One Scientist’s Wish List for STM Publishers Philip E. Bourne University of California San Diego [email protected] http://www.sdsc.edu/pb (see presentations and publications)
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One Scientist’s Wish List for STM Publishers Philip E. Bourne University of California San Diego [email protected] http://www.sdsc.edu/pb (see presentations and publications) My 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. • I am becoming increasingly interested in scholarly communication I Readily Acknowledge Each Discipline is Different Your Reaction to My Viewpoint Motivators: What is Wrong with Me? Well My Lab Anyway We Cannot Possibly Read a Fraction of the Papers We Should Drivers of Change Renear & Palmer 2009 Science 325:828-832 Hence We Are Scanning More Reading Less Drivers of Change Renear & Palmer 2009 Science 325:828-832 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 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 Drivers of Change Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 4(7): e1000136 The Not so Hidden Truth About Science • Scientists place more emphasis on writing and less on reading • We are H factor obsessed, but interested in other metrics • We are driven by (in order): – Grants – Papers – Teaching – Community service Drivers of Change Enough About Me – What About You? Drivers of Change Data and the Publication Are Disjoint • 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 Drivers of Change • 1078 databases reported in NAR 2008 • MetaBase http://biodatabase.org reports 2,651 entries edited 12,587 times Biosciences Data as of April 14, 2009 Publishing Limitations • A paper is an artifact of a previous era • It is not the logical end product of eScience, hence: – Work is omitted – Article vs supplement is a mess – Visualization may be limited – Interaction and enquiry are non-existent – Rich media can help, but are rarely used Drivers of Change The Traditional PDF is an Inferior Way to Convey the Science The Traditional PDF is not the Natural End Product of the Research Enterprise 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 The Game is Afoot It is being driven from the top down and the bottom up Database & Literature Integration www.rcsb.org/pdb/explore/literature.do?structureId=1TIM Context Drivers of Change BMC Bioinformatics Accepted Semantic Tagging of Database Content Drivers of Change http://www.pdb.org PLoS Comp. Biol. 6(2) e1000673 Interactive PDFs etc.. Article of the Future Drivers of Change Post-publication of Video and Paper www.scivee.tv Drivers of Change Pubcast – Video Integrated with the Full Text of the Paper Pubcasts - A Unique Technology Pubcasts - A Blend of Video, text, tables, figures, PowerPoints, comments, ratings… ALL SYNCHRONIZED FOR RAPID LEARNING Don’t understand what you are reading? Click and have the author pop-up and explain it! See the scientists and the experiments behind the research papers and textbooks Mashups – www.scivee.tv Postercasts Drivers of Change More on Semantic Tagging Semantic Tagging http://biolit.ucsd.edu ICTP Trieste, December 10, 2007 Drivers of Change 26 http://biolit.ucsd.edu 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 Drivers of Change BMC Bioinformatics 2010 11:103 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 Drivers of Change http://www.codeplex.com/ucsdbiolit Automatic Knowledge Discovery for Those with No Time to Read Cardiac Disease Literature Immunology Literature Shared Function Drivers of Change 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 4. 1. 1. A link brings up figures from the paper 2. 3. A composite view of journal and database content results 3. 2. Clicking the paper figure retrieves data from the PDB which is analyzed Here is What I Want 1. User clicks on thumbnail 2. Metadata and a webservices call provide a renderable image that can be annotated 3. Selecting a features provides a database/literature mashup 4. That leads to new papers PLoS Comp. Biol. 1(3) e34 Let Us Summarize Where We Are • Scientists (aka authors, consumers) have problems at home (aka lab.) • Publishers have problems at home (changing business models, demands etc.) • Change is afoot, both top down and bottom up Lets Catch Our Breath So What Do I Think We Should Do To Solve My Problems and Your Problems? What Should We Do? Consider Today’s Academic Workflow Reviews Curation Feds Research [Grants] Journal Article Publishers Poster Session Conference Paper Community Service/Data What Should We Do? Societies Blogs Consider Tomorrow’s Academic Workflow Reviews Curation Feds Ideas, Data, Hypotheses Research [Grants] Journal Article Publishers Poster Session Conference Paper Community Service/Data What Should We Do? Societies Blogs “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 End of May Maybe The Line is Somewhere Else? Scientist Laboratory Idea Experiment Data Conclusions What Should We Do? Publish Publisher Maybe The Line is Somewhere Else? Laboratory Scientist Idea Experiment Institution Data Lab Notebook What Should We Do? Conclusions Publish Publisher Problems with Publishing Workflows • • • • • • • Workflows are not linear Workflow : paper is not 1:1 Confidentiality Peer review Infrastructure Community acceptance Reward system What Should We Do? Solutions to Publishing Workflows? • New organizations (university as publisher?) • Appropriate reward system • Shared governance – author, institution, publisher • Crowd sourcing the electronic printing press What Should We Do? Crowd Sourcing the Electronic Printing Press (aka Workshop: Beyond the PDF) • Proposal to the US National Science Foundation: • 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 Logistics • UC San Diego • Sometime in the Fall/winter 2010 • Under the auspices of W3C • FoRC will have a follow on meeting Those Interested Thus Far Virginia Barbour Paul Ginsparg Colin Batchelor Carole Goble richard k belew Alexander Griekspoor Tanya Beradini Timo Hannay Geoffrey Bilder Eduard Hovy Peter Binfield Peter Jerram Theodora Bloom Heather Joseph Katy Borner Julia Lane Philip Bourne Barend Mons Jean-Claude Bradley peter murray-rust Patrick Brown Catherine Nancarrow Todd Carpenter Cameron Neylon Richard Cave David Patterson Tim Clark Mark Patterson Matthew Cockerill Tracy Pelon Matt Day Dan Pollock Lee Dirks [email protected] Jonathan Eisen Brian Schottlaender Michael Eisen Borya Shakhnovich Lynn Fink David Shotton Marc Friedman Elliot Siegel Pascale Gaudet [email protected] [email protected] Herbert Van de Sompel Question: What if Everyone Had An Electronic Printing Press? • • • • • • Peer review might change? Bibliometrics might change? Business models will likely change? What happens to the database/literature divide? Societies might do more self publishing? We might have improved the dissemination of science, but will we have improved the comprehension? General References • What Do I Want from the Publisher of the Future PLoS Comp Biol (in Press) http://www.sdsc.edu/pb • Fourth Paradigm: Data Intensive Scientific Discovery http://research.microsoft.com/enus/collabora tion/fourthparadigm/ References to Exemplars • Semantic Biochemical Journal - 2010: Using Utopia • Article of the Future, Cell, 2009: • Prospect, Royal Society of Chemistry, 2009: • Adventures in Semantic Publishing, Oxford U, 2009: • The Structured Digital Abstract, Seringhaus/Gerstein, 2008 • CWA Nanopublications – 2010 Acknowledgements • BioLit Team – – – – – Lynn Fink Parker Williams Marco Martinez Rahul Chandran Greg Quinn • Microsoft Scholarly Communications – – – – – Pablo Fernicola Lee Dirks Savas Parastitidas Alex Wade Tony Hey http://biolit.ucsd.edu http//www.pdb.org http://www.codeplex.com/ucsdbiolit • wwPDB team • SciVee Team – Apryl Bailey – Tim Beck – – – – – – http://www.scivee.tv Leo Chalupa Lynn Fink Marc Friedman (CEO) Ken Liu Alex Ramos Willy Suwanto [email protected] Questions?