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A new
dimension in
  scientific
 publishing
 has arrived

       www.BiochemJ.org
       Bringing life sciences to life
Amos Bairoch‟s lament
“It is quite depressive to think that we are spending
millions in grants for people to perform
experiments, produce new knowledge, hide this
knowledge in a often badly written text and then
spend some more millions trying to second guess
what the authors really did and found”

        Bairoch A (2009) The future of annotation/biocuration.
         Nature Precedings doi:10.1038/npre.2009.3092.1.
Utopia Documents...
Blends the best of The Semantic Web…
…with the ease of use, stability & elegance
  of PDF files

Articles remain as stable Versions of Record
  while being dynamic, interactive and
  evolving repositories of knowledge
Enriching document metadata
• Utopia documents „reads‟ a PDF much like a
  human would
• It recognizes the content of a document
  – Title, authors, keywords
  – Citations and references are automatically linked to
    online repositories
  – Identifies important features such as „materials and
    methods‟
Interacting with document content
• Utopia Documents brings static PDF files to
  life
• Interactive visualizations
  –   Molecules realised as 3D rotating images
  –   Protein sequences become live and interactive
  –   Tables of data become live „spreadsheets‟
  –   Graphs generated on the fly, linked to source data
• Dynamically include data/text-mining results
Still really impressed with how Utopia
Documents breathes life into research
papers by connecting them to
#LinkedData http://getutopia.com
Leigh Dodds (Talis)
Horizon…
Next release:
• Commenting (private and public)
Future releases:
• Utopia Library
• Integration of ChemSpider
• Utopia Conferences
Get other publishers involved
Our vision
•   PDF reader of choice for academics
•   Wide uptake by other organisations
•   Build into XML workflows
•   Enable researchers to unlock the vast
    array of knowledge currently in data tombs
And the Semantic Biochemical
          Journal
Utopia Documents
                     Watch video at:
             http://www.biochemj.org/demo

            Download Utopia Documents at:
                   Getutopia.com

              Read: Attwood, T.K. et al (2009)
„Calling International Rescue: knowledge lost in literature
                     and data landslide!‟
              Reference Biochem J. (2009) 424, 317-333

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Adam Marshall Charelston Utopia Presentation

  • 1. A new dimension in scientific publishing has arrived www.BiochemJ.org Bringing life sciences to life
  • 2. Amos Bairoch‟s lament “It is quite depressive to think that we are spending millions in grants for people to perform experiments, produce new knowledge, hide this knowledge in a often badly written text and then spend some more millions trying to second guess what the authors really did and found” Bairoch A (2009) The future of annotation/biocuration. Nature Precedings doi:10.1038/npre.2009.3092.1.
  • 3. Utopia Documents... Blends the best of The Semantic Web… …with the ease of use, stability & elegance of PDF files Articles remain as stable Versions of Record while being dynamic, interactive and evolving repositories of knowledge
  • 4. Enriching document metadata • Utopia documents „reads‟ a PDF much like a human would • It recognizes the content of a document – Title, authors, keywords – Citations and references are automatically linked to online repositories – Identifies important features such as „materials and methods‟
  • 5.
  • 6. Interacting with document content • Utopia Documents brings static PDF files to life • Interactive visualizations – Molecules realised as 3D rotating images – Protein sequences become live and interactive – Tables of data become live „spreadsheets‟ – Graphs generated on the fly, linked to source data • Dynamically include data/text-mining results
  • 7. Still really impressed with how Utopia Documents breathes life into research papers by connecting them to #LinkedData http://getutopia.com Leigh Dodds (Talis)
  • 8. Horizon… Next release: • Commenting (private and public) Future releases: • Utopia Library • Integration of ChemSpider • Utopia Conferences Get other publishers involved
  • 9. Our vision • PDF reader of choice for academics • Wide uptake by other organisations • Build into XML workflows • Enable researchers to unlock the vast array of knowledge currently in data tombs
  • 10. And the Semantic Biochemical Journal
  • 11. Utopia Documents Watch video at: http://www.biochemj.org/demo Download Utopia Documents at: Getutopia.com Read: Attwood, T.K. et al (2009) „Calling International Rescue: knowledge lost in literature and data landslide!‟ Reference Biochem J. (2009) 424, 317-333