gmane.comp.misc.ontology.protege.general

Penultimate CFP: 13th International Conferenceon Web Information System Engineering (WISE 2012)

Announcements — 2012-05-25T10:23:45

========================================================================
The 13th International Conference on Web Information System Engineering
                              (WISE 2012)

                    http://www.wise2012.cs.ucy.ac.cy

                November 28th-30th, 2012, Paphos, Cyprus
========================================================================

               *** EXTENDED DEADLINE: 22nd June 2012 ***


               *** CALL FOR PAPERS AND RESEARCH DEMOS ***

The aim of this thirteenth edition of the conference series on Web
Information Systems Engineering is to provide an international forum
for researchers, professionals, and industrial practitioners to share
their knowledge in the rapidly growing area of Web technologies,
methodologies and applications. Previous WISE conferences were held in
Hong Kong, China (2000), Kyoto, Japan (2001), Singapore (2002), Roma,
Italy (2003), Brisbane, Australia (2004), New York, USA (2005), Wuhan,
China (2006), Nancy, France (2007), Auckland, New

using owlapi to mimic tabbed subclasses plugin

Wynne, Robert (NIH/NCI) [C] — 2012-05-24T22:35:09

Hi everyone,

First, I apologize for cross posting.  I am not certain which list is best for my questions.

I am using P4 alpha with the Tabbed Subclasses plugin written by Nick Drummond in conjunction with a driver written with the OWL API (v2.2.0).  The purpose of the driver is to extract a branch (or branches) into a new OWL file.  I use Perl afterwards to remove any classes outside the branch, as well as outward pointing restrictions from classes within the branch.  By removing these axioms, a clean branch is produced.

Nick's plugin is excellent because I can quickly copy a hierarchy of classes based on a focus node, and provide this list of classes to the program for extraction.  Not only that, but rdfs:subClassOf and rdf:Descriptions (found in equivalent classes of Thesaurus) are properly represented in Tabbed Subclasses (and naturally P4).

The method I wrote long ago (line 212, getDescendants), using a focus node as a parameter, does not perform exactly the same as the plugin implementation.  For ex

Re: How to deal with the encoding problem during ontology storing?

Timothy Redmond — 2012-05-22T17:43:21


I suspect that this is an XML and not a UTF-8 problem.  Something is 
wrong with the

<?xml version="1.0"?>


line.  Also possibly you have a byte order mark in front of the "<"?   I 
don't know what the SAX parser does with a BOM.   You can check this 
with a hex editor to see if there are any characters before the "<".


On 5/22/12 3:17 AM, Wentao Zhou wrote:

I don't know that much about Jena but for the Chinese character issues I 
do have some hints (many of which you probably already know).

We have had some trouble with the database connection in the past.   You 
need to make sure that your connection to the MySQL database uses 
UTF-8.  This must be true both when reading and writing the database.  
In the past we have used a connection url for the database that looks 
like this:

            jdbc:mysql://localhost/protege?useUnicode=true&characterEncoding=UTF-8


but I think that on some occasions this has actually made things worse.

Also if you put Chinese characters in your source files without e

Re: Some tests later...

Timothy Redmond — 2012-05-22T17:23:26


You can't.  Protege 4 and Protege 3.4.8 are completely different 
programs and have little compatibility except in that they both edit OWL 
files.

-Timothy



On 5/21/12 1:42 PM, Fabio Aiub Sperotto wrote:

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How to deal with the encoding problem duringontology storing?

Wentao Zhou — 2012-05-22T10:17:04

Hi guys,

I have been trying to store the ontology into the MySQL database via one
kind of ontology storing method, everything is Ok except for an encoding
problem. My native language is chinese, so there are several concepts
described in chinese in the ontology file, while, during the process of
storing, the chinese characters cannot show normally in tables, all chinese
characters are showed as the characters '?'.

The error message is:

Exception in thread "main" com.hp.hpl.jena.shared.JenaException:
org.xml.sax.SAXParseException: Content is not allowed in prolog.

 at
com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler.fatalError(RDFDefaultErrorHandler.java:45)
 at
com.hp.hpl.jena.rdf.arp.impl.ARPSaxErrorHandler.fatalError(ARPSaxErrorHandler.java:35)
 at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:225)
 at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.fatalError(XMLHandler.java:255)
 at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
 at org.apache.xerces.impl.XMLErro

Re: Some tests later...

Fabio Aiub Sperotto — 2012-05-21T20:42:19

Thanks for answer Timothy.

Yes, in Protégé 4.1 the OWLViz e OntoGraph plugins, handling is good with
words accented (i'm developing a ontology in PT-BR and in this version is
all ok with concepts).

In Protégé 3.4.8 the Ontoviz plugin works, but showed wrong characters in
words accented. With OWLViz in this version, don't work (don't open the
visualization on screen, generating several Java exceptions).

How i can use the OWLViz inserted in Protégé 4, in Protégé 3.4.8 for
example?

Thanks.

