1. Helping Researchers Create
Scholarly Content
Martin Fenner
Department of Hematology,
Hemostaseology, Oncology
and Stem Cell Transplantation

2. Not by starting
from scratch …

3. … but by adding a few
missing pieces

4. Scholarly research is
content creation

5. Reading is often an intermediary
step in content creation

6. Reading is often an intermediary
step in content creation
Except …

7. Education

8. Health Care

9. Curiosity

10. These uses are often covered by
secondary literature
Review journals Textbooks Science blogs

11. Reading for content creation

12. Fulltext search of methods
section

13. Fulltext search of methods
section
Why only
Elsevier?

14. An alternative fulltext search

17. Table 3. Olaparib-Related Adverse Events Found in at Least 5% of the Safety Population, According to Olaparib Dose.*
Adverse Event
<100 mg, Daily
or Twice Daily,
2 of Every 3 Wk
(N = 18)
100 mg,
Twice Daily,
2 of Every 3 Wk
(N = 4)
100 mg,
Twice Daily,
Continuously
(N = 5)
200 mg
Twice Daily,
Continuously
(N = 20)
400 mg
Twice Daily,
Continuously
(N = 8)
600 mg
Twice Daily,
Continuously
(N = 5)
Total
(N = 60)
Figures and
tables
number of patients/total number (percent)
Anemia
Grade 1−2 1 (6) 0 0 0 0 1 (20) 2 (3)
Grade 3−4 0 0 0 1 (5) 0 0 1 (2)
Lymphopenia
Grade 1−2 0 0 0 0 0 0 0
Grade 3−4 0 0 0 2 (10) 1 (12) 0 3 (5)
Diarrhea
Grade 1−2 0 0 0 2 (10) 1 (12) 0 3 (5)
Grade 3−4 0 0 0 0 0 0 0
Dyspepsia
Grade 1−2 0 0 0 1 (5) 1 (12) 2 (40) 4 (7)
Grade 3−4 0 0 0 0 0 0 0
Nausea
Grade 1−2 6 (33) 1 (25) 0 7 (35) 0 3 (60) 17 (28)
Grade 3−4 0 0 0 0 1 (12) 1 (20) 2 (3)
Stomatitis
Grade 1−2 0 0 0 3 (15) 0 0 3 (5)
Grade 3−4 0 0 0 0 0 0 0
Vomiting
Grade 1−2 2 (11) 1 (25) 0 5 (25) 0 3 (60) 11 (18)
Grade 3−4 0 0 0 0 1 (12) 0 1 (2)
Anorexia
Grade 1−2 3 (17) 0 0 2 (10) 0 2 (40) 7 (12)
Grade 3−4 0 0 0 0 0 0 0
Dysgeusia
Grade 1−2 0 2 (50) 0 2 (10) 1 (12) 3 (60) 8 (13)
Grade 3−4 0 0 0 0 0 0 0
Fatigue
Grade 1−2 3 (17) 0 1 (20) 4 (20) 5 (62) 4 (80) 17 (28)
Grade 3−4 0 0 0 1 (5) 0 0 1 (2)
Dizziness
Grade 1−2 0 0 0 1 (5) 0 1 (20) 2 (3)
Grade 3−4 0 0 0 0 1 (12) 0 1 (2)
* The listed adverse events were classified as being possibly, probably, or definitely related to olaparib in the safety population. No grade 5
Fong et al. Inhibition of poly(ADP-ribose) polymerase in tumors from
BRCA mutation carriers. N Engl J Med 2009;361:123-34

18. Content licensing can be
automated …

19. Section 107 contains a list of the various purposes for
which the reproduction of a particular work may be
considered fair, such as criticism, comment, news
reporting, teaching, scholarship, and research.
Copyright protects the particular way an author has
expressed himself. It does not extend to any ideas,
systems, or factual information conveyed in the work.
U.S. Copyright Law
… but is confusing and too
restrictive for many researchers

20. How many researchers ask for
permissions?

21. CC license for tables and figures
better solution for reuse
Attribution
Share Alike
No derivative works
Non-commercial

