Trends in Scientific, Technical and - PowerPoint Presentation

Slide1

Trends in Scientific, Technical and Medical Publishing

Associação Brasileira de Editores Científicos VIII Workshop de Editoração Científica 10 a 13 Novembro 2014Campos do Jordão/SP

12/11/2014

Ganesha Associates

1Slide2

CV

BSc Physics 1971, PhD Neuroscience 1976, post doc Epidemiology 1975-1979Visiting Researcher, UFPe 1978-79, 1984Editor, Publisher, Director at Elsevier Science, 1979 – 2005Pubmed systems expert, NCBI, NIH 2006-2007STM business analyst, Outsell Inc, 2009-2011Visiting Professor UFPe, 2006-2008, 2012-2014Independent consultant Ganesha Associates 2006-2014

Consultant, European Bioinformatics Institute ELIXIR impact project 2015

12/11/2014

Ganesha Associates

2Slide3

Preparation

Journal Selection

Writing

Submission

Peer

Review

Publication

Success

determining

likelihood of acceptance

citation management

navigating

a submission system in

a second

language

writing

an

outline

comparing journals

assessing relevance to research topic

understanding comments

long decision timelines

decision

to

re-submit,

or try

a

different journal

Publication

ethics

writing in English

formatting

to

guidelines

Publishing is an essential research skillSlide4

13/08/2013

Ganesha Associateswww.ganesha-associates.comSlide5

Elephants in the room

Primary scientific content is predominantly in the form of articles with an IMRD structure (and in the future, related data)‘Grey literature’ (standards, guidelines, professional communications, etc) excluded.Science isn’t local or national“Quality”: Many publishing problems stem from lack of critical reading of the scientific literature, not ‘English’12/11/2014Ganesha Associates

5Slide6

Trends in STM publishing

Globalisation will trump nationalismTraditional publishing morphs into informaticsPublishing 2.0 is brokenWhat can we do to fix it?12/11/2014Ganesha Associates

6Slide7

12/11/2014

Ganesha Associates 7

The growing importance of metricsSlide8

12/11/2014

Ganesha Associates 8Slide9

Brasil:

12/11/2014Ganesha Associates 9Slide10

Source:

International Comparative Activity Performance – Elsevier 2011

BRIC output: documents

12/11/2014

Ganesha Associates

10Slide11

Citation quality is a problem

12/11/2014Ganesha Associates

11Slide12

12/11/2014

Ganesha Associates 12Slide13

EPI : English Proficiency Index by age

12/11/2014Ganesha Associates 13Slide14

12/11/2014

Ganesha Associates 14A brief history of scientific publishingAccording to Bishop Sprat's History of the Royal Society (1667), society members sought to reject "amplifications, digressions, and swellings of style...bringing all things as near the Mathematical plainness, as they can: and preferring the language of Artizans, Countrymen, and Merchants, before that, of Wits and Scholars."Slide15

12/11/2014

Ganesha Associates 15A brief history of scientific publishingSlide16

12/11/2014

Ganesha Associates

16

Scientific publishing is a very

profitableSlide17

Open access mandates

National Institute of Health (NIH) Public Access Policy – 2008Hargreaves Review of Intellectual Property and Growth – 2011EC says that it is aiming for 60% of all European publicly funded research articles to be open access by 2016 - 2012Finch Group Report – June 2012RCUK Policy on Open Access – July 2012, amended March 2013Fair Access to Science and Technology Research Act (FASTR) – February 2013White House Office of Science and Technology Policy (OSTP) – February 2013Green almost unanimously favoured over Gold (Exception UK)

12/11/2014

Ganesha Associates

17Slide18

12/11/2014

Ganesha Associates

18

The emergence of Open Access

Clockwise: Harold Varmus, Michael

Eisen

, Pat Brown and David

LipmanSlide19

History of sequence info => open access

12/11/2014Ganesha Associates 19Slide20

Data growth curves of 5 major EMBL-EBI resources (European Genome-

phenome Archive (EGA); European Nucleotide Archive (ENA); Proteomics data repository (PRIDE); Metabolomics resource (MetaboLights); and Functional genomics database (ArrayExpress) over the years 2005-2013. Source: EMBL-EBI.12/11/2014

