Beyond the Journal Article One Scientist’s Perspective  Philip E. Bourne University of California San Diego [email_address...
How I Got to Be Standing Here <ul><li>Researcher in  computational biology </li></ul><ul><li>Co-developed the Protein Data...
How I Got to Be Standing Here http://www.wwpdb.org/ Journals Database 2005:  Is a Biological Database Different from a Bio...
Author Submission via the Web Depositor Submission via the Web Syntax Checking Syntax Checking Review by Scientists & Edit...
So the processes are not that dissimilar it was the final product that was {is} perceived so differently I am not a Scient...
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 T...
But This is What I Really Came to Appreciate was a Wealth of Possibility <ul><li>All  published materials available on-lin...
From Someone Who Generates Scholarship And Cares, Have The Possibilities Been Realized Some Six Years Hence?  Not Really B...
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 Wha...
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 <ul><li>A very clever idea – The App model </li></ul><ul><li>Leverage content </li></ul><ul...
There is Competition Out There Why Don’ t We Have Such Developments in OA?
Why Don’ t We Have Such Developments in OA? <ul><li>OA publishers think in papers not research objects? </li></ul><ul><li>...
Content is not  consistently  available <ul><li>David Lipman  </li></ul><ul><li>“ Phil, What you are doing is illegal!” </...
The Good News is There Are People Out There Who Care <ul><li>“ Beyond the PDF” crowd </li></ul><ul><li>FORCE11 </li></ul><...
Scientists Themselves –  New OA Journal <ul><li>My knee jerk reaction – is this the best a bunch of great minds can come u...
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! <ul><li>Provide fully open content according to CC BY  The...
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 ...
We Are Scanning More Reading Less – Our Level of Detail is Dropping Renear & Palmer 2009 Science 325:828-832 Rule 2 Foster...
Automatic Knowledge Discovery for Those with No Time to Read Shared Function Rule 2 Foster Low Hanging Fruit Immunology Li...
This Requires That Publishers Exercise the NLM DTD as Far as Possible
Rule 3 Recognize Data <ul><li>Not sure that passing the buck to Dryad and others is the best solution?  </li></ul><ul><li>...
Data – The State of Play (A Scientist’s Perspective) <ul><li>Some disciplines have embraced data journals </li></ul><ul><l...
Data Becomes Part fo the Article <ul><li>User clicks on thumbnail </li></ul><ul><li>Metadata and a webservices call provid...
There Is a Real Opportunity for “Data Papers” <ul><li>Structured metadata about the dataset </li></ul><ul><li>Hence the op...
Rule 4 – Recognize Rich Media as Scholarship <ul><li>Currently video and podcasts are adjuncts to published work – they co...
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 <ul><li>It is a form of expression the current YouTubers embrace and may become as ubiquitous as papers and slide ...
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 <ul><li>Article level metrics are great but: </li></ul><ul><ul><l...
Rule 6 - Play Upon the Scientists Guilt re Reproducibility <ul><li>My views of reproducibility: </li></ul><ul><ul><li>We a...
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 <ul><li>Its h...
Yes The Workflow is Real Rule 6 Foster Reproducibility
Problems with Publishing Workflows <ul><li>Workflows are not linear </li></ul><ul><li>Workflow : paper is not 1:1 </li></u...
Rule 7 - Where Possible Promote the Use of Social Media and Citizen Science  <ul><li>Think of ways beyond blogging, tweeti...
The Wikipedia Experiment – Topic Pages <ul><li>Identify areas of Wikipedia that relate to the journal that are missing of ...
Rule 8 – Think of a Cycle Not an End Product Research [Grants] Journal Article Conference Paper Poster Session Reviews Blo...
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 F...
Here is an Idea to Get You Started <ul><li>Right now reward is defined almost solely by the H-index </li></ul><ul><li>Open...
Here is Another One.. http://richard.cyganiak.de/2007/10/lod/lod-datasets_2010-09-22_colored.html Rule 9 – Come up with Ki...
Rule 10 – Lobby Better <ul><li>Do more to solicit scientists to support legislation like the Hargreaves data mining propos...
General References <ul><li>What Do I Want from the Publisher of the Future PLoS Comp Biol  6(5): e1000787 </li></ul><ul><l...
References to Exemplars <ul><li>Semantic Biochemical Journal - 2010: Using Utopia </li></ul><ul><li>Article of the Future,...
