On Mar 25, 2009, at 4:31 PM, eric neumann wrote:
Bijan,
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?
This is the kind of "similar" used in most internal genomic/compound
systems...
<http://myOrg.com/sw/mxid/PHLP0005> :isIdentifiedwith <http://www.uniprot.org/uniprot/P16233
>
It really isn't probabilistic anymore since the scientists have all
agreed and defined their entry based on some of the info from the
public entity; for most situations it is an 'exact mapping' to the
referred molecules. I agree owl:sameAs was not intended for this
kind of relation, but is is extremely common, and a specialized
relation for this would be very much desired. : )
Remember also, even though these URIs may be of instances in terms
of records, the molecule referenced is not really "a specific single
molecule" found in nature (conceptually possible, but never thought
of this way in may experience). In fact, this is almost always the
case in molecular biology (genes, genomes, SNPs, proteins, etc),
while when dealing with macro-humans, we can refer to an exact
instance in the real world.
I assume that the intended referent is a 'typical molecule' or a
'molecular pattern' rather than a particular, single molecule. Yes, of
course: but that doesn't affect the use of sameAs. Whatever these
'molecules' are that your ontology is talking about, sameAs means the
same one of those.
Perhaps we really need a set of basic relations (and meta classing?)
for this scale of scientific phenomena to keep it distinct from
organism examples in clinical studies and experiments...
The basic ontology issues of identity and so on should work at any
scale from quarks to galaxy clusters.
Pat
Eric
On Wed, Mar 25, 2009 at 4:05 PM, Bijan Parsia <bpar...@cs.manchester.ac.uk
> wrote:
Oh, another possibility, 4) probabilistic sameAs. That's probably
more researchy than similarity logics, but more in the next few year
timeline rather than in the "have no idea" timeline.
Cheers,
Bijan.
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