UCSD Library Presentation 10182010
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The document discusses the challenges in scholarly communication, emphasizing the need for faster access to scientific data and improved interoperability. It proposes various solutions such as better communication, changing reward systems, and developing new tools for data analysis and sharing to accelerate scientific discovery. The author highlights the role of institutions in adopting these changes and facilitating more effective workflows in research publishing.
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UCSD Library Presentation 10182010
- 1. Why is Scholarly Communication Broken and What Can Be Done?In Celebration of Open Access WeekPhilip E. BourneUniversity of California San Diegopbourne@ucsd.eduUCSD LibrariesOct. 18, 2010
- 2. DisclaimerI am a domain (life) scientist not a computer or information scientistI am fortunate enough to have a major biological resource (the Protein Data Bank) and a major biological journal (PLoS Computational Biology) as my playgroundI am part of the long tailI am naïve, but I am the majorityOct. 18, 2010UCSD Libraries
- 3. AgendaMotivationWhat needs to be done?A few examplesThe role of the institutionOct. 18, 2010UCSD Libraries
- 4. The Scientific Process is Too Slow to Respond to a Crisis – Either Global or PersonalOct. 18, 2010UCSD LibrariesBy the time the paper is published we could all be deadhttp://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 ofthat data are paramountStructure Summary page activity forH1N1 Influenza related structuresJan. 2008Jan. 2009Jan. 2010Jul. 2009Jul. 2008Jul. 20103B7E: Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir1RUZ: 1918 H1 Hemagglutinin* http://www.cdc.gov/h1n1flu/estimates/April_March_13.htmMotivationOct. 18, 2010UCSD Libraries
- 6. If that is not enough…For some people the scientific process may be too slow to save their lifeOct. 18, 2010UCSD LibrariesMotivation
- 7. Josh Sommer – A Remarkable Young ManCo-founder & Executive Director the Chordoma FoundationOct. 18, 2010UCSD Librarieshttp://sagecongress.org/Presentations/Sommer.pdfMotivation
- 8. ChordomaA rare form of brain cancerNo known drugsTreatment – surgical resection followed by intense radiation therapyOct. 18, 2010UCSD Librarieshttp://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPGMotivation
- 9. Oct. 18, 2010UCSD Librarieshttp://sagecongress.org/Presentations/Sommer.pdfMotivation
- 10. Oct. 18, 2010UCSD Librarieshttp://sagecongress.org/Presentations/Sommer.pdfMotivation
- 11. Oct. 18, 2010UCSD Librarieshttp://sagecongress.org/Presentations/Sommer.pdfMotivation
- 12. Oct. 18, 2010UCSD LibrariesIf I have seen further it is only bystanding on the shoulders of giantsIsaacIsaac NewtonFrom Josh’s point of view the climb up just takes too long> 15 years and > $850M to be more preciseAdapted: http://sagecongress.org/Presentations/Sommer.pdfMotivation
- 13. Oct. 18, 2010UCSD Librarieshttp://sagecongress.org/Presentations/Sommer.pdfMotivation
- 14. Oct. 18, 2010UCSD Librarieshttp://sagecongress.org/Presentations/Sommer.pdfMotivation
- 15. Oct. 18, 2010UCSD Librarieshttp://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_FoundationMotivation
- 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, 2010UCSD LibrariesWhat Needs to be Done?
- 17. A Few Things to Accelerate the Rate of Scientific DiscoveryBetter 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 archivesWe need to be more open with bothWe need to think more about the tools that analyze, visualize and annotate data to maximize knowledge discoveryReward systems need to changeWe need scientist management toolsWe need to be less fixated on the big data problemsWe need to unleash the full power of the InternetOct. 18, 2010UCSD LibrariesHardEasy
- 18. We Need Data and Knowledge About That Data to InteroperateThe Knowledge and Data Cycle0. Full text of PLoS papers stored in a database4. The composite view haslinks to pertinent blocks of literature text and back to the PDBUser clicks on contentMetadata and webservices to data provide an interactiveview that can be annotatedSelecting features provides a data/knowledge mashupAnalysis leads to new content I can share4.1.3. A composite view ofjournal and databasecontent results1. A link brings up figures from the paper3.2.2. Clicking the paper figure retrievesdata from the PDB which isanalyzedPLoS 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 providersRewardMetadata standards for provenance, privacy etc.Exemplars ….Oct. 18, 2010UCSD LibrariesCaveat: Each discipline is different – I speak very much from a biomedicalsciences perspective
- 20. Certainly the Argument for Interoperability in the Biomedical Sciences is Strong1078 databases reported in NAR 2008MetaBase http://biodatabase.org reports 2,651 entries edited 12,587 timesPubMed contains 18,792,257 entries~100,000 papers indexed per monthIn Feb 2009:67,406,898 interactive searches were done92,216,786 entries were viewedData as of April 14, 2009PLoS Comp. Biol. 2005 1(3) e34What Needs to be Done?
- 21. Example Interoperability: The Database Viewwww.rcsb.org/pdb/explore/literature.do?structureId=1TIMBMC Bioinformatics 2010 11:220Oct. 18, 2010UCSD LibrariesWhat Needs to be Done?
- 22. Example Interoperability: The Literature Viewhttp://biolit.ucsd.eduNucleic Acids Research 2008 36(S2) W385-389Oct. 18, 2010UCSD LibrariesWhat Needs to be Done?
