5  Peer review

This was created by sharing my notes and sources with perplexity, and it generated this checklist for me.

5.1 Preparation

Research the topic. If you lack background knowledge, research the field before starting. This helps you assess whether the work represents a genuine contribution.1

Check for duplicates and prior work. Search for similar papers or earlier versions of this manuscript to ensure originality and identify any potential duplicate publication concerns.23

Verify your expertise and availability. Confirm the manuscript is in your area of expertise and that you have sufficient time to complete a thorough review.4

Check for competing interests. Identify any conflicts of interest that might affect your objectivity.5

5.2 Reading the Paper

First read: Scan the entire manuscript to understand the main message, study design, and overall direction. Ask yourself:

  • What contribution does this article make to the field?6
  • Is the manuscript original?7
  • Is the overall study design appropriate?8
  • What are the research question and key claims?9

Second read: Conduct a detailed, section-by-section review using the checklists below. Keep everything confidential throughout this process.1011

5.3 Section-by-Section Review

As you read each section, note specific concerns with page and line numbers. Categorize issues as major or minor as you go.1213

5.3.1 Title

  • Does it clearly express what the manuscript is about?14
  • Does it highlight the importance of the study?15
  • Does it contain unnecessary description?16

5.3.2 Abstract

  • Is it a short, clear summary of aims, key methods, important findings, and conclusions?17
  • Does it accurately communicate the main study contributions?18
  • Does it include enough information to stand alone?19
  • Does it contain unnecessary information?20

5.3.3 Keywords

Minor issues only: Are they appropriate and comprehensive?21

5.3.4 Introduction

  • Does it clearly summarize the current state of the topic?22
  • Does it address limitations of current knowledge?23
  • Does it clearly explain why the study was necessary?24
  • Does it clearly define the study aim, consistent with the rest of the manuscript?25
  • Does it concisely establish the rationale (significance of topic, knowledge gap, how gap will be addressed)?26
  • Is the research question clear and appropriate?27
  • Is the literature review up to date and appropriate?28

5.3.5 Methods

  • Are the study design and methods appropriate for the research question?29
  • Are all methods clearly and transparently described?30
  • Is there enough detail to repeat the experiments/reproduce the study?3132
  • Is it clear how samples were collected or participants recruited?33
  • Is there potential bias in the sample or recruitment?34
  • Are correct controls/validation included?35
  • Are potential confounding factors considered?36
  • Has randomization been done correctly?37
  • Is the time-frame sufficient to see outcomes?38
  • Is there sufficient power and appropriate statistics?39
  • Are there concerns related to internal or external validity?40
  • Are there ethical concerns (IRB review, informed consent, ethical design)?4142

5.3.6 Results

  • Are results presented clearly and accurately?43
  • Do the results match the methods?44
  • Have all relevant data been included?45
  • Is there risk of patients/participants being identified?46
  • Is data in text consistent with figures and tables?47
  • Have necessary analyses been performed to test the hypothesis?48
  • Could additional analyses more comprehensively test the hypothesis?49
  • Are results supported by the data?50
  • Have data been transparently represented?51
  • Are there concerns about accuracy of reported data or results?52

5.3.7 Discussion and Conclusion

  • Do authors logically explain the findings?53
  • Do authors compare findings with current research?54
  • Are implications for future research and applications discussed?55
  • Are conclusions supported by the data?5657
  • Have data been interpreted fairly and in a balanced manner?58
  • Have results been interpreted in context of existing literature?59
  • Are conclusions logical from the data?60
  • Have study limitations been comprehensively discussed?6162
  • Are contradictory data discussed?63

5.3.8 Tables and Figures

  • Are data presented clearly and appropriately?64
  • Is presentation consistent with text description?65
  • Do legends and headings clearly explain what is shown?66
  • Do they include measures of uncertainty (standard error, confidence intervals) and sample size where required?67
  • Are they clear and representative of the study?68
  • Are there concerns about data manipulation?69

5.3.9 References

  • Are key references missing?70
  • Do authors cite initial discoveries where suitable?71
  • Do they cite reviews where they should cite original papers?72
  • Do cited studies represent current knowledge?73

5.3.10 Open Scholarship Review (STARS criteria)

  • Used a reporting checklist?74
  • Deposited model in a public archive?75
  • Included ORCID in model metadata?76
  • Shared model under an open licence?77
  • Provided basic instructions to run and use model?78
  • Explained how dependencies are managed?79
  • Provided code for all scenarios, sensitivity analyses, tables, figures, and reported results?80

5.4 Categorizing Comments: Major vs. Minor

5.4.1 Major Issues

Definition: Significant concerns essential for publication that affect validity, interpretation, or impact. These require substantial changes and warrant re-review.8182838485

Examples:

  • Fundamental methodological flaws or bias8687
  • Missing or inadequate data analysis8889
  • Weak or missing theoretical framework9091
  • Unclear or unsupported arguments9293
  • Inadequate description preventing reproducibility94
  • Ethical concerns95
  • Results not supported by data96
  • Conclusions not logical from findings97
  • Entire sections needing rewriting or reorganization9899
  • Missing crucial experiments or analyses100
  • Relevance concerns for the journal’s scope101102

Rule of thumb: If you need to see the manuscript again to verify the issues were fixed, it’s a major issue.103

5.4.2 Minor Issues

Definition: Important improvements that typically won’t affect overall conclusions and aren’t essential for publication. These can often be reviewed by the editor alone without re-review.104105106107

