A presentation made to Elsevier VPs, Managers etc. on what scientisst what from publishers going forward.

1. What Do I Want from the Publisher of the Future? Philip E. Bourne University of California San Diego pbourne@ucsd.edu http://www.sdsc.edu/pb PLoS Comp Biol 2010 6(5): e1000787.

2. What is My Twisted Perspective? Background in both IT and science (chemistry, computational biology) My lab. distributes for free data equivalent to ¼ the Library of Congress every month I am a supporter of open access (provided there is a business model) and editor in chief of PLoS Computational Biology I am Co-founder of SciVee Inc. (conflict?) I am becoming increasingly interested in scholarly communication I Readily Acknowledge Each Discipline is Different

3. My Comments Are Heavily Influenced by a Recent Workshop –Beyond the PDF The most vibrant workshop I have attended in over 30 years of workshops https://sites.google.com/site/beyondthepdf/

4. Driver of Change With much of the STM research workflow now being digital it makes no sense to retrofit the finding of that workflow into something essentially analog

6. Blockbuster video

7. Newspapers (pay wall vs. mining)

8. iPads/tablets

9. YouTube

10. Social networking

12. Interactive PDFs

13. Article of the Future

14. ORCHID

15. Datacite, Dryad

16. Mendelay

17. Hubs, Currents…

18. Open publishing platforms

20. Interactive PDFs– baby steps

21. Article of the Future – already past

22. ORCHID – disambiguation of all content

23. Datacite, Dryad – data treated as publications

24. Hubs – new forms of integration

26. The Article of the Future is Not the Killer App – Yet? Semantic tagging to ontological terms is okay, but really only valuable when I gain new knowledge, not the meaning of a term I could look up any way. PaperFlick – maybe Tabs – hey it’s a web site after all Comments – well we know how well that works so far Tables in XLS format – yes! Bibliometrics – its not open

27. A Way to Reward a Different Model of Scholarly Achievement Would be the Tipping Point Change Reward You don’t get tenure for starting a PLoS hub!

28. Reward Scheme – One of Scholarship’s Dirty Secrets – We Claim to be Quantitative, Yet we Measure Ourselves Otherwise Journal Impact factors are not paper impact factors Other forms of scholarly discourse (blogs, database depositions, software etc) don’t rate … Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comp. Biol. 7(1) e1002001.

29. Why Will We Move Beyond the PDF Eventually? Scholarship Will Demand It

30. Publishing Limitations A paper is an artifact of a previous era It is not the logical end product of eScience, hence: Work is omitted Data and the knowledge of that data are disjoint Article vs supplement is a mess Visualization may be limited Interaction and enquiry are non-existent Rich media can help, but are rarely used There is no true aggregation Drivers of Change

31. We Cannot Possibly Read a Fraction of the Papers We Should Drivers of Change Renear & Palmer 2009 Science 325:828-832

32. Hence We Are Scanning More Reading Less Renear & Palmer 2009 Science 325:828-832 Drivers of Change

33. 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 Drivers of Change

34. 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 Drivers of Change

35. Here is What I Want as a Scholar The Knowledge and Data Cycle 0. Full text of PLoS papers stored in a database 4. The composite view has links to pertinent blocks of literature text and back to the PDB User clicks on content Metadata and webservices to data provide an interactiveview that can be annotated Selecting features provides a data/knowledge mashup Analysis leads to new content I can share 4. 1. 3. A composite view of journal and database content results 1. A link brings up figures from the paper 3. 2. 2. Clicking the paper figure retrieves data from the PDB which is analyzed PLoS Comp. Biol. 2005 1(3) e34

36. Cardiac Disease Literature Immunology Literature Here is What I Want as a Scholar:Automatic Knowledge Discovery Shared Function Drivers of Change

37. As a Consequence the Traditional PDF is an Inferior Way to Convey the Science Moreover, the Traditional PDF is not the Natural End Product of the Research Enterprise

38. A paper when complete is thrown over a high wall to a publisher and essentially forgotten – Perhaps it is time to climb the wall? Drivers of Change uzar.wordpress.com

39. So What Do I Think We Should Do To Solve My Problems and Your Problems? What Should We Do?

40. Consider Today’s Academic Workflow Reviews Feds Publishers Societies Blogs Community Service/Data Curation Research [Grants] Journal Article Poster Session Conference Paper What Should We Do?

41. Consider Tomorrow’s Academic Workflow Reviews Feds Publishers Societies Blogs Community Service/Data Curation Ideas, Data, Hypotheses Research [Grants] Journal Article Poster Session Conference Paper What Should We Do?

42. “We have an interaction with the publisher that does not begin when the scientific process ends, but begins at the beginning of the scientific process itself “ What Should We Do? PLoS Comp Biol 2010 6(5): e1000787

43. Maybe The Line is Somewhere Else? Scientist Laboratory Idea Experiment Data Conclusions Publisher Publish What Should We Do?

44. Maybe The Line is Somewhere Else? Laboratory Scientist Idea Experiment Institution Data Lab Notebook Conclusions Publisher Publish What Should We Do?

45. This Amounts to Publishing WorkflowsBut That Has its Problems Workflows are not linear Workflow : paper is not 1:1 Confidentiality Peer review Infrastructure Community acceptance Reward system What Should We Do?

46. What is Needed to Publish Workflows? New organizations (university as publisher?) Suitable support frameworks for research objects Provenance and appropriate reward systems for living entities Shared governance author, institution, publisher What Should We Do?

47. Define a Goal Make a positive contribution that would not otherwise happen in such a timely way https://sites.google.com/site/beyondthepdf/

48. What is Being Done? Research objects of the future (ROFs) – Entities that capture all aspects of scholarship: hypotheses, data, methods, results, presentations etc.) that are semantically enriched, interoperable and easily transmitted and comprehended Define a set of requirements to meet the needs of the SMA project. Agree on standards and architecture to support the requirements. Interface with existing efforts under the W3C umbrella. Illustrate that the effort has advanced our understanding of SMA beyond what would otherwise be possible. https://sites.google.com/site/beyondthepdf/

49. What is Being Done? Writing – Establishing a scholarly discourse that embraces the idea of ROFs. New writing tools should create ROF containers that contain all relevant files. These containers should be shared using appropriate network protocols. Evaluate existing tools for use in this regard. Settle on tools or agree to modify tools to address the SMA goal. Work to demonstrate the value of the tools in supporting data integration (with appropriate metadata). Have graduate students in several research groups evaluate the tools. https://sites.google.com/site/beyondthepdf/

50. What is Being Done? Attribution, Evaluation, Archiving Develop a use case for use by funding agencies to evaluate the effectiveness of funding. A tool to measure citation and attention based metrics across a broad spectrum of sources was proposed. Prototype an impact dashboard to be used by the SMA Foundation. https://sites.google.com/site/beyondthepdf/

51. In Summary – Crowd Source the Printing Press of the 21st Century https://sites.google.com/site/beyondthepdf/

53. pbourne@ucsd.edu Discussion