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On the Reproducibility of Science

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Melissa Haendel …

Melissa Haendel
March 18, 2013
Beyond the PDF2 - Amsterdam, NL

Science, Publishing, Open Access

Published in: Technology

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  • 1. On the reproducibilityof scienceMelissa HaendelBeyond the PDF220 March 2013@ontowonkahaendel@ohsu.edu
  • 2. Do we know if the infrastructure isactually broken?Slide  from  Gully  Burns  The  science  cycle  
  • 3. This is a broken data story.The  science  cycle  Image:  h6p://www.joinchangena=on.org/blog/post/roadblocks-­‐on-­‐the-­‐pathway-­‐to-­‐ci=zenship  
  • 4. Journal guidelines for methods areoften poor and space is limited“All  companies  from  which  materials  were  obtained  should  be  listed.”   -­‐  A  well-­‐known  journal  Reproducibility  is  dependent  at  a  minimum,  on  using  the  same  resources.  But…  
  • 5. Hypothesis:  AnAbodies  in  the  published  literature  are  not  uniquely  idenAfiable    An experiment in reproducibilityGather  journal  ar=cles  5  domains:  Immunology  Cell  biology  Neuroscience  Developmental  biology  General  biology  3  impact  factors:  High  Medium  Low  28  Journals  119  papers  454  an=bodies  408  commercial  an=bodies  46  non-­‐commercial  an=bodies  Iden=fying  ques=ons:  Is  the  an=body  iden=fiable  in  the  vendor  site?  Is  the  catalog  number  reported?  Is  the  source  organism  reported?  Is  the  an=body  target  iden=fiable?  
  • 6. The data shows…Approximately  half  of  anAbodies  are  not  uniquely  idenAfiable  in  119  publicaAons  Percent  idenAfiable  0%  10%  20%  30%  40%  50%  60%  Commercial  an=body   Non-­‐commerical  an=body  n=408  n=46  
  • 7. 0%  10%  20%  30%  40%  50%  60%  70%  80%  90%  100%  Immunology  Neuroscience   Dev  Bio   Cell  Bio   General  Bio  High  Medium  Low  Percent  iden=fiable  n=124   n=94  n=87  n=95  n=56  Unique  idenAficaAon  of  commercial  anAbodies  varies  across  discipline  and  impact  factor  In some domains high impact journals have worsereporting, and in others it is the opposite
  • 8. Maybe labs are just disorganized?
  • 9. Meet the Urban Lab
  • 10. Meet the Urban LabImage:  Gourami  Watcher  
  • 11. A+ organization!The  Urban  lab  anAbodies  
  • 12. Of 14 antibodies published in 45 articles,only 38% were identifiable 0%  10%  20%  30%  40%  50%  60%  70%  80%  90%  Commerical  Ab  iden=fiable  Non-­‐commercial  Ab  iden=fiable    Catalog  number  reported  Source  organism  reported  Target  uniquely  iden=fiable  Percent  idenAfiable  
  • 13. What does this tell us?
  • 14. Scientists really do put theirdata in cardboard boxes.
  • 15. Ø Promote  beJer  reporAng  guidelines  in  journals  Ø Include  reviewing  guidelines  Ø Provide  tools  to  reference  research  resources  with  unique  and  persistent  IDs/URIs    Ø Train  librarians  and  other  data  stewards  to  apply  data  standards  What are we going to do about it?