Transcript Document

Trends in Scientific, Technical and
Medical Publishing
Associação Brasileira de Editores Científicos
VIII Workshop de Editoração Científica
10 a 13 Novembro 2014
Campos do Jordão/SP
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CV
• BSc Physics 1971, PhD Neuroscience 1976, post doc
Epidemiology 1975-1979
• Visiting Researcher, UFPe 1978-79, 1984
• Editor, Publisher, Director at Elsevier Science, 1979 –
2005
• Pubmed systems expert, NCBI, NIH 2006-2007
• STM business analyst, Outsell Inc, 2009-2011
• Visiting Professor UFPe, 2006-2008, 2012-2014
• Independent consultant Ganesha Associates 20062014
• Consultant, European Bioinformatics Institute ELIXIR
impact project 2015
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www.ganesha-associates.com
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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’
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The growing importance of metrics
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BRIC output: documents
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Source: International Comparative Activity Performance – Elsevier 2011
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Citation quality is a problem
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EPI : English Proficiency Index by age
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The emergence of Open Access
Clockwise: Harold Varmus, Michael Eisen, Pat
Brown and David Lipman
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History of sequence info => open access
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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.
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ELIXIR: the European Research
Infrastructure for biological data
•
ELIXIR connects national
infrastructures and EMBL-EBI
– Launched in 2014
•
11 Member states + EMBL
signed agreement
– Czech 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
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Sustainable archives - value of data
reuse?
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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]
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Summary
• To be of use information resources need to be
interconnected and freely accessible
• The value of these resources will be constantly
assessed and reappraised
• This is not a job that can be undertaken by
publishers alone
• Funders and end-users will drive the big
changes
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Scientific assessment
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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…?
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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 2014
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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]
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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]
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Irreproducibility - 1
• Drug development: The biotechnology company Amgen
was unable to replicate the vast majority of published preclinical 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]
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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 networks
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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
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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!
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Publishing 3.0
• Not all journals will thrive
• Need more ambition in the aims and scope,
instructions to authors
• Objective, transparent editorial selection
process and clearer feedback to authors could
help increase IF.
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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.
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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.
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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
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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 groups
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