Protege-OWL Short Course, May 30 – June 1, 2012, Stanford University

Dear friends,

We are pleased to announce another offering of the Protege-OWL Short Course in late May of this year. The course will take place right before SemTech 2012, Semantic Tech & Business conference in San Francisco ( You can schedule your trip to the Bay Area to attend both events.

The Protege-OWL Short Course provides an in-depth introduction to ontology engineering and the Web Ontology Language (OWL). We cover best practices in ontology building and the latest Semantic Web technologies, including OWL 2, RDF, SPARQL, and SWRL.

During the hands-on portion of the course, participants will learn how to navigate the latest version of the Protege tool set, which supports the full OWL 2 standard. Protege is the most popular and widely used ontology editor, employed in projects by organizations such as the World Health Organization, eBay, and Yahoo!.

Dates & location: May 30 – June 1, 2012, Stanford University
Course content:
Course schedule:
Online registration:
Facebook event page:
All portions of the course will be taught by members of the Protege staff:

Matthew Horridge
Natasha Noy
Martin O’Connor
Timothy Redmond
Samson Tu
Tania Tudorache
Jennifer Vendetti
Questions? Contact protege-shortcourse at

Best Regards,

The Protege Team

National Center for Biomedical Ontology [NCBO] Hackathon – March 26-27, 2012

Do you have a task in biomedical or clinical informatics that will benefit from the use of ontologies or ontology-based technology? Want to brainstorm application design and development questions? Want help incorporating the NCBO Web services into your application?

Join us for the first-ever NCBO Hackathon. This event will include two days of intensive hands-on sessions to facilitate the development of applications using NCBO Web services. We will devote extensive time to your software development project and will have presentations covering a range of topics from application design to coding. You will:

  • Brainstorm ideas for applications
  • Discuss coding issues, performance tuning, and future development plans
  • Learn about the suite of NCBO Web services and how they are (and have been!) used in applications. Examples include access to ontologies, search, mappings, term proposals, text annotation, and biomedical resource search (the “Resource Index”)
  • Hear about the design of our RDF triple store and learn how to access the triple-store directly from your application using the SPARQL query language

Early registration is $25, but spots are limited so register online now.

Call for papers: International Workshop on Semantic Interoperability in Medical Informatics in conjunction with ESWC2012 (27th May 2012) – Heraklion (Crete), Greece

== Level 2 ==

=== Level 3 ===

==== Level 4 ====

===== Level 5 =====

====== Level 6 ======


Collaboratory Platforms

Alfresco –

Apache –

dotCMS –

DotNetNuke –

dotproject –

Drupal –

Joomla –

Mozilla –

OpenSuSE –

Red Hat –

Ubuntu –

Zoho –

Zimbra –

Zope –



WordPress P2 Theme




Second Annual VIVO Conference Call for National Networking Application

The Second Annual VIVO Conference will be held August 24 – 26 at the Gaylord National in Washington D.C. The conference is sponsoring a competition for applications using data coming from VIVO systems to support science.


Applications can be written in any language.

To qualify applications must:

  • Consume VIVO data from more than one VIVO consortium site. Applications consuming data from other sites will not be considered.
  • Be hosted outside the consortium (University of Florida, Cornell University, Indiana University, Washington University School of Medicine, Weill Cornell Medical College, The Scripps Research Institute, and Ponce School of Medicine).
  • Be accessible from a single persistent URL, accessible on the public Internet without authentication.

Criteria for Success

Applications will be judged on the following criteria:

  1. Value to scientists on the national network.
  2. Functionality. The application performs as described.
  3. Presentation. The application is well organized and attractive.


The first prize winner will have registration refunded, receive a cash prize and will be awarded a plaque at a recognition ceremony during the conference. Second and third prize winners will receive certificates.


To submit your application, please send an email to Applications are due July 31, 2011. Winners will be announced at the conference. Submissions must include:

  • Names, academic degree(s), affiliations, and locations of all authors. Brief (500 words or less) description of the application and its value to scientists.
  • A URL for the application.
  • Instructions regarding operation.
  • The judges will execute the application from the URL provided without assistance from the authors.

