gmane.comp.misc.ontology.protege.general

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 encoding 
them then you should be sure that the encoding is UTF-8 and that the 
compiler knows that the encoding is UTF-8.  The javac compiler has a 
encoding option that lets you set this.

-Timothy



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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.XMLErrorReporter.reportError(Unknown Source)
 at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
 at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
 at
org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown
Source)
 at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
Source)
 at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
 at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
 at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
 at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
 at com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:107)
 at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:158)
 at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:145)
 at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:183)
 at com.hp.hpl.jena.rdf.model.impl.ModelCom.read(ModelCom.java:192)
 at store.storeSchema.ceateDBModelFromFile(storeSchema.java:79)
 at store.storeSchema.main(storeSchema.java:358)
Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog.
 at
org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown
Source)
 ... 17 more

The relevant code is as follows:

    public static OntModel ceateDBModelFromFile(IDBConnection con, String
name, String filePath){
 ModelMaker maker = ModelFactory.createModelRDBMaker(con);
 Model base = maker.createModel(name);
 OntModel newmodel =
ModelFactory.createOntologyModel(getModelSpec(maker),base);
 Model defModel = maker.createModel(name);
 defModel.commit();
 FileInputStream read = null;
 try{
  read = new FileInputStream(filePath);
 }catch (FileNotFoundException e){
 e.printStackTrace();
 System.out.println("未找到要存储的本体文件，请检查文件地址及名称");
 }
 InputStreamReader in = null;
 try {
 in = new InputStreamReader((FileInputStream)read, "UTF-8");
 } catch (UnsupportedEncodingException e) {
 e.printStackTrace();
 System.out.println("不支持上述字符集。");
 }
 defModel.begin();
 defModel.read(in,null);
 try {
 in.close();
 } catch (IOException e){
 e.printStackTrace();
 System.out.println("无法关闭字节流文件。");
 }
 defModel.commit();
 System.out.println("数据转换执行完毕，已将本体文件存入数据库。");
 try{
 con.close();
 } catch (SQLException e){
 e.printStackTrace();
 System.out.println("文件无法关闭。");
 }
 System.out.println("已将本体文件持久化到数据库中");
 return newmodel;
 }


What are the probable causes could lead to the upper problem, and how to
deal with the problem mentioned above?
Any reply from you is really appreciated!
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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
conference. Tutorials enable attendees to fully appreciate current issues, main schools of thought,
and possible application areas.
Tutorial notes will be published separately in a companion booklet.

Topics of Interest
------------------
In order to meet these goals, tutorials should address topics that satisfy the following criteria:
- the topic falls in the general scope of EKAW 2012,
- there is a clear focus on a specific technology, problem or application, and
- there is a sufficiently large community interested in the topic.

In particular, we encourage the submission of tutorial proposals on:
- Knowledge Management
- Knowledge Engineering and Acquisition
- Social and Cognitive Aspects of Knowledge Representation and Reasoning
- User interaction, querying, and interfaces

Additionally, tutorials could also include:
practical parts in terms of examples or exercises to be carried out by the participants

Proposers of accepted tutorials have to prepare a tutorial webpage containing detailed information
about the tutorial.

Submission Guidelines
---------------------
Tutorial proposals should be submitted via EasyChair
https://www.easychair.org/conferences/?conf=ekaw2012workshopandt as a single PDF file of no more
than 5 pages, specifying “Tutorial Proposal”. Proposals should contain the following information:
- Title.
- Abstract (200 words)
- Motivation on why the topic is of particular interest at this time
- Relation to the conference topics.
- If the tutorial, or a very similar tutorial has been given elsewhere, explanation of the benefit
of presenting it again to the EKAW community
- Overview of content, description of the aims, presentation style, potential/preferred prerequisite
knowledge;
- Indication on whether the tutorial should be considered for a half-day or full-day.
- Intended audience and expected number of participants.
- Audio-visual or technical requirements and any special room requirements (for hands-on sessions,
any software needed and download sites must be provided by the tutorial presenters).
- Data of the presenters (name, affiliation, email address, homepage) and short CV including also
their expertise, experiences in teaching and in tutorial presentation.

