Joachim Baran | 17 Apr 19:47 2014

Feature Request


  Instead of going office-to-office, I thought it is easier to broadcast this feature request here. :)

  I use owl:equivalentClass a lot in one of my ontologies and that creates a visualization problem in the class hierarchy tree.

  I select "View" -> "Show only the active ontology" in Protege 4.3 Desktop, which nicely shows only my classes and equivalences to other ontologies (e.g., "Cell = cell").

  However, it also shows the same equivalence as "cell = Cell" under owl:Thing. This behavior causes a lot of clutter in the class hierarchy view.

  Would it be possible to hide the "reverse" equivalences when "Show only the active ontology" is selected?

Thank you,


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clemens utschig | 16 Feb 21:48 2014

Fwd: Re: [protege-dev] Problem with events and database backing

---------- Forwarded message ----------
From: clemens utschig <clemens.utschig <at>>
Date: Sunday, February 16, 2014
Subject: Fwd: Re: [protege-dev] [protege-discussion] Problem with events and database backing
To: Timothy Redmond <tredmond <at>>

So, i got to the point of sneaking a kb under the protege app at runtime - pretty much a new constructor in project (using the code from the one with uri, and calling all the methods) and then projectmanager.getpm.setcurrentproject... Almost there, but now i really need your help - all the default widgets are working - but when i click on an instance within the instance widget the form does not show? ... If i use the default project constructor (with a string) and do the same thing - it does show up.. Unfortunately i cant debug into this with all the threads running around, so i really need some advice here - is there some other magic?

On Sunday, February 16, 2014, clemens utschig <clemens.utschig <at>> wrote:
> Hey timothy - first of all thanks a ton for the reply.
> Yes i am on version 3.5.. The problem is that i cant create a server project first as i use the ontology to configure a (remote) application on the fly - and want to use the protege app to do configuration on top of that - think of the ontology as a graph within a deployable server app. And i dont want to start messing with two servers (my own and its lifecyle and the protege one ;-)
> I'll try to tweak the protege app tmrw a little - and see if i can sneak a project instance underneath it on the fly (rather than it *owning* and opening a uri..)..
> If you have some other super smart idea, any help is appreciated...
> Cheers from germany, i actually studied at stanford during my time in san francisco ;-)  
> On Saturday, February 15, 2014, Timothy Redmond <tredmond <at>> wrote:
>> Just in case you didn't see my reply.
>> -Timothy
>> -------- Original Message --------
>> Subject: Re: [protege-dev] [protege-discussion] Problem with events and database backing
>> Date: Sat, 15 Feb 2014 09:39:14 -0800
>> From: Timothy Redmond <tredmond <at>>
>> Reply-To: protege-dev <at>
>> To: protege-discussion <at>, protege-dev <at>
>> I am a bit confused getting this message because I think that the new
>> lists are protege-users and protege-dev. So I am forwarded this message
>> to protege-dev just in case.
>> On 02/15/2014 07:23 AM, clemens utschig wrote:
>>> folks - this is rather urgent...
>>> I try to get the listener magic to work (e.g. new instance created,
>>> frame update, browser text changed) - between the protege application
>>> and and multiple api based consumers all using the same - database
>>> backed - project.
>>> It seems somehow events / listeners are not firing / generated by
>>> default?
>>> Any help much appreciated.
>> This is just a thought and may not be related to what you are
>> experiencing. I am assuming that you are talking about Protege 3
>> although -- even though the implementations are completely different --
>> the same comments apply to Protege 4 and 5.
>> If you create two separate Protege knowledge bases (e.g. separate java
>> objects) that point to the same database then you will have several
>> problems. These problems only occur when modifying the knowledge bases;
>> I think that things will work if all the callers are in read-only mode.
>> The most obvious problem is that changes in one Protege knowledge base
>> will only generate events in that knowledge base and not in the other
>> knowledge bases. A less obvious problem is that, in certain
>> circumstances, changes made with one knowledge base will not be seen in
>> other knowledge bases. There may be other problems as well.
>> If this is in fact your problem then there are two obvious fixes to the
>> problem. If everything is happening in a single JVM, then it is
>> possible that you can refactor your code so that all callers requesting
>> a knowledge base will get the same one. Maybe there would be a static
>> method or something that manages the process of getting the knowledge
>> base. Since the code will no longer be reentrant, you may need to also
>> add some synchronization.
>> If you have more than one JVM or there is some other reason why the
>> above solution is not practical then the other approach is to use a
>> Protege server. If you have several clients accessing the same server
>> all the events and other synchronization will be taken care of. This is
>> easier than it sounds and there is a wiki page telling you how to do this:
>> Protege 3 --
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clemens utschig | 15 Feb 16:23 2014

