Transcript Basic reading, writing and informatics skills for
Basic reading, writing and informatics skills for biomedical research Segment 8. Getting a scientific article published
10 April 2008 Copyright: Ganesha Associates 2008 1
What is scientific publishing ?
• Scientific publishing is the process by which scientific progress is communicated to the community.
• So it is an essential part of the scientific process • If it isn’t published, it isn’t science… • …and you’ve wasted a lot of the tax-payer’s money • Scientific publishing is a commercial enterprise 10 April 2008 Copyright: Ganesha Associates 2008 2
Publishing drives the scientific process
New consensus view 10 April 2008 Old consensus view Copyright: Ganesha Associates 2008 3
Getting published is important for you because…
• Attribution of priority via peer review – It’s new (probably), you were the first !
• Verification via peer review – Your conclusions are clear and plausible, your methodology appropriate – But your conclusions may still later be proved to be incorrect… • Communication – Replication, integration into the consensus view – Permanent archive • Evaluation !!
– $$$$$ – CAPES Qualis 10 April 2008 Copyright: Ganesha Associates 2008 5
Which journal will you publish in ? (Field: developmental neuroscience)
– Tier A: high profile, broad readership journals such as Nature, Science and Cell – Tier B: the “highest quality” specialized journals, or less high quality broader journals such as Neuron, Nature Neuroscience, Genes & Development, and Development. If going for breadth, PNAS, Current Biology, EMBO Journal – Tier C: “safe bet” journals, such as Developmental Biology, J. Neuroscience, BioMedCentral journals – Tier D: the “just publish it” titles, such as Mechanisms of Development, Experimental Brain Research. Some authors would never publish in these journals – they would just as soon put their work in a drawer 10 April 2008 Copyright: Ganesha Associates 2008 6
Which journal will you publish in ? (Field: developmental neuroscience)
– “If I have a paper which I believe demonstrates a fundamental advance in our understanding of neural differentiation – what path do I take ?” – “….there are two underlying pressures determining the place to publish: the prestige of the journal and the need to be first.” – “….if the aim is to ‘establish turf’, if someone else comes out before you in any ‘respectable journal where you trust the quality of the science, then you have lost your ability to stake your claim to that particular piece of ‘turf’. – If there is more time, authors may go from one top tier journal to another before choosing to go to the next level.” 10 April 2008 Copyright: Ganesha Associates 2008 7
Which journal will you publish in ? (Field: cell biology)
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The mycology journal ‘ecosystem’
– Important journals - Mycology Dept, UFPE (2006) • Journal of Invertebrate Pathology • Phytopathology • Plant Pathology • Mycological Research • Plant Disease • Applied and Environmental Microbiology • Current Microbiology • Genetics and Molecular Biology • Molecular Plant Pathology • Medical Mycology • Mycopathology • Applied Soil Ecology • ………..and at least 10 more journals!
– Note only three titles contain a reference to mycology !
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Ecosystems
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Journal hierarchies
• General discoveries of high fundamental importance –
Nature
• Discoveries of high fundamental importance within a specialist discipline or field –
Journal of Neuroscience
• Confirmatory studies – Generalisation to other species – Qualification of boundary conditions –
Brain Research
• Me-too studies, esoteric fields –
Brain and Cognition
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Implications of discipline-specific journal ecosystems
• Identify the most important journals in your field • Check the impact factor • Remember, every journal has a well-defined role • So read the ‘Aims and Scope’ statements for each journal carefully • At the same time, make a copy of the journals’ ‘Instructions for Authors’, they will be different too 10 April 2008 Copyright: Ganesha Associates 2008 12
Cell
: Aims and Scope
•
Cell
publishes findings of unusual significance in any area of experimental biology, including but not limited to cell biology, molecular biology, neuroscience, immunology, virology and microbiology, cancer, human genetics, systems biology, signaling, and disease. • The basic criterion for considering papers is whether the results provide significant conceptual advances into, or raise provocative questions and hypotheses regarding an interesting biological question. 10 April 2008 Copyright: Ganesha Associates 2008 13
Genomics
: Aims and Scope
• The goal of
Genomics
challenging problems data mining and – Identification is to promote the understanding papers in all of the following areas: – Comparative genomics analysis that yields improvements regulation of transcriptomes and proteomes responses to drugs and other xenobiotics of the structure, function, and evolution of genomes in all kingdoms of life and the application of genome sciences and technologies to in biology and medicine. The scope of the journal is broad and we welcome original, full-length, and timely valuable insights into conserved and divergent aspects of function, regulation, and evolution – Bioinformatics and computational biology with particular emphasis on in data annotation and integration – Functional genomics approaches involving the use of large-scale and/or high-throughput methods to understand genome-scale function and of genes involved in disease and complex traits, including – Significant advances in genetic and genomics technologies and their applications, including chemical genomics 10 April 2008 Copyright: Ganesha Associates 2008 14
Gastroenterology
: Aims and Scope •
Gastroenterology
publishes novel clinical and basic studies on all aspects of the digestive system, including the liver and pancreas, as well as nutrition. • The types of articles
Gastroenterology
publishes include original papers, review articles, case reports, and special category manuscripts.