Examples:

  • Clarifying ambiguous statements108109
  • Typographical or grammatical errors110111
  • Citation inconsistencies or missing minor references112113
  • Fine-tuning figures, tables, or formatting114
  • Small additional context or citations115116
  • Syntax and language improvements117
  • Keywords and title refinements118

Rule of thumb: If the editor can verify the changes without your expertise, it’s a minor issue.119

5.5 Writing the Review

5.5.1 Structure Your Report

Use this standard format:120121122

  1. Summary paragraph
  2. Overall impression and recommendation
  3. Major comments (numbered)
  4. Minor comments (numbered)
  5. Confidential comments to editor (separate section)

5.5.2 1. Summary Paragraph

Write 3-5 sentences demonstrating you’ve read and understood the study. Include:123124125

  • Study objectives and design126
  • Key results127
  • Authors’ conclusions/interpretations128
  • Positive contributions made by the article129

This shows the editor you understand the paper and helps authors see your interpretation.130

5.5.3 2. Overall Impression and Recommendation

State your recommended decision (explained in next section) and provide your “take-home” message about the manuscript’s strengths and weaknesses.131132

5.5.4 3. Major Comments

Formatting:

  • Number each comment133134135
  • List most important concerns first136
  • Include page and line numbers for easy reference137138139
  • Give concrete examples with direct quotes (bolded or italicized)140
  • Be specific and actionable141142143

Content: Address critical concerns from your section-by-section review that fall into the major category. Focus on issues fundamental to the current study—not “next step” suggestions.144145

Tone:

  • Be direct but respectful146147148149
  • Be professional and constructive, not offensive150151152153
  • Focus on the research, not the researcher154155
  • Frame as suggestions: “Consider clarifying…” rather than demands156157158
  • Acknowledge authors’ effort159160
  • Avoid defensive or aggressive language161
  • Use neutral language without emotionally charged expressions162163

Example structure: “The methodology section lacks clarity on participant inclusion criteria (page 6, lines 120-125). This makes it difficult to assess whether the sample is representative. Consider adding a detailed explanation of your inclusion and exclusion criteria, including specific thresholds for each criterion.”164165166

5.5.5 4. Minor Comments

Use the same formatting and tone guidelines as major comments. List minor issues identified in your section-by-section review. Keep these brief. Don’t focus primarily on spelling and grammar—these are trivial.167168

5.5.6 5. Confidential Comments to Editor

Purpose: Discuss sensitive information or context that shouldn’t be shared with authors. You don’t have to write anything here—it’s optional.169170171172173

What to include:

  • Your overall assessment summary and rationale for your decision recommendation174175176
  • Novelty and rigor assessment177
  • Potential ethical issues (plagiarism, manipulated figures, duplicate publication, human subjects concerns, inappropriate authorship)178179
  • Sensitive concerns about the manuscript that might be too harsh for authors180181
  • Context the editor should know (e.g., previous interaction with this manuscript at another journal)182
  • Whether manuscript needs language/grammar editing183
  • Clarifications if your decision category doesn’t fully communicate your assessment184

Important: Never contradict your comments to authors here. All scientific evaluation should be in your comments to authors.185

5.6 Making Your Decision Recommendation

5.6.1 Decision Categories

Accept without revision: Very rare.186

Minor revisions: Limited changes needed. The manuscript is mostly sound but needs small refinements like clarifying text, fixing tables, adding minor citations, or tweaking arguments. High chance of acceptance if revisions are made properly. Often reviewed by editor only, not sent back to reviewers.187188189190191

Major revisions: Substantial work required. Examples include:192193

  • Substantial rewriting needed194
  • Key elements missing or inadequately described195
  • Significant data issues requiring additional or reanalysis196
  • Major structural reorganization needed197198
  • New experiments required199
  • Addressing whole new topics in arguments200
  • Existing analyses have flaws201

The manuscript will be sent back to reviewers for re-evaluation. Acceptance is not guaranteed after revision.202203204

Reject: Fundamental flaws that cannot be addressed through revision, inappropriate principle/method, or insufficient contribution. Use when reviewers recommend major revisions but suggest changes authors cannot actually make (e.g., fundamental design flaws).205206

5.6.2 Writing Your Recommendation to the Editor

In your confidential comments, explain the rationale for your recommendation, such as:207208

  • How the manuscript advances the field209
  • How it informs clinical care or practice210
  • Whether it motivates important new lines of investigation211
  • Whether issues are addressable through revision212
  • Any sensitive concerns213

5.7 Final Checks Before Submission

  • Have you given a brief summary and highlighted key messages?214
  • Have you given positive feedback as well as constructive criticism?215216
  • Have you clearly marked which concerns are major vs. minor?217218219
  • Are your concerns specific with examples where possible?220221222
  • Have you numbered comments and referred to page/line numbers?223224225
  • Is your feedback constructive and focused on the research?226227
  • If you were the author, would you understand how to improve the manuscript?228
  • If you were the editor, would your comments help them make a decision?229
  • Have you checked spelling and grammar in your report?230
  • Have you included comments in correct places in the online system (confidential vs. author-facing)?231
  • Is your tone professional and respectful throughout?232233234235
  • Have you included positive feedback alongside criticism?236
  • Have you indicated if you’re available to review the revised version?237
  • Will you finish on time?238 239240241242243244245246247248249250251252
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