Biocuration and scholarly communication cycle:    roles and opportunities for biocurators                  Panel Discussio...
Take-home / talking points / provocation• The needs and motivations of authors and  „users‟ of the literature differ• Some...
What authors want                      Kudos - “good                        journal”        Publication          credit   ...
What readers/users want                          Thorough         Reusability                          Complete           ...
Growth in the cost of traditional publishing
PLOS BiologyOctober, 2003            PLOS Medicine                         October, 2004     PLOS Community Journals     J...
Growth of PLOS journals and of Open Access  30,000                                                                        ...
PLOS ONE‟s Key Innovation: the editorialprocess  Editorial criteria    • Scientifically rigorous    • Ethical    • Properl...
Two types of study generating dataType 1: the structured data is the output• e.g. DNA sequence, protein structure, clinica...
Provocation: the solutions we‟re all proposingdon‟t deal with the main problems• Adding more steps and checks to publicati...
Do some   science Write adescription              Store some of the              data somewhere…
Do some science              Integrated collection              of methods, results,              data, metadata          ...
Where should data go?• Curated, subject-specific, open  access, long-term databases  (GenBank, ArrayExpress)• General non-...
Steps towards better data handling - 1What to do with „homeless‟ data?Partnership with Dryad (www.datadryad.org)• Unstruct...
Steps towards better data handling - 2Planning in hand for „data papers‟• Describes reusable dataset to support reuse• Pub...
Publish your BigReproducibility                    PaperInitiative                              Send it to Science        ...
PLOS + partnerships:
Take-home / talking points / provocation• The needs and motivations of authors and  „users‟ of the literature differ• Some...
Open Access       tbloom@plos.org                   19
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Society for biocuration panel discussion, April 2013

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Society for biocuration panel discussion, April 2013

  1. 1. Biocuration and scholarly communication cycle: roles and opportunities for biocurators Panel Discussion Theo Bloom, Editorial Director for Biology, PLOS Hinxton, April 2013
  2. 2. Take-home / talking points / provocation• The needs and motivations of authors and „users‟ of the literature differ• Some studies output structured data well• Many/most studies don‟t, and here‟s our biggest problem• We need to move towards universal solutions and away from bespoke ones• In the meantime there is a lot of help needed 2
  3. 3. What authors want Kudos - “good journal” Publication credit First / fast Easy Compliant 3
  4. 4. What readers/users want Thorough Reusability Complete Replicable Compliant 4
  5. 5. Growth in the cost of traditional publishing
  6. 6. PLOS BiologyOctober, 2003 PLOS Medicine October, 2004 PLOS Community Journals June-September, 2005 October, 2007 PLOS ONE December, 2006 6
  7. 7. Growth of PLOS journals and of Open Access 30,000 120,000 PLOS 25,000 100,000 Open access total (secondary axis) 20,000 80,000 15,000 60,000 10,000 40,000 5,000 20,000 0 0 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
  8. 8. PLOS ONE‟s Key Innovation: the editorialprocess Editorial criteria • Scientifically rigorous • Ethical • Properly reported • Conclusions supported by the data Editors and reviewers do not ask • How important is the work? • Which is the relevant audience? Everything that deserves to be published, will be published 8
  9. 9. Two types of study generating dataType 1: the structured data is the output• e.g. DNA sequence, protein structure, clinical trial results• Often large-scale / high-throughput• Curators and databases support these really well, even small-scale studiesType 2: the “paper” is the output• No structured database exists/ no widespread agreement on standards 9
  10. 10. Provocation: the solutions we‟re all proposingdon‟t deal with the main problems• Adding more steps and checks to publication makes it slow (unpopular with authors)• Assuming an expert editor handling each article makes it slow and expensive• Some authors are moving towards preprints, blog-style publications, and definitely away from traditional journals (e.g. PLOS ONE)• We need to fix the problems at the time the studies are done 10
  11. 11. Do some science Write adescription Store some of the data somewhere…
  12. 12. Do some science Integrated collection of methods, results, data, metadata Write a narrative Store all of the description that is data somewhere inextricably linked to the data and methods useful and link to publication
  13. 13. Where should data go?• Curated, subject-specific, open access, long-term databases (GenBank, ArrayExpress)• General non-specific repositories: Dryad, FigShare, Institutional (bigger is better? Can we have a „kite-marked‟ list?)• Supplementary files with the article (heterogeneous, poorly formatted, hard to collate/mine)• NOT: the author‟s website or file drawer 13
  14. 14. Steps towards better data handling - 1What to do with „homeless‟ data?Partnership with Dryad (www.datadryad.org)• Unstructured data „packages‟ associated with published articles• Freely available - CC0• A unique identifier (DOI) for each package• Statistics for access• Seamless tying together of article and dataPartnership with figshare (www.figshare.org)• figshare widget displays Supporting Information files directly in the article• search, magnify, download singly or as a package
  15. 15. Steps towards better data handling - 2Planning in hand for „data papers‟• Describes reusable dataset to support reuse• Publishes associated metadata • Structured data cross-referenced to its “natural home” (e.g., protein structures to PDB) • Unstructured data in PLOS Dataverse instance• Ensures valuable data actionable for reuse • actionable formats • curated to reasonable standard • accessible in a recognized, stable repository• Inherently reusable data • Valid experimental / observational design • Good quality control, ethical experiments • Data perceived to have “standalone” value
  16. 16. Publish your BigReproducibility PaperInitiative Send it to Science Exchange to reproduce Independent scientists attempt to reproduce the study Success! Science Failure! Authors Exchange issues a think long and hard certificate of about what they‟ve validation, which is done posted on the paper Reproduction is Hopefully publish in published in PLOS PLOS ONE although ONE and data is this is not required stored at figshare 16
  17. 17. PLOS + partnerships:
  18. 18. Take-home / talking points / provocation• The needs and motivations of authors and „users‟ of the literature differ• Some studies output structured data well• Many/most studies don‟t, and here‟s our biggest problem• We need to move towards universal solutions and away from bespoke ones• In the meantime there is a lot of help needed 18
  19. 19. Open Access tbloom@plos.org 19

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