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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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 [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
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
==================================================================