Important Dates
---------------
Event October 8-9, 2012
Tutorial submission May 16, 2012
Tutorial notifications June 10, 2012

Chairs
------
Claudia d’Amato, University of Bari, Italy
Krzysztof Janowicz, University of California, Santa Barbara, USA
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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 the relationship between genome-wide genetic variation and common 
human traits is a viable and cost-effective alternative to the 
traditional genome-wide association studies (GWAS).

Of course, such studies leverage the foundational work of the past 
decade on biomedical data integration (architectures, data models, 
ontologies, privacy, etc), which had paved the way for life sciences 
infrastructures, such as ELIXIR, the open source Informatics for 
Integrating Biology and the Bedside (i2b2) platform, and federated query 
tools, such as the Shared Health Research Information Network (SHRINE).

The increasing availability of "big data", coming from high-throughput 
analytical techniques, large clinical data repositories, the biomedical 
literature and online resources, offers exciting opportunities to 
researchers, but also poses new integration challenges.

DILS 2012 is the 8th in a series on international conferences that aim 
at fostering discussion, exchange, and innovation in research and 
development in the areas of data integration and data management for the 
life sciences. Researchers and professionals from biology, medicine, 
computer science and engineering are invited to share their knowledge 
and experience.

DILS 2012 will have three keynotes talks, peer-reviewed paper 
presentations, flash presentations, and a poster/demo session.

----------------
Poster/demo submission
----------------

DILS 2012 invites submissions for posters and demos to be presented in 
the poster/demo session at the conference.

Please submit poster/demo abstracts to dils2012conference at gmail.com 
as plain text files (up to 400 words, exclusive of title, authors and 
affiliations), clearly specifying the category (Poster or Demo).

The poster/demo abstracts are not part of the main DILS 2012 
proceedings, but will be published on the DILS web site and distributed 
at the conference. The organizers will provide a basic setup (easels, 
tables), but no computers or projectors.
The best posters will be selected for a flash presentation during the 
main conference.

Submission: May 31, 2012

----------------
Keynote speakers
----------------

     * Jim Ostell, NCBI, National Library of Medicine, NIH
       Entrez: The NCBI Search and Discovery Engine

     * Ken Barker, IBM Watson group
       Combining Structured and Unstructured Knowledge Sources for 
Question Answering in Watson

     * Jim Cimino, Clinical Center, NIH
       The Biomedical Translational Research Information System: 
Clinical Data Integration at the National Institutes of Health

----------------
Program
----------------

   - Foundations of Data Integration

     * InterOnto - Ranking Inter-Ontology Links
       Silke Trißl, Philipp Hussels and Ulf Leser

     * Finding Cross Genome Patterns in Annotation Graphs
       Joseph Benik, Caren Chang, Louiqa Raschid, Maria Esther Vidal, 
Guillermo Palma and Andreas Thor

     * Pay-as-you-go Ranking of Schema Mappings using Query Logs
       Ruhaila Binti Maskat, Norman W. Paton and Suzanne Embury

   - New Paradigms for Data Integration

     * Cancer Data Integration and Querying with GeneTegra
       E. Patrick Shironoshita, Yves R. Jean-Mary, Ray M. Bradley, 
Patricia Buendia and Mansur R. Kabuka

     * Integrating large, disparate biomedical ontologies to boost organ 
development network connectivity
       Chimezie Ogbuji and Rong Xu

     * Crowdsourcing for Validating Candidate Gene-Mutation Relations in 
MEDLINE Abstracts
       John D. Burger, Emily Doughty, Sam Bayer, David Tresner-Kirsch, 
Ben Wellner, John Aberdeen, Kyungjoon Lee, Maricel G. Kann and Lynette 
Hirschman

   - Integrating Clinical Data

     * ONCO-i2b2: improve patients selection through case-based 
information retrieval techniques
       Daniele Segagni, Riccardo Bellazzi, Alberto Zambelli, Silvia G. 
Priori, Matteo Gabetta and Valentina Tibollo

     * Syntactic-Semantic Frames for Clinical Cohort Identification Queries
       Dina Demner-Fushman and Swapna Abhyankar

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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" topics.

