Re: Less strong equivalences (was Re: blog: semantic dissonance in uniprot)

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"

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.

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...


Eric




On Wed, Mar 25, 2009 at 4:05 PM, Bijan Parsia
<bparsia@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.
>
>