Mansour, Michel | 10 Feb 16:57
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NullPointerException when logging

Hello,

Protege 3.4.8 is throwing a NullPointerException when the logging level is set to FINE or lower (i.e., FINER, FINEST, ALL). This only seems to happen when opening a project using the Java API by specifying a .pprj file, which contains the database connection information. The relevant portion of the stack trace is:

java.lang.NullPointerException
    at edu.stanford.smi.protege.storage.database.pool.DatabaseParam.hashCode(Unknown Source)
    at java.util.HashMap.get(HashMap.java:300)
    at edu.stanford.smi.protege.storage.database.pool.ConnectionPool.getConnectionPool(Unknown Source)
    at edu.stanford.smi.protege.storage.database.RobustConnection.<init>(Unknown Source)
    at edu.stanford.smi.protege.storage.database.AbstractDatabaseFrameDb.createConnection(Unknown Source)
    at edu.stanford.smi.protege.storage.database.AbstractDatabaseFrameDb.getCurrentConnection(Unknown Source)
    at edu.stanford.smi.protege.storage.database.IdleConnectionNarrowFrameStore.setIdle(Unknown Source)
    at edu.stanford.smi.protege.storage.database.IdleConnectionNarrowFrameStore.getName(Unknown Source)
    at edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.dumpFrameStores(Unknown Source)
    at edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.addActiveFrameStore(Unknown Source)
    at edu.stanford.smi.protege.model.Project.loadDomainKB(Unknown Source)
    at edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Unknown Source)
    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)

(The initial Project constructor being called is Project(String, Collection).)

And it seems to come down to this block of code in edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore#addActiveFrameStore(NarrowFrameStore, Collection) (lines 262-265):

        if (log.isLoggable(Level.FINE)) {
            log.fine("Added new active frame store");
            dumpFrameStores(Level.FINE);
        }

By the time it tries to create the connection in AbstractDatabaseFrameDb, all of the connection parameters are null, resulting in the NPE in DatabaseParam's hashCode() method. If logging is turned off (or set to a level higher than FINE), this error doesn't occur.

Please let me know if you need any more information.

Thank you,
Michel


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Alessandro Oltramari | 10 Feb 15:44
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SPARQL ASK

Hi all,

I've just noticed a problem with the SPARQL tab in Protege 4.2.0, Build 256. 
When I use an ASK form to query my ontology, I get this message:

"Error 316 Logged at Fri Feb 10 09:39:34 EST 2012
SparqlReasonerException: java.lang.IllegalArgumentException: query is not a tuple query"

I tried different ASK queries, even the simplest ones. 
On the contrary, SELECT works well, even when constraints keywords like FILTER and OPTIONAL are added. 

Do you know if ASK queries are supported or not not by the current version of the SPARQL tab?

Thanks for answer,

Alessandro
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robert Stevens | 10 Feb 09:57
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IVBO/FOIS Early Career Symposium

Apologies for multiple postings, please forward to any students and early 
career scientists who may be interested!

               ******************************************************

               EARLY CAREER SYMPOSIUM

               July 25, 2012

               Call for Papers

               International Conference on Biomedical Ontology (ICBO 2012)

               Formal Ontology in Information Systems (FOIS 2012)

               http://purl.org/icbofois2012/

               ******************************************************

IMPORTANT DATES:

* April 15, 2012: Deadline for submission of extended abstracts for Early 
Career Symposium.

* May 15, 2012: Notification of acceptance of colloquium submissions.

* June 30, 2012: Deadline for submission of camera-ready copy

* July 25, 2012: Doctoral and Postdoctoral Colloquium (approximately 
1:30pm-6:30pm)

SCOPE OF THE COLLOQUIUM

The ICBO and FOIS 2012 conferences will host a joint Early Career Symposium. 
This event is designed to provide an opportunity for current PhD students 
and postdoctoral researchers to give a short presentation of their research 
with ample time for feedback and mentorship. It will also allow participants 
to network with other early career scientists in ontology and biomedicine. 
While attendance is open to anyone registered for one of the main 
conferences, presenters should be active doctoral students or postdoctoral 
researchers.

