This was a presentation to the University of California San Diego (UCSD) Senate invited by the library.

1. Why is Scholarly Communication Broken and What Can Be Done?In Celebration of Open Access Week Philip E. Bourne University of California San Diego pbourne@ucsd.edu UCSD Libraries Oct. 18, 2010

2. Disclaimer I am a domain (life) scientist not a computer or information scientist I am fortunate enough to have a major biological resource (the Protein Data Bank) and a major biological journal (PLoS Computational Biology) as my playground I am part of the long tail I am naïve, but I am the majority Oct. 18, 2010 UCSD Libraries

3. Agenda Motivation What needs to be done? A few examples The role of the institution Oct. 18, 2010 UCSD Libraries

4. The Scientific Process is Too Slow to Respond to a Crisis – Either Global or Personal Oct. 18, 2010 UCSD Libraries By the time the paper is published we could all be dead http://knol.google.com/k/plos-currents-influenza# Motivation

5. In a time of crisis the need for fast access to accurate data and any knowledge of that data are paramount Structure Summary page activity for H1N1 Influenza related structures Jan. 2008 Jan. 2009 Jan. 2010 Jul. 2009 Jul. 2008 Jul. 2010 3B7E: Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir 1RUZ: 1918 H1 Hemagglutinin * http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm Motivation Oct. 18, 2010 UCSD Libraries

6. If that is not enough…For some people the scientific process may be too slow to save their life Oct. 18, 2010 UCSD Libraries Motivation

7. Josh Sommer – A Remarkable Young ManCo-founder & Executive Director the Chordoma Foundation Oct. 18, 2010 UCSD Libraries http://sagecongress.org/Presentations/Sommer.pdf Motivation

8. Chordoma A rare form of brain cancer No known drugs Treatment – surgical resection followed by intense radiation therapy Oct. 18, 2010 UCSD Libraries http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG Motivation

9. Oct. 18, 2010 UCSD Libraries http://sagecongress.org/Presentations/Sommer.pdf Motivation

10. Oct. 18, 2010 UCSD Libraries http://sagecongress.org/Presentations/Sommer.pdf Motivation

11. Oct. 18, 2010 UCSD Libraries http://sagecongress.org/Presentations/Sommer.pdf Motivation

12. Oct. 18, 2010 UCSD Libraries If I have seen further it is only by standing on the shoulders of giants Isaac Isaac Newton From Josh’s point of view the climb up just takes too long > 15 years and > $850M to be more precise Adapted: http://sagecongress.org/Presentations/Sommer.pdf Motivation

13. Oct. 18, 2010 UCSD Libraries http://sagecongress.org/Presentations/Sommer.pdf Motivation

14. Oct. 18, 2010 UCSD Libraries http://sagecongress.org/Presentations/Sommer.pdf Motivation

15. Oct. 18, 2010 UCSD Libraries http://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_Foundation Motivation

16. Now we are all hopefully motivated let us break this down to what actually needs to be done in my opinion Here are a few big things … Oct. 18, 2010 UCSD Libraries What Needs to be Done?

17. A Few Things to Accelerate the Rate of Scientific Discovery Better communication, data and knowledge access, and new modes of discovery, which means: We need data and knowledge about that data to interoperate i.e. we need new kinds of fast, versatile publications and data archives We need to be more open with both We need to think more about the tools that analyze, visualize and annotate data to maximize knowledge discovery Reward systems need to change We need scientist management tools We need to be less fixated on the big data problems We need to unleash the full power of the Internet Oct. 18, 2010 UCSD Libraries Hard Easy

18. We Need Data and Knowledge About That Data to Interoperate 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

19. We Need Data and Knowledge About That Data to Interoperate – What is Stopping US? Governance – publishers vs. database providers Reward Metadata standards for provenance, privacy etc. Exemplars …. Oct. 18, 2010 UCSD Libraries Caveat: Each discipline is different – I speak very much from a biomedical sciences perspective

20. Certainly the Argument for Interoperability in the Biomedical Sciences is Strong 1078 databases reported in NAR 2008 MetaBase http://biodatabase.org reports 2,651 entries edited 12,587 times PubMed contains 18,792,257 entries ~100,000 papers indexed per month In Feb 2009: 67,406,898 interactive searches were done 92,216,786 entries were viewed Data as of April 14, 2009 PLoS Comp. Biol. 2005 1(3) e34 What Needs to be Done?

21. Example Interoperability: The Database View www.rcsb.org/pdb/explore/literature.do?structureId=1TIM BMC Bioinformatics 2010 11:220 Oct. 18, 2010 UCSD Libraries What Needs to be Done?

22. Example Interoperability: The Literature Viewhttp://biolit.ucsd.edu Nucleic Acids Research 2008 36(S2) W385-389 Oct. 18, 2010 UCSD Libraries What Needs to be Done?

23. ICTP Trieste, December 10, 2007 Oct. 18, 2010 UCSD Libraries

24. Semantic Tagging & Widgets are a Powerful Tool to Integrate Data and Knowledge of that Data, But as Yet Not Used Much Oct. 18, 2010 UCSD Libraries Will Widgets and Semantic Tagging Change Computational Biology? PLoS Comp. Biol. 6(2) e1000673 What Needs to be Done?