- 23. ICTP Trieste, December 10, 2007Oct. 18, 2010UCSD Libraries
- 24. Semantic Tagging & Widgets are a Powerful Tool to Integrate Data and Knowledge of that Data, But as Yet Not Used MuchOct. 18, 2010UCSD LibrariesWill Widgets and Semantic Tagging Change Computational Biology? PLoS Comp. Biol. 6(2) e1000673What Needs to be Done?
- 25. Semantic Tagging of Database Content in The Literature or Elsewherehttp://www.rcsb.org/pdb/static.do?p=widgets/widgetShowcase.jspPLoS Comp. Biol. 6(2) e1000673Semantic Tagging
- 26. Oct. 18, 2010UCSD LibrariesWhat Needs to be Done?
- 27. The Publishers are Starting to Do ItOct. 18, 2010UCSD LibrariesFrom Anita de Waard, Elsevier What Needs to be Done?
- 28. This is Literature Post-processingBetter to Get the Authors InvolvedAuthors are the absolute experts on the contentMore effective distribution of laborAdd metadata before the article enters the publishing processOct. 18, 2010UCSD LibrariesWhat Needs to be Done?
- 29. Word 2007 Add-in for authorsAllows authors to add metadata as they write, before they submit the manuscriptAuthors are assisted by automated term recognitionOBO ontologiesDatabase IDsMetadata are embedded directly into the manuscript document via XML tags, OOXML formatOpenMachine-readableOpen source, Microsoft Public Licensehttp://www.codeplex.com/ucsdbiolitOct. 18, 2010UCSD LibrariesWhat Needs to be Done?
- 30. ChallengesAuthors Carrot IF one or more publishers fast tracked a paper that had semantic markup it might catch onPublishersCarrot Competitive advantageOct. 18, 2010UCSD LibrariesWhat Needs to be Done?
- 31. A Few Things to Accelerate the Rate of Scientific DiscoveryBetter 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 archivesWe need to be more open with bothWe need to think more about the tools that analyze, visualize and annotate data to maximize knowledge discoveryReward systems need to changeWe need scientist management toolsWe need to be less fixated on the big data problemsWe need to unleash the full power of the InternetOct. 18, 2010UCSD LibrariesHardEasy
- 32. Reward Systems Need to ChangeWhat is Needed?Author disambiguationAuditing (identification and metrics) of all scholarship - means new toolsSeniors need to promote alternative forms of scholarshipJuniors need to respondOct. 18, 2010UCSD LibrariesTen Simple Rules for Getting Promoted as a Computational Biologist in Academia PLoS Comp Biol to appearReward Systems Need to Change
- 33. Example ToolsOct. 18, 2010UCSD Librarieshttp://www.researcherid.com/http://pubnet.gersteinlab.org/http://www.biomedexperts.com
- 34. What Are these Alternative Forms of Scholarship?ReviewsCurationResearch[Grants]JournalArticlePosterSessionConferencePaperBlogsCommunity Service/DataReward Systems Need to ChangeOct. 18, 2010UCSD Libraries
- 35. Ideally the ID will be Tagged to Every Piece of Scholarly CommunicationI an Not a Scientist I am a NumberPLoS Comp. Biol. 2008 4(12) e1000247Reward Systems Need to ChangeOct. 18, 2010UCSD Libraries
- 36. A Few Things to Accelerate the Rate of Scientific DiscoveryBetter 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 archivesWe need to be more open with bothWe need to think more about the tools that analyze, visualize and annotate data to maximize knowledge discoveryReward systems need to changeWe need scientist management toolsWe need to be less fixated on the big data problemsWe need to unleash the full power of the InternetOct. 18, 2010UCSD LibrariesHardEasy
- 37. The Truth About My LaboratoryI have ?? mail folders!The intellectual memory of my laboratory is in those foldersThis is an unhealthy hub and spoke mentalityWe Need Scientist Management ToolsOct. 18, 2010UCSD Libraries
- 38. The Truth About My LaboratoryI generate way more negative that positive data, but where is it? Content management is a messSlides, posters…..Data, lab notebooks ….Collaborations, Journal clubs …Software is open but where is it?Farewell is for the data toohttp://artbyvida.com/portfolio.phpComputational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 2008 4(7): e1000136We Need Scientist Management Tools
- 39. Many Great Tools Out ThereOct. 18, 2010UCSD LibrariesTavernaWe Need Scientist Management Tools
- 40. Where I See the ProblemsThe long tail is confusedLack of interoperability between the optionsThe reward (publishing) is still removed from the available toolsOct. 18, 2010UCSD LibrariesWe Need Scientist Management Tools
- 41. Science is Increasingly a Digital WorkflowScientistLaboratoryIdeaExperimentDataConclusionsPublisherPublishThe Role of the Institution
- 42. Maybe The Line is Somewhere Else?LaboratoryScientistIdeaExperimentInstitutionDataLab NotebookConclusionsPublisherPublishThe Role of the Institution
- 43. This Amounts to Publishing WorkflowsBut That Has its ProblemsWorkflows are not linearWorkflow : paper is not 1:1ConfidentialityPeer reviewInfrastructureCommunity acceptanceReward systemThe Role of the Institution
- 44. Solutions to Publishing Workflows?New organizations (university as publisher?)Appropriate reward systemShared governance author, institution, publisherCrowd sourcing the electronic printing pressThe 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 requirementsEstablish a specification documentOpen source the development effortHave a commitment from a publisher to publish a research object using the systemAct as an exemplar for what can be doneThe Role of the Institution
- 46. LogisticsUC San DiegoJan 19-21, 2010Under the auspices of W3CFoRC will have a follow on meetingThe Role of the Institution
- 47. pbourne@ucsd.eduQuestions?Oct. 18, 2010UCSD Libraries