    Additional Resources

    VIVO uses Linked Data ( standards for data access via Resource Description Framework (RDF).  See the Linked Data site for more information regarding Linked Data, RDF and data processing. VIVO enjoys a robust open source, open community space on SourceForge. The VIVO software and ontology are publicly available at along with content that supports implementation, adoption, and development efforts around the world

    Call for Papers – WEB TECHNOLOGIES, a Track of the 27th Annual ACM Symposium on Applied Computing, 25 – 29 March 2012, Riva del Garda (Trento), Italy

    Call for Papers

    Aims and rationale

    The World Wide Web is changing. The advent of HTML 5, the increasing
    importance of AJAX and client-side scripting, the new frontiers of Semantic
    Web, the explosion of Web-based Social Networks as well as the advent of the
    Federated Social Web are only some examples of this general trend.

    Web applications are progressively evolving into rich and flexible
    environments where users can easily access documents, publish content, listen
    to music, watch videos, draw pictures and even play directly via
    browser. This new class of ubiquitous software systems is gaining momentum
    and fosters the evolution of new ways for people to interact and
    cooperate. Novel approaches and techniques, new tools and frameworks are
    needed to address the increasing complexity of these applications.

    The Web Technologies track of ACM SAC aims at bringing together researchers
    and practitioners from industry and academia working on practical and
    foundational aspects of Web technologies as well as other technologies that
    in the Web framework have found new and unexpected application fields. We
    seek original, unpublished contributions that are mainly focused on, but not
    necessarily limited to, the following aspects of Web technologies:

    • Collaboration on the Web: Wikis, Social Software, and Web 2.0
    • Electronic Publishing on the Web
    • Emerging Web Technologies
    • Expanding the reach of Social Software: Enterprise 2.0, Social Software,
      Business Process Management, …
    • Federated Social Web software and protocols
    • Hypertext, hypermedia, markup languages, and XML-related
    • Performance, Scalability and Quality of Service on the Web
    • Web Metrics, Monitoring and Analysis
    • (Process-aware) Web Information Systems
    • Rich User Experiences and Human Computer Interaction in Web
    • Semantic-enhanced Web applications
    • Web Browsers and Web Interfaces
    • Web Accessibility
    • Mobile Web and Cross-device Content Delivery
    • Web Searching

    Proceedings and Post-Proceedings

    Papers accepted for the Web Technologies track will be published by ACM both
    in the SAC 2012 proceedings and in the ACM Digital Library. Authors of
    selected papers will be invited to submit an extended version of their work
    to an international journal.

    Paper Submission

    Original papers from the above-mentioned or other related areas will be
    considered. This includes three categories of submissions:

    1. original and unpublished research;
    2. reports of innovative computing applications in the arts, sciences,
      engineering, business, government, education and industry;
    3. reports of successful technology transfer to new problem domains.

    Each submitted paper will undergo a blind review process and will be
    refereed by at least three referees.
    Accepted papers in all categories
    will be published in the ACM SAC 2012 proceedings.

    The camera-ready version of the accepted paper should be prepared using the
    ACM format (guidelines are given on
    the SAC 2012 web
    Accepted full papers should not exceed 6 pages in a double
    column format (with the option, at additional expense of USD 80 per page, to
    add 2 more pages).

    The submission system is not open yet.

    Relevant Dates

    • August 31, 2011: Paper submission deadline
    • October 12, 2011: Author notification
    • November 2, 2011: Camera-ready copies due


    Track chairs

    Davide Rossi, University of Bologna

    Angelo Di Iorio, University of Bologna

    Stefano Zacchiroli, Université Paris Diderot – Paris 7

    E-mail contact:

    PC members

    to be announced


    2010 VIVO Conference Schedule of Events, August 12-13, 2010

    Thursday, August 12

    7:00 AM – 4:00 PM Registration Auditorium
    8:00 AM – 12:00 PM VIVO Workshops (Breakfast for workshop attendees provided from 7 – 8 AM in the Auditorium Lobby):

    • Implementing VIVO at Your Institution

    • VIVO Ontology

    • VIVO Data Analysis & Visualization Services: How to Program, Extend & Utilize

    Break Out A

    Break Out B

    Break Out C

    12:00 – 1:00 PM Lunch (on your own)
    1:00 – 2:30 PM Opening Plenary Session – Mike Conlon & Kristi Holmes

    Keynote Speaker – Noshir Contractor – Using Web Science to Understand and Enable Research Networks

    2:30 – 3:00 PM Break (Refreshments provided) Auditorium Lobby
    3:00 – 4:00 PM Scientific Sessions & Speakers

