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Philip E. Bourne
Professional DevelopmentLecture 7
Understanding and Working the Publishing Process
Today’s Research Cycle
Research[Grants]
JournalArticle
ConferencePaper
PosterSession
Feds
Societies
Publishers
Reviews
BlogsCommunity Service/Data
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
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
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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
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
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The Growth of Open Access Literature
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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
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
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)
Example Journal Organization PLoS Comp. Biol. – Paper Flow
Editor in Chief
Advisory Editors
Deputy EICs
Associate Editors
Editorial Staff
Reviewers
Papers
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)
Example Journal Organization PLoS Comp. Biol. – Issues
Editor in Chief
Advisory Editors
Deputy EICs
Associate Editors
Editorial Staff
Reviewers
Final Decision
Demonstration of the Journal Management Process
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
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Some big “Ifs”
Lets take a step back and see where we are today
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
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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.net– MetaLab (Borya Shakhnovich)
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
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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
DataCollection
StructureSolution
StructureRefinement
Functional Annotation Publish
Remains more of an Art than a Science
http://kb.psi-structuralgenomics.org/
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
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
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ICTP Trieste, December 10, 2007 23
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
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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
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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
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
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
In Conclusion
• You will need to understand and work the publishing process
• Scientific publishing is changing