25. Semantic Tagging of Database Content in The Literature or Elsewhere http://www.rcsb.org/pdb/static.do?p=widgets/widgetShowcase.jsp PLoS Comp. Biol. 6(2) e1000673 Semantic Tagging

26. Oct. 18, 2010 UCSD Libraries What Needs to be Done?

27. The Publishers are Starting to Do It Oct. 18, 2010 UCSD Libraries From Anita de Waard, Elsevier What Needs to be Done?

28. This is Literature Post-processingBetter to Get the Authors Involved Authors are the absolute experts on the content More effective distribution of labor Add metadata before the article enters the publishing process Oct. 18, 2010 UCSD Libraries What Needs to be Done?

29. Word 2007 Add-in for authors Allows authors to add metadata as they write, before they submit the manuscript Authors are assisted by automated term recognition OBO ontologies Database IDs Metadata are embedded directly into the manuscript document via XML tags, OOXML format Open Machine-readable Open source, Microsoft Public License http://www.codeplex.com/ucsdbiolit Oct. 18, 2010 UCSD Libraries What Needs to be Done?

30. Challenges Authors Carrot IF one or more publishers fast tracked a paper that had semantic markup it might catch on Publishers Carrot Competitive advantage Oct. 18, 2010 UCSD Libraries What Needs to be Done?

31. A Few Things to Accelerate the Rate of Scientific Discovery Better communication, data and knowledge access, and new modes of discovery, which means: We need data and knowledge about that data to interoperate i.e. we need new kinds of fast, versatile publications and data archives We need to be more open with both We need to think more about the tools that analyze, visualize and annotate data to maximize knowledge discovery Reward systems need to change We need scientist management tools We need to be less fixated on the big data problems We need to unleash the full power of the Internet Oct. 18, 2010 UCSD Libraries Hard Easy

32. Reward Systems Need to ChangeWhat is Needed? Author disambiguation Auditing (identification and metrics) of all scholarship - means new tools Seniors need to promote alternative forms of scholarship Juniors need to respond Oct. 18, 2010 UCSD Libraries Ten Simple Rules for Getting Promoted as a Computational Biologist in Academia PLoS Comp Biol to appear Reward Systems Need to Change

33. Example Tools Oct. 18, 2010 UCSD Libraries http://www.researcherid.com/ http://pubnet.gersteinlab.org/ http://www.biomedexperts.com

34. What Are these Alternative Forms of Scholarship? Reviews Curation Research [Grants] Journal Article Poster Session Conference Paper Blogs Community Service/Data Reward Systems Need to Change Oct. 18, 2010 UCSD Libraries

35. Ideally the ID will be Tagged to Every Piece of Scholarly Communication I an Not a Scientist I am a Number PLoS Comp. Biol. 2008 4(12) e1000247 Reward Systems Need to Change Oct. 18, 2010 UCSD Libraries

36. A Few Things to Accelerate the Rate of Scientific Discovery Better communication, data and knowledge access, and new modes of discovery, which means: We need data and knowledge about that data to interoperate i.e. we need new kinds of fast, versatile publications and data archives We need to be more open with both We need to think more about the tools that analyze, visualize and annotate data to maximize knowledge discovery Reward systems need to change We need scientist management tools We need to be less fixated on the big data problems We need to unleash the full power of the Internet Oct. 18, 2010 UCSD Libraries Hard Easy

37. The Truth About My Laboratory I have ?? mail folders! The intellectual memory of my laboratory is in those folders This is an unhealthy hub and spoke mentality We Need Scientist Management Tools Oct. 18, 2010 UCSD Libraries

38. The Truth About My Laboratory 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 http://artbyvida.com/portfolio.php Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 2008 4(7): e1000136 We Need Scientist Management Tools

39. Many Great Tools Out There Oct. 18, 2010 UCSD Libraries Taverna We Need Scientist Management Tools

40. Where I See the Problems The long tail is confused Lack of interoperability between the options The reward (publishing) is still removed from the available tools Oct. 18, 2010 UCSD Libraries We Need Scientist Management Tools

41. Science is Increasingly a Digital Workflow Scientist Laboratory Idea Experiment Data Conclusions Publisher Publish The Role of the Institution

42. Maybe The Line is Somewhere Else? Laboratory Scientist Idea Experiment Institution Data Lab Notebook Conclusions Publisher Publish The Role of the Institution

43. 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 The Role of the Institution

44. Solutions to Publishing Workflows? New organizations (university as publisher?) Appropriate reward system Shared governance author, institution, publisher Crowd sourcing the electronic printing press The Role of the Institution

45. Crowd Sourcing the Electronic Printing Press(aka Workshop: Beyond the PDF) Funded by DDCF, Microsoft, NCI, Sage Bionetworks: Aims: Define user requirements Establish a specification document Open source the development effort Have a commitment from a publisher to publish a research object using the system Act as an exemplar for what can be done The Role of the Institution

46. Logistics UC San Diego Jan 19-21, 2010 Under the auspices of W3C FoRC will have a follow on meeting The Role of the Institution

47. pbourne@ucsd.edu Questions? Oct. 18, 2010 UCSD Libraries