Re: Less strong equivalences

Phil,
Wouldn't the structure of a molecule (seq for gene, bond connections for
chemical) be considered an instance in its own right? Consequently to your
point about 'classes',  the class of d-glucose molecules are really all
referring to the same Chem-Structure instance. Chemists will almost always
work with the structure entity and its associated (inferred) properties such
as mol weight, polarity, composition, etc.

Is it possible what we really need to address this "structure-identity"
issue for some of the points raised in this thread?


BTW, the "Carbon" in a periodic table is usually referred to by chemists as
an instance of type "Element".  Elements can be thought of as meta-classes
for atoms...
See,  scientists have already thought about the necessary differences when
it becomes necessary  ; )

cheers,
Eric


On Thu, Mar 26, 2009 at 8:16 AM, Phillip Lord
<phillip.lord@newcastle.ac.uk>wrote:

> Pat Hayes <phayes@ihmc.us> writes:
> >> From your descriptions, I can't tell which one would best handle the
> >> following situation:
> >>
> >> "Object 1 refers to exactly the same molecule (exemplar) as object 2
> refers
> >> to"
> >
> > That sure sounds like sameAs, applied to molecules. Why isn't sameAs good
> > enough here? What goes wrong?
>
> I can think of very few occasions when we want to talk about a molecule;
> we need to talk about classes of molecules. We can consider this as
> problematic even with a very simple example.
>
> Let's assume we have two databases with information about Carbon. Do we
> use "sameAs" to describe the atoms that they are talking about? Maybe,
> but what happens if one is talking about the structure of Carbon and
> it's location in the periodic table, while the other is talking about
> Carbon with the isotopic mix that we have in living organisms on earth?
>
> In biology, we have the same problem. Is porcine insulin the same as
> human insulin? Is "real" human insulin the same as recombinant
> human insulin? Well, the answer to all of these is no, even though most
> biologists will tell you that real and recombinant insulin are the same
> because they have the same primary sequence; a medic will tell you
> otherwise, because they have different effects. Why? Don't know.
>
> If you make the distinctions that you might need some of the time, all
> of the time, then you are going to end up with a very complicated model.
> Hence the evolutionary biologist says all the insulins are the same. The
> medic says that they are different. And neither of them care about
> different types of carbon (unless they are C14-dating).
>
> I don't think that there is a generic solution here which is not too
> complicated to use. The only solution (which is too complicated) I can
> think of is to do what we do when we have this problem in programming;
> you use a pluggable notion of equality, by using some sort of comparitor
> function or object. I don't think that this is an issue for OWL myself;
> I think it's something we may need to build on top of OWL.
>
> Phil
>
>