Re: Problem with events and database backing

folks - this is rather urgent...
I try to get the listener magic to work (e.g. new instance created, frame update, browser text changed) - between the protege application and and multiple api based consumers all using the same - database backed - project.

It seems somehow events / listeners are not firing / generated by default?

Any help much appreciated.

On Sat, Feb 15, 2014 at 4:22 PM, clemens utschig <clemens.utschig <at>> wrote:
folks - this is rather urgent...
I try to get the listener magic to work (e.g. new instance created, frame update, browser text changed) - between the protege application and and multiple api based consumers all using the same - database backed - project.

It seems somehow events / listeners are not firing / generated by default?

Any help much appreciated.

On Sat, Feb 15, 2014 at 4:19 PM, clemens utschig <clemens.utschig <at>> wrote:
folks - this is rather urgent...
I try to get the listener magic to work (e.g. new instance created, frame update, browser text changed) - between the protege application and and multiple api based consumers all using the same - database backed - project.

It seems somehow events / listeners are not firing / generated by default?

Any help much appreciated.

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Sean Zhang | 3 Feb 05:08 2014

Special Issue Call for Papers: "MapReduce and Big Data Infrastructure", in in International Journal of Big Data Intelligence.

Call for papers:
Special Issue on "MapReduce and Big Data Infrastructure", in International Journal of Big Data



This special issue solicits papers from an open call and extended papers partly selected from the

following conference(s):

CloudCom-Asia 2013: International Conference on Cloud Computing and Big Data

MR.BDI 2013: International Symposium on MapReduce and Big Data Infrastructure

Subject Coverage

Topics include, but are not limited to, the following:

•The 5Vs of the data landscape: volume, variety, velocity, veracity, value
•Big data science and foundations, analytics, visualisation and semantics
•Software and tools for big data management
•Security, privacy and legal issues specific to big data
•Big data economy, QoS and business models
•Intelligence and scientific discovery
•Software, hardware and algorithm co-design, high-performance computing
•Large-scale recommendation systems and graph analysis
•Algorithmic, experimental, prototyping and implementation
•Data-driven innovation, computational modelling and data integration
•Data intensive computing theorems and technologies
•Modelling, simulation and performance evaluation
•Hardware and infrastructure, green data centres/environmental-friendly perspectives
•Computing, scheduling and resource management for sustainability
•Complex applications in areas where massive data is generated

Notes for Prospective Authors

Submitted papers should not have been previously published nor be currently under consideration for

publication elsewhere. (N.B. Conference papers may only be submitted if the paper has been completely re-

written and if appropriate written permissions have been obtained from any copyright holders of the

original paper).
All papers are refereed through a peer review process.  Please read our information on preparing and

submitting articles.

1. All papers must be submitted online Information

about preparing articles:

2. Please add a short comment indicating the name of guest editor(s) and/or the name of conference where

your paper was selected. You can include this information in a cover letter or in the comment area in step

1 of the submission process.

Deadlines for Submission

Submission of Manuscripts: 15 March 2014

Notification to Authors: 30 April 2014

Final Versions Due: 15 May 2014

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Manal Haimour | 2 Feb 23:56 2014

Ontology Graph


I have a question regarding web-protege. How can I generate a graph after I am finished with specifying the classes and the properties? I have been trying all day to find something to generate a graph , ontology graph, but I couldnt.

I would appreciate any help I can find.

