A talk of what one scientist wants of publishers delivered to UK and European publishers at the UKSG meeting.

1. Digital Research Analog Publishing – One Scientist’s View Philip E. Bourne University of California San Diego pbourne@ucsd.edu http://www.sdsc.edu/pb 1 UKSG 2011

2. My Bias.. Computational biologist (only one of many domains) Open access advocate Maintainer of an important biological data resource (PDB) UKSG 2011 2

3. My Wish… As a scientist I want an interaction with a “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 Future PLoS Comp Biol 2010 6(5): e1000787 UKSG 2011

4. What Does That Mean? The “Publisher” becomes Part of the Scientific Workflow Scientist Laboratory Idea Experiment Data Conclusions Publisher uzar.wordpress.com Maybe The Line is Somewhere Else? Publish 4 UKSG 2011

5. Maybe The Line is Somewhere Else? Laboratory Scientist ? Idea Experiment Institution? Data Lab Notebook Conclusions Publisher Publish 5 UKSG 2011

6. ? Laboratory Scientist Idea Experiment Institution? Data Lab Notebook Conclusions Publisher Publish Maybe The Line is Somewhere Else? UKSG 2011 6

7. Why Do I Want This? UKSG 2011 7

8. I Want Interoperability with the Data and Applications that Understand That Data What is needed? Standard set of apps for data exploration Standard calling interfaces Who manages the data? Publisher Author Database 3rd party User annotates view Metadata stored with the article Fetches the data and provides a Staring point for interactive enquiry UKSG 2011

9. We Are Making Progress But it is Incremental UKSG 2011

11. Add/delete queries

12. Flag interesting entries

13. Add personal structure annotationsUKSG 2011

14. Why Do I Want This?Integrated Rich Media Can Improve Comprehension Already happening but post publication not Prepublication Lab discussions, presentations of the work etc. are part of the new discourse 11 UKSG 2011

15. Mashup with Content from Other Articles / Data Sure its happening already, but… It remains too difficult It must be at the point of capture not post anything UKSG 2011

16. Proposal - The TeachU Workflow Step 1 presenter starts PowerPoint Mac PC Step 4 slides are uploaded Slides Website Step 3 presenter stops recording and initiates upload Step 5 slides and podcast are automatically synchronized Step 2 presenter starts recording on smart phone Step 6 listener plays back synchronized presentation Sync File Podcast Android iPhone Windows Phone 7

17. Why Do I Want This?Semantic Linking of Data Can Lead to New Knowledge Discovery www.rcsb.org/pdb/explore/literature.do?structureId=1TIM BMC Bioinformatics 2010 11:220 14 UKSG 2011

18. Cardiac Disease Literature Immunology Literature Why Do I Want This?Semantic Linking of Data Can Lead to New Knowledge Discovery Shared Function 15 UKSG 2011

19. Why Do I Want This? ? Laboratory Scientist Idea Experiment Institution? Data Lab Notebook Conclusions Publisher Publish UKSG 2011 16

20. Why I Want This?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 17 UKSG 2011

21. Why I Want This?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 Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 4(7): e1000136 18 UKSG 2011

22. Why I Want ThisThe Truth About the Published Record Preservation of the digital record? Reproducibility? The need for the library to reinvent itself/ institutional repositories to invent themselves? Digital chaos in the long tail? 19 UKSG 2011

23. What Will It Take to Get There? As a scientist I want an interaction with a “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 Future PLoS Comp Biol 2010 6(5): e1000787 UKSG 2011

24. Open source cohesive tools New standards Business rights and IP Attribution/evaluation/archiving A “publisher” to take the plunge Beyond the PDF 21 UKSG 2011 What Will It Take to Get There? https://sites.google.com/site/beyondthepdf/

25. Sounds Insurmountable? UKSG 2011 22

26. But Wait..There Are Many Great Tools Out There Taverna We Need Scientist Management Tools 23 UKSG 2011

27. But Wait..There Are Many Great Ideas Out There Nano publications Semantic tagging of PDFs and beyond Citation ontologies Scholarly HTML Authoring tools UKSG 2011 24

28. A Test BedSpinal Muscular Atrophy (SMA) Coalesce a set of disparate tools Engage the publishers Make some progress on a treatable disease 25 UKSG 2011

29. Acknowledgements Beyond the PDF Workshop Funded by DDCF, Microsoft, NCI, Science Commons The SciVee Team including: Marc Friedmann, J. Lynn Fink, Alex Gramos, Willy Suwanto The PDB Team including: Andreas Prlic, DimitrisDimitanopolos 26 UKSG 2011

30. pbourne@ucsd.edu Discussion 27 UKSG 2011