The document discusses the need for a closer relationship between scientists and publishers throughout the scientific process rather than only at the publication stage. It emphasizes the importance of integrating data, tools, and workflows to create a more interactive and interoperable scientific discourse, advocating for innovations like nano publications and rich media integration. The author calls for a transformation in how scientific work is published and shared to improve data management, reproducibility, and collaboration within the scientific community.

1. Addressing the Discontinuity Between Doing Research and Disseminating ResearchPhilip E. BourneUniversity of California San Diegopbourne@ucsd.eduhttp://www.sdsc.edu/pb

2. Scientist vs. PublisherThere is a high wall separating a scientist and a publisherPerhaps a consequence of the analog worldThere is no need for this in a digital world Perhaps it is time to climb the wall?uzar.wordpress.comScientific Discourse Today

3. Stated Another Way…Scientific Discourse in the FutureAs a scientist I want 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 I want from a Publisher of the FuturePLoS Comp Biol 2010 6(5): e1000787

4. In the dream world I am creating here what would the end productof that relationship look like?Scientific Discourse in the Future

5. Yes I Want the Beauty of an Original Research Article with Semantic Tagging and Visual Embeds etc .. butScientific Discourse in the Future

6. I Want Interoperability with the Data and Applications that Understand That DataWhat is needed?Standard set of apps for data explorationStandard calling interfacesWho manages the data?PublisherAuthorDatabase3rd partyUser annotates viewMetadata stored with the articleFetches the data and provides a Staring point for interactive enquiryScientific Discourse in the Future

7. Already Being Done by Databases and on MobileTight Integration with MyPDBAccess to saved queries

8. Add/delete queries

9. Flag interesting entries

10. Add personal structure annotationsScientific Discourse in the Future

11. Integrated Rich MediaAlready happening but post publication not PrepublicationLab discussions, presentations of the work etc. are part of the new discourseScientific Discourse in the Future

12. Mashup with Content from Other Articles / DataDoable?Sure its happening already, but at the level of the article not the nano publicationNano implies being part of the research processScientific Discourse in the Future

13. Example of Nano Integration: The Database Viewwww.rcsb.org/pdb/explore/literature.do?structureId=1TIMBMC Bioinformatics 2010 11:220Scientific Discourse in the Future

14. I Also Want To Learn from the CorpusCardiac DiseaseLiteratureImmunology LiteratureAt this point the research article itself becomes a nano publicationShared FunctionScientific Discourse in the Future

15. A Consequence …ToolsAnnotation and new formatsUse cases and examplesBusiness rights and IPAttribution/evaluation/archivingBeyond the PDFSan Diego Jan 19-21

16. Crowd Sourcing the Electronic Printing Press(aka Workshop: Beyond the PDF)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 done

17. Wait a Minute There is More..So That Is the End Product What is the Beginning Product?We as scientists 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

18. Consider the Scientific WorkflowMaybe The Line is Somewhere Else?ScientistLaboratoryIdeaExperimentDataConclusionsPublisherPublishWe need to publish workflows

19. Maybe The Line is Somewhere Else?LaboratoryScientistIdeaExperimentInstitutionDataLab NotebookConclusionsPublisherPublishWe need to publish workflows

20. We Need to Publish WorkflowsWhat Would Drive This?Preservation of the digital recordReproducibilityThe need for the library to reinvent itselfDigital chaos in the long tail

21. The Truth About the Scientific eLaboratoryI have ?? mail folders!The intellectual memory of my laboratory is in those foldersThis is an unhealthy hub and spoke mentalityDrivers of Change

22. The Truth About the Scientific eLaboratoryI 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 tooComputational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 4(7): e1000136

23. Many Great Tools Out ThereTavernaWe Need Scientist Management Tools

24. Where I See the ProblemsThe long tail is confusedLack of interoperability between the optionsThe reward (publishing) is still removed from the available tools

25. As a scientist I want a different kind relationship with the publisher of the futureIs anyone interested?

26. AcknowledgementsBeyond the PDF WorkshopFunded by DDCF, Microsoft, NCI, Sage BionetworksThe SciVee TeamMarc Friedmann, J. Lynn Fink, Alex Gramos, Willy SuwantoThe PDB Team

27. pbourne@ucsd.eduDiscussion