One Scientist’s Wish List for Scientific Publishers

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Keynote presentation American Chemical Society Editors Meeting, La Jolla CA USA, Jan 6, 2012

Keynote presentation American Chemical Society Editors Meeting, La Jolla CA USA, Jan 6, 2012

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  • A PubCast is a scientific publication combined with a corresponding video. Really, that means --any video that is relevant to the work described in the publication can be combined to create a PubCast. The point is to draw attention to the research and promote the article’s readership, exposure and possible citation. There are many reasons why video combined with the paper helps accomplish this. But in order to gain the greatest benefit from a PubCast --it is MOST beneficial if the publication starts out as an open access publication…


  • 1. One Scientist’s Wish List for Scientific Publishers Philip E. Bourne University of California San Diego [email_address] Conference of ACS Editors Jan 6, 2012, La Jolla CA
  • 2. My {Biased} Perspective
    • I am a domain scientist (computational molecular biology)
    • I co-direct the RCSB Protein Data Bank
    • I co-founded and am EIC of one Public Library of Science (PLoS) open access journals – There must be a business model
    • I co-founded a company, SciVee Inc., that is attempting to leverage the perceived changes in scholarly communication
    • I support a small academic scholarly communication group
  • 3. What Drives Me…. The Story of Meredith
  • 4. Meredith was Successful Because….
    • She is an exceptional individual
    • Much of the data and knowledge she needed she had to beg for; she used the UCSD library
    • She easily got access to computer time
    • I want others less smart like myself to be successful too..
  • 5. What is Wrong Today?
    • Formal science communication:
      • Occurs too slowly
      • Reaches too few people
      • Costs too much
      • Ignores the data
      • Is very hard to reproduce
    • Is stuck in the era of the printing press – we need to move Beyond the PDF and use the power of the medium
  • 6. It’ s a Start…
    • We have scratched the surface, but have yet to explore the core
    • But look what we could do…
  • 7. My Dream
    • User reads a paper (one view of the info)
    • Clicks on a figure which can be analyzed
    • Clicking the figure gives a composite database + journal view
    • This takes you to yet more papers or databases
    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
  • 8. The Dream Can Only be Realized in the Context of the Complete Research Enterprise Literature Data Methods
  • 9. My Current Reality
  • 10. Let Me Try and Illustrate What is Possible Through Our Own Little Contributions
  • 11. Much of What We Try and Do Leverages Open Access Content 2008 Open Access: Taking Full Advantage of the Content PLoS Comp. Biol. 4(3) e1000037
  • 12. Literature: OA Biosciences
    • Meredith certainly benefited from the OA literature, but not enough …
    • … we have a long way to go in several respects
    PubMed Central Contents Nov 8, 2011 PubMed Contents Nov 8, 2011 Literature Data Methods
  • 13. Literature: Semantically Enriched Version of PubMed Central Literature Data Methods ; NAR 2008 36(S2) W385-389
  • 14. Literature: So What has Happened with This?
    • The value seems to be in restful services that enable databases to recognize where in the literature their data are referenced
    • We use this in the PDB in the following way….
    Literature Data Methods
  • 15. Data & Literature: Integration Literature Data Methods BMC Bioinformatics 2010 11:220
  • 16. Literature: Word Add-in for Authors
    • Allows authors to add metadata as they write, before they submit the manuscript
    • Authors are assisted by automated term recognition
      • OBO ontologies
      • Database IDs
    • Metadata are embedded directly into the manuscript document via XML tags, OOXML format
      • Open
      • Machine-readable
    • Open source, Microsoft Public License Literature Data Methods BMC Bioinformatics 2010 11:103.
  • 17. Literature: Knowledge Discovery Shared Function Literature Data Methods Immunology Literature Cardiac Disease Literature
  • 18. Lets Turn Our Attention to Data ….
  • 19. Data: Thoughts from the Biosciences
    • Growth – DNA sequence data are doubling every 5 months
    • NLM/NCBI is amazing
    • Other great resources – but a slow realization they are appearing stove piped
    • Data are undervalued (more on this)
    • We need a data registry for deep search and comparison
    Literature Data Methods
  • 20. Data: Data Journals – Lots of Talk
    • Nature Publishing Group
    • F1000
    • PLoS at Large
    • eLife
    • Global Biodiversity Information Facility
    • Some fields do it naturally – Astronomy, Earth Sciences …
    Literature Data Methods
  • 21. Data: PLoS Data Pages
    • To be introduced later this year
    • Shared metadata description?
    • Data in Dryad or equivalent
    • History could repeat itself – JMS revisited
    Literature Data Methods
  • 22. .. And Finally Methods
  • 23. Methods: Is Reproducibility a Myth?
    • My views of reproducibility:
      • We all express the importance, but the only time it is tested is when something is truly novel or error is suspected
      • Reproducability covers a spectrum of meaning – by whom and with how much effort
      • The longer the time lag the less likely something is reproducible
    Literature Data Methods Nature Reviews Drug Discovery 10, 643-644 (September 2011)
  • 24. PLoS Comp Biol Software
    • Requires source be deposited in an open source public repository
    • Encourages a copy of record be deposited with the article
    • Requires that the reviewer be able to test the software if they wish - implies data, documentation, test parameters and output be provided for checking
    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
  • 25. Methods: Workflow Tools Might be the Answer? Taverna Wings Literature Data Methods
  • 26. Methods: Workflows - Our Own Experience
    • Its hard and embarrassing
    • We have a working prototype using Wings
    • I can feel the potential productivity gains
    • My students are more doubtful
    • Its been a lot of fun and will enable us to improve our processes regardless of the workflow system itself
    Literature Data Methods
  • 27. Methods: Yes The Workflow is Real Literature Data Methods
  • 28. Methods: Problems with Publishing Workflows
    • Workflows are not linear
    • Workflow : paper is not 1:1
    • Confidentiality
    • Peer review
    • Infrastructure
    • Community acceptance
    • Reward system
    • No publisher seems willing to touch them
    Literature Data Methods
  • 29. And Now for Something Completely Different
  • 30. Experiments in Rich Media Mashups
  • 31. Pubcast – Video Integrated with the Full Text of the Paper
  • 32. 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
  • 33. 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
  • 34. Nothing is Going to Change Unless The Reward System Changes The Right Thing To Do Reward P.E. Bourne 2011 Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comp. Biol. 7(1) e1002001.
  • 35. Interim Solution: Use the Traditional Reward System The Wikipedia Experiment – Topic Pages
    • Identify areas of Wikipedia that relate to the journal that are missing of stubs
    • Develop a Wikipedia page in the sandbox
    • Have a Topic Page Editor Review the page
    • Publish the copy of record with associated rewards
    • Release the living version into Wikipedia
  • 36. 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
  • 37. 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?
  • 38. Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook ?
  • 39. Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook ?
  • 40. Questions? [email_address]