    • Semantic modeling for scientists

    • Panel Discussion – VIVO: users, interface design, and evaluation

    • Introduction to ORCID – Open Researcher & Contributor ID

    Break Out A

    Break Out B


    4:00 – 5:00 PM Scientific Sessions & Speakers

    • Smarter Campus: Catalyst for Research Collaboration through Optimal Assignment of Resources to Projects

    • CTSAIP: How a Small Project Produced Big Results; Deriving Physicians’ Expertise Profiles Based On ICD9-Coded Encounter Note Logs; Finding Specialists Using Interface Terminology and Concept-Based Hierarchical Reference Terminology

    • Next Steps for Research Networking in Science

    Break Out A

    Break Out B


    5:00 – 6:30 PM Reception and Posters (Hors d’oeuvres, beer and wine) Viscusi Area

    Friday, August 13

    7:30 – 10:00 AM Registration (Breakfast for conference attendees provided from 7 AM – 8 AM in the Viscusi Gallery) Auditorium
    8:00 – 9:00 AM Keynote Speaker – Jim Hendler – What is the Semantic Web really all about? Auditorium
    9:00 – 10:00 AM Scientific Sessions & Speakers

    • Panel Discussion – Implementation of VIVO

    • Shared Health Research Information Network (SHRINE); Research networking in the context of CV Management

    • Intergration Possibilities between VIVO & Google Apps for Education; What Faculty Members Want from a Research Information System; and From Bench to Bedside and Beyond: Potential Uses of VIVO in an Academic Medical Center Environment

    • Mapping Scientific Networks

    Break Out A

    Break Out B

    Break Out C


    10:00 – 10:30 AM Break (Refreshments provided) Viscusi Area
    10:30 – 11:30 AM Scientific Sessions & Speakers

    • Panel Discussion – Outreach & Adoption of VIVO

    • VIVO Development Overview

    • CTSciNet and VIVO: A Collaboration Aiming to Enhance Translational Research

    • Building an Australian user community for VIVO: Profiling Research Data for the Australian National Data Service

    Break Out A

    Break Out B

    Break Out C


    11:30 AM – 1:00 PM Lunch (Food provided) Viscusi Area
    1:00 – 2:00 PM Scientific Sessions & Speakers

    • Design and development of a modular harvestor for data ingest

    • Standardizing VIVO URLs: How Standard is Standard?

    • The Real Who’s Who: User & Computer-based Author Identification; Predicting author h-indexing using characteristics of the co-author network; Author disambiguation & VIVO: Building the Semantic Web by crawling

    • STAR METRICS: An Innovative U.S. Government-University Partnership to Create Data Infrastructure to Couple Scientists and Science Funding with Outcomes

    Break Out A

    Break Out B

    Break Out C


    2:00 – 3:00 PM Scientific Sessions & Speakers

    • Serving Niche and Orphan Research Communities through Network Extension and Augmentation, a User-centered Approach

    • Configuring a SPARQL End Point for VIVO; Drawing Organizational Charts Using VIVO; and Publications Research and Automated Author Disambiguation: Collaboration between University of Florida and Cornell University

    • Collexis and VIVO: Paving the Collexis Pathway to the National Research Network

    • The next step in knowledge evolution; Colonization of brains…

    Break Out A

    Break Out B

    Break Out C


    3:00 – 3:30 PM Break (Refreshments provided) Viscusi Area
    3:30 – 5:00 PM Closing Plenary Session – Mike Conlon & Kristi Holmes Auditorium

    5th International Semantic MediaWiki Conference (SMWCon Fall 2010) CALL FOR PARTICIPATION September 18-19, 2010 Amsterdam, The Netherlands

    SMWCon Fall 2010 is the 5th International Semantic MediaWiki Conference. It will be held on the weekend of September 18-19, 2010 at the Open Universiteit in Amsterdam, the Netherlands. The conference provides an informal and engaging environment for discussing cutting-edge and emerging Semantic MediaWiki tools, extensions and applications.

    General Information

    SMWCon brings together developers, users, and organizations from the Semantic MediaWiki (SMW) community around the world. As with the previous SMWCons, SMWCon Fall 2010 will include presentations and discussions about current applications and the future development of Semantic MediaWiki and its extensions and applications. Participants are invited to present their own work and to discuss experiences and ideas. While the conference will have scheduled presentations, each will encourage free discussion and a rapid exchange of ideas. Registration for participation and proposals for contributions can be entered on the conference wiki homepage (see below).