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Announce Announcements | 2 Feb 14:13 2014

DeSE 2014: First Call for Papers

*** First Call for Papers ***

Seventh International Conference on Developments in eSystems Engineering (DeSE '2014)

25th - 27th August 2014

Azia Hotel and Spa 5*, Paphos, Cyprus

Recent years have witnessed increasing interest and development in computerised systems and procedures,
which exploit the electronic media in order to offer effective and sophisticated solutions to a wide range of
real-world applications. Innovation and research development in this rapidly evolving area of eSystems has
typically been reported on as part of cognate fields such as, for example: Information and Communications
Technology, Computer Science, Systems Science, Social Science and engineering. This conference, on the
developments in eSystems Engineering will act as a platform for disseminating and discussing new research
findings and ideas in this emerging field.

Papers are invited on all aspects of eSystem Engineering, modelling and applications, to be presented at a
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experts and accepted papers will appear in the conference proceedings published by the Conference
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especially attractive opportunity for professional discussion, socialising and sightseeing.

DeSE 2014 conference is technically co-sponsored by IEEE. DeSE 2014 comprises an exciting spectrum of
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o eSecurity and e-Forensics
o eEntertainment and Creative Technologies
o eNetworking and Wireless Environments
o eUbiquitous Computing and Intelligent Living
o Green and Sustainable Technologies
o eCulture and Digital Society
o eSport Science
o eSystems Engineering (Main Stream)
o Sustainable Construction and Renewable Energy

All submitted papers will be peer-reviewed. Accepted and presented papers may be published in the final
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approval by the Conference Technical Committee.

Azia Resort and Spa 5*, Paphos, Cyprus
Built as three different sections on adjacent grounds, with plethora of magnificent spaces for carefree living,
the Azia Resort has all the diversity to keep its guests contented for a week or longer. Each element of the
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Announce Announcements | 1 Feb 13:22 2014

WiMob 2014: First CFP and Call for Workshop Proposals

*** First Call for Papers ***
*** Call for Workshop Proposals ***

The 10th IEEE International Conference on Wireless and Mobile
Computing, Networking and Communications
WiMob 2014

Golden Bay Hotel, Larnaca, Cyprus
October 8-10, 2014

Deadline for Workshop Proposals: March 31, 2014
Deadline for Paper Submissions: May 1, 2014

(Proceedings will be published by IEEE)

The IEEE WiMob conference is an international forum for the exchange of
experience and knowledge among researchers and developers concerned with
wireless and mobile technology. For nine years, the International IEEE WiMob
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in Wireless Communications, Mobile Networking and Ubiquitous Computing.

IEEE WiMob 2014 will take place at Larnaca, Cyprus, between October 8 to
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IEEE WiMob 2014 is soliciting high quality technical papers addressing
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applications. Papers should present original work validated via analysis,
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also are welcome.

IEEE WiMob 2014 will host three parallel symposiums, including but not limited
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1. Wireless Communications
Broadband Wireless Communication Systems
Signal Separation and Interference Rejection
Wireless Personal Communications
Multimedia Communications over Wireless
Advances in Satellite Communication
DSP Applications to Wireless Systems
Adaptive Antennas for Wireless Systems
Modulation and Coding
Multiple Access Techniques
Multiuser Detection
Channel Measurement and Characterization
Location Estimation and Tracking
OFDM and CDMA Technologies and Systems
Resource Allocation and Interference Management
MIMO Channels
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Link and System Capacity
Spectrum Usage and Cognitive radio systems
Cognitive and cooperative MAC
Cognitive Radio Applications and Spectrum Management

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Inter-working of 2G, 3G and 4G Wireless Networks
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Cross-layer Design and Optimization
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Delay Tolerant Networks
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Optimization models and algorithms

3. Ubiquitous Computing, Services and Applications
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communications, pervasive computing and networking, and its
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* Ebrahim Bagheri, Ryerson University, bagheri <at>
* Joaquin Garcia-Alfaro, Telecom SudParis, garcia_a <at>
* Joan Garcia Haro, Universidad Politecnica de Cartagena, joang.haro <at>
* Luis Orozco Barbosa, Universidad de Castilla-La Mancha, luis.orozco <at>

Acceptance/rejection notification will be sent to workshop organizers.

