RE: [BIONT] Teleconference on Tuesday, 5th September 2006

Thanks, Kei Cheung!

This is one of the design issues I had raised. The issue of granularity is a
very important one, and you have provided an interesting use case.

Regards,

---Vipul

=======================================
Vipul Kashyap, Ph.D.
Senior Medical Informatician
Clinical Informatics R&D, Partners HealthCare System
Phone: (781)416-9254
Cell: (617)943-7120
http://www.partners.org/cird/AboutUs.asp?cBox=Staff&stAb=vik
 
To keep up you need the right answers; to get ahead you need the right questions
---John Browning and Spencer Reiss, Wired 6.04.95

> -----Original Message-----
> From: kei cheung [mailto:kei.cheung@yale.edu]
> Sent: Tuesday, September 05, 2006 10:41 AM
> To: Kashyap, Vipul
> Cc: William Bug; public-semweb-lifesci@w3.org
> Subject: Re: [BIONT] Teleconference on Tuesday, 5th September 2006
> 
> Hi Vipul, Bill et al.,
> 
> Thanks for your efforts. I think the seed (global) ontology is a good
> start. I'd also suggest to include modeling at the neuronal level that
> allows study of neuronal properties that are involved in Parkinson
> Disease. For example, the following OWL ontology
> 
> <owl:Class rdf:ID="#Cerebellar_purkinje_cell">
> <owl:equivalentClass>
> <owl:intersectionOf >
> <owl:Class rdf:id="purkinje neuron" />
> <owl:Restriction>
> <owl:onProperty rdf:resource="#locatedInBrainRegion" />
> <owl:allValuesFrom
> rdf:resource="#Cerebellum" />
> </owl:Restriction>
> <owl:intersectionOf />
> </owl:equivalentClass>
> </owl:Class>
> 
> It captures the knowledge that there are purkinje cells located in the
> cerebellum region of the brain. The interesting thing is that NeuronDB
> and CCDB, for example, represent this knowledge differently. In
> NeuronDB, there is a concept called "CerebellarPurkinjeNeuron", while in
> CCDB it's broken down into the following triples: PurkinjeNeuron,
> locatedInBrainRegion, Cerebellum. The above OWL ontology (or bridging
> ontology) indicates how to use the equivalentClass construct to
> establish mapping between NeuronDB and CCDB. OWL is just one way to do
> it. There are also other ways to do the same thing.
> 
> Cheers,
> 
> -Kei
> 
> Kashyap, Vipul wrote:
> 
> > For the time being, I have uploaded the JPEG and GIF versions of the
> > Ontology in UML.
> >
> > ---Vipul
> >
> > ------------------------------------------------------------------------
> >
> > *From:* William Bug [mailto:William.Bug@DrexelMed.edu]
> > *Sent:* Tuesday, September 05, 2006 12:01 AM
> > *To:* Kashyap, Vipul
> > *Cc:* public-semweb-lifesci@w3.org
> > *Subject:* Re: [BIONT] Teleconference on Tuesday, 5th September 2006
> >
> > Many thanks, Vipul.
> >
> > I think this is a nice, concrete start and will certainly provide a
> > solid foundation for discussion as we move forward - as will the
> > Design Issues page you've created.
> >
> > If it's OK, I'd like to make a small request re: the UML file. I see
> > MS has created an XMI export feature for Visio
> > (http://www.microsoft.com/downloads/details.aspx?FamilyID=3DD3F3BE-656D-
> 4830-A868-D0044406F57D&displaylang=en
> > <http://www.microsoft.com/downloads/details.aspx?FamilyID=3DD3F3BE-656D-
> 4830-A868-D0044406F57D&displaylang=en>).
> > Would it be possible for you to export the UML from Visio in XMI
> > format? This way I'll be able to use one of several open source
> > modeling tools that use XMI as there persistence file format. I assume
> > I'm not the only one on the list without a copy of Visio on hand. I
> > expect there may be some associations that don't translate perfectly,
> > but as it now stands, I'm not able to take advantage of the fruit's of
> > your labor. As a side note, I often provide a PNG version when
> > distributing models, just so others who either don't have the tools or
> > the knowledge of how to use open source equivalents can at least view
> > the model in a web browser.
> >
> > Many thanks again. I think it will be immensely helpful to have made
> > this concrete step forward. It also provides the BioRDF WG an
> > opportunity to comment on how this ontology will mesh with the
> > requirements they've been identifying for the Parkinsonian
> > Syndrome-related data sources.
> >
> > Cheers,
> >
> > Bill
> >
> > On Sep 4, 2006, at 10:43 PM, Kashyap, Vipul wrote:
> >
> >
> >
> > BIONT Teleconference on Tuesday, 5^th September from 11:00am - 12:00pm
> > US Eastern
> >
> > Phone: +1 617 761 6200, conference 24668 ("BIONT")
> >
> > IRC irc://irc.w3.org:6665/hcls
> >
> > Browser-based IRC client: http://www.w3.org/2001/01/cgi-irc
> >
> > *Agenda:*
> >
> > We will discuss the initial "seed ontology" for the Bench to Bedside
> > Ontology
> >
> > This is based on the use case specification available at:
> >
> > http://esw.w3.org/topic/HCLS/ParkinsonUseCase
> >
> > We will focus on the Cellular and Molecular Biologist view.
> >
> > The seed ontology is available at:
> >
> > http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology
> >
> > The seed ontology in the UML format (Visio File) is available at:
> >
> >
> http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology?action=AttachF
> ile&do=get&target=SeedOntologyUML.vsd
> >
> <http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology?action=Attach
> File&do=get&target=SeedOntologyUML.vsd>
> >
> > A discussion of Design Choices and other issues is available at:
> >
> > http://esw.w3.org/topic/HCLS/OntologyTaskForce/DesignIssues
> >
> > Cheers,
> >
> > ---Vipul
> >
> > =======================================
> >
> > Vipul Kashyap, Ph.D.
> >
> > Senior Medical Informatician
> >
> > Clinical Informatics R&D, Partners HealthCare System
> >
> > Phone: (781)416-9254
> >
> > Cell: (617)943-7120
> >
> > http://www.partners.org/cird/AboutUs.asp?cBox=Staff&stAb=vik
> > <http://www.partners.org/cird/AboutUs.asp?cBox=Staff&stAb=vik>
> >
> > To keep up you need the right answers; to get ahead you need the right
> > questions
> >
> > ---John Browning and Spencer Reiss, Wired 6.04.95
> >
> >
> >
> > Bill Bug
> >
> > Senior Research Analyst/Ontological Engineer
> >
> > Laboratory for Bioimaging & Anatomical Informatics
> >
> > www.neuroterrain.org
> >
> > Department of Neurobiology & Anatomy
> >
> > Drexel University College of Medicine
> >
> > 2900 Queen Lane
> >
> > Philadelphia, PA 19129
> >
> > 215 991 8430 (ph)
> >
> > 610 457 0443 (mobile)
> >
> > 215 843 9367 (fax)
> >
> > Please Note: I now have a new email - William.Bug@DrexelMed.edu
> > <mailto:William.Bug@DrexelMed.edu>
> >
> >
> >
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>

Received on Tuesday, 5 September 2006 14:43:07 UTC