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Re: [HCLSIG] homologs for yeast proteins?

From: Andrew D. Farmer <adf@ncgr.org>
Date: Wed, 1 Feb 2006 12:17:37 -0700 (MST)
To: Brian Osborne <osborne1@optonline.net>
cc: lin@ncgr.org, <vpin@ncgr.org>, <moby-dev@biomoby.org>, chris mungall <cjm@fruitfly.org>, <public-semweb-lifesci@w3.org>, <jluciano@predmed.com>
Message-ID: <Pine.LNX.4.44.0602011046490.9512-100000@alberich.ncgr.org>

replying to the following (and apologies for some cross-posting):

> 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.
> > 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?

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:

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
(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."
Received on Wednesday, 1 February 2006 19:18:11 UTC

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