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Björn Brembs 
Universität Regensburg 
http://brembs.net
Life 
changes
yesterday 
today
yesterday 
today
Institutions produce publications, data 
and software
Dysfunctional scholarly literature
• Limited access 
• No global search 
• No functional hyperlinks 
• No flexible data 
visualization 
• No submission 
standards 
• (Almost) no statistics 
• No text/data-mining 
• No effective way to sort, 
filter and discover 
• No scientific impact 
analysis 
• No networking feature 
• etc. 
…it’s like the 
web in 1995!
Scientific data in peril
Report on Integration of Data and Publications, ODE Report 2011 
http://www.alliancepermanentaccess.org/wp-content/plugins/download-monitor/download.php?id=ODE+Report+on+Integration+of+Data+and+Publications
Non-existent software archives
• Institutional email 
• Institutional webspace 
• Institutional blog 
• Library access card 
• Open access repository 
• No archiving of texts 
• No archiving of code 
• No archiving of data
Only read publications from high-ranking journals
Only publish in high-ranking journals
Is journal rank like astrology?
Introduced in 1950’s by Eugene Garfield: ISI 
A1 A2 
C12 
citations 
published 
time 
articles 
published 
year 1 year 2 year 3 
퐼퐹(푦푒푎푟 3) = +
Introduced in 1950’s by Eugene Garfield: ISI 
40 60 
100 
citations 
published 
time 
articles 
published 
year 1 year 2 year 3 
퐼퐹(푦푒푎푟 3) 
= =1 
+
Journal X IF 2013= 
All citations from TR indexed journals in 2013 to papers in journal X 
Number of citable articles published in journal X in 20011/12 
€30,000-130,000/year subscription rates 
Covers ~11,500 journals (Scopus covers ~16,500)
• Negotiable 
• Irreproducible 
• Mathematically 
unsound
• PLoS Medicine, IF 2-11 (8.4) 
(The PLoS Medicine Editors (2006) The Impact Factor Game. PLoS Med 3(6): e291. 
http://www.plosmedicine.org/article/info:doi/10.1371%2Fjournal.pmed.0030291) 
• Current Biology IF from 7 to 11 in 
2003 
– Bought by Cell Press (Elsevier) in 2001…
• Rockefeller University Press bought their data from Thomson Reuters 
• Up to 19% deviation from published records 
• Second dataset still not correct 
Rossner M, van Epps H, Hill E (2007): Show me the data. The Journal of Cell 
Biology, Vol. 179, No. 6, 1091-1092 http://jcb.rupress.org/cgi/content/full/179/6/1091
• Left-skewed distributions 
• Weak correlation of individual 
article citation rate with journal IF 
Seglen PO (1997): Why the impact factor of journals should not be used for evaluating research. BMJ 1997;314(7079):497http://www.bmj.com/cgi/content/full/314/7079/497
The weakening relationship between the Impact Factor and papers' citations in the digital age (2012): George A. Lozano, Vincent Lariviere, Yves Gingras arXiv:1205.4328
Brembs, B., Button, K., & Munafò, M. (2013). Deep impact: unintended consequences of journal rank. Frontiers in Human Neuroscience, 7. doi:10.3389/fnhum.2013.00291
Munafò, M., Stothart, G., & Flint, J. (2009). Bias in genetic association studies and impact factor Molecular 
Psychiatry, 14 (2), 119-120 DOI: 10.1038/mp.2008.77
Brown, E. N., & Ramaswamy, S. 
(2007). Quality of protein crystal 
structures. Acta Crystallographica 
Section D Biological Crystallography, 
63(9), 941–950. 
doi:10.1107/S0907444907033847
Fang et al. (2012): Misconduct accounts for the majority of retracted scientific publications. PNAS 109 no. 42 17028-17033
Data from: Fang, F., & Casadevall, A. (2011). RETRACTED SCIENCE AND THE RETRACTION INDEX Infection and Immunity DOI: 10.1128/IAI.05661-11
Journal rank is a figment of our imagination.
“High-Impact” journals attract the 
most unreliable research
“Do you trust scientists?”
“Who can you trust these days?”
