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

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."

 

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Donald Doherty, Ph.D.
Brainstage Research, Inc.
412-478-4552