This year's "hot" topic is the representation of
physiology. Physiology is the science of the functions and
functionings of biological systems, and significant resources have
been invested in biology and medicine to describe and simulate
physiological processes. In particular, researchers in systems biology
and systems medicine have generated a large number of computational
models to predict the outcome of physiological processes on a
sub-cellular, cellular, tissue and organ-level scale, and projects
such as the Virtual Physiological Human aim to extend this work
further and create a computational model of human physiology. While
ontologies are now widely applied to integrate biomedical data in many
domains, the complexity of the physiology domain has limited the
success of ontologies so far. We aim to address this problem in the
OBML workshop by organizing a special session on the ontology of
physiology. This session will bring together researchers in ontology,
biomedicine, systems biology and knowledge representation to present
their solutions and requirements for the domain of physiology.


Topics
------

We invite submissions in all areas of biomedical ontology, including
the following topics:
- applications of ontologies and terminologies in biology, medicine,
  and clinical research
- methods and tools for the construction and management of ontologies
- ontologies for knowledge representation, methods of
  reasoning, integration and interoperability of ontologies
- applications of the Semantic Web and knowledge representation
  formalisms in biomedicine and the life sciences
- new biomedical ontologies and updates to existing ontologies

For our special session on "ontology of physiology", we are
particularly interested in 
- ontology and systems biology
- ontology of processes
- ontology of functions, functionings, dispositions and tendencies
- links between physiology, phenotypes and disease
- use of ontologies for the description of parameters, inputs,
  simulations and simulation results of computational models


Submission instructions
-----------------------
Submissions to the workshop should comprise 2-4 pages and must be
written in English. The preferred file format for submissions is PDF,
other admitted formats are Microsoft Word (DOC and DOCX) and
Postscript (PS). Please use the corresponding template for
submissions, either the LaTeX template or the Microsoft Word
template.

Submissions must be submitted via Easychair at

[2] http://www.easychair.org/conferences/?conf=obml2012


Dates
-----

Submission deadline:      August 01, 2012
Author notification:      August 31, 2012
Submission of
camera-ready manuscripts: September 16, 2012
OBML Workshop:            September 27-28, 2012


Location
--------

The OBML Workshop 2012 will take place in Dresden, Germany,
presumably at the Biotechnology Center of the Technical University.


Invited Speakers
----------------

Francisco Couto   (Universidade de Lisboa)
Michael Schroeder (Technical University Dresden)
George Gkoutos    (University of Cambridge)


Organization
------------

Robert Hoehndorf (chair)
Martin Boeker    (program chair)
Heinrich Herre   (program chair)
Frank Loebe      (co-organizer)


Local Organization
------------------
Michael Schroeder
(Biotechnology Center, Technical University Dresden)


Program committee
-----------------
 TBA
(see [1] for updates)


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

[2] Submission system
    http://www.easychair.org/conferences/?conf=obml2012
    


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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 central to reducing the complexity of
designing and understanding ontologies, and to facilitating ontology
verification, reasoning, development, maintenance and integration.

Recent research on ontology modularity shows substantial progress in
foundations of modularity, techniques of modularization and modular
development, distributed reasoning and empirical evaluation. These
results provide a solid foundation and exciting prospects for further
research and development.

The workshop continues a series of successful events that have been an
excellent venue for practitioners and researchers to discuss latest
and current work; the most recent WoMOs were held at FOIS 2010 and
ESSLLI 2011.

TOPICS include, but are not limited to:

- What is modularity?: kinds of modules and their properties; modules
vs. contexts; design patterns; granularity of representation;

- Logical/foundational studies: conservativity; modular ontology
languages; reconciling inconsistencies across modules; formal
structuring of modules; heterogeneity;

- Algorithmic approaches: distributed and incremental reasoning;
modularization and module extraction; sharing, linking, reuse;
privacy; evaluation of modularization approaches; complexity of
reasoning; implemented systems;

- Applications: semantic web; life sciences; bio-ontologies; natural
language processing; space and time; ambient intelligence; social
intelligence; collaborative ontology development and ontology
versioning.