    Organizing Committee

    Lloyd Rutledge, Open Universiteit Henk Scholten, BI-Team Michael Cariaso, KeyGene Daniel Hansch, Ontoprise GmbH Yaron Koren, WikiWorks Markus Krötzsch, University of Oxford Denny Vrandečić, KIT Jesse Wang, Vulcan Inc.

    Venue and Accommodation

    The Open Universiteit Amsterdam Study Center is very close to public transport, the highway and Schiphol, Amsterdam’s international airport. The Study Center has wireless and non-stop free coffee. A variety of hotels are available in the neighborhood of the venue. For more information, see the conference wiki homepage, or send an email to

    NETTAB 2010 on Biological Wikis: Call for Contribution

    NETTAB 2010 on "Biological Wikis"
    November 29 – December 1, 2010, Naples, Italy
    See below for Topics, Contributions sought, Deadlines, Instructions and Committees.
    It is now clear that wiki systems offer a variety of advantages for the management of biological data and information.
    Some of the specific aims of wikis for biology (bio-wikis) include:
       * Collaborative development and sharing of knowledge
       * Collaborative annotation of database contents
       * Collaborative creation of database contents
    The collaborative development and sharing of documentation and knowledge allows communities to promote, exploit, discuss and reach consensus on procedures, data, experiences, news, and other varied information. Indeed valuable expertise and interests in special topics are usually distributed, and are rarely concentrated in a unique site or research group.
    The collaborative annotation of biological databases is increasingly under consideration because extended and accurate curation of an ever increasing volume of data is extremely costly and time consuming. Such distributed networks can help to improve and extend databases curation beyond that which is possible with, typically, limited numbers of curation staff. It allows users to contribute their expertise and observations  independently of database central organizations. Although the contents of the database are collaboratively annotated, the underlying databases themselves are left unchanged.
    Furthermore, collaborative creation of community databases can capture emerging structure in rapidly developing fields. These database-wikis are indexes of biologically relevant data that emerge from focused and rapidly developing communities. They form a stopgap between unstructured discussion in fora and on mailing lists and the ‘mature’ databases that emerge subsequently. Hence they can be useful for discerning trends and promoting best practices, as well as  collect unique and timely information.
    In the future, collaborative ‘wiki’ updates of almost all database contents can be envisaged. However several important issues need to be addressed:
       * How reliable are user contributions?
       * What format should annotations take?
       * How is this information feed back into ‘authoritative’ databases?
    Procedures should be implemented to support assessment of users’ contributions, extraction of structured data from annotations, uptake of original data into reference databases. The authoritativeness of contributions is essential: how can quality be assessed? How do we deal with contributions from casual end users, since these are usually not considered adequate when compared with professional annotation at service centers. Can the open edition model of many wiki systems, e.g. Wikipedia, be as successful in life sciences?  Alternatively, should the usual criteria for assessing quality of research be applied, including peer-evaluation of contributions and identification of users? Crediting users for their contributions (e.g. authorship assignment) may be necessary to stimulate  the broadest possible participation.  Which further benefits may be imagined to acknowledge user investment (subscriptions to services, journals, …)?
    Special features may be required to cater for the specificity of biological data: textual information is only a small part of biological data, how can the numerous and heterogeneous biological data types be catered for, e.g.  images, plots, diagrams? An adaptation of current wiki systems is needed. A survey of existing systems as well as current development efforts will be useful, so that possible synergies can be identified and supported, as well as ensure a coherent set of interoperable biological wikis.
    The following list is not meant to be exclusive of any further topics as stated above.
    Submitted contributions should address one or more of the following topics:
       * Wiki development tools
             o Wikimedia
             o Wikimedia extensions
             o Semantic Wikis
             o Wiki-coupled CMSs
             o Other wikis
       * Arising issues for the biomedical domain:
             o Authoritativeness of contributions and sites
             o Quality assessment
             o Users acknowledgement
             o Stimulatation of quality contributions
             o Authorships management and reward
             o ‘Scientific production’ value for contributions
             o Management of bioinformatics data types
