Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review
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Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review
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peer-review.SKILL.md
---name: peer-review
description: Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation.
allowed-tools: Read Write Edit Bash
license: MIT license
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---# Scientific Critical Evaluation and Peer Review
## Overview
Peer review is a systematic process for evaluating scientific manuscripts. Assess methodology, statistics, design, reproducibility, ethics, and reporting standards. Apply this skill for manuscript and grant review across disciplines with constructive, rigorous evaluation.
## When to Use This Skill
This skill should be used when:
- Conducting peer review of scientific manuscripts for journals
- Evaluating grant proposals and research applications
- Assessing methodology and experimental design rigor
- Reviewing statistical analyses and reporting standards
- Evaluating reproducibility and data availability
- Checking compliance with reporting guidelines (CONSORT, STROBE, PRISMA)
- Providing constructive feedback on scientific writing
**Related Resource:** The **venue-templates** skill provides `reviewer_expectations.md` with detailed guidance on what reviewers look for at different venues (Nature/Science, Cell Press, medical journals, ML conferences). Use this to calibrate your review standards to the target venue.
## Visual Enhancement with Scientific Schematics
**When creating documents with this skill, always consider adding scientific diagrams and schematics to enhance visual communication.**
If your document does not already contain schematics or diagrams:
- Use the **scientific-schematics** skill to generate AI-powered publication-quality diagrams
- Simply describe your desired diagram in natural language
- Nano Banana Pro will automatically generate, review, and refine the schematic
**For new documents:** Scientific schematics should be generated by default to visually represent key concepts, workflows, architectures, or relationships described in the text.
- **Objectivity:** Are results presented without over-interpretation?
- **Completeness:** Are all relevant results included, including negative results?
- **Reproducibility:** Are raw data or summary statistics provided?
**Common issues to identify:**
- Selective reporting of results
- Inappropriate statistical tests
- Missing error bars or measures of variability
- Over-fitting or circular analysis
- Batch effects or confounding variables
- Missing controls or validation experiments
#### Discussion
- **Interpretation:** Are conclusions supported by the data?
- **Limitations:** Are study limitations acknowledged and discussed?
- **Context:** Are findings placed appropriately within existing literature?
- **Speculation:** Is speculation clearly distinguished from data-supported conclusions?
- **Significance:** Are implications and importance clearly articulated?
- **Future directions:** Are next steps or unanswered questions discussed?
**Red flags:**
- Overstated conclusions
- Ignoring contradictory evidence
- Causal claims from correlational data
- Inadequate discussion of limitations
- Mechanistic claims without mechanistic evidence
#### References
- **Completeness:** Are key relevant papers cited?
- **Currency:** Are recent important studies included?
- **Balance:** Are contrary viewpoints appropriately cited?
- **Accuracy:** Are citations accurate and appropriate?
- **Self-citation:** Is there excessive or inappropriate self-citation?
### Stage 3: Methodological and Statistical Rigor
Evaluate the technical quality and rigor of the research with particular attention to common pitfalls.
**Statistical Assessment:**
- Are statistical assumptions met (normality, independence, homoscedasticity)?
- Are effect sizes reported alongside p-values?
- Is multiple testing correction applied appropriately?
- Are confidence intervals provided?
- Is sample size justified with power analysis?
- Are parametric vs. non-parametric tests chosen appropriately?
- Are missing data handled properly?
- Are exploratory vs. confirmatory analyses distinguished?
**Experimental Design:**
- Are controls appropriate and adequate?
- Is replication sufficient (biological and technical)?
- Are potential confounders identified and controlled?
- Is randomization properly implemented?
- Are blinding procedures adequate?
- Is the experimental design optimal for the research question?
**Computational/Bioinformatics:**
- Are computational methods clearly described and justified?
- Are software versions and parameters documented?
- Is code made available for reproducibility?
- Are algorithms and models validated appropriately?
- Are assumptions of computational methods met?
- Is batch correction applied appropriately?
### Stage 4: Reproducibility and Transparency
Assess whether the research meets modern standards for reproducibility and open science.
**Data Availability:**
- Are raw data deposited in appropriate repositories?
- Are accession numbers provided for public databases?
- Are data sharing restrictions justified (e.g., patient privacy)?
- Are data formats standard and accessible?
**Code and Materials:**
- Is analysis code made available (GitHub, Zenodo, etc.)?
- Are unique materials available or described sufficiently for recreation?
- Are protocols detailed in sufficient depth?
