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3rd Tinnitus Research Initiative Meeting                           24-26 June 2009, Stresa, Italy




       Tinnitusbook: a proposal for an
       advanced scientific web community
       for tinnitus research
        G. Attanasio (a,f), P. Ciccarese (b,c), E. Wu (e),
           T. Clark (b,c,d), E. Pecis (f), R. Filipo(a)
       a: Dept. Neurology and Otolaryngology, University La Sapienza, Rome, IT;
       b: Massachusetts Gen. Hosp., Boston, MA;
       c: Harvard Med. School, Boston, MA;
       d: Harvard Initiative in Innovative Computing, Cambridge, MA;
       e: Alzheimer Res. Forum Found., Boston, MA;
       f: Acufeni.net Association onlus
Acufeni.net forum
www.acufeni.net
OUR PROJECT

     To create a new interdisciplinary online
      resource connecting researchers with
    researchers, to facilitate rapid progress in
                Tinnitus research


COMMUNITY                        COMMUNITY
OF PATIENTS                    OF SCIENTISTS
3rd Tinnitus Research Initiative Meeting                           24-26 June 2009, Stresa, Italy




  Building Online Communities for Scientists
          Tinnitusbook: a proposal for an advanced
        scientific web community for tinnitus research
                                   Paolo Ciccarese, PhD
                         Mass General Hospital / Harvard Medical School



                                                       In collaboration with
paolo.ciccarese@gmail.com                              Alzheimer Research Forum
Alzheimer Research Forum

• Created in 1996 www.alzforum.org
• 58,000 Alzheimer Disease (AD) Related
  Papers
• 1800 AD Related News Articles
• Curated 14,700 Antibodies
• 5000 Members (AD Scientists)
• 6300 Scientists’ Comments
• Over 80 live discussions

         > The CNN of Alzheimer
Alzheimer Research Forum
www.alzforum.org
58,000 AD Related Papers
6300 Scientists’ Comments
Over 80 Live Discussions
ARF - People

•   Executive Editor (June Kinoshita)
•   2 Managing Editors
•   3 Science Writers
•   3 Consultants (Elizabeth Wu for Knowledge Managment)
•   1 Drug Database Curator (Gwen Wong, PhD)
•   1 Event Coordinator
•   1 Web Developer
•   1 Production Assistant
•   10 Advisory Board

              …and 5000 Scientists!!!
SWAN - Semantic Web
    Applications in Neuromedicine
• Define Hypotheses, Claims, Research
  Questions, Comments, Experiments
  – To relate them in between each others
  – To relate them to Gene, Protein, Antibodies,
    Organisms
• Annotate Publications (manual and semi-
  automatic)
• Efficient browsing of the knowledge base
• Knowledge sharing across communities
SWAN Model
http://hypothesis.alzforum.org
                                 SWAN Homepage
SWAN Hypotheses
SWAN Hypothesis
SWAN Claim


             Qualifiers

             Supportive
             Evidence

             Relationships
             with other
             statements in
             the KB


             Lses
SWAN Graph [1]
SWAN Graph [2]
SWAN Graph [3]
Schizophrenia Research Forum
High Number of Resources
•   PubMed                •   Reagents
•   Mash Terminology      •   Experiments
•   Entrez Gene           •   Neuro Imaging
•   UniProt               •   Models
•   Gene Ontology         •   Annotations
•   Alzforum Gene         •   Discussions
•   Alzforum Antibodies   •   Commentaries
•   Experimental Data     •   …
Science Collaboration Framework

• Reusable software that can be used to
  develop web-based, collaborative, scientific
  communities
• Support interdisciplinary scientists in
  publishing, annotating, sharing and
  discussing content such as articles,
  perspectives, interviews and news items, as
  well as assert personal biographies and
  research interests
stembook.org
stembook.org

• It is an open access collection of invited,
  original, peer-reviewed chapters (46 a few
  days ago) covering a range of topics related
  to stem cell biology written by top
  researchers in the field at the Harvard Stem
  Cell Institute and worldwide.
• ISSN 1940-3429
Table of Contents
Example: Link to genes
Other Stem Book features

• eAlert
• Commenting and discussion forums
• Semiautomatic annotation of Genes in new
  articles
• Access to the under-development clouds of
  resources for life science (genes, proteins,
  antibodies, organisms…)
PDonline.org
What we can offer