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Agricultural and Forest Meteorology
•
Agricultural and Forest Meteorology
is an international journal for the publication of original articles and reviews on the inter-relationship between meteorology and the fields of plant, animal and soil sciences, ecology, and biogeochemistry. Emphasis is on basic and applied scientific research relevant to practical problems in agriculture, forestry, and natural ecosystems. Articles must appeal to an international audience. Theoretical models should be tested against experimental data. Special issues devoted to single topics are also published.
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Inside a primary journal:
Cell
• •
Cell the
was launched in 1974 as journal of exciting biology.
• Now a part of Elsevier’s Cell Press, a family of ten journals,
Cell
’s Ph.D.-trained scientific editors work with authors, reviewers, and editorial board members with the goal of publishing 26 issues of the most interesting discoveries in biology every year 10 April 2008 Copyright: Ganesha Associates 2008 17
Cell
’s editorial structure
• In-house Editor – Employed by the journal’s publisher to carry out administrative and copy-editing roles • Editor-in-Chief – Major figure in the field • Editorial Board – Represent all of the major sub-fields, act as advisors to the Editor-in-Chief. Usually recognised experts in their respective fields • Referees – Selected by the Editorial Board, usually an expert in the specific area covered by the manuscript 10 April 2008 Copyright: Ganesha Associates 2008 18
Editorial evaluation process -
Cell
• All submissions are initially evaluated in depth by the Editor-in-Chief or sent to an appropriate member of the Editorial Board. • Papers that do not conform to the general criteria for publication will be returned to the authors without detailed review, typically within 3-5 days. • Otherwise, manuscripts will be sent to reviewers who have agreed in advance to assess the paper rapidly. • The editors will make every effort to reach decisions on these papers within 3 weeks of the submission date.
• Accepted papers will be published within 3 months of acceptance. 10 April 2008 Copyright: Ganesha Associates 2008 19
What is the Editor looking for ?
• Plausibility
– Is the experimental design robust ?
– How effectively have the alternative hypotheses been excluded ?
• Topicality
– Is the work original – Is it interesting ?
– Is it relevant ?
– Is it useful ?
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The most likely outcome of the editorial process is rejection
•
Nature, Science, Cell
and other top ranking journals have rejection rates of over 95% • Most high quality journals have a rejection rate of over 80% • Most journals with an Impact Factor >1 have a rejection rate > 66% • All Editors want their journals to be better than their rivals. • So they select only the best articles to publish.
• Some manuscripts may not even be sent for full peer review • Authors of accepted papers will often be asked for revisions and reductions in length 10 April 2008 Copyright: Ganesha Associates 2008 21
Define: Triage
A system for allocating scarce resources; it provides the maximum resources to individuals of highest priority, and few or no resources to individuals of lowest priority.
Derived from practices used to prevent medical systems from being overwhelmed when there are many sick or injured.
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Triage quality varies
• Journal of Biological Chemistry, Biochemistry, and Biochimica Biophysica Acta all have rejection rates > 80% • Impact Factors of 7.4, 5.1. 2.5
• 21%, 34%, 55% of published articles receive 1 or 0 citations • High Impact Factor journals have higher false negative rates – they reject a lot that is good • Low Impact Factor Journals have higher false positive rates – they publish a lot that is not good 10 April 2008 Copyright: Ganesha Associates 2008 23
The importance of rejection rates
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How to avoid rejection ?
Author Journal staff Editor-in-Chief Referees Publication Copyright: Ganesha Associates 2008 Rejection Rejection Rejection 25
Major reasons for rejection - Editors
• Subject falls outside of the aims and scope of the journal • Subject is not of sufficient importance or novelty for publication in the journal so it will not appeal to a broad audience • Manuscript not written in the appropriate style or format for the journal • Manuscript too long • Manuscript incomplete • Quality of English not perfect 10 April 2008 Copyright: Ganesha Associates 2008 26
The role of peer review
– History – Anonymous – Multiple, to avoid bias – Validation/accreditation – Selecting the best – Or de-selecting the worse ?
