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

From: kei cheung <kei.cheung@yale.edu>
Date: Fri, 19 May 2006 15:31:38 -0400
To: eneumann@teranode.com
Cc: donald.doherty@brainstage.com, public-semweb-lifesci@w3.org
Message-id: <446E1D1A.2080708@yale.edu>

Hi Eric,

As a baby step towards making a stronger connection between the SenseLab 
task (http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/SenseLab) and 
the neuroscience community, I made some update on the SenseLab task 
description based on some people's suggestions (e.g., Susie suggestion 
on including my OWL-based integration work reported at the HBP meeting 
and Alan's suggestion on providing some examples of mapping SenseLab 
concepts to standard neuro-ontologies). I have added two new sections 
which are: "Work in Progress" and "Mapping to existing standard ontologies".

Best,

-Kei

 Eric Neumann wrote:

>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 Friday, 19 May 2006 19:31:49 GMT

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