Push-back, Questions? [email_address]
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Ten Simple Rules for Open Access Publishers

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  • 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)
  • Ten Simple Rules for Open Access Publishers

    1. 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. 2. How I Got to Be Standing Here <ul><li>Researcher in computational biology </li></ul><ul><li>Co-developed the Protein Data Bank (PDB) </li></ul><ul><li>Felt my field was not well served by the current literature </li></ul><ul><li>Saw an opportunity to work through a society </li></ul><ul><li>Thought OA was a good idea, but was not passionate about it </li></ul><ul><li>Co-founded and remain the EIC of PLoS Computational Biology </li></ul>
    3. 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. 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. 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. 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. 7. But This is What I Really Came to Appreciate was a Wealth of Possibility <ul><li>All published materials available on-line free to all (author pays model) </li></ul><ul><li>Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s) </li></ul><ul><li>Copyright remains with the author </li></ul>PLoS Comp Biol 2008 4(3) e1000037
    8. 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. 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. 10. I realized last night that the catalyst could be for reasons of profit or service to science or something in between
    11. 11. There is Competition Out There <ul><li>A very clever idea – The App model </li></ul><ul><li>Leverage content </li></ul><ul><li>Provide an open API </li></ul><ul><li>Get the community to do all the work </li></ul><ul><li>Drive folks to buy content </li></ul>Why Don’ t We Have Such Developments in OA?
    12. 12. There is Competition Out There Why Don’ t We Have Such Developments in OA?
    13. 13. Why Don’ t We Have Such Developments in OA? <ul><li>OA publishers think in papers not research objects? </li></ul><ul><li>No R&D budgets? </li></ul><ul><li>No/unidentifiable competitions? </li></ul><ul><li>Not enough content? </li></ul><ul><li>Content is not consistently available? </li></ul><ul><li>Not a collective vision? </li></ul><ul><li>Too early? </li></ul><ul><li>All of the above </li></ul>
    14. 14. Content is not consistently available <ul><li>David Lipman </li></ul><ul><li>“ Phil, What you are doing is illegal!” </li></ul><ul><li>PMC content available under different licensing conditions </li></ul><ul><li>Content conforms to the NLM DTD to different degrees </li></ul><ul><li>The latter may come back to haunt us </li></ul>
    15. 15. The Good News is There Are People Out There Who Care <ul><li>“ Beyond the PDF” crowd </li></ul><ul><li>FORCE11 </li></ul><ul><li>Individual investigators </li></ul><ul><li>Librarians forging a new role for themselves </li></ul><ul><li>Funding agencies, foundations </li></ul><ul><li>Scientists themselves </li></ul><ul><li>Commercial companies e.g. Microsoft </li></ul>
    16. 16. Scientists Themselves – New OA Journal <ul><li>My knee jerk reaction – is this the best a bunch of great minds can come up with! </li></ul><ul><li>My more thoughtful reaction – every little bit helps – it will broaden awareness of the value of OA like nothing else </li></ul>
    17. 17. Ten Simple Rules for What OA Publishers Can Do to Move the Ball Forward
    18. 18. Rule 1 – Continue to Do What You Do But Better – More Openness! <ul><li>Provide fully open content according to CC BY The future of OA might be tied to new business models associated with using the corpus </li></ul><ul><li>Lower costs with more efficient journal management systems – OA publishers are beholden to legacy bloated expensive systems – a recognized and committed joint open source development effort is important </li></ul>
    19. 19. Rule 2. Foster Low Hanging Fruit
    20. 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. 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. 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. 23. This Requires That Publishers Exercise the NLM DTD as Far as Possible
    24. 24. Rule 3 Recognize Data <ul><li>Not sure that passing the buck to Dryad and others is the best solution? </li></ul><ul><li>Need more than a DOI </li></ul><ul><li>Maybe the only short term solution? </li></ul>
    25. 25. Data – The State of Play (A Scientist’s Perspective) <ul><li>Some disciplines have embraced data journals </li></ul><ul><li>Some journals have ignored data </li></ul><ul><li>Institutional repositories are “roach motels” </li></ul><ul><li>The long tail problem is dying to be addressed </li></ul><ul><li>Scientists would love a data citation that looks like a paper citation </li></ul><ul><li>There are some wonderful opportunities… </li></ul>Rule 3 Recognize Data
    26. 26. Data Becomes Part fo the Article <ul><li>User clicks on thumbnail </li></ul><ul><li>Metadata and a webservices call provide a renderable image that can be annotated </li></ul><ul><li>Selecting a features provides a database/literature mashup </li></ul><ul><li>That leads to new papers </li></ul>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
    27. 27. There Is a Real Opportunity for “Data Papers” <ul><li>Structured metadata about the dataset </li></ul><ul><li>Hence the opportunity to discover the data </li></ul><ul><li>Hence the opportunity to establish metrics on the use of the data </li></ul><ul><li>And this is a big one… the opportunity to develop apps (centralized and standardized software) that operate on the data </li></ul>Rule 3 Recognize Data