– Alternatives • Nature • PLos One 10 April 2008 Copyright: Ganesha Associates 2008 27
The role of peer review
• A peer is someone who is of the same or equal standing as another. Thus peer review is review performed by individuals considered to be professional equals.
• The process forces authors to meet the standards of their discipline and achieve scientific objectivity.
• Publications and awards that have not undergone peer review are likely to be regarded with suspicion by scholars and professionals in many fields.
• Peer review is important to achieve clear, precise writing. This is just as true for professional scientists as it is for students.
• Peer review can result in acceptance, conditional acceptance or rejection 10 April 2008 Copyright: Ganesha Associates 2008 28
Peer review – the pros
– A peer is someone who is of the same or equal standing as another. Thus peer review is review performed by individuals considered to be professional equals.
– The process forces authors to meet the standards of their discipline and achieve scientific objectivity.
– Publications and awards that have not undergone peer review are likely to be regarded with suspicion by scholars and professionals in many fields.
– Peer review is important to achieve clear, precise writing. This is just as true for professional scientists as it is for students.
– Peer review can result in acceptance, conditional acceptance or rejection 10 April 2008 Copyright: Ganesha Associates 2008 29
Peer review – the cons
– A peer is likely to be a competitor. How objective are they going to be ?
– Most articles get published and the quality of articles published in high impact titles such as Nature is highly variable.
– Authors are encouraged by the publishing process to exaggerate their claims and even be selective of the data being published, leading to bias – Negative findings are rarely published, leading to further bias when judging the effectiveness say of new medical technologies – “There is increasing concern that most current published research findings are false” John Ioannidis, PLoS 2005 10 April 2008 Copyright: Ganesha Associates 2008 30
Reviewer comments - example
This paper describes clinical and cytogenetic finding in a child with retinoblastoma who had an aggressive fatal course. The authors postulate that this may be related to changes in chromosome 6. However, it is difficult to see how the findings here either promote or negate that hypothesis. In addition several other problems should be addressed: a. Abstract, line 9: could (not should) b. Abstract: define IO c. Staging details at the time of initial diagnosis are inadequate. Were scans done of the head? chest? abdomen? pelvis? bone?
d. One assumes that the right eye was normal at initial diagnosis but this is not stated.
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Reviewer comments – example, cont’d
e.Staging details at the time of initial relapse are inadequate. Were scans done of the head? chest? abdomen? pelvis? bones?
f. What was the csf cytology at the time of initial relapse?
g. What cytologic studies were performed on the ocular, marrow and other tumors at the initial relapse to prove that this was retinoblastoma?
h. What is MADIT?
i. If the authors are going to postulate that chromosome 6 abnormalities are important then other publications require more careful review and more detailed presentation of findings. How does one more case advance the hypothesis?
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Reviewer Comments – main problems
Author’s Hypothesis:
This case represents a particularly aggressive form of retinoblastoma which can be diagnosed by the observation of a rare chromosomal abnormality
Referees Hypotheses:
The initial treatment of the retinoblastoma was ineffective But assuming it wasn’t: Several chromosomal abnormalities described – no evidence that specific chromosomal defect chosen was connected with Copyright: Ganesha Associates 2008 33
A Referee’ Check List
• Taken from the journal Respiratory Care • Structured to focus on each section of the manuscript
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PLoS One
• PLoS ONE is an international, peer-reviewed, open access, online publication. PLoS ONE welcomes reports on primary research from any scientific discipline. It provides: – Open-access—freely accessible online, authors retain copyright – Fast publication times – Peer reviewed by expert, practicing researchers – Post-publication tools to indicate quality and impact – Community-based dialogue on articles – Worldwide media coverage • “All papers that make a valuable contribution to the scientific literature, that are replicable, that are clearly written, and whose conclusions are supported by the data deserve publication.” 10 April 2008 Copyright: Ganesha Associates 2008 35
Neuroscience Peer-Review Consortium
• The NPRC was created to reduce the inefficiency that arises when an author submits a manuscript to a journal after the same manuscript has been reviewed and rejected by another journal. • In many cases, publication of good manuscripts —which may have been rejected solely because of space or scope limitations — is delayed as editors from each journal attempt to find reviewers, send the reviews, and wait for the reviews to be returned. Often the same reviewer is asked to review the same manuscript multiple times.
• The NPRC streamlines this process by allowing reviews solicited by one journal to be forwarded and re-used by other member journals.
• However, ultimate control of manuscript submission remains in the hands of authors as reviews are forwarded only when the author requests this service.
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Introduction
• Is the background information adequate to introduce the research problem ?
• Are the references adequate ?
• Are specific study objectives or hypotheses stated ?