SUBMISSION GUIDELINES

Intending participants should submit an extended abstract, which may be a 
description of their current or planned research, an abstract of their PhD 
proposal, or a description of a related issue such as methodology. The 
research should either have a significant ontology component already or a 
plan to utilize ontologies in the future. All topics that fall into the 
scope of the conference are welcome.

Submission is via EasyChair 
(https://www.easychair.org/conferences/?conf=icbo-2012), according to the 
template provided on the conference web site (up to two pages):

http://www.kr-med.org/icbofois2012/doccons.htm

PRESENTATION

Presentations at the ECS will be given by doctoral or early postdoctoral 
researchers which have to register for the ECS. Accepted submissions will be 
presented as short talks (timing will depend on the final number of accepted 
submissions), with additional time for questions and discussion. Accepted 
submissions will be published in a symposium booklet (PDF).

TRAVEL FUNDS

A limited number of travel grants for the conferences may become available. 
Interested applicants should send an e-mail to ludger.jansen <at> uni-rostock.de. 
We will contact them with further details on how to submit an application 
once the funds have been secured.

CONTACT

For all queries about the Early Career Symposium, please contact Ludger 
Jansen (ludger.jansen <at> uni-rostock.de).

Robert Stevens
Reader in bioHealth Informatics
School of Computer Science
University of Manchester
Oxford Road
Manchester
United Kingdom
M13 9PL

robert.stevens <at> manchester.ac.uk
Blog: http://robertdavidstevens.wordpress.com
Home: http://www.cs.man.ac.uk/~stevensr
+44 161 275 6251

KBO 

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[CFP] 1st CfP: OWL Reasoner Evaluation Workshop (ORE 2012)

[Apologies for cross-posting]


-----------------------------------------------------------------------------------------------------
                                  1st CALL FOR PAPERS  
                     OWL Reasoner Evaluation Workshop (ORE 2012)
                        Collocated with IJCAR 2012 Conference
                    http://www.cs.ox.ac.uk/isg/conferences/ORE2012/
-----------------------------------------------------------------------------------------------------


OBJECTIVES
--------------------------------------------------------------------------

OWL is a logic-based ontology language standard designed to promote interoperability, particularly in
the context of the (Semantic) Web. The standard has encouraged the development of numerous OWL reasoning
systems, and such systems are already key components of many applications.

The goal of this workshop is to bring together the developers of reasoners for (subsets of) OWL,
including systems focusing on both intensional (ontology) and extensional (data) query answering.
The workshop will give developers a perfect opportunity to promote their systems.


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

Submissions are solicited from developers interested in describing OWL reasoning and query answering systems.
We invite submission of both SHORT SYSTEM DESCRIPTION papers and LONG SYSTEM DESCRIPTION AND EVALUATION papers.
Papers should include a description of the system in question, including:

    * language subset(s) supported;

    * syntax(es) and interface(s) supported;

    * reasoning algorithm(s) implemented;

    * important optimisation techniques used;

    * particular advantages (or disadvantages);

    * application focus (e.g., large datasets, large ontologies, complex ontologies, etc.);

    * other novel or interesting features.


Full papers should also include an evaluation (see guidelines), preferably using (some of) the datasets provided.
Short papers may also include a brief performance analysis.


EVALUATION GUIDELINES
--------------------------------------------------------------------------

If possible, evaluations should use the standard datasets provided and present results for the following reasoning
tasks (where relevant for the system being evaluated):

    * Classification. The dataset consists of a set of OWL ontologies. The total time taken to load and classify
each ontology should be reported. It would also be interesting to report on comparisons of the computed taxonomy
with the "reference" taxonomies that are provided with the dataset (in preparation).

    * Class satisfiability. The dataset consists of a set of OWL ontologies, and for each ontology one or more
class URIs. The time taken to perform each test along with the satisfiability result for each class should be reported.