22. Table 2: Univariate associations between cancer and other patient characteristics
BMC Medicine
Characteristic Cancer patients Non-cancer patients Odds ratio P
% or mean (sd) n % or mean (sd) n
Research article
Number of subjects
TZD therapy 32.5%
126
126 Association between0.09
25.3%
877
877 1.42 cancer prevalence a
Pioglitazone
Rosiglitazone
13.5%
19.1%
126
126
thiazolidinediones: results from the Verm
13.6%
11.9%
877
877
0.99
1.75
0.98
0.03
Sulfonylurea therapy
Biguanide therapy
34.9%
39.7%
126
126
System 877
38.2%
40.0% 877
0.87
0.99
0.48
0.94
Nateglinide therapy 0.8% 126 Maria E Ramos-Nino*†10.62
0.5% 877 1.75 , Charles D MacLean†2
Men 42.1% 126 46.1% 877 0.85 0.40
Age, years 69.1 (10.2) 126 64.2 (12.1) 877 1.04 <0.001
White ethnicity 97.6% 125 Address:
97.3% 1University of Vermont, Department of Pathology, Vermont 05405, USA, 2Univ
875 1.15 0.83
A1C, mean % 7.0 (1.3) 126 7.2 (1.3) USA and871
05401, 3University of Vermont, College of Nursing and Health Sciences, Burlin
0.88 0.12
Insulin therapy 15.9% 126 18.8% Maria E Ramos-Nino*0.81
Email: 877 0.43
- Maria.Ramos@uvm.edu; Charles D MacLean - Charles.M
Body mass index, kg/m2 32.7 (6.8) 125 34.0 (7.5) Littenberg - Benjamin.Littenberg@vtmednet.org
Benjamin 865 0.97 0.06
Alcohol drinking 25.4% 126 27.6%
* Corresponding876 0.89
author †Equal contributors 0.60
Cigarette smoking 11.1% 126 17.8% 876 0.58 0.06
Median annual income, $ 15000–29999 114 15000–29999 813 1.02 0.75
Duration of diabetes, years 10.2 (9.7) 124 10.2 (10.4) 829 1.00 0.98
High comorbidity 71.4% 126 46.2% 877 2.91 <0.001
Published: 21 June 2007 Received: 4 No
Number of prescription medications 7.3 (4.3) 126 6.6 (3.7) 877 1.05 0.05
Accepted: 21 Ju
Number of anti-diabetic drugs 1.2 (1.0) 126 BMC Medicine 2007, 5:17 doi:10.1186/1741-7015-5-17
1.2(0.9) 877 1.01 0.92
Physical functional status 40.9 (13.7) 125 42.3 (12.7) is available from: http://www.biomedcentral.com/1741-7015/5/17
This article 871 0.99 0.27
Mental functional status 50.5 (10.5) 126 49.4 (10.9) 875 1.01 0.30
© 2007 Ramos-Nino et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribu
sd, standard deviation; n, number of patients for which data were available; TZD, thiazolidinedione. permits unrestricted use, distribution, and reproduction in any medium, provided the o
which
Tables from papers don‘t Abstract
Background: Peroxisome proliferator-activated receptors (P
drug targets for diabetes. Drugs that activate PPAR , such as
display well in presentations
widely used for treatment of Type 2 diabetes mellitus. PPAR
neoplastic role in several in vitro models, although conflicting
models. The effects of TZDs on cancer risk in humans needs
prescribed for long periods of time in patients with diabetes.
Methods: A total of 1003 subjects in community practice set

23. Provide table and figure data …

24. Anorexia Nausea Vomiting Dysgeusia
18% 13%
28% 28%
… and visualize them as needed

25. www.sciencemag.org/cgi/content/full/328/5979/710/DC1
Supporting Online Material for
A Draft Sequence of the Neandertal Genome
Richard E. Green,* Johannes Krause, Adrian W. Briggs, Tomislav Maricic,
Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai,
Markus Hsi-Yang Fritz, Nancy F. Hansen, Eric Y. Durand, Anna-Sapfo Malaspinas,
Jeffrey D. Jensen, Tomas Marques-Bonet, Can Alkan, Kay Prüfer, Matthias Meyer,
Hernán A. Burbano, Jeffrey M. Good, Rigo Schultz, Ayinuer Aximu-Petri, Anne Butthof,
Barbara Höber, Barbara Höffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum,
Eric S. Lander, Carsten Russ, Nathaniel Novod, Jason Affourtit, Michael Egholm,
Christine Verna, Pavao Rudan, Dejana Brajkovic, !eljko Kucan, Ivan Gu"ic,
Vladimir B. Doronichev, Liubov V. Golovanova, Carles Lalueza-Fox,
Marco de la Rasilla, Javier Fortea, Antonio Rosas, Ralf W. Schmitz, Philip L. F. Johnson,
Evan E. Eichler, Daniel Falush, Ewan Birney, James C. Mullikin, Montgomery Slatkin,
Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich,* Svante Pääbo*
*To whom correspondence should be addressed. E-mail: green@eva.mpg.de (R.E.G.);
reich@genetics.med.harvard.edu (D.R.); paabo@eva.mpg.de (S.P.)
Published 7 May 2010, Science 328, 710 (2010)
DOI: 10.1126/science.1188021
This PDF file includes:
Materials and Methods
SOM Text
Access to
Figs. S1 to S51
Tables S1 to S58
References research data