“Politicians? Financial experts? Realtors?“
Costs [thousand US$/article] 
Legacy SciELO 
(Sources: Van Noorden, R. (2013). Open access: The true cost of science publishing. Nature 495, 426–9; Packer, A. L. (2010). The SciELO Open 
Access: A Gold Way from the South. Can. J. High. Educ. 39, 111–126)
Costs [thousand US$/article] 
Legacy SciELO 
(Sources: Van Noorden, R. (2013). Open access: The true cost of science publishing. Nature 495, 426–9; 
Packer, A. L. (2010). The SciELO Open Access: A Gold Way from the South. Can. J. High. Educ. 39, 111–126)
The disaster that is our digital 
infrastructure
Science, tear down this paywall!
Potential for innovation: 9.8b p.a. 
Costs [thousand US$/article] 
Legacy SciELO 
(Sources: Van Noorden, R. (2013). Open access: The true cost of science publishing. Nature 495, 426–9; 
Packer, A. L. (2010). The SciELO Open Access: A Gold Way from the South. Can. J. High. Educ. 39, 111–126)
• Sustainable, global search and access for all 
literature, code and data 
• Intelligent sort, filter and discover 
functionalities 
• Scientific, evidence-based reputation system 
• Authoring tools for collaborative writing and 
single-click submission 
• Orders of magnitude cheaper: US$90/paper 
(e.g. SciELO) vs. US$5,000/paper (subscription)
One person is not an 
institutional infrastructure
Software to control the experiment and save the data
Software to analyze and visualize the data
Same type of experiments → same 
script 
Default: → same categories 
→ same tags 
→ same authors 
→ same links 
→ same description 
→ One complete article, in one click. 
Update the figure: 
Higher sample size directly published 
while analysed, your boss may see the 
results before you do! (or you may see 
the results of your student before they 
do) 
Possibility to make it public and citable 
in one click or directly in the R code.
http://dx.doi.org/10.6084/m9.figshare.97792
The desolate state of our scientific infrastructure
The desolate state of our scientific infrastructure
The desolate state of our scientific infrastructure
The desolate state of our scientific infrastructure
The desolate state of our scientific infrastructure
The desolate state of our scientific infrastructure

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The desolate state of our scientific infrastructure

  • 1. Björn Brembs Universität Regensburg http://brembs.net
  • 7. • Limited access • No global search • No functional hyperlinks • No flexible data visualization • No submission standards • (Almost) no statistics • No text/data-mining • No effective way to sort, filter and discover • No scientific impact analysis • No networking feature • etc. …it’s like the web in 1995!
  • 9. Report on Integration of Data and Publications, ODE Report 2011 http://www.alliancepermanentaccess.org/wp-content/plugins/download-monitor/download.php?id=ODE+Report+on+Integration+of+Data+and+Publications
  • 10.
  • 11.
  • 12.
  • 13.
  • 15.
  • 16.
  • 17. • Institutional email • Institutional webspace • Institutional blog • Library access card • Open access repository • No archiving of texts • No archiving of code • No archiving of data
  • 18.
  • 19. Only read publications from high-ranking journals
  • 20. Only publish in high-ranking journals
  • 21. Is journal rank like astrology?
  • 22. Introduced in 1950’s by Eugene Garfield: ISI A1 A2 C12 citations published time articles published year 1 year 2 year 3 퐼퐹(푦푒푎푟 3) = +
  • 23. Introduced in 1950’s by Eugene Garfield: ISI 40 60 100 citations published time articles published year 1 year 2 year 3 퐼퐹(푦푒푎푟 3) = =1 +
  • 24. Journal X IF 2013= All citations from TR indexed journals in 2013 to papers in journal X Number of citable articles published in journal X in 20011/12 €30,000-130,000/year subscription rates Covers ~11,500 journals (Scopus covers ~16,500)
  • 25. • Negotiable • Irreproducible • Mathematically unsound
  • 26. • PLoS Medicine, IF 2-11 (8.4) (The PLoS Medicine Editors (2006) The Impact Factor Game. PLoS Med 3(6): e291. http://www.plosmedicine.org/article/info:doi/10.1371%2Fjournal.pmed.0030291) • Current Biology IF from 7 to 11 in 2003 – Bought by Cell Press (Elsevier) in 2001…
  • 27.