**Reporting Standards:**
- Does the manuscript follow discipline-specific reporting guidelines (CONSORT, PRISMA, ARRIVE, MIAME, MINSEQE, etc.)?
- See `references/reporting_standards.md` for common guidelines
- Are all elements of the appropriate checklist addressed?
### Stage 5: Figure and Data Presentation
Evaluate the quality, clarity, and integrity of data visualization.
**Quality Checks:**
- Are figures high resolution and clearly labeled?
- Are axes properly labeled with units?
- Are error bars defined (SD, SEM, CI)?
- Are statistical significance indicators explained?
- Are color schemes appropriate and accessible (colorblind-friendly)?
- Are scale bars included for images?
- Is data visualization appropriate for the data type?
**Integrity Checks:**
- Are there signs of image manipulation (duplications, splicing)?
- Are Western blots and gels appropriately presented?
- Are representative images truly representative?
- Are all conditions shown (no selective presentation)?
**Clarity:**
- Can figures stand alone with their legends?
- Is the message of each figure immediately clear?
- Are there redundant figures or panels?
- Would data be better presented as tables or figures?
### Stage 6: Ethical Considerations
Verify that the research meets ethical standards and guidelines.
**Human Subjects:**
- Is IRB/ethics approval documented?
- Is informed consent described?
- Are vulnerable populations appropriately protected?
- Is patient privacy adequately protected?
- Are potential conflicts of interest disclosed?
**Animal Research:**
- Is IACUC or equivalent approval documented?
- Are procedures humane and justified?
- Are the 3Rs (replacement, reduction, refinement) considered?
- Are euthanasia methods appropriate?
**Research Integrity:**
- Are there concerns about data fabrication or falsification?
- Is authorship appropriate and justified?
- Are competing interests disclosed?
- Is funding source disclosed?
- Are there concerns about plagiarism or duplicate publication?
### Stage 7: Writing Quality and Clarity
Assess the manuscript's clarity, organization, and accessibility.
**Structure and Organization:**
- Is the manuscript logically organized?
- Do sections flow coherently?
- Are transitions between ideas clear?
- Is the narrative compelling and clear?
**Writing Quality:**
- Is the language clear, precise, and concise?
- Are jargon and acronyms minimized and defined?
- Is grammar and spelling correct?
- Are sentences unnecessarily complex?
- Is the passive voice overused?
**Accessibility:**
- Can a non-specialist understand the main findings?
- Are technical terms explained?
- Is the significance clear to a broad audience?
## Structuring Peer Review Reports
Organize feedback in a hierarchical structure that prioritizes issues and provides actionable guidance.
### Summary Statement
Provide a concise overall assessment (1-2 paragraphs):
- Brief synopsis of the research
- Overall recommendation (accept, minor revisions, major revisions, reject)
- Key strengths (2-3 bullet points)
- Key weaknesses (2-3 bullet points)
- Bottom-line assessment of significance and soundness
### Major Comments
List critical issues that significantly impact the manuscript's validity, interpretability, or significance. Number these sequentially for easy reference.
**Major comments typically include:**
- Fundamental methodological flaws
- Inappropriate statistical analyses
- Unsupported or overstated conclusions
- Missing critical controls or experiments
- Serious reproducibility concerns
- Major gaps in literature coverage
- Ethical concerns
**For each major comment:**
1. Clearly state the issue
2. Explain why it's problematic
3. Suggest specific solutions or additional experiments
4. Indicate if addressing it is essential for publication
### Minor Comments
List less critical issues that would improve clarity, completeness, or presentation. Number these sequentially.
**Minor comments typically include:**
- Unclear figure labels or legends
- Missing methodological details
- Typographical or grammatical errors
- Suggestions for improved data presentation
- Minor statistical reporting issues
- Supplementary analyses that would strengthen conclusions
- Requests for clarification
**For each minor comment:**
1. Identify the specific location (section, paragraph, figure)
2. State the issue clearly
3. Suggest how to address it
### Specific Line-by-Line Comments (Optional)
For manuscripts requiring detailed feedback, provide section-specific or line-by-line comments:
- Reference specific page/line numbers or sections
- Note factual errors, unclear statements, or missing citations
- Suggest specific edits for clarity
### Questions for Authors
List specific questions that need clarification:
- Methodological details that are unclear
- Seemingly contradictory results
- Missing information needed to evaluate the work
- Requests for additional data or analyses
## Tone and Approach
Maintain a constructive, professional, and collegial tone throughout the review.
