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Beyond the Journal Article One Scientist’s Perspective  Philip E. Bourne University of California San Diego [email_address] http://www.sdsc.edu/pb Relevant Work from Us: http ://www.sdsc.edu/pb/SummaryScholarComm. pdf http://www.slideshare.net/pebourne/?? COASP Sept 21, 2011 Or..  Ten Simple Rules for OA Publishers   
How I Got to Be Standing Here ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
How I Got to Be Standing Here http://www.wwpdb.org/ Journals Database 2005:  Is a Biological Database Different from a Biological Journal? PLoS Comp. Biol. 2005 1(3) e34
Author Submission via the Web Depositor Submission via the Web Syntax Checking Syntax Checking Review by Scientists & Editors Review by Annotators Corrections by Author Corrections by Depositor Publish – Web Accessible Release – Web Accessible Similar Processes Lead to Similar Resources
So the processes are not that dissimilar it was the final product that was {is} perceived so differently I am not a Scientist I am a Number PLoS Comp. Biol.  2008 4(12) e1000247
Yet What is Better.. A Paper only Ever Cited by the Folks who Wrote it or a Dataset That is Downloaded and Used 100’s of Times? We will come back to this…
But This is What I Really Came to Appreciate was a Wealth of Possibility ,[object Object],[object Object],[object Object],PLoS Comp Biol  2008  4(3)  e1000037
From Someone Who Generates Scholarship And Cares, Have The Possibilities Been Realized Some Six Years Hence?  Not Really But I Like to Think  the Process Has Started
So I am Here To Tell You Not What is Right with OA – You Know That Already. I Am Here To Tell You in My Humble Opinion What Needs to Be Done To Realize the Promise. Not Necessarily by Publishers, but Catalyzed by Publishers
I realized last night that the catalyst could be for reasons of profit or service to science or something in between
There is Competition Out There ,[object Object],[object Object],[object Object],[object Object],[object Object],Why Don’ t We Have Such Developments in OA?
There is Competition Out There Why Don’ t We Have Such Developments in OA?
Why Don’ t We Have Such Developments in OA? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Content is not  consistently  available ,[object Object],[object Object],[object Object],[object Object],[object Object]
The Good News is There Are People Out There Who Care ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Scientists Themselves –  New OA Journal ,[object Object],[object Object]
Ten Simple Rules for What OA Publishers Can Do to Move the Ball Forward
Rule 1 – Continue to Do What You Do But Better – More Openness! ,[object Object],[object Object]
Rule 2. Foster Low Hanging Fruit
We Cannot Possibly Read a Fraction of the Papers We Should Rule 2 – Foster Low Hanging Fruit Renear & Palmer 2009 Science 325:828-832
We Are Scanning More Reading Less – Our Level of Detail is Dropping Renear & Palmer 2009 Science 325:828-832 Rule 2 Foster Low Hanging Fruit
Automatic Knowledge Discovery for Those with No Time to Read Shared Function Rule 2 Foster Low Hanging Fruit Immunology Literature Cardiac Disease Literature
This Requires That Publishers Exercise the NLM DTD as Far as Possible
Rule 3 Recognize Data ,[object Object],[object Object],[object Object]
Data – The State of Play (A Scientist’s Perspective) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Rule 3 Recognize Data
Data Becomes Part fo the Article ,[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 PLoS Comp. Biol. 2005 1(3) e34
There Is a Real Opportunity for “Data Papers” ,[object Object],[object Object],[object Object],[object Object],Rule 3 Recognize Data
Rule 4 – Recognize Rich Media as Scholarship ,[object Object]
Yes YouTube Can Increase the Rate of Discovery Rule 4 Recognize Rich Media  as Scholarship
Pubcast – Video Integrated with the Full Text of the Paper
Lessons ,[object Object],[object Object],Rule 4 Recognize Rich Media  as Scholarship
Rule 5 Play Upon a Scientists Guilt re The Reward Sytem The Right Thing To Do Reward
Rule 5 Play Upon a Scientists Guilt re The Reward System ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Rule 6 - Play Upon the Scientists Guilt re Reproducibility ,[object Object],[object Object],[object Object],[object Object]
Workflow Tools Might be the Answer Taverna Rule 6 Foster Reproducability Wings
Consider an Example: Our Own Experience in Capturing the Scientific Process to Make it Open and Reproducable ,[object Object],[object Object],[object Object],[object Object],[object Object],Rule 6 Foster Reproducibility
Yes The Workflow is Real Rule 6 Foster Reproducibility
Problems with Publishing Workflows ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Rule 6 Foster Reproducibility
Rule 7 - Where Possible Promote the Use of Social Media and Citizen Science  ,[object Object],[object Object]
The Wikipedia Experiment – Topic Pages ,[object Object],[object Object],[object Object],[object Object],[object Object],Rule 7 Foster Social Media and Citizen Science
Rule 8 – Think of a Cycle Not an End Product Research [Grants] Journal Article Conference Paper Poster Session Reviews Blogs Community Service/Data Curation
Rule 9 – Think of Killer Apps That Could be an OA Game Changer P.E.Bourne, J.L.Fink, M.Gerstein 2008 Open Access: Taking Full Advantage of the Content  PLoS Comp. Biol .  4(3) e1000037
Here is an Idea to Get You Started ,[object Object],[object Object],[object Object],[object Object],Rule 9 – Come up with Killer Apps
Here is Another One.. http://richard.cyganiak.de/2007/10/lod/lod-datasets_2010-09-22_colored.html Rule 9 – Come up with Killer Apps
Rule 10 – Lobby Better ,[object Object],[object Object]
General References ,[object Object],[object Object]
References to Exemplars ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Push-back, Questions? [email_address]

