Re: BioGateway

Eric,

   the SSB team clearly aims at collaborating around specific SB 
applications (such as therapeutic development). We (Ward, Mikel, I, and 
some others from the SSB team) will be at the SWAT4LS meeting 
(http://www.swat4ls.org/) next 28 Nov. Will you be there? We could 
perhaps take the opportunity to initiate some discussions (e.g. URIs) 
within the panel session to set out the ground for a tentative F2F to 
specifically deal with such issues as you suggested.

cheers,
Erick

eric neumann wrote:
> Ward,
>
> 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 use". 
>
> 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,
> Eric
>
>
>
> On Wed, Oct 29, 2008 at 10:10 AM, Ward Blondé <wablo@psb.ugent.be 
> <mailto: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/
>     <http://search.cpan.org/%7Eeasr/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
>     <mailto: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 Monday, 3 November 2008 22:19:46 UTC