**Best Practices:**
- **Be constructive:** Frame criticism as opportunities for improvement
- **Be specific:** Provide concrete examples and actionable suggestions
- **Be balanced:** Acknowledge strengths as well as weaknesses
- **Be respectful:** Remember that authors have invested significant effort
- **Be objective:** Focus on the science, not the scientists
- **Be thorough:** Don't overlook issues, but prioritize appropriately
- **Be clear:** Avoid ambiguous or vague criticism
**Avoid:**
- Personal attacks or dismissive language
- Sarcasm or condescension
- Vague criticism without specific examples
- Requesting unnecessary experiments beyond the scope
- Demanding adherence to personal preferences vs. best practices
- Revealing your identity if reviewing is double-blind
## Special Considerations by Manuscript Type
### Original Research Articles
- Emphasize rigor, reproducibility, and novelty
- Assess significance and impact
- Verify that conclusions are data-driven
- Check for complete methods and appropriate controls
### Reviews and Meta-Analyses
- Evaluate comprehensiveness of literature coverage
- Assess search strategy and inclusion/exclusion criteria
- Verify systematic approach and lack of bias
- Check for critical analysis vs. mere summarization
- For meta-analyses, evaluate statistical approach and heterogeneity
### Methods Papers
- Emphasize validation and comparison to existing methods
- Assess reproducibility and availability of protocols/code
- Evaluate improvements over existing approaches
- Check for sufficient detail for implementation
### Short Reports/Letters
- Adapt expectations for brevity
- Ensure core findings are still rigorous and significant
- Verify that format is appropriate for findings
### Preprints
- Recognize that these have not undergone formal peer review
- May be less polished than journal submissions
- Still apply rigorous standards for scientific validity
- Consider providing constructive feedback to help authors improve before journal submission
### Presentations and Slide Decks
**⚠️ CRITICAL: For presentations, NEVER read the PDF directly. ALWAYS convert to images first.**
When reviewing scientific presentations (PowerPoint, Beamer, slide decks):
#### Mandatory Image-Based Review Workflow
**NEVER attempt to read presentation PDFs directly** - this causes buffer overflow errors and doesn't show visual formatting issues.
- Recommendation (ready to present, minor revisions, major revisions)
**Layout and Formatting Issues (By Slide Number):**
```
Slide 3: Text overflow - bullet point 4 extends beyond right margin
Slide 7: Element overlap - figure overlaps with caption text
Slide 12: Font size - axis labels too small to read from distance
Slide 18: Alignment - title not centered
```
**Content and Structure Feedback:**
- Adequacy of background context and citations
- Clarity of research question and objectives
- Quality of methods summary
- Effectiveness of results presentation
- Strength of conclusions and implications
**Design and Accessibility:**
- Overall visual appeal and professionalism
- Color contrast and readability
- Colorblind accessibility
- Consistency across slides
**Timing and Scope:**
- Whether slide count matches intended duration
- Appropriate level of detail for talk type
- Balance between sections
#### Example Image-Based Review Process
```
[14:30:00] PEER REVIEW: Starting review of presentation
[14:30:05] PEER REVIEW: Presentation detected - converting to images
[14:30:10] PDF REVIEW: Running pdf_to_images.py on presentation.pdf
[14:30:15] PDF REVIEW: Converted 25 slides to images in review/ directory
[14:30:20] PDF REVIEW: Inspecting slide 1/25 - title slide
[14:30:25] PDF REVIEW: Inspecting slide 2/25 - introduction
...
[14:35:40] PDF REVIEW: Inspecting slide 25/25 - acknowledgments
[14:35:45] PDF REVIEW: Completed image-based review
[14:35:50] PEER REVIEW: Found 8 layout issues, 3 content issues
[14:35:55] PEER REVIEW: Generating structured feedback by slide number
```
**Remember:** For presentations, the visual inspection via images is MANDATORY. Never attempt to read presentation PDFs as text - it will fail and miss all visual formatting issues.
## Resources
This skill includes reference materials to support comprehensive peer review:
### references/reporting_standards.md
Guidelines for major reporting standards across disciplines (CONSORT, PRISMA, ARRIVE, MIAME, STROBE, etc.) to evaluate completeness of methods and results reporting.
### references/common_issues.md
Catalog of frequent methodological and statistical issues encountered in peer review, with guidance on identifying and addressing them.
