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Re: [HCLSIG] Human Brain Project meeting notes...very cool!

From: Eric Neumann <eneumann@teranode.com>
Date: Mon, 1 May 2006 15:01:32 -0400 (EDT)
Message-ID: <59173.24.63.202.161.1146510092.squirrel@www.teranode.com>
To: donald.doherty@brainstage.com, public-semweb-lifesci@w3.org


Don,

Good to hear from you again, and I am really pleased that SW had a chance
to be discussed at HBP... wish I was there to have heard it. If you need
any additional help for your planned RDF-OWL activities, please do not
hesitate to ask any of the mmebers in HCLSIG or the larger SW working
group (I hope Eric Miller is listening ;-) ).

I would like to ensure your BIRN wiki use-cases get cross-posted (or
cross-linked) with the HCLSIG wiki's:
http://esw.w3.org/topic/CategoryHclsig. Perhaps Kei can help us out here.

best,
Eric

--- Donald Doherty <donald.doherty@brainstage.com> wrote:

> The Human Brain Project (HBP) meeting last week was
> very productive and
> extremely relevant to the work here at the HCLSIG.
>
>
>
> First of all, the word is out about RDF and OWL
> amongst the HBP
> neuroscientists, in large part due to the efforts of
> Karen Skinner, Bill
> Bug, Kei-Hoi Cheung, Maryann Martone, and some
> others. (Also, Eric Neumann's
> visit at the end of March educated many.)
>
>
>
> Most important for the HCLSIG team is that the HBP
> Ontologies and Standards
> working group has set as one of its three or four
> goals to try to make each
> of the neuroscience databases available in RDF or
> OWL so that cross-database
> integration/querying may be tried using semantic web
> technologies. The
> working group also agreed that they would share
> their use cases. Use cases
> from all of the HBP teams will be posted on a wiki
> at the BIRN site.
>
>
>
> Note that at least the following has already been
> accomplished:
>
>
>
> Kei-Hoi Cheung who is collaborating with Gordon
> Shepherd's laboratory and is
> also participating with the HCLSIG has created OWL
> versions of the NeuronDB
> and CoCoDat databases and performed cross-database
> queries on them. His
> example query was:
>
>
>
> "Find the receptors contained in the apical dendrite
> compartment of all
> types of pyramidal neurons in the neocortex which
> have been measured for an
> ionic sodium current having a voltage threshold of
> at least -35 mV"
>
>
>
> Kei posted the URL to his HBP meeting slides today:
>
>
>
> http://twiki.med.yale.edu/kei_web/sw_group/hbp2006_meeting_uupdate_hclsig.pp
> t
>
>
>
> Bret Peterson and Mark Ellisman spoke about the
> Biomedical Informatics
> Research Network (BIRN) and brought up the semantic
> web. Maryann Martone has
> created what looks to be an extensive OWL ontology
> for BIRN. The mouse-BIRN
> group is focusing on Parkinson's disease with
> example queries like the
> following:
>
>
>
> "Give me all images of medium spiny neuron
> tract-traces and histology of
> surrounding regions from the Parkinson's
> alpha-synuclein mouse model."
>
>
>
> -----
>
> Donald Doherty, Ph.D.
> Brainstage Research, Inc.
> 412-478-4552
>
>
>



Eric Neumann, PhD
co-chair, W3C Healthcare and Life Sciences,
and Senior Director Product Strategy
Teranode Corporation
83 South King Street, Suite 800
Seattle, WA 98104
+1 (781)856-9132
www.teranode.com
Received on Monday, 1 May 2006 19:01:51 GMT

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