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From: Ward Blondé <wablo@psb.ugent.be>
Date: Wed, 29 Oct 2008 15:10:28 +0100
Message-ID: <49086ED4.3020004@psb.ugent.be>
To: public-semweb-lifesci@w3.org
CC: Matthias Samwald <samwald@gmx.at>


There were still some questions about BioGateway 
(http://www.semantic-systems-biology.org/) that emerged during the F2F 
meeting, but couldn't be discussed fully as the schedule was very tight. 
The key question was whether BioGateway is compatible with the HCLS 
initiatives, and BioRDF in particular. That is not so clear, mainly 
because of the URIs.

Which RDF did we use?
We made our own RDF-translations trough Onto-Perl 
(http://search.cpan.org/~easr/ONTO-PERL-1.13/), an in-house programming 
library, to have optimal queryability and integration of all the 
imported resources. Everything is fully automatic from downloading the 
original sources, to loading the created RDF into Virtuoso.

Why didn't we use existing OWL files, to use its RDF syntax?
We found out that SPARQL gave us the best results for querying. As 
Onto-Perl allows RDF-exports, we could optimize the RDF to get less 
verbose queries and quicker answers. The RDF syntax of OWL contains a 
sort of mini-graphs between related classes. That makes it a heavy 
burden for SPARQL querying, although SPARQL can not exploit this for 
reasoning purposes.

About the URIs:
We created our own URIs, because it was not clear to us which URIs 
should be preferred for usage. And also because that made it easy during 
the development, and realized too late how important this is. We think 
that common URIs is very important to make the Semantic Web work. Just 
like common tools and formats, we need common URIs! This is not crucial 
for http-URIs for web browsing by human, because a redirect to a 
synonymous URI will cost only a small fraction of the time, and web 
developers can maintain the redirects manually. But this is completely 
different for query systems and reasoning systems that have to do 
complex operations on millions of such URIs in a very short time.
Large synonym lists might solve this problem technically, but should be 
avoided if possible, I think.



Matthias Samwald wrote:
> Are the minutes from our F2F meeting [1] last week in Mandelieu 
> already online? I can only find some fragments, but not all of them.
> Thanks,
> Matthias Samwald
> [1] http://esw.w3.org/topic/HCLSIG/F2F/2008-10_F2F

Ward Blondé                                     wablo@psb.ugent.be
PhD student
Tel:+32 (0)9 331 38 24                        fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
Received on Wednesday, 29 October 2008 14:11:00 UTC

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