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Elsevier - Labs on Line


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Webinar presented to Elsevier Nov. 15, 2011

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Elsevier - Labs on Line

  1. 1. Its Not Just About Papers Anymore Philip E. Bourne University of California San Diego [email_address]
  2. 2. My Perspective <ul><li>I am a domain scientist (computational molecular biology) </li></ul><ul><li>I co-founded and am EIC of one Public Library of Science (PLoS) open access journals </li></ul><ul><li>I co-founded a company, SciVee Inc., that is attempting to leverage the perceived changes in scholarly communication </li></ul><ul><li>I support a small academic scholarly communication group </li></ul>
  3. 3. What is Wrong Today? <ul><li>Formal science communication: </li></ul><ul><ul><li>Occurs too slowly </li></ul></ul><ul><ul><li>Reaches too few people </li></ul></ul><ul><ul><li>Costs too much </li></ul></ul><ul><ul><li>Ignores the data </li></ul></ul><ul><ul><li>Is very hard to reproduce </li></ul></ul><ul><li>Is stuck in the era of the printing press – we need to move Beyond the PDF and use the power of the medium </li></ul>
  4. 4. The Research Enterprise Literature Data Methods
  5. 5. My Current Reality
  6. 6. My Dream <ul><li>User reads a paper (one view of the info) </li></ul><ul><li>Clicks on a figure which can be analyzed </li></ul><ul><li>Clicking the figure gives a composite database + journal view </li></ul><ul><li>This takes you to yet more papers or databases </li></ul>1. A link brings up figures from the paper 0. Full text of PLoS papers stored in a database 2. Clicking the paper figure retrieves data from the PDB which is analyzed 3. A composite view of journal and database content results 4. The composite view has links to pertinent blocks of literature text and back to the PDB 1. 2. 3. 4. The Knowledge and Data Cycle
  7. 7. Our Own Little Contributions
  8. 8. Semantically Enriched Version of PubMed Central Literature Data Methods
  9. 9. Word Add-in for Authors <ul><li>Allows authors to add metadata as they write, before they submit the manuscript </li></ul><ul><li>Authors are assisted by automated term recognition </li></ul><ul><ul><li>OBO ontologies </li></ul></ul><ul><ul><li>Database IDs </li></ul></ul><ul><li>Metadata are embedded directly into the manuscript document via XML tags, OOXML format </li></ul><ul><ul><li>Open </li></ul></ul><ul><ul><li>Machine-readable </li></ul></ul><ul><li>Open source, Microsoft Public License </li></ul> Literature Data Methods
  10. 10. Knowledge Discovery Shared Function Literature Data Methods Immunology Literature Cardiac Disease Literature
  11. 11. Data & Literature Integration Literature Data Methods
  12. 12. PLoS Data Pages <ul><li>Currently being worked out </li></ul><ul><li>Shared metadata description? </li></ul><ul><li>Data in Dryad or equivalent </li></ul><ul><li>History could repeat itself – JMS revisited </li></ul>Literature Data Methods
  13. 13. Myth: Reproducibility <ul><li>My views of reproducibility: </li></ul><ul><ul><li>We all express the importance, but the only time it is tested is when something is truly novel or error is suspected </li></ul></ul><ul><ul><li>Reproducability covers a spectrum of meaning – by whom and with how much effort </li></ul></ul><ul><ul><li>The longer the time lag the less likely something is reproducible </li></ul></ul>Literature Data Methods
  14. 14. PLoS Comp Biol Software <ul><li>Requires source be deposited in an open source public repository </li></ul><ul><li>Encourages a copy of record be deposited with the article </li></ul><ul><li>Requires that the reviewer be able to test the software if they wish (implies data, documentation, test parameters and output be provided for checking </li></ul>Motivation: S.Veretnik, J.L.Fink, and P.E. Bourne 2008 Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. . 4(7): e1000136 Literature Data Methods
  15. 15. Workflow Tools Might be the Answer Taverna Wings Literature Data Methods
  16. 16. Our Own Experience <ul><li>Its hard and embarrassing </li></ul><ul><li>We have a working prototype using Wings </li></ul><ul><li>I can feel the potential productivity gains </li></ul><ul><li>My students are more doubtful </li></ul><ul><li>Its been a lot of fun and will enable us to improve our processes regardless of the workflow system itself </li></ul>Literature Data Methods
  17. 17. Yes The Workflow is Real Literature Data Methods
  18. 18. Problems with Publishing Workflows <ul><li>Workflows are not linear </li></ul><ul><li>Workflow : paper is not 1:1 </li></ul><ul><li>Confidentiality </li></ul><ul><li>Peer review </li></ul><ul><li>Infrastructure </li></ul><ul><li>Community acceptance </li></ul><ul><li>Reward system </li></ul><ul><li>No publisher seems willing to touch them </li></ul>Literature Data Methods
  19. 19. And Now for Something Completely Different
  20. 20. Experiments in Rich Media Mashups
  21. 21. Pubcast – Video Integrated with the Full Text of the Paper
  22. 22. Rich Media as Scholarship Products Application Product Primary Customers Journals PubCast Journals, publishers, societies Meetings PosterCast Societies, conference orgs. SlideCast Comm. PaperCast Societies, journals Podcast SlideCast Education PosterCast Societies, universities SlideCast Books BookCast Publishers, book sellers
  23. 23. Android iPhone Windows Phone 7 Step 1 presenter starts PowerPoint Step 2 presenter starts recording on smart phone Step 3 presenter stops recording and initiates upload Slides Website Step 5 slides and podcast are automatically synchronized Sync File Podcast Step 6 listener plays back synchronized presentation Podium Capture Mac PC Step 4 slides are uploaded
  24. 24. Nothing is Going to Change Unless The Reward System Changes The Right Thing To Do Reward
  25. 25. Interim Solution: Use the Traditional Reward System The Wikipedia Experiment – Topic Pages <ul><li>Identify areas of Wikipedia that relate to the journal that are missing of stubs </li></ul><ul><li>Develop a Wikipedia page in the sandbox </li></ul><ul><li>Have a Topic Page Editor Review the page </li></ul><ul><li>Publish the copy of record with associated rewards </li></ul><ul><li>Release the living version into Wikipedia </li></ul>Literature Data Methods
  26. 26. In Summary: I Do Not Want to Do Any of This – I Want You to Do It P.E. Bourne 2010 What Do I Want from the Publisher of the Future? PLoS Comp Biol 6(5): e1000787
  27. 27. What Does That Mean? The “Publisher” becomes Part of the Scientific Workflow Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Maybe The Line is Somewhere Else?
  28. 28. Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook ?
  29. 29. Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook ?
  30. 30. Questions? [email_address]