RE: Semantic web for life sciences: vision vs. reality

- Greg,

> The data model that UniProt uses is record based, each 
> protein has a unique LSID identifier, where as the Reactome 
> data uses bnodes for protein identifiers. The protein 
> resources in BioPAX have cross reference properties but these 
> point to literal UniProt identifiers not LSID UniProt 
> identifiers. That means I have no way of knowing that the 
> resource identified by 'urn:lsid:UniProt.org:UniProt:Q96LC9' 
> in the UniProt data is the same as the resource identified by 
> 'UniProt_Q96LC9_BMF_protein' in the reactome data (besides 
> the fact that bnodes are not globally unique).

So, the problem is a social problem.  All "standardization" problem is.
That is not the problem of SW per se.  SW is a framework, it offers a bed of
possibilities.  How we can make out of the possibilities is up to the
practioner not designer, right?  If two ontologies don't use the same URI to
refer to the same resource, there is no other way around except manual
mapping.  This is why we need standardization.
 
> But what about ontologies ? In Biology they seem to be having 
> their own problems at the moment [2]. 

I share very much with
[2](http://www.nature.com/nbt/journal/v23/n9/full/nbt0905-1095.html) that
picked MGED apart.  I hope no one get offened here.  But I think MGED people
are still in the thinking of OO.  The MGED ontology is still an OO model but
with an RDF disguise.  

> So how to get there ?

Standardization and education.  A lot of social issues.  This is actually
what I hope this discussion group can bring to biologiest.  In the
meanwhile, you just have to keep doing what you do to get your job done.
This is just an unfortunate reality.  And besides, we cannot wait for all
the ontologies and standard to fall into places before we can do meaningful
thing.  But the future, however a fantasy it might be, is bright and we got
to give it a try, don't we?

Received on Friday, 30 September 2005 03:34:08 UTC