Chris wrote:
alternatively you can go down what I guess is more the biopax-obo route;
make your reaction a subclass of the GO function, use classes to
represent the proteins and chemicals involved, with some kind of
participation relation between the participants and the reaction
Of course one would need to be aware that the GO molecular function branch
represents FUNCTIONS, not processes. At least that seems to be the way we
should interpret it from a BFO perspective. A molecular function like
'binding' cannot have participants (such as molecules). The molecular
function can be realized as a binding process, and this process can then be
described through its participants (molecules).
Of course, this is not very practical. It seems quite problematic to me that
certain things (such as molecular binding) are only represented in the GO
molecular function branch, but are not represented in the GO biological
process branch.
Cheers,
Matthias Samwald
Semantic Web Company, Austria // DERI Galway, Ireland
