- 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
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 UTC