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=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)
>
> 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 14:41:07 UTC