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Re: BioGateway

From: eric neumann <ekneumann@gmail.com>
Date: Fri, 31 Oct 2008 10:45:28 -0400
Message-ID: <92e86c7d0810310745g29360bedndd81f60f70679d4e@mail.gmail.com>
To: "Ward Blondé" <wablo@psb.ugent.be>
Cc: public-semweb-lifesci@w3.org, "Matthias Samwald" <samwald@gmx.at>
This indeed will be interesting to follow and compare to other Systems
Biology initiatives within industry (especially those that include an
ontological component). For example, I am currently working with one
pharmaceutical on such an project, and it indeed would be useful to see how
much can be gained by various approaches groups are taking, e.g., reliance
on reasoning vs other approaches. How this will compare with large-scale
data approaches that apply statistics on top of reasoning (e.g., to propose
class restrictions) will help the community identify effective
methodologies, and SB is certainly an area rich in that regard. May I ask if
the SSB is interested to interact with other companies (biotech and
pharmaceutical) around specific SB applications in therapeutic development?
It's always good to ground activities around business needs.

Regarding your question concerning URI compatibility, I think it may depend
on which way one is looking, since many of us feel most models discussed so
far from within HCLS would be generally supported, e.g., allow Linked Data.
Is there anything in particular in your URI model that may perhaps increase
constraints? One rule of thumb I see working is "do not force URIs to rely
too heavily on ontological constraints; it prevents uptake and ease of

I strongly believe the best way forward is to host some form of F2F that
specifically addresses the URI issues and benefits; such a gathering is at
least an order of magnitude more effective than online discussions. I
personally hope we can organize such a meeting or workshop early in 2009.
What are your thoughts?

best regards,

On Wed, Oct 29, 2008 at 10:10 AM, Ward Blondé <wablo@psb.ugent.be> wrote:

> Hello,
> 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.
> regards,
> Ward
> 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
> http://www.psb.ugent.be/cbd/people_ward_blonde.php
> ==================================================================
Received on Friday, 31 October 2008 14:46:05 UTC

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