• Is the writing in this section clear and concise ?
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Methods
• Are there outcome variables described for each study objective or hypothesis ?
• Are there appropriate descriptions of how calculated values were determined ?
• Are outcome variables that do not relate to the objectives or hypotheses avoided ?
• Are the measurement procedures appropriate for the study objectives or hypotheses ?
• Is there enough detail to judge validity and for readers to replicate the study ?
• Were appropriate statistical methods chosen for this study design ?
• Is the writing in this section clear and concise ?
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Results
• Are there complete data for each procedure or test described in the Methods section ?
• Do the data, or descriptions on the data, appear to be valid ?
• Are data that do not relate to the study objectives or hypotheses avoided ?
• Are the tables and illustrations adequate ?
• Does the text avoid presenting the same data as the Tables and Illustrations ?
• Is the writing clear and concise ?
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Discussion
• Is there an explanation of how the results address the problem statement or hypothesis ?
• Are theoretical and practical aspects of the results discussed ?
• Do you agree with the interpretation of the results ?
• Is there a comparison of this study with previously published studies ?
• Are the references adequate ?
• Is there a discussion of the limitations of the study ?
• Is there a section that clearly states the authors conclusions ?
• Is the writing of this section clear and concise ?
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Major reasons for rejection - Referees
• Inappropriate or incomplete statistics • Over-interpretation of results • Inappropriate instrumentation • Sample too small or unbiased • Text too difficult to follow • Insufficient problem statement • Inaccurate or inconsistent data reported • Incomplete, inaccurate, or outdated literature review • Insufficient data presented • Defective tables or figures 10 April 2008 Copyright: Ganesha Associates 2008 41
Main reasons for rejection - Brasil
• Submitted to the wrong journal • Journal aims and scope not followed • Purpose of the work unclear • Work does not relate to current areas of research interest • Too long • English
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Ten simple rules to help you get published
– Read many papers, and learn from both the good and the bad work of others. It is never too early to become a critic – The more objective you can be about your work, the better that work will ultimately become.
– Good editors and reviewers will be objective about your work.
– If you do not write well in the English language, take lessons early; it will be invaluable later.
– Learn to live with rejection.
– Philip E. Bourne, PLoS – http://compbiol.plosjournals.org/perlserv/?request=get document&doi=10.1371/journal.pcbi.0010057
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Ten simple rules to help you get published
– The ingredients of good science are obvious - novelty of research topic, comprehensive coverage of the relevant literature, good data, good analysis including strong statistical support, and a thought-provoking discussion – Start writing the paper the day you have the idea of what questions to pursue – Become a reviewer early in your career.
– Decide early on where to try to publish your paper.
– Quality is everything – Philip E. Bourne, PLoS – http://compbiol.plosjournals.org/perlserv/?request=get document&doi=10.1371/journal.pcbi.0010057
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Some more suggestions to help you get published
– Choosing a problem • Something that you have a personal interest in • is based on a current experimental paradigm recognized by the international scientific community • for which experimental resources are available, affordable • and for which you have intellectual support, e.g. experimental design, data interpretation, etc – Mestrado/Doutorado projects • Choose a supervisor with a good research track record • Specify the research problem during the first year • Try to shape first year course work around these specific needs • Pay more attention to experimental design, not just statistics • Don’t attempt one big experiment, but plan several • Seek progress reviews at regular intervals 10 April 2008 Copyright: Ganesha Associates 2008 45
• • • • • • • • • • • • • • • • • • • • • •
Practical activity 8 - The role of peer review
Using the guidelines provided, act as a group to review the research project proposals for the group as a whole. The group will provide a critical assessment and then ach student to review and discuss this feedback.
Reviewer's Check List
( Download a copy) Please record the author’s name/manuscript identifier below, then answer the following four questions by highlighting the rating given according to the following scale: 2 = very clear, 0 = very unclear, 1= could be clearer.
Author/Manuscript:
1. Is it clear why the problem is of importance, for example: Is the economic or medical significance defined ? What are the underlying key scientific issues ? Do the references used make it clear how these link to the consensus view in the literature ? Score: 0 1 2 2. Is it clear how the problem is to be addressed experimentally ?
Has an appropriate model system been chosen ? Is it clear what information needs to be collected ? Is it clear which methods have been chosen for this purpose and why ? Score: 0 1 2 3. Limitations Have the most-likely reasons for failure been identified ? What is the ‘Fail early’ strategy ? Score: 0 1 2 4. Literature review Is it up-to-date ? Are all key points of logical development in the text backed by an appropriate reference ? Score: 0 1 2 10 April 2008 Copyright: Ganesha Associates 2008 46