Proposals for workshops should be no more than 2 pages in
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1) A draft of the CFP of the workshop (includes title, description, topics and dates)
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5) Organizing committee
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8) Can be submitted in PDF or plain text
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Workshop chair(s) will be responsible for the following:

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Workshop Proposals Deadline: March 31, 2014
Workshops Proposals Acceptance Notification: April 15, 2014
Paper Submission Deadline: May 1, 2014
Notification of Acceptance: July 25, 2014
Camera Ready: August 25, 2014

Organization Committees

General Chair
Abderrahim Benslimane, University of Avignon, France

General Co-Chairs
George Angelos Papadopoulos, University of Cyprus, Cyprus
Ali Miri, Ryerson University, Canada

Steering Committee Chair
Samuel Pierre, École Polytechnique de Montréal, Canada

Steering Committee
Abderrahim Benslimane, University of Avignon, France
Dovan Thanh, Telenor & Norwegian Univ. of Science& Technology, Norway
Hussein Mouftah, University of Ottawa, Canada
Ibrahim Habib, City University of New York, USA
Khaled Ben Letaief, Hong Kong University of Sci. & Tech.
Pierre Boucher, Ericsson Research Canada
Samuel Pierre, École Polytechnique de Montréal, Canada

TPC Co-Chairs
Li CHEN, Sun Yat-Sen University, China - wireless communication track
Milena Radenkovic, University of Nottingham, UK - ubiquitous, service and application track
Lin Xiaodong, University of Ontario Institute of Technology, Canada- wireless networking, mobility and nomadicity track

Workshop Co-Chairs
Ebrahim Bagheri, Ryerson University, Canada
Joaquin Garcia-Alfaro, Telecom SudParis, France
Joan Garcia Haro, Universidad Politecnica dede Cartagena, Spain
Luis Orozco Barbosa, Universidad de Castilla-La Mancha, Spain

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André Luiz Tietböhl Ramos | 30 Jan 21:32 2014

Re: protege-discussion Digest, Vol 90, Issue 18

Dear Timothy,

Thanks for the very good explanation. Read below please.

On Ter, 2014-01-28 at 12:05 -0800, protege-discussion-request <at> wrote:

Message: 2 Date: Mon, 27 Jan 2014 13:12:12 -0800 From: Timothy Redmond <tredmond <at>> To: protege-discussion <at> Hello, My guess is that with a little more detail we will be able to quickly figure this out. First, if possible it would be nice to see the ontology. > I do have an Individual (own#real) What is the full name of this individual? If for example, you meant that the name is owl:real so that the full name is

In order to solve this issue I deleted the individual however the error still shows up. How so? Would there be a "hidden" individual somewhere as cleverly show below?

then this is probably the source of your problem. Using reserved names (such as the names of datatypes) for your own use can lead to ambiguous parsing by different owl parsers. It is possible that the parser used by FaCT++ generated a different in memory version of your ontology than the Protege parser did. It may be a bit tricky to tell by looking at the rdf what the full name of the resource is. > that does not exist in my ontology (it is not shown in Proteg?'s > Indivuduals tab) but exists according to the reasoner (FACT++). By what means did FaCT++ tell you that the individual exists. Did you run FaCT++ from the command line or otherwise? This may not be important if my guess about your ontology is correct.

I run FACT++ from the GUI.  The message shown is:

ReasonerInternalException. Unsupported datatype ''

You would want to only change those that occur as the individual.  You should also at some point (maybe after getting this ontology to parse in Protege as you expect it) change the namespace of these individuals so that they are not in the owl: namespace.

Ok, thanks! I will when I'm good enough using Protege for I still don't know how to accomplish it effectively.

> Version: 4.1 If by this you mean Protege 4.1, I would recommend that you upgrade to Protege 4.2 if you can.

Yes, it is Protege version 4.1. Using 4.2b or 4.3 doesn't help much either.


