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

Tue, 05 Sep 2006 13:56:45 -0700 


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:[EMAIL PROTECTED]
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:[EMAIL PROTECTED]
*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 - [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> 
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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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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.

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