Discussion about the Protege ontology editor and knowledge-acquisition tool

Taylor Cowan | 2 Aug 2007 04:41

Re: Racer reasoner

Pellet
http://pellet.owldl.com/download

nice integration with protege 3.3 via DIG interface.

----- Original Message ----
From: Jorge Barba <jbarba23 <at> gmail.com>
To: User support for Core Protege and the Protege-Frames editor <protege-discussion <at> lists.stanford.edu>
Sent: Monday, July 30, 2007 1:13:55 PM
Subject: Re: [protege-discussion] Racer reasoner

Thanks for your response!

What other reasoner do you recommend that I can download for free and work within Protege?

Regards!
Jorge

On 7/28/07, Samson Tu <swt <at> stanford.edu> wrote:

Racer is a commercial software now. See
http://www.racer-systems.com/products/racerpro/index.phtml

Jorge Barba wrote:
> Hi all,
>
> I am trying to use Racer within Protege. The website is
> http://www.sts.tu-harburg.de/~r.f.moeller/racer/
>
> but it is unavailable. The only thing there is:
>
>
>     Announcements
>
> RacerPro 1.9.1 beta is available now.
>
> This page will be updated really soon now to show the latest performance
> improvements.
>
>
> It's been like that for a while. There is another place where I can get
> Racer reasoner? Is this free software?
>
>
> Regards!
>
> Jorge
>
>
> ------------------------------------------------------------------------
>
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--
Samson Tu                    email: swt <at> stanford.edu
Senior Research Scientist    web: www.stanford.edu/~swt/
Stanford Medical Informatics phone: 1-650-725-3391
Stanford University          fax: 1-650-725-7944

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Jennifer Vendetti | 3 Aug 2007 04:35

Protege-OWL Short Course, Sept. 10-12, 2007, Stanford University

Dear Protege Community,

We are pleased to announce that we will be holding a Protege-OWL Short 
Course at Stanford University from September 10th-12th, 2007.  This will 
be a hands-on course taught by members of the Protege team in facilities 
located on the Stanford University campus.  Enrollment is limited to 
ensure optimal learning experiences.

Online registration is now available on the short course website:

http://protege.stanford.edu/shortcourse/protege-owl/200709/

We plan to make the full course schedule available by the end of this 
week.  If you have questions about the course, please do not hesitate to 
contact the course organizers:

protege-shortcourse <at> lists.stanford.edu

We look forward to meeting some of you in September!

Best Regards,
The Protege Team

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Jennifer Vendetti | 4 Aug 2007 00:06

Re: Open Source Reasoner?

There is also Fact++ from the University of Manchester, which is 
available under the GNU public license:

http://owl.man.ac.uk/factplusplus/

They have been working on this recently and added optimizations that 
have improved performance.  I believe the correct place for download is 
now Google Code:

http://code.google.com/p/factplusplus/

Jennifer

Gary Kopp wrote:
> My thanks to you, Michael and Taylor. Now I remember that Pellet was on my
> short list when I was looking at OWL almost a year ago, in a research
> project that I put on the shelf.
>
> --Gary
>
> -----Original Message-----
> From: protege-discussion-bounces <at> lists.stanford.edu
> [mailto:protege-discussion-bounces <at> lists.stanford.edu] On Behalf Of Michael
> Grove
> Sent: Wednesday, July 18, 2007 5:37 AM
> To: protege-discussion <at> lists.stanford.edu
> Subject: Re: [protege-discussion] Open Source Reasoner?
>
> I would tend to agree with Taylor, your best bet for an open source reasoner
>
> is definately Pellet.  You can find out more about how to set up its DIG 
> interface and its general use at the Pellet site (http://pellet.owldl.com)
>
> Cheers,
>
> Michael
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion <at> lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>   

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Bo Hu | 6 Aug 2007 11:40

CFP: Semantic Web in Ubiquitous Healthcare

Event highlights

Location and date: Busan, Korea, 12 November 2007
Registration deadline: October 2007
Paper submission deadline: 12 August 2007

------------------------------

--------------------------------------------

                          CALL FOR PAPERS
--------------------------------------------------------------------------

      The ISWC Workshop on Semantic Web in Ubiquitous Healthcare
                          (SemUbiCare)
            http://fountain.ecs.soton.ac.uk/semUbiCare/
November 12, 2007, ISWC'07 + ASWC'07 Workshop Program, Busan, Korea

------------------------------------------------------------------------
Motivation
------------------------------------------------------------------------

Ubiquitous healthcare refers to an emerging paradigm that is gradually
reshaping the old "patient-seeing-doctor" scenario into one in which
health services and information (e.g. clinical advices and warning,
patient status monitoring and feedback, etc.) become just "one-click" away.
At the heart of this envisioned "anywhere and anytime" healthcare is
empowering miniature computing devices with the ability to acquire and
understand data in a real-time and distributed environment, identify and
locate other devices to work together by forming an ad-hoc network, and
communicate with end-users in a human friendly fashion. While the advance
in technology has prepared us with essential hardware (e.g. sensors, HCI
devices, etc.), we are facing unprecedented challenges that are posed by
the vast amount of data and the distributed nature of the new approach
towards healthcare.

