The evidence code of the annotation (IEA, TAS, ....) explain what is the origin of this relationship between gene and gene ontology. and the relations (is_a, part_of, ...), explains what is the relationship between GO terms
So far the tools I know to be used for Gene-GO analysis, doesn't use them, at most the inferred from electronic annotation is optionally excluded. But the relationship between GO are not used AFAIK in several tools like topGO, DAVID, AmiGO, GOStats, and the similarity scores of GO, like Resnik, Lin, Jiang, Rel and Wang.
Are there tools that use this information (and I have been simply clueless)? I am mainly interested in tools focused to humans.