IMPORTANT DATES

Paper Submission: May 18, 2012
Notification: June 19, 2012
Camera ready: July 6, 2012
Workshop: July 24, 2012

SUBMISSION GUIDELINES:

We welcome submissions on modularity in a broad sense. The workshop is
open to papers of theoretical or practical nature. Submissions should
be of up to 11 pages in length, formatted according to Springer LNCS
style (see http://www.springer.com/comp/lncs/Authors.html), prepared
in PDF format and submitted no later than May 18, 2012, through the
EasyChair Submission System (see
http://www.easychair.org/conferences/?conf=womo2012).

Submitted papers will be peer-reviewed by members of the program
committee. Accepted papers will be made available in the proceedings
to be published electronically in the CEUR Workshop Proceedings series
(see http://www.ceur-ws.org).

(Find the WoMO 2010 and 2011 proceedings here
http://www.booksonline.iospress.nl/Content/View.aspx?piid=16268 and
http://www.booksonline.iospress.nl/Content/View.aspx?piid=20369)

WORKSHOP CHAIRS:

Thomas Schneider, University of Bremen, Germany
Dirk Walther, Technical University of Madrid (UPM), Spain

PROGRAM COMMITTEE:

Kenneth Baclawski, Northeastern University, Boston, MA, USA
Stefano Borgo, Italian National Research Council, Trento, Italy
Oscar Corcho, Universidad Politecnica de Madrid, Spain
Bernardo Cuenca Grau, University of Oxford, UK
Mike Dean, Raytheon BBN Technologies, Ann Arbor, MI, USA
Silvio Ghilardi, Universita degli Studi di Milano, Italy
Michael Gruninger, University of Toronto, Canada
Janna Hastings, EMBL-EBI, Cambridge, UK
Robert Hoehndorf, University of Cambridge, UK
Boris Konev, University of Liverpool, UK
Roman Kontchakov, Birkbeck College, London, UK
Thomas Meyer, Meraka Institute, CSIR, Pretoria, South Africa
Till Mossakowski, University of Bremen, Germany
Immanuel Normann, Birkbeck College, London, UK
Leo Obrst, MITRE, McLean, VA, USA
Adrian Paschke, Free University of Berlin, Germany
David Perez del Rey, Universidad Politecnica de Madrid, Spain
Uli Sattler, University of Manchester, UK
Luciano Serafini, Fondazione Bruno Kessler, Trento, Italy
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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 scientists' time and
effort. The scientific literature continues to grow and is becoming more
and more unmanageable for researchers operating in the most active
disciplines. Better interfaces for collaboration, visualization, and
understanding would significantly improve scientific practice.
Scientific data, publications, and tools could be published in open
formats with appropriate semantic descriptions and metadata annotations
to improve sharing and dissemination. Opportunities for broader
participation in well-defined scientific tasks enable human contributors
to provide large amounts of data, annotations, or complex processing
results that could not otherwise be obtained. These are just some
examples of areas where there are opportunities for artificial
intelligent techniques could make a difference. Improvements and
innovations across the spectrum of scientific processes and activities
will have a profound impact on the rate of scientific discoveries.

This symposium will provide a forum for researchers interested in
understanding the role of AI techniques in improving or innovating
scientific processes.

 

We seek submissions that: (1) report on success stories that illustrate
the potential of future research in this field; (2) discuss lessons
learned in the process of addressing challenging aspects of the
scientific process; (3) analyze the impact of a particular technique in
an area of science and reflect on its potential for broader
applicability in other sciences; and (4) propose future concepts
grounded in lessons learned and an understanding of the challenges in
the scientific discovery process.