    * Ontology satisfiability. That dataset consists of a set of OWL ontologies. The total time taken to load and test
the satisfiability of each ontology should be reported, along with the satisfiability result for each ontology.

    * Logical entailment. The dataset consists of a set of pairs of OWL ontologies. The total time take to determine if
the first ontology entails the second ontology should be reported, along with the entailment result (true or false).

    * Instance retrieval. The dataset is an OWL ontology and a class expression. For each ontology the total time taken
to load the ontology and retrieve the sets of instances for each class expression should be reported. It would also be
interesting to report on comparisons of the retrieved instances with the "reference" set that are provided with the dataset.

It is suggested that full results of any evaluations performed are made available via the web, with summaries of the results
 being included in the papers submission as space permits.


SUBMISSIONS
--------------------------------------------------------------------------

Long papers must be no longer than 12 pages, while short papers must be no longer than 6 pages.

Submissions must be in PDF and should be formatted according to the Springer LNCS guidelines.
Submission is electronic through easychair.

All submissions will be peer-reviewed by the program committee. Selected papers are to be published as a
volume of CEUR workshop proceedings.


IMPORTANT DATES
--------------------------------------------------------------------------

    * Submission of abstracts: April 9th, 2012

    * Paper submission deadline: April 16th, 2012

    * (Optional) Submission of systems to SEALS platform: April 16th, 2012

    * Notification of acceptance: May 7th, 2012

    * Camera-ready papers due: May 25th, 2012

    * Workshop: July 1st, 2012 (Half-day)


ORGANISATION
--------------------------------------------------------------------------

    * Ian Horrocks, University of Oxford, UK
    * Mikalai Yatskevich, University of Oxford, UK
    * Ernesto Jiménez-Ruiz, University of Oxford, UK
    * Franz Baader, TU Dresden, Germany
    * Jérôme Euzenat, INRIA, Grenoble, France
    * Pavel Klinov, Clark & Parsia, USA
    * Jeff Heflin, Lehigh University, PA, USA
    * Francisco Martin-Recuerda, Universidad Politécnica de Madrid, Spain
    * Bijan Parsia, University of Manchester, UK
    * Stefan Schlobach, Vrije Universiteit Amsterdam, The Netherlands

For enquiries, please contact the Organisers at ore2012 <at> easychair.org




--
Ernesto Jiménez-Ruiz
Research Assistant
Department of Computer Science
University of Oxford
Wolfson Building, Parks Road, Oxford OX1 3QD, UK

http://krono.act.uji.es/people/Ernesto
http://www.cs.ox.ac.uk/people/ernesto.jimenez-ruiz/



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rperro88 | 9 Feb 10:07
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Biomedical ambit

Hi! I've solve the problem with the error of the Client-server version!

I know that the software protègè born for the biomedical application: I'm interested to this, so, i want to ask to you if i can see, some example of the use of protègè in this ambit!
thank you!

Roberta
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Frank Loebe | 9 Feb 00:48
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FINAL REMINDER: Feb 12: FOIS 2012 submission deadline (strict) (Formal Ontology in Information Systems, Jul 24-27, Graz, Austria)

   (apologies for cross-posting)  ...  (deadline approaching)
-----------------------------------------------------------------

 FINAL REMINDER of    -------------
 Call for Papers     |  FOIS 2012  |    Jul 24-27, Graz, Austria
                      -------------

>>> EXTENDED, STRICT DEADLINE APPROACHING <<<
   Conference paper submission:   Sunday, Feb 12, 2012  <--

             [1]  http://purl.org/icbofois2012

------------------------------------------------
TITLE AND CO-LOCATION
------------------------------------------------

Seventh International Conference on
   Formal Ontologies in Information Systems (FOIS 2012)
                               July, 24-27, 2012 in Graz, Austria

               held together with the

Third International Conference on Biomedical Ontology (ICBO 2012)

------------------------------------------------
IMPORTANT DATES
------------------------------------------------

We are calling for papers to be considered for inclusion
in FOIS 2012.

Conference paper submission:      Feb 12, 2012 <-- APPROACHING
Conference paper notification:    Mar 16, 2012  <- updated!
Camera-ready conference papers:   Mar 31, 2012  <- updated!

For the submission categories poster and workshop paper
see the conference website [1].  (Their corresponding initial
deadlines are between Mar 15 and May 01, 2012.)

------------------------------------------------
AUTHOR INSTRUCTIONS FOR CONFERENCE PAPERS
------------------------------------------------

Submitted papers must not exceed 14 pages, including the
bibliography and an abstract of no more than 300 words.
Papers should be submitted electronically as PDF files prepared
in accordance with the IOS formatting guidelines [2].

Submissions should be made via Easychair at the following address:

[3] https://www.easychair.org/account/signin.cgi?conf=fois2012

Proceedings will be published by IOS Press and will be available
at the time of the conference. Please note that at least one
author must register for the conference in order for an accepted
paper to be published in the proceedings.

------------------------------------------------
KEYNOTE SPEAKERS
------------------------------------------------

Steven R. Ray   (Carnegie Mellon Silicon Valley, California, USA)
Laure Vieu      (CNRS-IRIT, Toulouse, France)
Edward N. Zalta (Stanford University, California, USA)

------------------------------------------------
CONFERENCE ORGANISATION
------------------------------------------------

Conference chair:
   Michael Gruninger   (University of Toronto, Canada)

Program chairs:
   Maureen Donnelly    (University at Buffalo, USA)
   Giancarlo Guizzardi (Fed. Univ. of Espirito Santo, Brazil)

Local organization:
   Stefan Schulz       (Graz University, Austria)

------------------------------------------------
FURTHER INFORMATION
------------------------------------------------

For further information on FOIS, the flagship conference of the
International Association for Ontology and its Applications
(IAOA) [4], please consult the website of FOIS 2012 [1] or
the conference series website [5] for past conferences.

------------------------------------------------
LINKS
------------------------------------------------

[1] http://purl.org/icbofois2012
 ==  http://www.kr-med.org/icbofois2012
    FOIS and ICBO 2012 website

[2] http://www.iospress.nl/authco/instruction_crc.html
    IOS Press formatting guidelines

[3] https://www.easychair.org/account/signin.cgi?conf=fois2012
    Submission at EasyChair

[4] http://www.iaoa.org
    International Association for Ontology and its Applications

[5] http://www.formalontology.org/
    FOIS conference series

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

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Sören Auer | 8 Feb 20:25
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Semantic Web PhD & PostDoc positions available in Bern, Switzerland

2 PHD and 1 POSTDOC POSITION at
Business School of Bern University of Applied Sciences

For collaborative international research projects in the area of
intelligent information management, the Business School of Bern
University of Applied Sciences (BUAS) in cooperation with research group
Agile Knowledge Engineering and Semantic Web (AKSW) at Universität
Leipzig opens positions for:

2 PhD and 1 PostDoc Position in Knowledge Engineering / Semantic Web

The positions are primarily based at BUAS (Switzerland) and funded by
European FP7 projects and possibly Swiss national research grants. A
close collaboration and ca. 4 research visits per year at AKSW research
group at Universität Leipzig (Germany) are envisaged for the PhD
students to complete their PhD program.

*We offer*
* The stimulating environment of two research institutes in the fields
of Business Informatics, Semantic Web, Ontology Engineering, Linked Data
Web, Knowledge Management, Data integration and Service-Oriented
Architectures;
* Long-term collaboration with well-known academic institutions and
major companies around the world;
* A multicultural working place with state-of-the-art infrastructure, a
competitive salary and resources including funding for attending
international conferences, PhD symposia, summer schools, etc.;
* competitively funded PhD positions close to the rate of the Swiss
National Science Foundation (currently ca. CHF 41’000);
* competitively paid Postdoc positions commensurate with the pay scale
of BUAS (starting at CHF 80’000 depending on experience).