2012/5/21 <protege-discussion-request< at >lists.stanford.edu>

Re: Accent characters OWLViz and Ontoviz

Timothy Redmond — 2012-05-21T13:47:19

No problem - this is the right place.


You can't use Protege 4 plugins in Protege 3.  I am glad it is working 
in Protege 4.  I have some worries about the handling of UTF-8 in OWL 
viz so this is good news.

-Timothy



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Accent characters OWLViz and Ontoviz

Fabio Aiub Sperotto — 2012-05-19T02:45:42

Hello,

I really don't know where ask about this, sorry for any inconvenience.

I'm using Protégé 3.4.8 and OWLViz don't function with accent characters
(OWLViz build 17). With OWLViz build 18, in Protégé 4, the problem
apparently is solved. There's no way to use de last build (18) of OWLViz on
Protégé 3.4.8? Or some other way to fix this?

Ontoviz have the same problem, don't accept accent characters.

Thanks for any feedback.

[EKAW 2012] Call for Tutorial proposals -Deadline Approaching

Claudia d'Amato — 2012-05-16T10:06:47

--------------Apologies for cross posting--------------

*********************************************************************************
Call for Tutorial Proposals http://ekaw2012.ekaw.org/node/63
at the International Conference on Knowledge Engineering and Knowledge Management
a 2012 http://www.ekaw.org/
*********************************************************************************

Introduction
------------
The International Conference on Knowledge Engineering and Knowledge Management (EKAW) is concerned
with all aspects of eliciting, acquiring, modeling and managing knowledge, as well as its role in
the construction of knowledge-intensive systems and services for the semantic web, knowledge
management, e-business, natural language processing, and intelligent information integration. The
focus of the 18th edition of EKAW will be on "Knowledge Engineering and Knowledge Management that
matters".
Besides a research track, EKAW will host a number of tutorials on topics related to the theme of the
confere

Call for Posters,Demos and Participation -- DILS 2012

Olivier Bodenreider — 2012-05-15T18:44:51

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

                   DILS 2012 Call for Participation

++++++++++++                                             ++++++++++++
         Registration is open: http://www.cvent.com/d/9cq14w/1Q
             Deadline for posters and demos: May 31, 2012
++++++++++++                                             ++++++++++++

8th International Conference on Data Integration in the Life Sciences

                       College Park, MD, USA,
                          June 28-29, 2012
              http://sites.google.com/site/webdils2012

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


-------------------
About the Conference
-------------------

Applications of data integration in the life sciences have started to 
provide significant results. For example, the eMERGE Network has 
recently demonstrated that combining phenotype information extracted 
from electronic medical records with genotype information in order to 
study th

Re: Import

Timothy Redmond — 2012-05-14T16:15:29

Or for a simpler but less complete technology you can click 
Refactor->Merge Ontologies in Protege 4.2.

-Timothy



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Re: Real time data reg

Timothy Redmond — 2012-05-14T16:05:40

I think that someone would have to write a plugin to make this work.

-Timothy



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OBML 2012: 1st Call for Papers (4th Workshopon Ontologies in Biomedicine and Life Sciences, Sep 27-28,Dresden, Germany)

2012-05-11T15:46:33

     (apologies for cross-posting)  ...  (please distribute)
     -------------------------------------------------------

 Call for Papers   >>  OBML 2012  <<   Sep 27-28, Dresden, Germany
                      
             Submission deadline:   Aug 01, 2012

[1]  https://wiki.imise.uni-leipzig.de/Gruppen/OBML/Workshops/2012

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

  Fourth Workshop of 
         Ontologies in Biomedicine and Life Sciences (OBML 2012)


Goals of OBML
-------------

The workshop series on "Ontologies in Biomedicine and Life Sciences"
(OBML workshop) was initiated by the working group for OBML of the
German Society for Computer Science in 2009. The OBML workshop aims to
bring together scientists who are working on all areas of ontologies
applied to biomedicine and the life sciences to exchange ideas,
discuss new results, start collaborations and to initiate new
projects. The OBML workshop is held annually and deals with all
aspects of biomedical ontologies as well as additional "hot" t

Final CfP+deadline extension: WoMO 2012 - 6th Int'l Workshop on Modular Ontologies

WoMO 2012 — 2012-05-10T21:53:08

========================================================
     6th Int'l Workshop on Modular Ontologies (WoMO)
              Graz, Austria, July 24, 2012
           held in conjunction with FOIS 2012

             --- Final Call for Papers ---
========================================================
   +++ EXTENDED SUBMISSION DEADLINE: May 18, 2012 +++
========================================================

+++ Following requests, we have extended the submission deadline to
MAY 18, 2012. +++

INVITED SPEAKERS:

* Thomas Eiter, Vienna University of Technology, Austria
  Title TBA

* Luciano Serafini, Fondazione Bruno Kessler, Trento, Italy
  Multi context logics: a formal support for structuring knowledge and
beliefs (Tentative title)


http://www.informatik.uni-bremen.de/~ts/womo2012

MODULARITY, studied for years in software engineering, allows
mechanisms for easy and flexible reuse, generalization, structuring,
maintenance, design patterns, and comprehension. In formal and applied
ontology, modularity is