Andre Luiz

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Jennifer Vendetti | 30 Jan 20:31 2014

Protege Support Mailing List Changes

Dear Protege Community,

The purpose of this email is to inform you of some upcoming changes to our free support mailing lists.  Over the last two decades, the number of Protege mailing lists has proliferated beyond what is practical for our modestly sized team to maintain.  On Monday, February 3rd, all of our support mailing lists will be condensed to the following two options:


End user support for all versions of the WebProtege and Protege Desktop applications.  Anyone currently subscribed to protege-discussion, protege-owl, p4-feedback, and/or webprotege-feedback will be automatically moved to the protege-user list.  If you have concerns about the volume of email on protege-user, please note that you will have the option of modifying your subscription to digest mode.  If you wish to unsubscribe from any of our support lists before February 3rd, please do so via the list information pages at the bottom of this correspondence.


Developer support for all versions of WebProtege and Protege Desktop.  Please note that no one will be automatically subscribed to this list.  If you have questions about Protege source code, developing plug-ins for Protege, programmatic access of ontologies from your applications, etc., please subscribe yourself via the list information page to post your questions:

We look forward to continuing our efforts to support and interact with you on our new lists.

Best Regards,
The Protege Team


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Jackie Blanco | 28 Jan 11:40 2014

CFP (Deadline Approaching) Third ICEEE2014 - Kuala Lumpur, Malaysia

First Submission Deadline: February 18, 2014

The Third International Conference on E-Learning and E-Technologies in Education (ICEEE2014)
March 18-20, 2014
Asia Pacific University of Technology and Innovation (APU)
Kuala Lumpur, Malaysia

The conference is part of The Second World Congress on Computing and Information Technology (WCIT2014) which aims to enable researchers build connections between different digital applications.


:: Accessibility to Disabled Users
:: Assessment Software Tools
:: Authoring Tools and Content Development
:: Collaborative Learning
:: Computer-Aided Assessment
:: Distance Education
:: E-Learning Hardware and Software
:: E-Learning Success Cases
:: Errors in E-Learning
:: Higher Education vs. Vocational Training
:: Joint Degrees
:: Metrics and Performance Measurement
:: Ontologies and Meta-Data Standards
:: Security Aspects
:: Standards and Interoperability
:: Synchronous and Asynchronous Learning
:: Web-based Learning, Wikis and Blogs
:: AV-Communication and Multimedia
:: Blended Learning
:: Community Building
:: Context Dependent Learning
:: Course Design and E-Learning Curriculae
:: Digital Libraries for E-Learning
:: Distance and E-Learning in a Global Context
:: E-Learning Platforms, Portals
:: E-Testing and new Test Theories
:: Educating the Educators
:: Groupware Tools
:: Immersive Learning
:: Intelligent Tutoring Systems
:: International Partnerships in Teaching
:: Learning Organization
:: Medical Applications
:: Mobile Learning (M-learning)
:: Teacher Evaluation
:: Technology Support for Pervasive Learning
:: Virtual Labs and Virtual Classrooms

ALL registered papers will be published in the proceedings and will be included in the publisher's Digital Library.
In addition, BEST SELECTED PAPERS will be published in the INDEXED JOURNALS:

+ IJDIWC (ISSN: 2225-658X; IndexCopernicus, DOAJ, etc.)
+ IJCSDF (ISSN: 2305-0012; Scirus, EBSCOhost, etc.)
+ IJEEI (ISSN: 1947-8585; Cabell's Directories, DBLP, etc.)
+ IJISSS (ISSN: 1935-5688; INSPEC, SCOPUS, etc.)
+ IJESMA (ISSN: 1941-627X; Ulrich's Periodicals Directory, etc.)
+ Journal of Higher Education (e-ISSN 2146-7978)


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André Luiz Tietböhl Ramos | 27 Jan 21:29 2014

Find and changa an Individual in a .owl file


I do have an Individual (own#real) that does not exist in my ontology (it is not shown in Protegé's Indivuduals tab) but exists according to the reasoner (FACT++).  The only similar Individual I have is called Real (notice the CAPS).  I cannot use a DL SELECT command either because the reasoner complies about this issue. Thus, I opened the .owl file and found several owl#real occurrences. My question is: can i simply change real by Real in the .owl file with no side affects?


Andre Luiz

Version: 4.1
OS: ubuntu 13.10
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