*We expect*
* A strong background in Computer Science or related disciplines;
* Excellent software engineering skills with demonstrated proficiency in
modern software development;
* The willingness to work in an international environment and combine
formal scientific work with application-oriented research in order to
solve real-world problems;
* Research interest and expertise in at least one of the following:
knowledge representation and ontology languages, natural language
processing, data management and integration, Semantic Web standards,
business aspects of semantic systems;
* Prospective PhD students should fulfill the doctorate entrance
requirements of Universität Leipzig (i.e. masters degree or equivalent)
* Proficiency in English and the willingness to learn one of the
official Swiss languages (e.g. German, French, Italian).

*To apply*
Applicants should include a cover letter, curriculum vitae incl. list of
publications, a research statement and the names and addresses of two
referees, via email (PDF only) to ksm1 <at> bfh.ch (Dr. Michael Kaschewsky,
Head of Research Group, Bern University of Applied Sciences, Business
School). Positions are open until filled, but candidates are advised to
apply by 1 March 2012. In addition, qualified Postdoctoral researchers
have the opportunity to get funding for their position and additionally
for a doctoral position that they supervise independently but must apply
by 15 February 2012 - if you are interested please contact us asap.

*About us*
Bern University of Applied Sciences (BUAS) is the regional leader in
applied science and research with seven departments across three cities.
Research at the Business School in Bern is nationally leading and
internationally renowned in the field of e-government and applied
informatics in the public sector.
AKSW research group at the Universität Leipzig is establishing
theoretical results and scalable implementations for the Semantic Data
Web (e.g. DBpedia, OntoWiki, DL-Learner). Particular emphasis is given
to areas such as ontology creation and manipulation, knowledge
extraction, ontology learning and information & data integration on the
Semantic Data Web.
Additional information regarding our research and projects as well as
further information concerning these positions is available at
http://bfh.ch and http://aksw.org.
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Deus, Helena | 8 Feb 15:48
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Semantic Web and Linked Data uses in Cancer Chemoprevention at DERI

[Apologies for cross-posting]

 

We have open positions to work on the EU funded GRANATUM project. 
The vision of the GRANATUM project is to bridge the information, knowledge and collaboration gap among biomedical researchers in Europe (at least) ensuring that the biomedical scientific community has homogenized, integrated access to the globally available information and data resources needed to perform complex cancer chemoprevention experiments and conduct studies on large-scale datasets.

 

Experience in software development - server side Java; HTML; JavaScript; etc

Experience with Jena/semantic web frameworks is an advantage.

 

Please send an application letter, CV and name of two references to helena.deus <at> deri.org

 

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Jean-Louis JANIN | 1 Feb 23:13
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GraphWidget with Protégé 3.4.8

Hello,

Is-it possible to make a graph widget available with Protégé 3.4.8, in 
the form tab, for some classes, in order to draw and export the images 
obtained in the instance tab, as presented in the GraphWidget with class 
Organization and San José Mercury News ?

How ?

Jean-Louis Janin

--

-- 

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shobana priya | 31 Jan 06:14
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help for converting UML TO OWL

Can any one pls help me with the step by step procedure for  converting UML class diagram (Exported in XMI format) to OWL CODE using protege....




regards,
shofana

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jayadianti herlina | 30 Jan 19:05
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NullPointerException:null

Hi all,
I am using Protege 4.2.0 (build 249), I am working with 3 ontologies and then importing them into 1 ontology.
I try to map and match between 3 ontologies. Everything going well.
I am using DL Query (Version 1.1.0) and select a reasoner (hermit 1.3.5 and faCT++).
All as I expected, the query done very well, and mapped out perfectly :)
 
Then I save the file as usual, and then I tried to open it again.
I do a query with DLquery as usual and appeared dialog box: NullPointerException: null - whereas before all goes well.
is this a known bug?
Thank you very much for your help
 
Warm Regards
Jayadianti
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Gmane