an object model for functional genomics experiments. Its specification (with XML examples) is at http://fuge.sourceforge.net/dev/V1Final/FuGEv1-refManual.html. Because of its precision (it aims at describing all possible steps performed in the laboratory) it has grown quite complex and detailed. It is also quite general (e.g. Material, for biological sources, only has a characteristics collection of ontology terms). It's main structural entities are Investigation (describing the experiment), Protocol (describing the followed procedures), Material (describing the biological sources/samples) and Data (essentially the results of protocol application as recorded by instruments).
Some parts of the FuGE object model, rendered in UML, that are relevant for the dbNP project: