- From: kei cheung <kei.cheung@yale.edu>
- Date: Tue, 05 Sep 2006 16:53:52 -0400
- To: William Bug <William.Bug@drexelmed.edu>
- Cc: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, public-semweb-lifesci@w3.org
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