------------------------------------------------------------------------
Aim and Scope
------------------------------------------------------------------------

The main focus of this workshop is on providing an overview of existing
ubiquitous care platforms and elaborating on how semantic web technologies
can impinge on such existing efforts. We would particularly like to invite
developers and researchers of undergoing health/medical projects to share
with us their experience and lessons learnt. The workshop topics include,
but are not limited to:

* *Knowledge and EHR management in Ubiquitous Healthcare*
       o Healthcare knowledge acquisition, representation and
         visualisation
       o Healthcare knowledge modelling, healthcare ontologies,
         "lightweight" medical ontologies
       o Use-based ontology segmentation
       o EHR storage and semantic annotation
       o Digitising clinical guidelines
       o Knowledge sharing in healthcare organisations
       o Data interoperability and integration
* *Multimedia and Ubiquitous Healthcare*
       o Medical image/vedio clip annotation
       o Medical data retrieval
* *Healthcare services*
       o Workflow modelling in ubiquitous healthcare settings
       o Healthcare interventions modelling
       o Modelling decision making strategies
       o Device and functionality discovery and composition
       o Context modelling and context ontologies
* *Security, Dependability and Trust in Ubiquitous Healthcare*

We are particularly soliciting short papers describing deployed systems
in hospitals and clinical centres. Developers and Researchers who want to
participate in discussion are strongly encouraged to submit position papers.
Please state clearly in the position paper your expertise, what particular
problem you are interested, what solution you are looking for, and why
the statement is expected to be relevant to both the workshop and the community

------------------------------------------------------------------------
Programme Committee
------------------------------------------------------------------------

Olivier Bodenreider          National Library of Medicine, USA
Srinandan Dasmahapatra       University of Southampton, UK
John Fox                     Oxford University & Cancer Research UK, UK
Horacio Gonzalez-Velez       University of Edinburgh, UK
Warner ten Kate              Philips Research Lab, Eindhoven, Netherlands
Paul Lewis                   University of Southampton, UK
Mark Musen                   Stanford University, USA
David Robertson              University of Edinburgh, UK
Daniel L. Rubin              National Center for Biomedical Ontology, USA
Nigel Shadbolt               University of Southampton, UK
Carles Sierra             CSIS, Spain
Irma Velazquez               EHT, WHO, Switzerland
Takahira Yamaguchi           Keio University, Japan

------------------------------------------------------------------------
Important dates
------------------------------------------------------------------------

Paper submission:           12 August 2007
Acceptance notification:    8 September 2007
Camera-ready papers:        22 September 2007
Workshop:                   12 November 2007

------------------------------------------------------------------------
Paper submission and publication
------------------------------------------------------------------------

Electronic submissions of technical papers, short system description
papers and position papers will be accepted in MS Words, PDF. Selected
papers will be invited to submit to a journal special issue. Please visit
the main conference submission page for further information.

------------------------------------------------------------------------
Supported by
------------------------------------------------------------------------

EU HealthAgents Consortium
MicroArt, Spain
University of Southampton, UK

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Lanse | 7 Aug 2007 06:04

Protégé Query Results


Hi,
I am working on a program that analyzes the output from the query tab in
Protégé.  Would it be possible to include the names of slots in the output
file?
Thanks.
--

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View this message in context: http://www.nabble.com/Prot%C3%A9g%C3%A9-Query-Results-tf4227983.html#a12028167
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Jorge Barba | 8 Aug 2007 03:53

Re: Open Source Reasoner?

Hi Jennifer,

Thank you very much for the recommendations.

I am starting with Protege and I already learned how to create the Pizza Ontology on the tutorial.

Thanks again for your good references for the reasoner.

