- From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
- Date: Tue, 5 Sep 2006 12:23:08 -0400
- To: "William Bug" <William.Bug@DrexelMed.edu>
- Cc: <helen.chen@agfa.com>, <public-semweb-lifesci@w3.org>
- Message-ID: <2BF18EC866AF0448816CDB62ADF6538104C16210@PHSXMB11.partners.org>
Bill,
Thanks for the info...
Will install it and see if it works...
---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
________________________________
From: William Bug [mailto:William.Bug@DrexelMed.edu]
Sent: Tuesday, September 05, 2006 12:21 PM
To: Kashyap, Vipul
Cc: helen.chen@agfa.com; public-semweb-lifesci@w3.org;
public-semweb-lifesci-request@w3.org
Subject: 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-A86
8-D0044406F57D&displaylang=en
<http://www.microsoft.com/downloads/details.aspx?FamilyID=3DD3F3BE-656D-4830-A86
8-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
<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=AttachFile&do
=get&target=SeedOntologyUML.vsd
<http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology?action=AttachFile&d
o=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 - William.Bug@DrexelMed.edu
<mailto:William.Bug@DrexelMed.edu>
This email and any accompanying attachments are confidential.
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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
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 16:23:49 UTC