UKSG Meeting April 4, 2011
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UKSG Meeting April 4, 2011

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A talk of what one scientist wants of publishers delivered to UK and European publishers at the UKSG meeting.

A talk of what one scientist wants of publishers delivered to UK and European publishers at the UKSG meeting.

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UKSG Meeting April 4, 2011 UKSG Meeting April 4, 2011 Presentation Transcript

  • Digital Research Analog Publishing – One Scientist’s View
    Philip E. Bourne
    University of California San Diego
    pbourne@ucsd.edu
    http://www.sdsc.edu/pb
    1
    UKSG 2011
  • My Bias..
    Computational biologist (only one of many domains)
    Open access advocate
    Maintainer of an important biological data resource (PDB)
    UKSG 2011
    2
  • My Wish…
    As a scientist I want an interaction with a “publisher” that does not begin when the scientific process ends, but begins at the beginning of the scientific process itself
    What I want from a Publisher of the Future
    PLoS Comp Biol 2010 6(5): e1000787
    UKSG 2011
  • What Does That Mean? The “Publisher” becomes Part of the Scientific Workflow
    Scientist
    Laboratory
    Idea
    Experiment
    Data
    Conclusions
    Publisher
    uzar.wordpress.com
    Maybe The Line is Somewhere Else?
    Publish
    4
    UKSG 2011
  • Maybe The Line is Somewhere Else?
    Laboratory
    Scientist
    ?
    Idea
    Experiment
    Institution?
    Data
    Lab Notebook
    Conclusions
    Publisher
    Publish
    5
    UKSG 2011
  • ?
    Laboratory
    Scientist
    Idea
    Experiment
    Institution?
    Data
    Lab Notebook
    Conclusions
    Publisher
    Publish
    Maybe The Line is Somewhere Else?
    UKSG 2011
    6
  • Why Do I Want This?
    UKSG 2011
    7
  • I Want Interoperability with the Data and Applications that Understand That Data
    What is needed?
    Standard set of apps for data exploration
    Standard calling interfaces
    Who manages the data?
    Publisher
    Author
    Database
    3rd party
    User annotates
    view
    Metadata stored with the article
    Fetches the data and provides a
    Staring point for interactive enquiry
    UKSG 2011
  • We Are Making Progress But it is Incremental
    UKSG 2011
  • Already Being Done by Databases and on Mobile
    Tight Integration with MyPDB
    • Access to saved queries
    • Add/delete queries
    • Flag interesting entries
    • Add personal structure annotations
    UKSG 2011
  • Why Do I Want This?Integrated Rich Media Can Improve Comprehension
    Already happening but post publication not Prepublication
    Lab discussions, presentations of the work etc. are part of the new discourse
    11
    UKSG 2011
  • Mashup with Content from Other Articles / Data
    Sure its happening already, but…
    It remains too difficult
    It must be at the point of capture not post anything
    UKSG 2011
  • Proposal - The TeachU Workflow
    Step 1
    presenter starts
    PowerPoint
    Mac
    PC
    Step 4
    slides are
    uploaded
    Slides
    Website
    Step 3
    presenter stops
    recording and
    initiates upload
    Step 5
    slides and podcast
    are automatically
    synchronized
    Step 2
    presenter starts
    recording on
    smart phone
    Step 6
    listener
    plays back
    synchronized
    presentation
    Sync File
    Podcast
    Android
    iPhone
    Windows Phone 7
  • Why Do I Want This?Semantic Linking of Data Can Lead to New Knowledge Discovery
    www.rcsb.org/pdb/explore/literature.do?structureId=1TIM
    BMC Bioinformatics 2010 11:220
    14
    UKSG 2011
  • Cardiac Disease
    Literature
    Immunology Literature
    Why Do I Want This?Semantic Linking of Data Can Lead to New Knowledge Discovery
    Shared Function
    15
    UKSG 2011
  • Why Do I Want This?
    ?
    Laboratory
    Scientist
    Idea
    Experiment
    Institution?
    Data
    Lab Notebook
    Conclusions
    Publisher
    Publish
    UKSG 2011
    16
  • Why I Want This?The Truth About the Scientific eLaboratory
    I have ?? mail folders!
    The intellectual memory of my laboratory is in those folders
    This is an unhealthy hub and spoke mentality
    17
    UKSG 2011
  • Why I Want This?The Truth About the Scientific eLaboratory
    I generate way more negative that positive data, but where is it?
    Content management is a mess
    Slides, posters…..
    Data, lab notebooks ….
    Collaborations, Journal clubs …
    Software is open but where is it?
    Farewell is for the data too
    Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 4(7): e1000136
    18
    UKSG 2011
  • Why I Want ThisThe Truth About the Published Record
    Preservation of the digital record?
    Reproducibility?
    The need for the library to reinvent itself/ institutional repositories to invent themselves?
    Digital chaos in the long tail?
    19
    UKSG 2011
  • What Will It Take to Get There?
    As a scientist I want an interaction with a “publisher” that does not begin when the scientific process ends, but begins at the beginning of the scientific process itself
    What I want from a Publisher of the Future
    PLoS Comp Biol 2010 6(5): e1000787
    UKSG 2011
  • Open source cohesive tools
    New standards
    Business rights and IP
    Attribution/evaluation/archiving
    A “publisher” to take the plunge
    Beyond the PDF
    21
    UKSG 2011
    What Will It Take to Get There?
    https://sites.google.com/site/beyondthepdf/
  • Sounds Insurmountable?
    UKSG 2011
    22
  • But Wait..There Are Many Great Tools Out There
    Taverna
    We Need Scientist Management Tools
    23
    UKSG 2011
  • But Wait..There Are Many Great Ideas Out There
    Nano publications
    Semantic tagging of PDFs and beyond
    Citation ontologies
    Scholarly HTML
    Authoring tools
    UKSG 2011
    24
  • A Test BedSpinal Muscular Atrophy (SMA)
    Coalesce a set of disparate tools
    Engage the publishers
    Make some progress on a treatable disease
    25
    UKSG 2011
  • Acknowledgements
    Beyond the PDF Workshop
    Funded by DDCF, Microsoft, NCI, Science Commons
    The SciVee Team including:
    Marc Friedmann, J. Lynn Fink, Alex Gramos, Willy Suwanto
    The PDB Team including:
    Andreas Prlic, DimitrisDimitanopolos
    26
    UKSG 2011
  • pbourne@ucsd.edu
    Discussion
    27
    UKSG 2011