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

From: kc28 <kei.cheung@yale.edu>
Date: Wed, 03 May 2006 21:39:11 -0400
To: donald.doherty@brainstage.com
Cc: public-semweb-lifesci@w3.org
Message-id: <44595B3F.3080605@yale.edu>


For those of you who are interested, the powerpoint presentation of our 
pilot OWL-based integration of NeuronDB and CoCoDat is available at:



Donald Doherty 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.ppt
> 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
Received on Thursday, 4 May 2006 01:44:18 UTC

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