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Re: [moby] Re: [MOBY-dev] [HCLSIG] homologs for yeast proteins?

From: Mark Wilkinson <markw@illuminae.com>
Date: Wed, 01 Feb 2006 11:32:04 -0800
To: Core developer announcements <moby-dev@biomoby.org>
Cc: public-semweb-lifesci@w3.org
Message-Id: <1138822324.4897.41.camel@bioinfo.icapture.ubc.ca>

The web-service branch of BioMOBY is up and running happily (and is
being well-used!) but is somewhat locked-in to a legacy XML format that
was designed a couple of years before RDF became "the norm".  This is
unfortunate, since the MOBY XML format was designed to do a very similar
job - that is, serialize an ontology.  

Nevertheless, we are muddling through, and though the messages that are
being passed between service and client are in this MOBYesque XML
format, we do use ontological queries to achieve the "semantic mapping"
between a client with a piece of data, and the various services that
could operate on that data.  The guts of MOBY are very rapidly being
migrated to use OWL/RDF to enhance and simplify this semantic mapping
using a reasoner, but the messaging format will remain a legacy problem
for quite a while since we have so many services that use it now...  It
seems, however, that we can inter-convert our XML with RDF fairly easily
and reliably, so this may not be as big a problem as we had initially

Eric Miller (on this list) has seen my presentation of MOBY and talked
to me briefly about it, so he may have some comments on how close/far we
are from a "true" semantic-web-service vision... given that we built
this in 2001, I think we got it ALMOST right! ...personal bias, of
course ;-)


On Wed, 2006-02-01 at 12:17 -0700, Andrew D. Farmer wrote:
> replying to the following (and apologies for some cross-posting):
> <snip1>
> > Basically that's why I'm in this group. A challenging question for any
> > existing Bio* package is whether it can meet the _next_ set of challenges,
> > like integrating the data. Without attempting to answer that question I'll
> > say it's easy to imagine that "BioRDF", or the equivalent, would make an
> > excellent alternative.
> </snip1>
> <snip2>
> > > one-stop web portal that can answer this query right now. But it it
> > > doesn't really help with the generalised case of ontology-aware queries
> > > of disparate data sources. BioMoby may be able to do something like
> > > this. Any BioMoby folks on the list?
> </snip2>
> Hi all-
> I've been somewhat involved in the various BioMOBY projects (though by
> no means an official spokeperson- hopefully others from that community will
> chime in), but I picked up on Chris' reference. These things are certainly
> very much the space at which the BioMOBY efforts are aimed and the use of 
> semantic web technologies, though still a bit nascent, is beginning to take off
> in some of the MOBY-related development efforts.
> As one example, you might care to look at a prototypical system based on 
> an early version of the "semantic MOBY" branch of the project at:
> http://lin.ncgr.org
> There are a few sets of slides off the help link that give a bit more details
> than I will here.
> It uses OWL-based service descriptions for "data-driven" service discovery and
> RDF graphs for transmission of data in service invocation and response graphs,
> which enables some interesting aggregative behavior, hooks nicely into some
> "rich clients" for visulization and interaction with the data, and at least
> sets the stage for us to engage in some of the nifty promises offered by the
> higher levels of the semantic web stack. Coincidentally, the central "use
> case" we chose to highlight the prototype was in fact right along the lines
> of the question that started this thread, namely exploring 
> homology/orthology/paralogy relationships among functionally annotated
> sequences (though our focus is on legume data, in which these issues are
> even more interesting than yeast, IMHO! note, too, that plant biology is 
> also very important to the issues of human health that appear to be the
> main focus of the "life sci" half of this interest group...)
> It is very much a prototype at this point (in terms of functionality,
> documentation, and "production-readiness", i.e. please don't retrieve
> a set of 10000 sequences and send it to the BLAST service!), 
> but early indications from the plant biologists to whom we have demoed to 
> indicate that we have gone a fair way to helping our user community begin to
> understand the "semantic value proposition".  We hope to evolve it to tap 
> into even more of the potential of the semantic web technologies, we have a
> lot of ideas about next steps and welcome any help in this direction from
> interested parties. 
> I guess that is probably enough for the purposes of this list, if anyone
> is interested in further conversations in this direction, they can get in
> touch with either our small project (lin@ncgr.org) or the larger
> MOBY development community (subscribe to lists at biomoby.org).
> Thanks for listening...
> Andrew Farmer
> adf@ncgr.org
> (505) 995-4464
> Database Administrator/Software Developer
> National Center for Genome Resources
> ---
> "To live in the presence of great truths and eternal laws,
> to be led by permanent ideals-
> that is what keeps a man patient when the world ignores him,
> and calm and unspoiled when the world praises him."
> -Balzac
> ---
> _______________________________________________
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> MOBY-dev@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-dev
....his last words were 'Hey guys!  Watch this!'
Mark Wilkinson
Asst. Professor
Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics
St. Paul's Hospital
Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274

"For most of this century we have viewed communications as a conduit, 
       a pipe between physical locations on the planet. 
What's happened now is that the conduit has become so big and interesting 
      that communication has become more than a conduit, 
       it has become a destination in its own right..."

                Paul Saffo - Director, Institute for the Future
Received on Wednesday, 1 February 2006 22:56:15 UTC

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