26. www.sciencemag.org/cgi/content/full/328/5979/710/DC1
Supporting Online Material for
A Draft Sequence of the Neandertal Genome
Richard E. Green,* Johannes Krause, Adrian W. Briggs, Tomislav Maricic,
Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai,
Markus Hsi-Yang Fritz, Nancy F. Hansen, Eric Y. Durand, Anna-Sapfo Malaspinas,
Jeffrey D. Jensen, Tomas Marques-Bonet, Can Alkan, Kay Prüfer, Matthias Meyer,
Hernán A. Burbano, Jeffrey M. Good, Rigo Schultz, Ayinuer Aximu-Petri, Anne Butthof,
Barbara Höber, Barbara Höffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum,
Eric S. Lander, Carsten Russ, Nathaniel Novod, Jason Affourtit, Michael Egholm,
Christine Verna, Pavao Rudan, Dejana Brajkovic, !eljko Kucan, Ivan Gu"ic,
Vladimir B. Doronichev, Liubov V. Golovanova, Carles Lalueza-Fox,
Marco de la Rasilla, Javier Fortea, Antonio Rosas, Ralf W. Schmitz, Philip L. F. Johnson,
Evan E. Eichler, Daniel Falush, Ewan Birney, James C. Mullikin, Montgomery Slatkin,
Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich,* Svante Pääbo*
*To whom correspondence should be addressed. E-mail: green@eva.mpg.de (R.E.G.);
reich@genetics.med.harvard.edu (D.R.); paabo@eva.mpg.de (S.P.)
Published 7 May 2010, Science 328, 710 (2010)
DOI: 10.1126/science.1188021
PDF with
This PDF file includes:
Materials and Methods
SOM Text
Access to
175 pages?
Figs. S1 to S51
Tables S1 to S58
References research data

27. Video and
other multimedia content

28. Is supplementary information
the right format?

29. Or shouldn‘t research data
rather be stored in a repository?

30. DataCite
Or shouldn‘t research data
rather be stored in a repository?

32. Why only
Connotea?

34. 7880 papers?

35. Unique author identifiers help
find research by same author

36. Encourage electronic letters
RESEARCH
Adequacy of authors’ replies to criticism raised in electronic
letters to the editor: cohort study
Peter C Gøtzsche, director,1 Tony Delamothe, editor,2 Fiona Godlee, editor,2 Andreas Lundh, PhD student1
1
Nordic Cochrane Centre, ABSTRACT publication of the research report. Guidelines for edi-
Rigshospitalet and University of Objective To investigate whether substantive criticism in tors are also sparse.3-5
Copenhagen, Dept 3343,
Blegdamsvej 9, DK-2100 electronic letters to the editor, defined as a problem that We have noticed that when the criticism is serious,
Copenhagen, Denmark could invalidate the research or reduce its reliability, is such as suggesting a fatal flaw, authors sometimes
2
BMJ, BMA House, Tavistock adequately addressed by the authors. avoid addressing it in their reply and instead discuss
Square, London
Design Cohort study. minor issues, or they misrepresent their research or
Correspondence to: P C Gøtzsche
pcg@cochrane.dk SettingBMJ between October 2005 and September 2007. the criticism. It is not known how common evasive
Inclusion criteria Research papers generating substantive replies are or how often editors assess whether authors
Cite this as: BMJ 2010;341:c3926 have addressed criticisms appropriately and honestly
doi:10.1136/bmj.c3926
criticism in the rapid responses section on bmj.com.
Main outcome measures Severity of criticism (minor, and ask for changes when this is not the case. We inves-
moderate, or major) as judged by two editors and extent tigated whether authors responded adequately to sub-
to which the criticism was addressed by authors (fully, stantive criticism after publication and whether the
partly, or not) as judged by two editors and the critics. critics and the editors were satisfied with the replies.
Results A substantive criticism was raised against 105 of
350 (30%, 95% confidence interval 25% to 35%) METHODS
included research papers, and of these the authors had Our objectives were to study whether substantive criti-
responded to 47 (45%, 35% to 54%). The severity of the cism in letters to the editor was adequately addressed
criticism was the same in those papers as in the 58 by authors, and whether the replies were less adequate
without author replies (mean score 2.2 in both groups, when the criticism was serious. We defined substantive
P=0.72). For the 47 criticisms with replies, there was no criticism as a problem that could invalidate the
relation between the severity of the criticism and the research or reduce its reliability.