    28. 28. Rule 4 – Recognize Rich Media as Scholarship <ul><li>Currently video and podcasts are adjuncts to published work – they could be it (e.g., Jove) or better integrated. </li></ul>
    29. 29. Yes YouTube Can Increase the Rate of Discovery Rule 4 Recognize Rich Media as Scholarship
    30. 30. Pubcast – Video Integrated with the Full Text of the Paper
    31. 31. Lessons <ul><li>It is a form of expression the current YouTubers embrace and may become as ubiquitous as papers and slide presentations in the next few years </li></ul><ul><li>Its only going to work if it is easy to publish and the reward is obvious </li></ul>Rule 4 Recognize Rich Media as Scholarship
    32. 32. Rule 5 Play Upon a Scientists Guilt re The Reward Sytem The Right Thing To Do Reward
    33. 33. Rule 5 Play Upon a Scientists Guilt re The Reward System <ul><li>Article level metrics are great but: </li></ul><ul><ul><li>Lets have more of them and more transparency </li></ul></ul><ul><ul><li>Lets standardize and so.. </li></ul></ul><ul><ul><li>Lets use them more effectively </li></ul></ul><ul><li>Example – you looked at this article therefore you might be interested in this one – within a journal and across journals! </li></ul><ul><ul><li>Its like PubMed but based on usage patterns </li></ul></ul>
    34. 34. Rule 6 - Play Upon the Scientists Guilt re Reproducibility <ul><li>My views of reproducibility: </li></ul><ul><ul><li>We all express the importance, but the only time it is tested is when something is truly novel or error is suspected </li></ul></ul><ul><ul><li>Reproducability covers a spectrum of meaning – by whom and with how much effort </li></ul></ul><ul><ul><li>The longer the time lag the less likely something is reproducible </li></ul></ul>
    35. 35. Workflow Tools Might be the Answer Taverna Rule 6 Foster Reproducability Wings
    36. 36. Consider an Example: Our Own Experience in Capturing the Scientific Process to Make it Open and Reproducable <ul><li>Its hard and embarrassing </li></ul><ul><li>We have a working prototype using Wings </li></ul><ul><li>I can feel the potential productivity gains </li></ul><ul><li>My students are more doubtful </li></ul><ul><li>Its been a lot of fun and will enable us to improve our processes regardless of the workflow system itself </li></ul>Rule 6 Foster Reproducibility
    37. 37. Yes The Workflow is Real Rule 6 Foster Reproducibility
    38. 38. Problems with Publishing Workflows <ul><li>Workflows are not linear </li></ul><ul><li>Workflow : paper is not 1:1 </li></ul><ul><li>Confidentiality </li></ul><ul><li>Peer review </li></ul><ul><li>Infrastructure </li></ul><ul><li>Community acceptance </li></ul><ul><li>Reward system </li></ul><ul><li>No publisher seems willing to touch them </li></ul>Rule 6 Foster Reproducibility
    39. 39. Rule 7 - Where Possible Promote the Use of Social Media and Citizen Science <ul><li>Think of ways beyond blogging, tweeting, social bookmarking etc. </li></ul><ul><li>Example – The Wikipedia experiment </li></ul>
    40. 40. The Wikipedia Experiment – Topic Pages <ul><li>Identify areas of Wikipedia that relate to the journal that are missing of stubs </li></ul><ul><li>Develop a Wikipedia page in the sandbox </li></ul><ul><li>Have a Topic Page Editor Review the page </li></ul><ul><li>Publish the copy of record with associated rewards </li></ul><ul><li>Release the living version into Wikipedia </li></ul>Rule 7 Foster Social Media and Citizen Science
    41. 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. 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. 43. Here is an Idea to Get You Started <ul><li>Right now reward is defined almost solely by the H-index </li></ul><ul><li>Open access to data, rich media, presentations, etc, etc could begin to change that .. If one could measure the value of other types of open access content </li></ul><ul><li>Google scholar, MS Academic Search does it to some degree, but it is not accurate </li></ul><ul><li>Help make alternative metrics more available and accurate – need ORCID, need good metadata </li></ul>Rule 9 – Come up with Killer Apps
    44. 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. 45. Rule 10 – Lobby Better <ul><li>Do more to solicit scientists to support legislation like the Hargreaves data mining proposal </li></ul><ul><li>NSF and NIH have new data sharing policies – how can these be mapped to OA activities? </li></ul>
    46. 46. General References <ul><li>What Do I Want from the Publisher of the Future PLoS Comp Biol 6(5): e1000787 </li></ul><ul><li>Fourth Paradigm: Data Intensive Scientific Discovery http://research.microsoft.com/enus/ collaboration/fourthparadigm/ </li></ul>
    47. 47. References to Exemplars <ul><li>Semantic Biochemical Journal - 2010: Using Utopia </li></ul><ul><li>Article of the Future, Cell, 2009:
 </li></ul><ul><li>Prospect, Royal Society of Chemistry, 2009:
 </li></ul><ul><li>Adventures in Semantic Publishing, Oxford U, 2009: </li></ul><ul><li>The Structured Digital Abstract, Seringhaus/Gerstein, 2008
 </li></ul><ul><li>CWA Nanopublications – 2010 
 </li></ul><ul><li>https://sites.google.com/site/beyondthepdf/ </li></ul><ul><li>https://sites.google.com/site/futureofresearchcommunications/ </li></ul>
    48. 48. Push-back, Questions? [email_address]
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