• Experience in creating and maintain online
  communities
• Reusable software that can speed up the
  process of creation of a new community
• Access to biomedical knowledge bases
• Access to new methods and technologies
  as result of our research
• Be part of a community of communities
Thank you
•   Tim Clark                  • Sudeshna Das
•   Gwen Wong                  • Benjamin Melançon
•   June Kinoshita
•   Marco Ocana
•   Elizabeth Wu


                 Paolo Ciccarese, PhD
                 paolo.ciccarese@gmail.com

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Tinnitusbook

  • 1. 3rd Tinnitus Research Initiative Meeting 24-26 June 2009, Stresa, Italy Tinnitusbook: a proposal for an advanced scientific web community for tinnitus research G. Attanasio (a,f), P. Ciccarese (b,c), E. Wu (e), T. Clark (b,c,d), E. Pecis (f), R. Filipo(a) a: Dept. Neurology and Otolaryngology, University La Sapienza, Rome, IT; b: Massachusetts Gen. Hosp., Boston, MA; c: Harvard Med. School, Boston, MA; d: Harvard Initiative in Innovative Computing, Cambridge, MA; e: Alzheimer Res. Forum Found., Boston, MA; f: Acufeni.net Association onlus
  • 3. OUR PROJECT To create a new interdisciplinary online resource connecting researchers with researchers, to facilitate rapid progress in Tinnitus research COMMUNITY COMMUNITY OF PATIENTS OF SCIENTISTS
  • 4. 3rd Tinnitus Research Initiative Meeting 24-26 June 2009, Stresa, Italy Building Online Communities for Scientists Tinnitusbook: a proposal for an advanced scientific web community for tinnitus research Paolo Ciccarese, PhD Mass General Hospital / Harvard Medical School In collaboration with paolo.ciccarese@gmail.com Alzheimer Research Forum
  • 5. Alzheimer Research Forum • Created in 1996 www.alzforum.org • 58,000 Alzheimer Disease (AD) Related Papers • 1800 AD Related News Articles • Curated 14,700 Antibodies • 5000 Members (AD Scientists) • 6300 Scientists’ Comments • Over 80 live discussions > The CNN of Alzheimer
  • 9. Over 80 Live Discussions
  • 10. ARF - People • Executive Editor (June Kinoshita) • 2 Managing Editors • 3 Science Writers • 3 Consultants (Elizabeth Wu for Knowledge Managment) • 1 Drug Database Curator (Gwen Wong, PhD) • 1 Event Coordinator • 1 Web Developer • 1 Production Assistant • 10 Advisory Board …and 5000 Scientists!!!
  • 11. SWAN - Semantic Web Applications in Neuromedicine • Define Hypotheses, Claims, Research Questions, Comments, Experiments – To relate them in between each others – To relate them to Gene, Protein, Antibodies, Organisms • Annotate Publications (manual and semi- automatic) • Efficient browsing of the knowledge base • Knowledge sharing across communities
  • 16. SWAN Claim Qualifiers Supportive Evidence Relationships with other statements in the KB Lses
  • 21. High Number of Resources • PubMed • Reagents • Mash Terminology • Experiments • Entrez Gene • Neuro Imaging • UniProt • Models • Gene Ontology • Annotations • Alzforum Gene • Discussions • Alzforum Antibodies • Commentaries • Experimental Data • …
  • 22. Science Collaboration Framework • Reusable software that can be used to develop web-based, collaborative, scientific communities • Support interdisciplinary scientists in publishing, annotating, sharing and discussing content such as articles, perspectives, interviews and news items, as well as assert personal biographies and research interests
  • 24. stembook.org • It is an open access collection of invited, original, peer-reviewed chapters (46 a few days ago) covering a range of topics related to stem cell biology written by top researchers in the field at the Harvard Stem Cell Institute and worldwide. • ISSN 1940-3429
  • 27. Other Stem Book features • eAlert • Commenting and discussion forums • Semiautomatic annotation of Genes in new articles • Access to the under-development clouds of resources for life science (genes, proteins, antibodies, organisms…)
  • 29. What we can offer • Experience in creating and maintain online communities • Reusable software that can speed up the process of creation of a new community • Access to biomedical knowledge bases • Access to new methods and technologies as result of our research • Be part of a community of communities
  • 30. Thank you • Tim Clark • Sudeshna Das • Gwen Wong • Benjamin Melançon • June Kinoshita • Marco Ocana • Elizabeth Wu Paolo Ciccarese, PhD paolo.ciccarese@gmail.com