Best Regards!
Jorge

On 8/3/07, Jennifer Vendetti <vendetti <at> stanford.edu> wrote:

There is also Fact++ from the University of Manchester, which is
available under the GNU public license:

http://owl.man.ac.uk/factplusplus/

They have been working on this recently and added optimizations that
have improved performance. I believe the correct place for download is
now Google Code:

http://code.google.com/p/factplusplus/

Jennifer

Gary Kopp wrote:
> My thanks to you, Michael and Taylor. Now I remember that Pellet was on my
> short list when I was looking at OWL almost a year ago, in a research
> project that I put on the shelf.
>
> --Gary
>
> -----Original Message-----
> From: protege-discussion-bounces <at> lists.stanford.edu
> [mailto: protege-discussion-bounces <at> lists.stanford.edu] On Behalf Of Michael
> Grove
> Sent: Wednesday, July 18, 2007 5:37 AM
> To: protege-discussion <at> lists.stanford.edu
> Subject: Re: [protege-discussion] Open Source Reasoner?
>
> I would tend to agree with Taylor, your best bet for an open source reasoner
>
> is definately Pellet. You can find out more about how to set up its DIG
> interface and its general use at the Pellet site (http://pellet.owldl.com)
>
> Cheers,
>
> Michael
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion <at> lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>

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Raúl García Castro | 8 Aug 2007 10:06

CFP: (Deadline extension: 12th August) EON2007 workshop at ISWC2007

Apologies for cross-postings

----------------------------------------------------
                   CALL FOR PAPERS
----------------------------------------------------

         5th International EON Workshop on
Evaluation of Ontologies and Ontology-based tools
                    (EON2007)
    http://km.aifb.uni-karlsruhe.de/ws/eon2007/

               November 11th, 2007
             Located at the ISWC 2007
                  Busan, Korea

OBJECTIVES

The successful series of EON workshops have provided a meeting facility 
for the discussion and enhancement of technology evaluation in the 
Semantic Web. Ontologies and Semantic Web technologies are moving 
towards industrial application, and thus require evaluations and 
benchmarks to be available to a broader range of users and developers. 
The main goal of this workshop is to gather, share and reuse methods, 
tools and metrics for Web Ontology Evaluation and Semantic Web 
Technology Evaluation (ontology development tools, ontology merging and 
alignment tools, ontology-based annotators, etc.).

The previous workshops proposed a series of experiments for evaluating 
different aspects of ontology tools (EON2002, EON2003 and EON2004), e.g. 
their expressiveness and interoperability capabilities, and different 
aspects of ontologies. The aim of the EON series is to attract attention 
to a number of evaluation topics since we believe this to be a highly 
relevant issue for the adaptation of Semantic Web technologies by 
partners outside the Semantic Web community.

This year we aim to obtain methods, tools and metrics that can be reused 
by the whole community in ontology evaluation and ontology technology 
evaluation tasks. We propose a experiment in the ontology evaluation 
area, while for ontology technology evaluation we will ask for short 
papers that provide existing benchmark suite descriptions with the 
information needed to use them and that will be evaluated according to 
their usability by an expert committee.

Both the proposed evaluation methods, tools and metrics and well as 
their results will be collected and made available to the research 
community by means of the Ontoworld wiki. Therefore, they can be 
extended while research advances in these topics.

TOPICS OF INTEREST

Main topics of interest in the areas of ontology and ontology technology 
evaluation include but are not limited to:

  * Evaluation methodologies and methods
  * Tools and benchmark suites
  * Metrics
  * Certification
  * Web Ontology Evaluation
  * Ontology Content Evaluation and Criteria for Ontology Content Evaluation
  * Task-oriented Evaluation / Task-independent Evaluation
  * Formal/Informal Ontology Evaluation
  * Evaluation of Heavily Interconnected Ontologies / Networks of Ontologies
  * Interoperability of tools
  * Integration of tools into frameworks
  * Performance and scalability evaluations and benchmarks

SUBMISSION AND PROCEEDINGS

This year, papers will be submitted via the main ISWC2007 submission 
system. Papers should be formatted according to the guidelines of the 
ISWC2007 conference.

Papers must not exceed 10 pages. Short papers, experiment contributions, 
evaluation descriptions, and demo descriptions must not exceed 4 pages.

We will pursue a journal special issue with the topics of the workshop 
if we receive an appropriate number of high-quality submissions.

IMPORTANT DATES

  * Deadline for paper submissions: August 12th, 2007 (*extended*)
  * Deadline for experiment descriptions and demos: August 12th, 2007 
(*extended*)
  * Notification of acceptance (papers and demos): September 7th, 2007
  * Camera-ready versions: September, 28th, 2007
  * Workshop: November 11th, 2007

WORKSHOP ORGANIZING COMMITTEE

  * Raúl García-Castro (Contact Person), Ontology Engineering Group at 
Universidad Politécnica de Madrid (ES)
  * Denny Vrandecic, Institute AIFB at University of Karlsruhe (DE)
  * Asunción Gómez-Pérez, Ontology Engineering Group, at Universidad 
Politécnica de Madrid (ES)
  * York Sure (EON series inventor), Institute AIFB at University of 
Karlsruhe (DE)
  * Zhisheng Huang, Artificial Intelligence Group at Vrije University of 
Amsterdam (NL)

This event is supported by Knowledge Web and NeOn.