Topics of interest include but are not limited to:

* Ontologies and knowledge bases that model particular areas of
scientific knowledge

* Semantic representations of metadata for all aspects of scientific
processes

* Techniques for organizing scientific literature

* Workflow systems to manage complex data analysis processes

* Knowledge discovery techniques that are embedded in the context of
scientific investigations

* Integrative approaches of machine learning and scientific model
induction

* Automated systems for experiment design, data analysis, and hypothesis
generation and refinement

* User-centered design of intelligent systems that partner with
scientists to perform complex tasks

* Integrated approaches to visualizing data, models, and the connections
between them to foster new insights

* Cognitive-centered design of scientist aids

* Social computing systems that let novice participants contribute to
scientific tasks

 

Submissions can be up to 6 pages, using the AAAI style files.
Submissions should be uploaded to the submission site no later than June
5 2012 before midnight on the timezone of your choice.

 

 

ORGANIZING COMMITTEE

 

Co-Chairs:

 

* Will Bridewell, Stanford University

* Yolanda Gil, University of Southern California

* Haym Hirsh, Rutgers University

* Kerstin Kleese van Dam, Pacific Northwest National Laboratory

* Karsten Steinhaeuser, University of Minnesota

 

Program Committee:

 

* Cecilia Aragon, University of Washington

* Phil Bourne, University of California San Diego

* Elizabeth Bradley, University of Colorado

* Paolo Ciccarese, Harvard University

* Susan Davidson, University of Pennsylvania

* Helena Deus, Digital Enterprise Research Institute

* Tom Dietterich, Oregon State University

* Yolanda Gil, University of Southern California

* Clark Glymour, Carnegie Mellon University

* Carla Gomes, Cornell University

* Alexander Gray, Georgia Institute of Technology

* Larry Hunter, University of Colorado Denver

* David Jensen, University of Massachusetts Amherst

* Vipin Kumar, University of Minnesota

* Pat Langley, Arizona State University

* Hod Lipson, Cornell University

* Huan Liu, Arizona State University

* Yan Liu, University of Southern California

* Miriah Meyer, University of Utah

* Mark Musen, Stanford University

* Andrey Rzhetsky, University of Chicago

* Steve Sawyer, Syracuse University

* Alex Schliep, Rutgers University

* Christian Schunn, University of Pittsburgh

* Nigam Shah, Stanford University

* Alex Szalay, The Johns Hopkins University

* Loren Terveen, University of Minnesota

* Raul E. Valdes-Perez, Vivisimo Inc.

* Evelyne Viegas, Microsoft Research

 

IMPORTANT DATES:

*      Submission deadline: June 5, 2012 
*      Notification to authors: June 30, 2012 
*      Camera-ready due: September 7, 2012 
*      Registration deadline: September 14, 2012 
*      Symposium: November 2-4, 2012

 

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

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

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/#%21/protegeproject>

Best Regards,
The Protege Team

[1] http://protege.cim3.net/cgi-bin/wiki.pl?SWRLTab
[2] http://www.jboss.org/drools

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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 humanitarian fields, especially when the solution
of large and complex problems must cope with tight timing schedules.

CSE 2012 is the next event, in a series of highly successful IEEE
International Conferences on Computational Science and Engineering,
held mainly as the International Workshop on High Performance
Scientific and Engineering Computing for 10 editions. The previous
CSE-11 was held in Dalian, China, August 24-26, 2011.

CSE 2012 is to bring together computer scientists, applied
mathematicians, engineers in different disciplines and researchers to
present, discuss and exchange ideas, results and experiences in the
area of advanced computing for problems in science and engineering
applications and inter-disciplinary. We are inviting new and unpublished
papers on, but not limited to, the following topics:

*   Intelligent and Bio-inspired Computing
*   Distributed and Parallel Computing
*   Database and Data Mining
*   Cluster, Grid, P2P and Cloud Computing
*   Mobile Computing and Wireless Communications
*   CSE Education
*   Scientific and Engineering Computing
*   Embedded and Ubiquitous Computing
*   Advanced Networking and Applications
*   Security, Privacy and Trust
*   Service and Internet Computing - Dependable, Reliable and Autonomic
    Computing
*   CSE applications

EUC 2012

Embedded and ubiquitous computing is an exciting paradigm that promises
to provide computing and communication services to the end users all the
time and everywhere. Its systems are now invading in every aspect of our
daily life and promise to revolutionize our life much more profoundly
than elevators, electric motors or even personal computer evolution ever
did. The emergence of this technology is a natural outcome of research
and technological advances in a variety of areas including embedded
systems, pervasive computing and communications, wireless networks,
mobile computing, distributed computing and agent technologies.

