Hello everybody,
We (RSC) also need to be able to describe at least some molecular models of non-existent molecules, so here goes, and I'd be delighted to hear what the BFO people have to say about this. But I'm in no special hurry, because they're all GDCs.
It's the "aboutness" that's the problem.
--8<--
An effective method, I read, is a sequence of instructions which if followed will result in the completion of a given task. (This is an idea in computer science; hopefully the people who are thinking of ontology work as a branch of computer science will know all about it.)
So what I shall call an _effective_ specification is a specification which can be followed and doesn't involve any creative input on the part of the follower. It's "about" the steps you would take, I think. IAO's "plan specification" is one of these.
Connection tables, DNA sequences, RNA sequences and protein sequences all specify molecules. However, unless you are Maxwell's demon (and I know I amn't) it's impossible to take a connection table and manoeuvre atoms into the specified places and end up with a molecule. There are actually ways of synthesizing DNA molecules and proteins with a given sequence, step-by-step, but they only work for short sequences and not the sort of thing you get in GMODs. And you can work out the connection table for a natural product molecule rather quickly but it could take decades and dozens of PhD theses to work out how to make the molecule in the lab.
So these molecular models are _non-effective_ specifications. And any "properties" you can extract from them, by means of data transformations, are really predictions. If the molecule exists, then there is an aboutness relation between the connection table and the molecule, and aboutness relations between the predictions and the molecule, but not otherwise.
--8<--
Does that sound sensible? So in summary, molecular structures are GDCs, specifically non-effective specifications, derived "properties" are GDCs too, specifically predictions, and they only have aboutness relations if the molecule actually exists. And we need not worry about aboutness for many many intermediate bits of data we might be passing around in RDF.
Best wishes,
Colin.
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