--

-- 

Raúl García Castro
http://delicias.dia.fi.upm.es/~rgarcia/

Ontology Engineering Group (http://www.oeg-upm.net/)
Universidad Politécnica de Madrid
Campus de Montegancedo, s/n - Boadilla del Monte - 28660 Madrid
Phone: +34 91 336 36 70 - Fax: +34 91 352 48 19

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Tania Tudorache | 8 Aug 2007 21:30

Re: Protégé Query Results

Hi,

I have made the export configurable, so that you can specify whether you 
would like to export the slot names as the first line in the file. This 
feature will be available in the next Protege build.

Cheers,
Tania

Lanse wrote:
> Hi,
> I am working on a program that analyzes the output from the query tab in
> Protégé.  Would it be possible to include the names of slots in the output
> file?
> Thanks.
>   

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Ehud Reiter | 9 Aug 2007 11:56

How do I modify slot values from Java API?

I am trying to modify the default value of a class slot in Protege
Frames 3.2, using the Java API.  Essentially I want to force a class
"ancestor" to have the same slot values as one of its children "child"
(inheritance up the taxonomy, not down).

The code is as follows
									 
ancestor.setTemplateSlotDefaultValues(s,child.getTemplateSlotDefaultValues(s));
							

This works *if* the ancestor class doesn't already have a default value
defined for the slot.  However, this fails if the ancestor class already
has a value defined, in this case I get something like

[Before above call] [MORPHINE is a child of PAIN RELIEF in the taxonomy]
Class Cls(PAIN RELIEF); slot Slot(importance); value is [20.0]
Class Cls(MORPHINE); slot Slot(importance); value is [50.0]

[after above call]
Class Cls(PAIN RELIEF); slot Slot(importance); value is [20.0, 50.0]

Ie, the setTemplateSlotDefaultValues seems to be adding the new value
(50.0) to the existing value (20.0), resulting in the list [20.0 50.0],
instead of replacing the 20.0 by the 50.0 (which is what I want
to happen).  The slot in question (importance)
is defined as a slot which can only have one value

Any suggestions?

Many thanks
					Ehud Reiter
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daniel.goergen | 9 Aug 2007 12:43

Antwort: How do I modify slot values from Java API?

Hello,

I cannot reproduce your problem.
I did the following:

ancestor = kb.getCls("PAIN_RELIEF");
child = kb.getCls("MORPHINE");
slt = kb.getSlot("importance");
ancestor.setTemplateSlotDefaultValues(slt , child.getTemplateSlotDefaultValues(slt));

this works fine

maybe your problem is the following:
if you add a default value for the slot in the ancestor class the child will get this value as well
if you now create a new default value for the same slot in the child class it will have two values (the inherited and the created)
note that even if a slot is multiple it may have more than one default value but only the first is used when creating instances

so I the code does what it should - it copies both values....

i hope this helps

Kind regards,

i. A. Daniel Goergen
Therapy Manager

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Mail: daniel.goergen <at> biotronik.com

protege-discussion-bounces <at> lists.stanford.edu schrieb am 09.08.2007 11:56:10:

> I am trying to modify the default value of a class slot in Protege
> Frames 3.2, using the Java API. Essentially I want to force a class
> "ancestor" to have the same slot values as one of its children "child"
> (inheritance up the taxonomy, not down).
>
> The code is as follows
>
> ancestor.setTemplateSlotDefaultValues(s,child.
> getTemplateSlotDefaultValues(s));
>
>
> This works *if* the ancestor class doesn't already have a default value
> defined for the slot. However, this fails if the ancestor class already
> has a value defined, in this case I get something like
>
> [Before above call] [MORPHINE is a child of PAIN RELIEF in the taxonomy]
> Class Cls(PAIN RELIEF); slot Slot(importance); value is [20.0]
> Class Cls(MORPHINE); slot Slot(importance); value is [50.0]
>
> [after above call]
> Class Cls(PAIN RELIEF); slot Slot(importance); value is [20.0, 50.0]
>
> Ie, the setTemplateSlotDefaultValues seems to be adding the new value
> (50.0) to the existing value (20.0), resulting in the list [20.0 50.0],
> instead of replacing the 20.0 by the 50.0 (which is what I want
> to happen). The slot in question (importance)
> is defined as a slot which can only have one value
>
> Any suggestions?
>
> Many thanks
> Ehud Reiter
> _______________________________________________
> protege-discussion mailing list
> protege-discussion <at> lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.
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