Helping Researchers Create Scholarly Content

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

Not by starting from scratch …

… but by adding a few missing pieces

Scholarly research is content creation

Reading is often an intermediary step in content creation

Reading is often an intermediary step in content creation Except …

Education

Health Care

Curiosity

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

Reading for content creation

Fulltext search of methods section

Fulltext search of methods section Why only Elsevier?

An alternative fulltext search

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

Content licensing can be automated …

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

How many researchers ask for permissions?

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

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

Provide table and ﬁgure data …

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

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

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

Video and other multimedia content

Is supplementary information the right format?

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

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

Why only Connotea?

7880 papers?

Unique author identiﬁers help ﬁnd research by same author

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.

Manuscript writing

Writing is collaborative

References should be shared during writing

Current writing tools are not ideal for scholarly papers

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

Remember Publicon?

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). À 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.

tributing papers should also submit via the Web. Corresponding PNAS Information for Authors authors of communicated and contributed papers will be provided 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 material.) 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-

Facilitate discussion prior to publication

Facilitate peer review

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

… more authors will be happy

http://blogs.plos.org/mfenner

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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

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Helping Researchers Create Scholarly Content

by Martin Fenner

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