Ganesha Associates

20Slide21

12/11/2014

Ganesha Associates 21Slide22

ELIXIR: the European Research Infrastructure for biological data

ELIXIR connects national infrastructures and EMBL-EBI

Launched in 2014

11 Member states + EMBL signed agreementCzech Republic, Estonia, Denmark,

Finland,Israel

, Netherlands,

Norway,Portugal

, Switzerland, Sweden, UK

6 countries have signed

MoU

and prepare national signature

Belgium, Greece, France, Italy, Slovenia, Spain

12/11/2014

Ganesha Associates

22Slide23

23

medicine

agriculture

bioindustries

environment

ELIXIR connects national centres and EMBL-EBI to build a sustainable European

infrastructure for biological

research data.

ELIXIR underpins life

science research – across academia and industry.

www.elixir-europe.org

12/11/2014

Ganesha Associates Slide24

S

ustainable archives - value of data reuse?24

12/11/2014

Ganesha Associates Slide25

The future

Publicly funded and large biomedical research funders are committed to open access publishing. Smaller charitable funders are supportive of the aims of open access, but are concerned about the practical implications for their budgets and their funded researchers. Biomedical research funders are now turning their attention to other priorities for sharing research outputs, including data, protocols and negative results. Publishing priorities of biomedical research funders [BMJ Open 17 Sept 2014]12/11/2014

Ganesha Associates

25Slide26

Summary

As the markets of emerging countries mature, focus will move from commodity-based economies to knowledge-based economies. Basic research funding will increasingly be directed towards areas that can demonstrate high impact on subsequent levels of technological innovation.Science and economics know no borders, global collaborations will be the norm.National governments will actively manage the intellectual property that they create with the objective of attracting global companies to invest with them. 12/11/2014

Ganesha Associates

26Slide27

Summary

To be of use information resources need to be interconnected and freely accessibleThe value of these resources will be constantly assessed and reappraisedThis is not a job that can be undertaken by publishers alone Funders and end-users will drive the big changes12/11/2014Ganesha Associates 27Slide28

The Publishing 2.0 business model is broken…

Open access alone is not yet the answer. PLoS 2013 income tax return: Turnover $33.43mProfit margin 17%. CEO salary $479k. “Bad open-access publishers are still growing like crazy.” [Nature, 7 August 2014]

12/11/2014

Ganesha Associates

28Slide29

Scientific assessment

12/11/2014Ganesha Associates 29Slide30

Scientific assessment - 1

“Subjective assessments of the merit and likely impact of scientific publications are routinely made by scientists during their own research, and as part of promotion, appointment, and government committees.”The San Francisco Declaration on Research Assessment (DORA, 2012) intends to halt the practice of correlating the journal impact factor with the merits of a specific scientist's contributions.But then what…?12/11/2014

Ganesha Associates

30Slide31

Scientific assessment - 2

“In a large cohort of NHLBI-funded cardiovascular R01 grants, we were unable to find an association between better percentile ranking and higher scientific impact as assessed by citation metrics.” [Circulation Research 9 January 2014]“Peer review should be able to tell us what research projects will have the biggest impacts,” Lauer contends. In fact, we explicitly tell scientists it’s one of the main criteria for review. But what we found is that peer review is not predicting outcomes at all. And that’s quite disconcerting.” Michael Lauer, NHLBI, NIH, Science August 201412/11/2014

Ganesha Associates

31Slide32

Scientific assessment - 3

“Using two large datasets (F1000 and Wellcome Trust) in which scientists have made qualitative assessments of scientific merit, we show that scientists are poor at judging scientific merit and the likely impact of a paper, and that their judgment is strongly influenced by the journal in which the paper is published. We also demonstrate that the number of citations a paper accumulates is a poor measure of merit and we argue that although it is likely to be poor, the impact factor, of the journal in which a paper is published, may be the best measure of scientific merit currently available.” [PLoS Biology 2013]12/11/2014Ganesha Associates

