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

Hi, Vipul

Thanks for putting a head start on this task. 

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. 

Maybe, as a best practice in this group, we should try to use RDF/OWL and 
find some visualization tools for display?  We could even use visio to 
draw some graphs to express design ideas of the ontology to be developed, 
yet better avoid using direct UML notation.

My two cents.

Kind regards.

Helen









"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
 
 


 


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