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

On Mar 25, 2009, at 5:27 PM, eric neumann wrote:

Several different issues here.

>
>
> 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?

It doesn't help me. We need to have a 'semantic' answer. What kinds of  
thing are being talked about here? What do the URIs refer to? (Records  
or chemicals?) Because the use of sameAs depends on the answer to this  
question very crucially.

>
> (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?

If your URIs are referring to the entities, then use sameAs when you  
are sure you are talking about the same entity, no matter what your  
records say about it. If they are referring to the records, then I  
would guess that sameAs would be true only when two URIs resolve to  
the same resource using GET.

>
>
>
> 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

Braaagh! Semantic alarm!  Identity is NOT similarity. Identity really  
does mean being EXACTLY the same thing. If A similarTo B, then we are  
talking about two things which are similar. If A sameAs B, then we are  
talking about ONE THING which happens to have two names.

> 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

None of these are identity.

> (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)

None of these are identity.

One way to use identity here is to try to map the original things to a  
'sort' or 'similarity class' or similarity type' or <choose your own  
buzzword>, and then use identity reasoning on these 'types'. So [ A  
similar-to B] is glossed as [(similarity-type A) sameAs (similarity- 
type B)]  but this only takes you so far: you still get transitivity,  
for example, so notions like 'very close' don't work this way. Still,  
it might be one way to approach the issue.


>
> ... 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?

This is just a basic ontology issue. You need to distinguish a  
particular molecule from a molecular 'pattern' from a class of  
isomers, etc.., BUt you can;'t expect OWL to do all this kind of work  
for you automatically.

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

Right, exactly. Classes weren't meant to carry this kind of conceptual  
load. You will just have to do some real ontologizing, my friend :-)

>
>
>
> 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.

Good: you have a clear ontology and a clear identity criterion for  
sameAs. You are talking about chemical structures. I'd suggest, if you  
really want to talk about molecules, having properties  
has_chemical_structure (domain: molecule; range; chemstruct) and  
is_a_molecule_of as its inverse. Don't use the class structure for  
Avogadro.

Pat Hayes

>
>
> 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.
>

------------------------------------------------------------
IHMC                                     (850)434 8903 or (650)494 3973
40 South Alcaniz St.           (850)202 4416   office
Pensacola                            (850)202 4440   fax
FL 32502                              (850)291 0667   mobile
phayesAT-SIGNihmc.us       http://www.ihmc.us/users/phayes