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

On Wed, Mar 25, 2009 at 5:47 PM, Bijan Parsia
<bparsia@cs.manchester.ac.uk>wrote:

> Eric,
>
> Thanks for the use case!
>
> On 25 Mar 2009, at 21:31, eric neumann wrote:
>
<snip>

>
>
>  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>
>>
>
> Can you explicate this a bit more for me? I.e., could you present what you
> expect this to do or not do?
>

Certainly... I want look up what myOrg knows about a uniprot protein, but
since they do their own internal data-keeping on things like "druggability"
which aren't included (yet) in uniprot, I need to make sure my extra data is
mapped to the public protein object.

Does this help you?

(Of course, in a SW world this could have all been done with internal
triples added to the uniprot URI locally...)


>
>  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.
>>
>
> Is it that most, but not all of the time, you can treat is as sameAs but
> sometimes you don't want to?


Well, the question we ask of experts like you is: should we are should we
not use owl:sameAs for exact mappings to entities with different records?


>
>
>  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. : )
>>
>
> We need to make me understand the relation :)


There are other "identiity" or "similar" relations in mol biology:

- homolog (symmetric) ; similar function in different species
- paralog (symmetric, sub-property of homolog )  ; similar origin
duplication in same species
- ortholog (symmetric; sub-property of homolog)  ; similar function in
different species
(also Ohnology and Xenology, see
http://en.wikipedia.org/wiki/Homology_(biology))
- variant of (a non-subsumptive form of specialization within genes)
- modified form of  (a non-subsumptive form of specialization for protein
gene products), includes splice variants (see
http://www.affymetrix.com/community/publications/affymetrix/tmsplice/index.affx
)
- similar chem structures (symmetric for compounds)

... I'm sure there a re dozens more.


>
>  Remember also, even though these URIs may be of instances in terms of
>> records,
>>
>
> instances of what?


For a "collective grouping" of similar instances of (physical) molecules...
d-glucose is 'a' specific molecular structure, but there are over 10^25 of
glucose molecules in a teaspoon of dextrose sweetener.... Not the usual OWL
concept of "instance of class Molecule" is it?

Defining 'glucose' as a Class just pushes the definition of Molecule up to
become more akin to a meta-Class...


>
>  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.
>>
>
> We cannot?


No one in pharma is interested in mapping URIs to an individual exact,
physical molecule; IP is always around the chemical structure (which IS
unique) rather than the molecule.

>
>
>  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...
>>
>
> I suspect there's more weight on "exemplar" than I know how to give at the
> moment :)


Well, try keeping a URI tracking a single molecule-- there's no business
value in that! ; )

Eric


>
>
> Cheers,
> Bijan.
>