EUC 2012 is the next event, in a series of highly successful IEEE
International Conferences on Embedded and Ubiquitous Computing (EUC),
previously held as ICDCS-ECS04 (Tokyo, Japan, March 2004), EUC-04
(Aizu, Japan, August 2004), EUC-05 (Nagasaki, Japan, December 2005),
EUC-06 (Seoul, Korea, August 2006), EUC-07 (Taipei, Taiwan, December
2007), EUC-08 (Shanghai, China, December 2008), EUC-09 (Vancouver,
Canada, August 2009), EUC-10 (Hong Kong, December 2010) and EUC 2011
(Melbourne, Australia, October 2011).

Topics of particular interest include, but are not limited to:

Embedded Computing
*   Embedded System Software and Optimization
*   Embedded System Architectures
*   Hardware/Software Co-design and Design Automation
*   Real-Time Systems and Operating Systems
*   Application-Specific Processors and Devices
*   Power-Aware Computing
*   Sensor Networks
*   System/Network-on-Chip
*   Reconfigurable Computing Systems and Applications
*   Cyber-Physical Systems

Ubiquitous Computing
*   Pervasive Computing and Communications
*   Middleware and Peer-to-Peer Computing
*   Internet Computing and Applications
*   Multimedia and Data Management
*   Human-Computer Interaction
*   Network Protocols
*   Wireless Communication & Networks
*   Mobile Computing
*   Agents and Distributed Computing
*   Security and Fault Tolerance Applications

Submission Guidelines

Submitted papers must not substantially overlap papers that have been
published or that are simultaneously submitted to a journal or a
conference with proceedings. Papers should be at most 8 pages
including the bibliography and well-marked appendices, and should
follow the IEEE 8.5" x 11" Two-Column Format. Committee members are
not required to read the appendices, and so the paper should be
intelligible without them. Submissions are to be made to the
submission web site. Only pdf files will be accepted. Submissions
not meeting these guidelines risk rejection without consideration
of their merits. Papers must be received by the submission deadline.
Authors of accepted papers must guarantee that their papers will be
presented at the conference. Accepted papers will be published in
the IEEE conference proceedings (EI indexed). Selected best papers
will be published in special issues of high quality journals
(currently under negotation).

Important Dates

*   Submission Deadline: 10 June
*   Notification of Acceptance: 15 July
*   Camera-ready Versions Submitted: 31 July
*   Author Registration: 31 July


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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)

Sichere Business Infrastrukturen, Wissenschaftl. Mitarbeiter

Steinplatz 2, 10623 Berlin, Germany

Telefon: +49 (0)30/24 306-324

 <mailto:hannes.restel< at >fokus.fraunhofer.de>
mailto:hannes.restel< at >fokus.fraunhofer.de

 <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 directly?

 

thank you!

 

roberta 

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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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DataMaster question

Bakalov, Vesselina D. — 2012-05-08T20:21:49

I hope this is the right place to post this question. The question is
related to the DataMaster plugin.

 

Is it possible to exclude columns when importing a table? I have a CLOB
column that I don't want to incude.

 

Thanks a lot,

Vessie

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Re: Import XML schemas to OWL using Protege

Timothy Redmond — 2012-05-08T17:25:02


I think that it is possible.  I did a quick google search for "xsd to 
owl" and the first hit was:

      http://rhizomik.net/html/redefer/xsd2owl/


I don't know much about these tools but I suspect that the mapping will 
be imperfect (but perhaps sufficient).


Not that I know of.

-Timothy



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