32Slide33

Scientific assessment - 4

“Most journals exchange some manuscripts with at least one other journal. Resubmission flows occurred preferentially within subgroups of journals. Partitioning of the network … revealed seven principal journal clusters. These were strongly consistent with subject categories as defined by the Institute for Scientific Information” [Science 23 November 2012]12/11/2014

Ganesha Associates

33Slide34

Scientific assessment - 5

“A complete citation network was constructed from all PubMed indexed English literature papers addressing the belief that β amyloid, a protein accumulated in the brain in Alzheimer’s disease, is produced by and injures skeletal muscle of patients with inclusion body myositis. We found that citation was often used to generate inappropriate information cascades resulting in unfounded authority of claims.” [BMJ 2009]12/11/2014Ganesha Associates

34Slide35

12/11/2014

Ganesha Associates 35Slide36

Irreproducibility - 1

Drug development: The biotechnology company Amgen was unable to replicate the vast majority of published pre-clinical research studies - only 6 out of 53 landmark cancer studies could be replicated, a success rate of 11%. [Nature 28 March 2012]Cancer research: There are many technical reasons why experimental results, particularly in cancer research, cannot be reproduced, including unrecognized variables in the complex experimental model, poor documentation of procedures, selective reporting of the most-positive findings, misinterpretation of technical noise as biological signal and, in the most extreme cases, fabrication of data. [Nature Reviews Clinical Oncology, 1 October 2013]12/11/2014Ganesha Associates

36Slide37

Irreproducibility - 2

The Consort Statement is an evidence-based, minimum set of recommendations for reporting randomized trials. It offers a standard way for authors to prepare reports of trial findings, facilitating their complete and transparent reporting, and aiding their critical appraisal and interpretation [2010, BMJ, NEJM, Lancet, JAMA]Nature research journals introduce editorial measures to address the problem by improving the consistency and quality of reporting in life-sciences articles. See [Nature 24 April 2013] NIH plans to enhance reproducibility [Nature 24 January 2014]12/11/2014

Ganesha Associates

37Slide38

Journals unite for reproducibility

A group of editors representing more than 30 major journals; representatives from funding agencies; and scientific leaders assembled at the American Association for the Advancement of Science’s headquarters in June 2014 to discuss principles and guidelines for preclinical biomedical research. The gathering was convened by the US National Institutes of Health, Nature and Science (see Science 346, 679; 2014).The attendees agreed on a common set of Principles and Guidelines in Reporting Preclinical Research (see go.nature.com/ezjl1p

) that list proposed journal policies and author reporting requirements in order to promote transparency and reproducibility.

12/11/2014

Ganesha Associates

38Slide39

Conflicts of interest

Publication of industry-supported trials was associated with an increase in journal impact factors. Sales of reprints may provide a substantial income. We suggest that journals disclose financial information in the same way that they require them from their authors, so that readers can assess the potential effect of different types of papers on journals’ revenue and impact. [PLoS Medicine October 2010] Statins. The BMJ and authors withdraw statements suggesting that adverse events occur in 18-20% of patients due to misunderstanding of statistical results. [BMJ 2014]12/11/2014Ganesha Associates

39Slide40

Summary

Bibliometrics, citation network analysis and informatics can provide insight into how the publishing process is working and can be improved.Impact factors may help in predicting author submission preferences but scientific impact can probably only be inferred by human annotation of citation networks12/11/2014Ganesha Associates 40Slide41

Publishing 3.0

The growth of information (articles, data, etc) is effectively exponential – discovery, curation and analysis are now bigger problems than creation of new content.Funders will need to drive the reconstruction of the publishing process – NCBI/EBI as models of information use rather launching eLife

Disruptive impact of mega-journals such as PLoS ONE, Brain Research,

BBA will grow.

12/11/2014

Ganesha Associates

41Slide42

Publishing 3.0

Publishing cycle: Funder[Strategy]> Author[Proposal]> Funder[Peer Review: Likely outcome]> Researcher [Manuscript]> Editor[Peer Review: Methodology+?]> Publisher[Standards]> User[Usefulness] The funder and the reader determine “purpose” and “usefulness”. 

