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Its Not Just About Papers Anymore Philip E. Bourne University of California San Diego [email_address] www.sdsc.edu/pb http://www.slideshare.net/pebourne
My Perspective ,[object Object],[object Object],[object Object],[object Object]
What is Wrong Today? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],https://sites.google.com/site/beyondthepdf/ http://www.force11.org
The Research Enterprise Literature Data Methods
My Current Reality http://www.flickr.com/photos/51282757@N05/5585299226/lightbox/
My Dream ,[object Object],[object Object],[object Object],[object Object],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
Our Own Little Contributions
Semantically Enriched Version of PubMed Central http://biolit.ucsd.edu Literature Data Methods
Word Add-in for Authors ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],http://www.codeplex.com/ucsdbiolit Literature Data Methods
Knowledge Discovery Shared Function Literature Data Methods Immunology Literature Cardiac Disease Literature
Data & Literature Integration www.rcsb.org/pdb/explore/literature.do?structureId=1TIM Literature Data Methods
PLoS Data Pages ,[object Object],[object Object],[object Object],[object Object],Literature Data Methods
Myth: Reproducibility ,[object Object],[object Object],[object Object],[object Object],Literature Data Methods
PLoS Comp Biol Software ,[object Object],[object Object],[object Object],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
Workflow Tools Might be the Answer Taverna Wings Literature Data Methods
Our Own Experience ,[object Object],[object Object],[object Object],[object Object],[object Object],Literature Data Methods
Yes The Workflow is Real Literature Data Methods
Problems with Publishing  Workflows ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Literature Data Methods
And Now for Something Completely Different http://www.scivee.tv
Experiments in Rich Media Mashups http://www.scivee.tv
Pubcast – Video Integrated with the Full Text of the Paper http://www.scivee.tv
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 http://www.scivee.tv
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 http://www.scivee.tv
Nothing is Going to Change Unless The Reward System Changes The Right Thing To Do Reward
Interim Solution:  Use the Traditional Reward System The Wikipedia Experiment – Topic Pages ,[object Object],[object Object],[object Object],[object Object],[object Object],Literature Data Methods
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
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? uzar.wordpress.com
Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook ?
Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook ?
Questions? [email_address]

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Elsevier - Labs on Line

  • 1. Its Not Just About Papers Anymore Philip E. Bourne University of California San Diego [email_address] www.sdsc.edu/pb http://www.slideshare.net/pebourne
  • 2.
  • 3.
  • 4. The Research Enterprise Literature Data Methods
  • 5. My Current Reality http://www.flickr.com/photos/51282757@N05/5585299226/lightbox/
  • 6.
  • 7. Our Own Little Contributions
  • 8. Semantically Enriched Version of PubMed Central http://biolit.ucsd.edu Literature Data Methods
  • 9.
  • 10. Knowledge Discovery Shared Function Literature Data Methods Immunology Literature Cardiac Disease Literature
  • 11. Data & Literature Integration www.rcsb.org/pdb/explore/literature.do?structureId=1TIM Literature Data Methods
  • 12.
  • 13.
  • 14.
  • 15. Workflow Tools Might be the Answer Taverna Wings Literature Data Methods
  • 16.
  • 17. Yes The Workflow is Real Literature Data Methods
  • 18.
  • 19. And Now for Something Completely Different http://www.scivee.tv
  • 20. Experiments in Rich Media Mashups http://www.scivee.tv
  • 21. Pubcast – Video Integrated with the Full Text of the Paper http://www.scivee.tv
  • 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 http://www.scivee.tv
  • 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 http://www.scivee.tv
  • 24. Nothing is Going to Change Unless The Reward System Changes The Right Thing To Do Reward
  • 25.
  • 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. 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? uzar.wordpress.com
  • 28. Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook ?
  • 29. Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook ?

Notas do Editor

  1. 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…