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

On Sep 29, 2005, at 11:33 PM, wangxiao wrote:

>
> - 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.

Manual mapping per se is not bad. What is bad is when this mapping is  
not able to be reused outside of application it was intended for. The  
notion of "as needed" data integration / mapping is an important one.  
If one does realize these resources are the same, using the Semantic  
Web, they can and write this "mapping" back into the web for the next  
person / application to benefit from.  In essence, recording their  
knowledge of how things connect in a way that others can reuse.

If communities can come up with common naming conventions for  
identifying resources thats great, they should! But this is not a  
requirement. What is, is a common framework for expressing this  
information that can be used by everyone.

Again, this reduces to what works best for any particular community  
which (again) reduces to a social problem. Getting folks around the  
table to contribute to the discussion and find out what works and  
what doesn't is a huge step to addressing this problem. That said,  
from my perspective, this step is being taken and thats an important  
indicator of success.

--
eric miller                              http://www.w3.org/people/em/
semantic web activity lead               http://www.w3.org/2001/sw/
w3c world wide web consortium            http://www.w3.org/

Received on Friday, 30 September 2005 13:24:50 UTC