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

I strongly agree with Helen's point here.

Vipul, to answer your question regarding a graphical view of the  
ontology:

If - as I believe Alan suggested - we represent our ontology in OWL,  
then there are tools for displaying the contents visually using  
Protege-OWL.  These come in the form of two plug-ins:
	Jambalaya:
		http://www.thechiselgroup.org/~chisel/projects/jambalaya/ 
jambalaya.html
		(visualization built on SHriMP - http://www.thechiselgroup.org/shrimp)

	OntoViz:
		http://protege.cim3.net/cgi-bin/wiki.pl?OntoViz
		(visualization built on GraphViz - http://www.graphviz.org/)

I'm pretty certain both of these come installed with the "Full"  
version of Protege.

Cheers,
Bill



On Sep 5, 2006, at 10:58 AM, Kashyap, Vipul wrote:

> Helen,
>
>
>
> Thanks for bringing these issues up:
>
>
>
> I have one observation on expressing ontology in UML notation.
>
> As we know that UML and ontology language in semantic web (RDF and  
> OWL) are based on very different theory, although the hierarchical  
> structures of OWL classes and UML classes do look like the same  
> from the first glance.   But they are really different concepts.   
> Expressing your ontology in UML notation, even just for  
> visualization purpose, is quite misleading.
>
> [VK] I agree that UML and OWL have different meta-models and  
> semantics. At the initial stage, all we are doing is identifying  
> classes, relationships and properties. The goal is to represent  
> these into OWL but I hesitate
>       to do that unless the use case and requirements have  
> solidified. As you know the same piece of knowledge can be  
> represented in multiple ways in OWL (for which we hope to develop  
> best practices), so I do not want to commit to OWL semantics at  
> this early stage… OWL is not merely a notation, it has well  
> specified semantics…
>
> So at this stage, we are not committing to any UML semantics, we  
> are just using it for the visualization facilities.
>
> I would be happy to switch to another OWL-based tool which offers  
> the visualization capabilities offered by Visio… Any suggestions?
>
> Regards,
>
> ---Vipul
>
>
>
>
>
>
>
> "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
> Sent by: public-semweb-lifesci-request@w3.org
>
> 09/05/2006 10:03 AM
>
> To
>
> "William Bug" <William.Bug@DrexelMed.edu>
>
> cc
>
> <public-semweb-lifesci@w3.org>
>
> Subject
>
> RE: [BIONT] Teleconference on Tuesday, 5th September 2006
>
>
>
>
>
>
>
>
>
>
>
>
> 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).   
> 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, 5th 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
>
> 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
>
> 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
>
>
>
>
>
>
>
>
> This email and any accompanying attachments are confidential.
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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)


Please Note: I now have a new email - William.Bug@DrexelMed.edu







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