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

Vipul,
 
Not trying to self-promote.  But I have designed a visual langauge that is
targeted specifically at the RDF/OWL based ontology formalism.  It is
extensible and self-descriptive (i.e., you can define your own notations for
specific concept). If you are interested, you might give it a try.  Here is
the project page, http://www.charlestoncore.org/dlg2/.  There is a visio
template to download too.
 
Xiaoshu


  _____  

From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Kashyap, Vipul
Sent: Tuesday, September 05, 2006 10:58 AM
To: helen.chen@agfa.com
Cc: public-semweb-lifesci@w3.org; public-semweb-lifesci-request@w3.org
Subject: RE: [BIONT] Teleconference on Tuesday, 5th September 2006



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
<http://www.microsoft.com/downloads/details.aspx?FamilyID=3DD3F3BE-656D-4830
-A868-D0044406F57D&displaylang=en> &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>
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>
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>
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=AttachFi
le&do=get&target=SeedOntologyUML.vsd>
http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology?action=AttachFil
e&do=get&target=SeedOntologyUML.vsd 
  
A discussion of Design Choices and other issues is available at: 
 <http://esw.w3.org/topic/HCLS/OntologyTaskForce/DesignIssues>
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 
  
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 -  <mailto:William.Bug@DrexelMed.edu>
William.Bug@DrexelMed.edu 
  
  


  



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