  • 28.
  • 29.
  • 30.
  • 31.
  • 32. • Rockefeller University Press bought their data from Thomson Reuters • Up to 19% deviation from published records • Second dataset still not correct Rossner M, van Epps H, Hill E (2007): Show me the data. The Journal of Cell Biology, Vol. 179, No. 6, 1091-1092 http://jcb.rupress.org/cgi/content/full/179/6/1091
  • 33. • Left-skewed distributions • Weak correlation of individual article citation rate with journal IF Seglen PO (1997): Why the impact factor of journals should not be used for evaluating research. BMJ 1997;314(7079):497http://www.bmj.com/cgi/content/full/314/7079/497
  • 34. The weakening relationship between the Impact Factor and papers' citations in the digital age (2012): George A. Lozano, Vincent Lariviere, Yves Gingras arXiv:1205.4328
  • 35. Brembs, B., Button, K., & Munafò, M. (2013). Deep impact: unintended consequences of journal rank. Frontiers in Human Neuroscience, 7. doi:10.3389/fnhum.2013.00291
  • 36. Munafò, M., Stothart, G., & Flint, J. (2009). Bias in genetic association studies and impact factor Molecular Psychiatry, 14 (2), 119-120 DOI: 10.1038/mp.2008.77
  • 37. Brown, E. N., & Ramaswamy, S. (2007). Quality of protein crystal structures. Acta Crystallographica Section D Biological Crystallography, 63(9), 941–950. doi:10.1107/S0907444907033847
  • 38. Fang et al. (2012): Misconduct accounts for the majority of retracted scientific publications. PNAS 109 no. 42 17028-17033
  • 39. Data from: Fang, F., & Casadevall, A. (2011). RETRACTED SCIENCE AND THE RETRACTION INDEX Infection and Immunity DOI: 10.1128/IAI.05661-11
  • 40. Journal rank is a figment of our imagination.
  • 41. “High-Impact” journals attract the most unreliable research
  • 42.
  • 43. “Do you trust scientists?”
  • 44. “Who can you trust these days?”
  • 46. Costs [thousand US$/article] Legacy SciELO (Sources: Van Noorden, R. (2013). Open access: The true cost of science publishing. Nature 495, 426–9; Packer, A. L. (2010). The SciELO Open Access: A Gold Way from the South. Can. J. High. Educ. 39, 111–126)
  • 47. Costs [thousand US$/article] Legacy SciELO (Sources: Van Noorden, R. (2013). Open access: The true cost of science publishing. Nature 495, 426–9; Packer, A. L. (2010). The SciELO Open Access: A Gold Way from the South. Can. J. High. Educ. 39, 111–126)
  • 48.
  • 49.
  • 50.
  • 51. The disaster that is our digital infrastructure
  • 52. Science, tear down this paywall!
  • 53.
  • 54. Potential for innovation: 9.8b p.a. Costs [thousand US$/article] Legacy SciELO (Sources: Van Noorden, R. (2013). Open access: The true cost of science publishing. Nature 495, 426–9; Packer, A. L. (2010). The SciELO Open Access: A Gold Way from the South. Can. J. High. Educ. 39, 111–126)
  • 55.
  • 56.
  • 57.
  • 58. • Sustainable, global search and access for all literature, code and data • Intelligent sort, filter and discover functionalities • Scientific, evidence-based reputation system • Authoring tools for collaborative writing and single-click submission • Orders of magnitude cheaper: US$90/paper (e.g. SciELO) vs. US$5,000/paper (subscription)
  • 59. One person is not an institutional infrastructure
  • 60.
  • 61. Software to control the experiment and save the data
  • 62. Software to analyze and visualize the data
  • 63.
  • 64.
  • 65.
  • 66.
  • 67.
  • 68.
  • 69.
  • 70.
  • 71.
  • 72.
  • 73.
  • 74. Same type of experiments → same script Default: → same categories → same tags → same authors → same links → same description → One complete article, in one click. Update the figure: Higher sample size directly published while analysed, your boss may see the results before you do! (or you may see the results of your student before they do) Possibility to make it public and citable in one click or directly in the R code.