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

Dear Bill et al.,

Thanks for the articles and the explanation. I agree that we should 
consider mutliple brain regions in the case of Parkinson's Disease (as 
well as other neurological diseases). I just gave a specific example 
(purkinje cell is located in cerebellum).  There are other types of 
neurons located in other brain regions. At the ontology level, we 
probably should have a neuron class that has an "is_located_in" property 
linking to the brain-region class (neuronames can be a candidate 
standard taxonomy of brain regions). Also you mentioned that neuron has 
another property "contains". For example, dopaminergic_neuron contains 
tyrosine_hydroxylase  which is an enzyme. The interesting question here 
is that should we treat tyrosine_hydroxylase as a subclass or instance 
of the enzyme class? Also, another related question is that what can a 
neuron contain (pigment is not an enzyme)? Just my 2-cent thought.

Best,

-Kei

William Bug wrote:

> 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 
> <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 
> <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 
>> <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 
>>> <mailto: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 
>>>> <mailto: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>
>>>> <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>
>>>> <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 
> <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.
>

Received on Tuesday, 5 September 2006 20:54:02 UTC