The editorial process checks that basic methodology is appropriate, argumentation clear, rules of scientific writing met, etc.

The publisher creates the XML, links, applies data standards

12/11/2014

Ganesha Associates

42Slide43

Publishing 3.0

Each field will support a small hierarchy of journals but only journals near the top and at the very bottom will be strong brands.And the one at the bottom will probably be PLoS ONE or another mega journal!

12/11/2014

Ganesha Associates

43Slide44

12/11/2014

Ganesha Associates 44Slide45

Publishing 3.0

Not all journals will thriveNeed more ambition in the aims and scope, instructions to authorsObjective, transparent editorial selection process and clearer feedback to authors could help increase IF. 12/11/2014Ganesha Associates

45Slide46

Aims and scope/Instructions to authors

Aims and scope: Our mission is to promote scientific knowledge generated in the rigor of the research methodology and ethics. The purpose of *** is to publish the outcomes of original research to advance the practice of *** in the medical, surgical management, education, research and information technology and communication. Abstracts: The summary should be structured into five sections (Background, Objectives, Methods, Results, Conclusions) when it is an Original Article, avoiding abbreviations and considering the maximum number of words.Figures: Figure legends should be double-spaced, and be numbered and placed before the References.

12/11/2014

Ganesha Associates

46Slide47

Referee’s comments

1. I do not see any substantial improvement over the current literature regarding the association between atopic diseases and childhood leukemia. The study design of this paper still suffers from the possibility of reverse causality and does not contribute anything novel to the literature.2. A key strength of this study is that it examines these associations in a different population with a different immune profile than has previously been examined - a population that per the authors in lines 166-167 has a high incidence of parasite infection. Important limitations include the sample size and the methods of exposure assessment.12/11/2014Ganesha Associates

47Slide48

Publishing 3.0

Reasons for rejection. Hypothesis unclear and/or unoriginal, submitted to the wrong journal, badly written (Portuguese/English). The metaphor of “dwarfs standing on the shoulders of giants” expresses the meaning of "discovering truth by building on previous discoveries". But where are the giants and how do you climb on their shoulders? The virtual library, science without borders: reading English, collaboration

12/11/2014

Ganesha Associates

48Slide49

Publishing 3.0

The role of national journals, The Brazilian Journal of… vs. The Journal of the Brazilian… A stepping stone on the path to excellence or permanent gateway to mediocrity? Aim high(er)!Examples: The Caatinga, the malnourished Nordestino rat, nursing care pathways for catheterisation in a hospital in Sao Paulo. The role of SciELO as a publishing platform: Professionalization, internationalization, financial sustainability. Meeting 2 December

12/11/2014

Ganesha Associates

49Slide50

Advantages to being a

Canadian national publisher?“

Canadian voice”

Research community support

University support

Community knowledge

Language

Trusted

brand

12/11/2014

Ganesha Associates

50Slide51

Conclusions

The STM publishing environment is changing rapidly.Brazilian STM publishers have an opportunity to reinvent themselves in a form that can be globally competitive.In order to achieve this goal they must professionalise their services and partner with key funders and user groups12/11/2014Ganesha Associates 51Slide52

Referee’s comments

1.The statistical analysis is incomplete. It is not clear why a chi-square association test was performed in Table 3, instead of the multivariable logistic regression. In addition, age, sex, and SES should be adjusted. 
2.The literature discussion is incomplete and biased. There should be a fair assessment and discussion since not all studies reported an inverse association between atopic diseases and childhood leukemia.
3.The discussion about the paper by Chang et al regarding potential biases seems unfair, and the author failed to mention another medical record-based paper by Logan Spector (EJC 2004) that also reported a positive association between atopic diseases and childhood ALL.
4.Overall, I do not see any substantial improvement over the current literature regarding the association between atopic diseases and childhood leukemia. The study design of this paper still suffers from the possibility of reverse causality and does not contribute anything novel to the literature.5. A key strength of this study is that it examines these associations in a different population with a different immune profile than has previously been examined - a population that per the authors in lines 166-167 has a high incidence of parasite infection. Important limitations include the sample size and the methods of exposure assessment.

12/11/2014

Ganesha Associates

52