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

Absolutely, thanks Kei!

Though - for Parkison's - we're going to need to deal with neurons in  
the substantia nigra and the locus coeruleus.  For instance, see:

Relationship among alpha-synuclein accumulation, dopamine synthesis,  
and neurodegeneration in Parkinson disease substantia nigra.
Mori F, Nishie M, Kakita A, Yoshimoto M, Takahashi H,  Wakabayashi K
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? 
db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16896314&query_hl=32& 
itool=pubmed_docsum

One of the problems with these areas of the brain is the cell types  
are much less clearly characteristic than cerebellar Purkinje  
neurons.  They aren't completely without distinctive character and  
some details can be given, as they are in the above research article:

	:neuron :contains :pigment
	:neuron :contains :tyrosine_hydroxylase

It's just neither of these are properties commonly used to classify  
neuronal type, though the latter is a property of:

	:neuron :is_a :dopaminergic_neuron

but as Gordon Shepherd and Michele Migliore have pointed out, this  
tradition of typing neurons by transmitter is very problematic:

	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? 
db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=11988775&query_hl=35& 
itool=pubmed_docsum

Oops - time to call in.

Cheers,
Bill


On Sep 5, 2006, at 10:42 AM, Kashyap, Vipul wrote:

> 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>
>>>
>>>
>>>
>>> This email and any accompanying attachments are confidential.
>>> This information is intended solely for the use of the individual
>>> to whom it is addressed. Any review, disclosure, copying,
>>> distribution, or use of this email communication by others is  
>>> strictly
>>> prohibited. If you are not the intended recipient please notify us
>>> immediately by returning this message to the sender and delete
>>> all copies. Thank you for your cooperation.
>>>
>>
>

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







This email and any accompanying attachments are confidential. 
This information is intended solely for the use of the individual 
to whom it is addressed. Any review, disclosure, copying, 
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prohibited. If you are not the intended recipient please notify us 
immediately by returning this message to the sender and delete 
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