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Digital Research Analog Publishing – One Scientist’s View

Digital Research Analog Publishing – One Scientist’s View. Philip E. Bourne University of California San Diego pbourne@ucsd.edu http://www.sdsc.edu/pb. My Bias. Computational biologist (only one of many domains) Open access advocate Maintainer of an important biological data resource (PDB).

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Digital Research Analog Publishing – One Scientist’s View

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  1. Digital Research Analog Publishing – One Scientist’s View Philip E. Bourne University of California San Diego pbourne@ucsd.edu http://www.sdsc.edu/pb UKSG 2011

  2. My Bias.. • Computational biologist (only one of many domains) • Open access advocate • Maintainer of an important biological data resource (PDB) UKSG 2011

  3. 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

  4. 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? UKSG 2011 Publish

  5. Maybe The Line is Somewhere Else? Laboratory Scientist ? Idea Experiment Institution? Data Lab Notebook Conclusions Publisher UKSG 2011 Publish

  6. Maybe The Line is Somewhere Else? ? Laboratory Scientist Idea Experiment Institution? Data Lab Notebook Conclusions Publisher UKSG 2011 Publish

  7. Why Do I Want This? UKSG 2011

  8. 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

  9. We Are Making Progress But it is Incremental UKSG 2011

  10. 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

  11. 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 UKSG 2011

  12. 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

  13. 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

  14. Why Do I Want This?Semantic Linking of Data Can Lead to New Knowledge Discovery UKSG 2011 www.rcsb.org/pdb/explore/literature.do?structureId=1TIM BMC Bioinformatics 2010 11:220

  15. Cardiac Disease Literature Immunology Literature Why Do I Want This?Semantic Linking of Data Can Lead to New Knowledge Discovery Shared Function UKSG 2011

  16. Why Do I Want This? ? Laboratory Scientist Idea Experiment Institution? Data Lab Notebook Conclusions Publisher UKSG 2011 Publish

  17. 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 UKSG 2011

  18. 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 UKSG 2011

  19. 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? UKSG 2011

  20. 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

  21. What Will It Take to Get There? • Open source cohesive tools • New standards • Business rights and IP • Attribution/evaluation/archiving • A “publisher” to take the plunge Beyond the PDF https://sites.google.com/site/beyondthepdf/ UKSG 2011

  22. Sounds Insurmountable? UKSG 2011

  23. But Wait..There Are Many Great Tools Out There Taverna UKSG 2011 We Need Scientist Management Tools

  24. 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

  25. A Test BedSpinal Muscular Atrophy (SMA) • Coalesce a set of disparate tools • Engage the publishers • Make some progress on a treatable disease UKSG 2011

  26. 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, Dimitris Dimitanopolos UKSG 2011

  27. pbourne@ucsd.edu Discussion UKSG 2011

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