37. Manuscript writing

38. Writing is collaborative

39. References should be shared
during writing

40. Current writing tools are not
ideal for scholarly papers

41. Why fonts, Why margins,
font sizes? line heights?
Why no
document
structure?

42. Remember Publicon?

43. Facilitate reference creation
Bollen, J., Van de Sompel, H., Hagberg, A. & Chute, R. A
principal component analysis of 39 scientific impact measures.
PloS ONE 4, e6022+ (2009).
J. Bollen, H. Van de Sompel, A. Hagberg, R. Chute, PloS ONE 4,
e6022+ (2009).
Bollen Johan, Sompel Herbert, Hagberg Aric, Chute Ryan. A
principal component analysis of 39 scientific impact measures. PloS
ONE. 2009;4:e6022+.
J. Bollen, et al. (2009). `A principal component analysis of 39
scientific impact measures.'. PloS ONE 4(6):e6022+.
This important paper provides evidence that scientific impact can
not be adequately measured by any single indicator.

44. tributing papers should also submit via the Web. Corresponding
PNAS Information for Authors
authors of communicated and contributed papers will be pro-
vided a URL for file submission after the member has initiated
the process by providing his or her endorsement and copies of
REVISED November also be submitted online.
the reviews received. SI must 2009
Digital Figures. Only TIFF, EPS, and high-resolution PDF for
Mac or PC are allowedSCOPE that will appear in the print
PURPOSE AND for figures
journal. (See Supporting Information below for online-only ma-
terial.) Color images must theinNational Academy of Sciences U
The Proceedings of be RGB (red, green, blue) mode.
(PNAS) publishes research reports, commentaries, perspecti -
erably 1 column width (8.7 cm). Figures wider with 1 column
and colloquium papers. In accordance than the guiding prin
should be between 10.5 and 18.0 cm wide. Numbers, letters,
ples established be no smallerEllery Hale in 1914,and no publis
and symbols should
by George than 6 points (2 mm) PNAS
larger than 12 points (6 mm) after reduction and must be con- foreign
brief first announcements of Academy members’ and
sociates’ (hereafter referred to as members) more important c
sistent. Composite figures must be preassembled. Figures must
be submitted as separate files, notof work thatmanuscriptto a membe
tributions to research and embedded in appears text.
See www.pnas.org/site/misc/digitalart.pdf oris a general science jour
be of particular importance. PNAS contact pnas_spe-
cialist@dartmouthjournals.com.
Facilitate figure creation
with a broad scientific audience. All papers should be intellig
Tables. Each table should have a brief title, be on a separate
page,this audience.
to and be double-spaced. Tables must be submitted as sepa-

45. Facilitate discussion prior to
publication

46. Facilitate peer review

47. Facilitate peer review

48. By connecting the missing
pieces using open standards …
ORCID CSL …
…
DataCite DOI
Creative
NLM DTD Commons

49. … more
authors will
be happy

51. http://blogs.plos.org/mfenner

52. Credits
http://www.flickr.com/photos/dhammza/91435718/
http://www.flickr.com/photos/gb_fotos/250133728/
http://www.flickr.com/photos/historyinphotos/2473688448/
http://www.flickr.com/photos/whatsthatpicture/4872953249/
http://www.flickr.com/photos/nucho/3340151745/
http://www.flickr.com/photos/olivander/999389454/
http://www.flickr.com/photos/photonquantique/1751839932/
http://www.nasaimages.org/luna/servlet/detail/
nasaNAS~5~5~24355~127738:Original-Members-of-GIRD
http://www.flickr.com/photos/kkanouse/2827557438/

53. http://www.flickr.com/photos/horiavarlan/4273913228/
http://www.flickr.com/photos/johnmcnab/4153178921/
http://www.flickr.com/photos/bishi/2852863455/
http://www.flickr.com/photos/michaeljy/3682379207/
http://www.flickr.com/photos/the-g-uk/3709881283/
http://www.flickr.com/photos/iisg/4699046845/
http://www.flickr.com/photos/flyzipper/342012313/
http://www.flickr.com/photos/kwerfeldein/3037976252/
http://www.flickr.com/photos/msiebuhr/987572658/
http://www.flickr.com/photos/wwworks/4759535950/
http://www.flickr.com/photos/redstamp/4222841910/

54. http://dx.doi.org/10.1056/NEJM194806032382301
http://dx.doi.org/10.1038/nature09442
http://dx.doi.org/10.1371/journal.pone.0006022
http://dx.doi.org/10.1056/NEJMoa0900212
http://dx.doi.org/10.1186/1741-7015-5-17
http://www.jneurosci.org/cgi/reprint/30/32/10599
http://dx.doi.org/10.3791/2059

55. This presentation can be
copied and distributed
provided that proper
credit is given.