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:[EMAIL PROTECTED]
*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=AttachFile&do=get&target=SeedOntologyUML.vsd
<http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology?action=AttachFile&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)
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