       * Wikis and collaborative systems for:
             o Genomics, proteomics, metabolomics, any -omics
             o Proteins analysis and visualization
             o gene and proteins interactions
             o metabolic pathways
             o oncology research
       * Issues to be tackled by wiki and collaborative research for:
             o Genomics, proteomics, metabolomics, any -omics
             o Proteins analysis and visualization
             o gene and proteins interactions
             o metabolic pathways
             o oncology research
    The following possible contributions are sought:
       * Oral communications
       * Posters
       * Software demos
    All accepted contributions will be published in the proceedings of the workshop.
    *  September 24, 2010: Oral communications submission
             o Decisions announced: October 24, 2010
    * October 17, 2010: Posters submission
             o Decisions announced: October 24, 2010
    * October 29, 2010: Early registration ends
    * November 29 – December 1, 2010: Workshop and Tutorials
    Kindly follow the instructions carefully when preparing your contribution and submit your contribution through the EasyChair system at
    All contributions should follow the same format, as specified here:
    font type: Times New Roman, font size: 12 pti, page size: A4, left and right margins: 2.0 cm, upper margin: 2.5 cm, lower margin: 2.0 cm.
    The lenght of contributions for oral communications should be between 3 and 5 pages, including tables and figures.
    They should include: Abstract, Introduction, Methods, Results and Discussion, References.
    All contributions for oral communications will be evaluated by at least three referees.
    The length of contributions for posters should be no more then 3 pages, including tables and figures.
    They should include: Introduction, Methods, Results, References.
    All posters will be evaluated on the basis of their relevance fot the workshop’s topics only.
    For any further information or clarification, please contact the organization by email at
       * Angelo Facchiano, CNR-ISA, Avellino, Italy
       * Paolo Romano, National Cancer Research Institute, Genoa, Italy
    Scientific Committee
       * Claudia Angelini, IAC, National Research Council, Napoli, Italy
       * Roland Barriot, Université Paul Sabatier – CNRS, Toulouse, France
       * Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
       * Dan Bolser, University of Dundee, Scotland, United kingdom
       * Philip E. Bourne, University of California, San Diego UCSD, La Jolla, USA
       * Mike Carasio, Keygene N.V., Wageningen, The Netherlands
       * Maria Luisa Chiusano, University of Napoli "Federico II", Napoli, Italy
       * Italia De Feis, IAC, National Research Council, Napoli, Italy
       * Angelo Facchiano, ISA, National Research Council, Avellino, Italy
       * Carl Herrmann, Université de la Méditerranée, Marseille, France
       * Pascal Hingamp, Université de la Méditerranée, Marseille, France
       * Eran Hodis, Weizmann Institute of Science, Rehovot, Israel
       * Robert Hoehndorf, Department of Genetics, University of Cambridge, United Kingdom
       * Robert Hoffmann, Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, USA
       * Thomas Kelder, BiGCaT Bioinformatics, University of Maastricht, The Netherlands
       * Alexander Pico, The Gladstone Institutes, University of California, San Francisco, USA
       * Jaime Prilusky, Bioinformatics, Weizmann Institute of Science, Rehovot, Israel
       * Paolo Romano, Bioinformatics, National Cancer Research Institute, Italy
       * Andrew Su, Bioinformatics, Genomics Institute of the Novartis Research Foundation, San Diego, USA
       * Joel Sussman, Weizmann Institute of Science, Rehovot, Israel
       * Tim Vickers, Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, USA
       * Wyeth Wasserman, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
       * and further members yet to be confirmed
    Organizing Committee
       * Claudia Angelini, IAC, National Research Council, Napoli, Italy
       * Maria Luisa Chiusano, University of Napoli "Federico II", Napoli, Italy
       * Italia De Feis, IAC, National Research Council, Napoli, Italy
       * Angelo Facchiano, ISA, National Research Council, Avellino, Italy
       * Paolo Romano, Bioinformatics, National Cancer Research Institute, Genoa, Italy
    Supporting Institutes, Scientific Societies and Projects
    This list is still under definition.
      * National Research Council (CNR), Italy
      * National Cancer Research Institute (IST), Genoa, Italy
      * Italian Network for Oncology Bioinformatics (RNBIO)
    Sponsorships are still under definition. You are welcome to email us for further information if you are interested in sponsoring this workshop.
    We look forward to meeting you in Naples!
    Paolo Romano and Angelo Facchiano
    on behalf of the Scientific Committee
    Paolo Romano (
    National Cancer Research Institute (IST)
    Largo Rosanna Benzi, 10, I-16132, Genova, Italy
    Tel: +39-010-5737-288  Fax: +39-010-5737-295  Skype: p.romano