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"
<[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED] 09/05/2006 10:03 AM |
|
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
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="">
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)
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