CFP: Discovery Informatics Symposium,Deadline June 5

Deus, Helena — 2012-05-10T13:24:08

[apologies for cross-posting]

=======================================

CALL FOR PAPERS

 

Discovery Informatics Symposium: 

The Role of AI Research in Innovating Scientific Processes


November 2-4, 2012, Arlington, VA (USA)
AAAI Fall Symposium Series

http://www.discoveryinformaticsinitiative.org/dis2012

 

(To receive further notifications about this and related meetings please
subscribe to:

http://discoveryinformaticsinitiative.org/mailman/listinfo/dii)

 

 

Addressing the ambitious research agendas put forward by many scientific
disciplines requires meeting a multitude of challenges in intelligent
systems, information sciences, and human-computer interaction. There are
many aspects of the scientific discovery process that our community
could help automate, facilitate, or make more efficient through
artificial intelligence techniques. For example, although considerable
efforts have been directed toward data modeling and integration, these
activities continue to demand large investments of scientist

Protege 3.5 Beta

Jennifer Vendetti — 2012-05-09T22:58:22

We are pleased to announce availability of the first beta build of 
Protege 3.5:

http://protege.stanford.edu/download/registered.html#p3.5

The main focus of the 3.5 series is the SWRLTab's [1] support of the 
Drools [2] rule engine, thus providing a completely free and open source 
solution for executing SWRL rules in Protege-OWL.

Release notes
-------------------
- Collection of minor bug fixes for the SWRLTab.
- Removed the Algernon, UMLS tab, and WordNet tab plug-ins from the 
distribution, as they are no longer maintained.

Other helpful links
--------------------------
Online version of these release notes: 
http://protegewiki.stanford.edu/wiki/Protege_3.5_Beta_Release_Notes
Release notes archive: 
http://protegewiki.stanford.edu/wiki/Protege_Release_Notes
Protege 3 documentation: 
http://protegewiki.stanford.edu/wiki/Protege3UserDocs
Protege on Facebook: 
https://www.facebook.com/pages/Protege-Project/136205016405270
Protege on Twitter: https://twitter.com/#!/protegeproject 
<https://twitter.com/#%2

Re: Real time data reg

kala devi ramar — 2012-05-09T19:16:08


Hello all
 
I want to use real time data in CSV and XML formats into protege.How to use the live data in owl?
Pls help me. I want it for my research work
 
Thanks 
 
R.Kaladevi_______________________________________________
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IEEE CSE/EUC 2012: Call for Papers (extendeddeadline!)

Announcements — 2012-05-09T09:22:59

                        *** Call for Papers ***

  The 15th IEEE International Conference on Computational Science and
                      Engineering (IEEE CSE 2012)

                    http://www.cse2012.cs.ucy.ac.cy/

 The 10th IEEE/IFIP International Conference on Embedded and Ubiquitous
                     Computing (IEEE/IFIP EUC 2012)

                    http://www.euc2012.cs.ucy.ac.cy/

                    3-5 October 2012, Paphos, Cyprus

               *** EXTENDED DEADLINE: 10th June 2012 ***


CSE 2012

The Computational Science and Engineering area has earned prominence
through advances in electronic and integrated technologies beginning
in the 1940s. Current times are very exciting and the years to come
will witness a proliferation in the use of various advanced computing
systems. It is increasingly becoming an emerging and promising
discipline in shaping future research and development activities in
academia and industry, ranging from engineering, science, finance,
economics, arts and hum

Re: Import

anji reddy — 2012-05-09T08:37:36

Hi all,
       Anybody knows, how to access OWL-S file to read the IOPE information
programatically through .net/java.....
( .net prefers).

Thanks inadvance
Regards
Anji
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Re: Import

Restel, Hannes — 2012-05-09T08:26:49

Yes You can!

..using the integrated tab plugin PROMPT.

See: http://protege.cim3.net/cgi-bin/wiki.pl?Prompt

 

All the best,

Hannes

 

--

Beschreibung: Beschreibung: FOKUS-logo-www - Kopie

 

M.Sc. Hannes Restel | Fraunhofer-Institut für Offene Kommunikationssysteme

 

Kompetenzzentrum eGovernment und Applikationen (ELAN)

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 <http://www.fokus.fraunhofer.de/> http://www.fokus.fraunhofer.de

 

Von: protege-discussion-bounces< at >mailman.stanford.edu
[mailto:protege-discussion-bounces< at >mailman.stanford.edu] Im Auftrag von
rperro88< at >hotmail.com
Gesendet: Mittwoch, 9. Mai 2012 10:04
An: protege-discussion< at >mailman.stanford.edu
Betreff: [protege-discussion] Import

 

HI, I have different ontology and I would merge these in a single one. So,
can I, starting from one ontology, import the others directl

Import

2012-05-09T08:04:22

HI, I have different ontology and I would merge these in a single one. So, can I, starting from one ontology, import the others directly?
thank you!
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