Hi,
For those of you who are interested, the powerpoint presentation of our
pilot OWL-based integration of NeuronDB and CoCoDat is available at:
http://twiki.med.yale.edu/kei_web/sw_group/hbp_2006_4_24_sw_neurodb_int2.ppt
-Kei
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
