1. Philip E. Bourne pbourne@ucsd.edu Professional Development Lecture 7 Understanding and Working the Publishing Process

2. Today’s Research Cycle Research [Grants] Journal Article Conference Paper Poster Session Feds Societies Publishers Reviews Blogs Community Service/Data

3. How Much Biomedical Literature? 18.8 million entries from 5000 journals (2/09)* Est. 45000 papers added each week! * Enter 1800:2100[dp] for current list 1000’s

4. Scientific Publishing is Changing More journals Journals moving to on-line only Changing publishing models eg open access, hybrids, open review Copyright is changing Journals are becoming more like databases Databases are becoming more like journals Support for other media eg JOVE PLoS Comp. Biol. 2005 1(3) e34

5. 5 NIH Public Access Policy “The research supported by the National Institutes of Health (NIH) is essential to improving human health. Public access to this research is vital – today and for generations to come.” From a letter from NIH Director Zerhouni to grantees, February 3rd, 2005

6. Open Access (Creative Commons License) 1.All published materials available on-line free to all (author pays model) 2.Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s) 3.Copyright remains with the author 6

7. The Growth of Open Access Literature 7

8. Publishing Expectations are Changing Expected to publish ever more papers Increased quantification –Impact factors –H factor –Google Scholar –ResearcherID PLoS Comp. Biol. 2008 4(12):e1000247

9. Putting It All Together The publishing process is under stress –Number of submissions is increasing –Review numbers and quality is declining –There is a growing perception of Science/Nature vs. the rest –We are increasingly fixated on numbers You Need to Work and Thrive in this Environment

10. Journal Models In-house editors – Science, Nature, PLoS Biology (est. publish 5% of submissions) Community Editors – PLoS Genetics, J. Mol. Evol. (est. publish 25% of submissions) PLoS ONE (est. publish 50% of submissions) arXiv.org (publish 100% of submissions)

11. Example Journal Organization PLoS Comp. Biol. – Paper Flow Editor in Chief Advisory Editors Deputy EICs Associate Editors Editorial Staff Reviewers Papers

12. Example Journal Organization PLoS Comp. Biol. – Paper Flow Editor in Chief Advisory Editors Deputy EICs Associate Editors Editorial Staff Reviewers Papers (1) (9) Reviews and Front Matter are Handled Differently (10) (~50) (100’s)

13. Example Journal Organization PLoS Comp. Biol. – Issues Editor in Chief Advisory Editors Deputy EICs Associate Editors Editorial Staff Reviewers Final Decision

14. Demonstration of the Journal Management Process

15. The Future - What If… What if … negative data was as easily obtainable as positive data What if … the source of learning was expanded dramatically from noisy data to include automatically captured human knowledge on a scale not previously possible What if … that knowledge included rich media What if … the value of that knowledge could be weighted according to the authority of the source 15

16. Some big “Ifs” Lets take a step back and see where we are today

17. Tomorrows Research Cycle The relationship between scientist and publisher is quite different The publisher is a warehouse for the workflow of scientific endeavor not just a repository for the end product 17

18. Tomorrows Research Cycle: Evidence Publishers hubs: –Elsevier portals –PLoS collections Open Access/open review e.g. Biology Direct NIH Roadmap requires data be accessible New Resources: –www.researchgate.netwww.researchgate.net –MetaLab (Borya Shakhnovich)

19. What If… What if … negative data was as easily obtainable as positive data What if … the source of learning was expanded dramatically from noisy data to include automatically captured human knowledge What if … that knowledge included rich media What if … the value of that knowledge could be weighted according to the authority of the source 19

20. Example: The Protein Structure Initiative The X-ray Crystallography Pipeline What if … negative data was as easily obtainable as positive data Basic Steps Target Selection Crystallomics Isolation, Expression, Purification, Crystallization Data Collection Structure Solution Structure Refinement Functional Annotation Publish Remains more of an Art than a Science http://kb.psi-structuralgenomics.org/

21. Positive and Negative Data are Required by the NIH to be deposited immediately Data are described by an ontology Perhaps some underlying principles can be learnt, particularly as the amount of data is increasing rapidly http://pepcdb.pdb.org/PepcDB/documentation/pepcDB-v9.3.jpg

22. What If… What if … negative data was as easily obtainable as positive data What if … the source of learning was expanded dramatically from noisy data to include automatically captured human knowledge What if … that knowledge included rich media What if … the value of that knowledge could be weighted according to the authority of the source 22

23. ICTP Trieste, December 10, 2007 23

24. What If… What if … negative data was as easily obtainable as positive data What if … the source of learning was expanded dramatically from noisy data to include automatically captured human knowledge What if … that knowledge included rich media What if … the value of that knowledge could be weighted according to the authority of the source 24

25. Pubcast – Video Integrated with the Full Text of the Paper 25

26. What If… What if … negative data was as easily obtainable as positive data What if … the source of learning was expanded dramatically from noisy data to include automatically captured human knowledge What if … that knowledge included rich media What if … the value of that knowledge could be weighted according to the authority of the source 26

27. First You Have to Identify the Source What if … the value of that knowledge could be weighted according to the authority of the source http://openid.nethttp://www.researcherid.com

28. How Do we Weight the Various Knowledge Sources? Peer reviewed literature Reviews (papers, grants, proceedings) Blog postings Database entries What if … the value of that knowledge could be weighted according to the authority of the source

29. How Do we Weight the Various Knowledge Sources? A token system Tokens can be authenticated by any user of that content Page ranking ?? What if … the value of that knowledge could be weighted according to the authority of the source PLoS Comp. Biol. 2008 4(12):e1000247

30. In Conclusion You will need to understand and work the publishing process Scientific publishing is changing