Adam Marshall Charelston Utopia Presentation

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Adam Marsall of Portland Press provides an exclusive look at how they built and launched Utopia

Adam Marsall of Portland Press provides an exclusive look at how they built and launched Utopia

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  • 1. A newdimension 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 spendingmillions in grants for people to performexperiments, produce new knowledge, hide thisknowledge in a often badly written text and thenspend some more millions trying to second guesswhat 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 filesArticles 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. 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
  • 6. Still really impressed with how UtopiaDocuments breathes life into researchpapers by connecting them to#LinkedData http://getutopia.comLeigh Dodds (Talis)
  • 7. Horizon…Next release:• Commenting (private and public)Future releases:• Utopia Library• Integration of ChemSpider• Utopia ConferencesGet other publishers involved
  • 8. 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
  • 9. And the Semantic Biochemical Journal
  • 10. 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