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Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
Ucsd library10182010
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Ucsd library10182010

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  • 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 LibrariesOct. 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 Motivation http://knol.google.com/k/plos-currents-influenza# By the time the paper is published we could all be dead
  • 5. * http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm Jan. 2008 Jan. 2009 Jan. 2010Jul. 2009Jul. 2008 Jul. 2010 1RUZ: 1918 H1 Hemagglutinin Structure Summary page activity for H1N1 Influenza related structures 3B7E: Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir In a time of crisis the need for fast access to accurate data and any knowledge of that data are paramount 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 Man Co-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 Motivation http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG
  • 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 Adapted: http://sagecongress.org/Presentations/Sommer.pdf Motivation Isaac If I have seen further it is only by standing on the shoulders of giants Isaac Newton From Josh’s point of view the climb up just takes too long > 15 years and > $850M to be more precise
  • 13. Oct. 18, 2010 UCSD Libraries http://sagecongress.org/Presentations/Sommer.pdf Motivation
  • 14. Oct. 18, 2010 UCSD Libraries Motivation http://sagecongress.org/Presentations/Sommer.pdf
  • 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 Easy Hard
  • 18. 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 We Need Data and Knowledge About That Data to Interoperate 1. User clicks on content 2. Metadata and webservices to data provide an interactive view that can be annotated 3. Selecting features provides a data/knowledge mashup 4. Analysis leads to new content I can share 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
  • 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 • 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 • 1078 databases reported in NAR 2008 • MetaBase http://biodatabase.org reports 2,651 entries edited 12,587 times Data as of April 14, 2009 PLoS Comp. Biol. 2005 1(3) e34 What Needs to be Done?
  • 21. www.rcsb.org/pdb/explore/literature.do?structureId=1TIM Example Interoperability: The Database View BMC Bioinformatics 2010 11:220 Oct. 18, 2010 UCSD Libraries What Needs to be Done?
  • 22. Example Interoperability: The Literature View http://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) e1000673Semantic 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-processing Better 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 Easy Hard
  • 32. Reward Systems Need to Change What 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 Reward Systems Need to Change Ten Simple Rules for Getting Promoted as a Computational Biologist in Academia PLoS Comp Biol to appear
  • 33. Example Tools Oct. 18, 2010 UCSD Libraries http://pubnet.gersteinlab.org/ http://www.researcherid.com/ http://www.biomedexperts.com
  • 34. What Are these Alternative Forms of Scholarship? Research [Grants] Journal Article Conference Paper Poster Session Reviews Blogs Community Service/Data Curation 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 Easy Hard
  • 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 Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 2008 4(7): e1000136 We Need Scientist Management Tools http://artbyvida.com/portfolio.php
  • 39. Many Great Tools Out There Oct. 18, 2010 UCSD Libraries We Need Scientist Management Tools Taverna
  • 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 Idea Experiment Data Conclusions PublishThe Role of the Institution Laboratory Publisher
  • 42. Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution Lab Notebook The Role of the Institution
  • 43. This Amounts to Publishing Workflows But 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. Questions? pbourne@ucsd.edu Oct. 18, 2010 UCSD Libraries

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