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Ten Simple Rules for Open Access Publishers

  • 1. Beyond the Journal Article One Scientist’s Perspective  Philip E. Bourne University of California San Diego [email_address] http://www.sdsc.edu/pb Relevant Work from Us: http ://www.sdsc.edu/pb/SummaryScholarComm. pdf http://www.slideshare.net/pebourne/?? COASP Sept 21, 2011 Or.. Ten Simple Rules for OA Publishers  
  • 2.
  • 3. How I Got to Be Standing Here http://www.wwpdb.org/ Journals Database 2005: Is a Biological Database Different from a Biological Journal? PLoS Comp. Biol. 2005 1(3) e34
  • 4. Author Submission via the Web Depositor Submission via the Web Syntax Checking Syntax Checking Review by Scientists & Editors Review by Annotators Corrections by Author Corrections by Depositor Publish – Web Accessible Release – Web Accessible Similar Processes Lead to Similar Resources
  • 5. So the processes are not that dissimilar it was the final product that was {is} perceived so differently I am not a Scientist I am a Number PLoS Comp. Biol. 2008 4(12) e1000247
  • 6. Yet What is Better.. A Paper only Ever Cited by the Folks who Wrote it or a Dataset That is Downloaded and Used 100’s of Times? We will come back to this…
  • 7.
  • 8. From Someone Who Generates Scholarship And Cares, Have The Possibilities Been Realized Some Six Years Hence? Not Really But I Like to Think the Process Has Started
  • 9. So I am Here To Tell You Not What is Right with OA – You Know That Already. I Am Here To Tell You in My Humble Opinion What Needs to Be Done To Realize the Promise. Not Necessarily by Publishers, but Catalyzed by Publishers
  • 10. I realized last night that the catalyst could be for reasons of profit or service to science or something in between
  • 11.
  • 12. There is Competition Out There Why Don’ t We Have Such Developments in OA?
  • 13.
  • 14.
  • 15.
  • 16.
  • 17. Ten Simple Rules for What OA Publishers Can Do to Move the Ball Forward
  • 18.
  • 19. Rule 2. Foster Low Hanging Fruit
  • 20. We Cannot Possibly Read a Fraction of the Papers We Should Rule 2 – Foster Low Hanging Fruit Renear & Palmer 2009 Science 325:828-832
  • 21. We Are Scanning More Reading Less – Our Level of Detail is Dropping Renear & Palmer 2009 Science 325:828-832 Rule 2 Foster Low Hanging Fruit
  • 22. Automatic Knowledge Discovery for Those with No Time to Read Shared Function Rule 2 Foster Low Hanging Fruit Immunology Literature Cardiac Disease Literature
  • 23. This Requires That Publishers Exercise the NLM DTD as Far as Possible
  • 24.
  • 25.
  • 26.
  • 27.
  • 28.
  • 29. Yes YouTube Can Increase the Rate of Discovery Rule 4 Recognize Rich Media as Scholarship
  • 30. Pubcast – Video Integrated with the Full Text of the Paper
  • 31.
  • 32. Rule 5 Play Upon a Scientists Guilt re The Reward Sytem The Right Thing To Do Reward
  • 33.
  • 34.
  • 35. Workflow Tools Might be the Answer Taverna Rule 6 Foster Reproducability Wings
  • 36.
  • 37. Yes The Workflow is Real Rule 6 Foster Reproducibility
  • 38.
  • 39.
  • 40.
  • 41. Rule 8 – Think of a Cycle Not an End Product Research [Grants] Journal Article Conference Paper Poster Session Reviews Blogs Community Service/Data Curation
  • 42. Rule 9 – Think of Killer Apps That Could be an OA Game Changer P.E.Bourne, J.L.Fink, M.Gerstein 2008 Open Access: Taking Full Advantage of the Content PLoS Comp. Biol . 4(3) e1000037
  • 43.
  • 44. Here is Another One.. http://richard.cyganiak.de/2007/10/lod/lod-datasets_2010-09-22_colored.html Rule 9 – Come up with Killer Apps
  • 45.
  • 46.
  • 47.

Editor's Notes

  1. Specifically, our aim is to achieve open access to the literature, whereby journal articles are freely available immediately upon publication their use is unrestricted, so that readers can download, print off, reanalyse, extract data and so on authors retain the copyright, and specifically the right to be appropriately cited papers are also deposited separately from the publisher in a public online archive (PMC)