Opening up the Research Communications Ecosystem

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talk by Tim Clark at Beyond the PDF workshop, San Diego CA, 19-21 Jan 2011

talk by Tim Clark at Beyond the PDF workshop, San Diego CA, 19-21 Jan 2011

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  • 1.  
  • 2. Tim Clark Harvard Medical School & Massachusetts General Hospital January 19, 2011 Copyright 2011 Massachusetts General Hospital. All rights reserved.
  • 3.
    • … [we] parked our egos and
    • intellectual-property noses
    • outside the door and agreed
    • that all of our data would be
    • public immediately.”
    • John Trojanowski, MD, PhD
    • U Penn Medical School
    Sharing of Data Leads to Progress on Alzheimer’s , NY Times, 12 Aug 2010
  • 4. MCI progressors non progressors PET imaging of PIB (radiolabelled compound binds amyloid beta A4 protein) MRI imaging of brain structure showing loss of hippocampal volume Brain. 2010 Nov;133(Pt 11):3336-3348 . = 218 subjects +
  • 5. create hypothesis design experiment run experiment collect data interpret data share interpretations synthesize knowledge
  • 6. dopaminergic pathway α-synuclein, β-amlyoid α-synuclein, Tau chr 16p11.2 CNV chr 16p11.2 CNV CRF, glutaminergic system, dopamine, amygdala … Alzheimer Disease Parkinson’s Disease Schizophrenia Autism Bipolar Disorder Drug Addiction Huntington’s Disease ALS Depression SIRT2
  • 7. 1667 2010 Printing Press Web
  • 8. We scientists do not attend professional meetings to present our findings ex cathedra, but in order to argue. John Polanyi, FRS
  • 9. Genes Proteins Biological Processes Chemical Compounds Antibodies Cells Brain anatomy …
  • 10. Text Shared metadata
  • 11.  
  • 12. Dr. Paolo Ciccarese – Oct 8, 2010
  • 13.  
  • 14.  
  • 15.
    • <rdf:Description rdf:about=&quot;http://swan.mindinformatics.org/annotationset/6&quot;>
    • <rdf:type rdf:resource=&quot;http://purl.org/ao/AnnotationSet&quot;/>
    • <rdfs:label>Species</rdfs:label>
    • </rdf:Description>
    • <rdf:Description rdf:about=&quot;http://swan.mindinformatics.org/annotationitem/11&quot;>
    • <rdf:type rdf:resource=&quot;http://purl.org/ao/types/Qualifier&quot;/>
    • <pav:createdOn rdf:datatype=&quot;java:java.sql.Timestamp&quot;>2011-01-06T13:58:29.000000000-05:00</pav:createdOn>
    • </rdf:Description>
    • <rdf:Description rdf:about=&quot;http://swan.mindinformatics.org/agentperson/2&quot;>
    • <rdf:type rdf:resource=&quot;http://xmlns.com/foaf/0.1/Person&quot;/>
    • <foaf:mbox>paolo.ciccarese@gmail.com</foaf:mbox>
    • <foaf:firstName>Paolo</foaf:firstName>
    • <foaf:img>
    • http://swan.mindinformatics.org/imgs/people/paolo-ciccarese_.jpg
    • </foaf:img>
    • <foaf:lastName>Ciccarese</foaf:lastName>
    • <foaf:homepage>http://www.hcklab.org/paolo-ciccarese-cv.html</foaf:homepage>
    • <foaf:name>Paolo Ciccarese</foaf:name>
    • </rdf:Description>
    • <rdf:Description rdf:about=&quot;http://swan.mindinformatics.org/annotationitem/11&quot;>
    • <pav:createdBy rdf:resource=&quot;http://swan.mindinformatics.org/agentperson/2&quot;/>
    • </rdf:Description>
    • <rdf:Description rdf:about=&quot;http://swan.mindinformatics.org/prefixpostfixtextselector/1&quot;>
    • <rdf:type rdf:resource=&quot;http://purl.org/ao/selectors/PrefixPostfixTextSelector&quot;/>]
  • 16.  
  • 17.  
  • 18.
    • SWAN Annotation
      • http://vimeo.com/18510599
    • Utopia Annotation
      • http://www.scivee.tv/node/26720
  • 19. Parkinson’s Disease Stem Cell Technology
  • 20.
    • Opening up the static document on the Web
    • Integrating the Web of documents with the Web of data (semantic web)
    • Exploiting synergies with textmining apps
    • Creating an ecosystem of semantic metadata on scientific publications
  • 21.
    • New models of Semantic Publishing in Science
    • Guest Editors:
      • P Bourne, T Clark, A de Waard,
      • C Goble, S Pettifer, D Shotton
    • Call for papers next week
    • Send us your best work!