git:20260721.831d49e to v2.0

- 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

- required_environment_variables: [{"name": "OPENROUTER_API_KEY", "prompt": "OpenRouter API key for the skill's LLM-powered steps.", "required_for": "optional features"}]

- metadata: {"version": "1.3", "skill-author": "K-Dense Inc.", "openclaw": {"primaryEnv": "OPENROUTER_API_KEY", "envVars": [{"name": "OPENROUTER_API_KEY", "required": false, "description": "OpenRouter API key for the skill's LLM-powered steps."}]}}

- ---

-

- # 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.

-

- **How to generate schematics:**

- ```bash

- python scripts/generate_schematic.py "your diagram description" -o figures/output.png

- ```

-

- The AI will automatically:

- - Create publication-quality images with proper formatting

- - Review and refine through multiple iterations

- - Ensure accessibility (colorblind-friendly, high contrast)

- - Save outputs in the figures/ directory

-

- **When to add schematics:**

- - Peer review workflow diagrams

- - Evaluation criteria decision trees

- - Review process flowcharts

- - Methodology assessment frameworks

- - Quality assessment visualizations

- - Reporting guidelines compliance diagrams

- - Any complex concept that benefits from visualization

-

- For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.

-

- ## Peer Review Workflow

-

- Conduct peer review systematically through the following stages, adapting depth and focus based on the manuscript type and discipline.

-

- ### Stage 1: Initial Assessment

-

- Begin with a high-level evaluation to determine the manuscript's scope, novelty, and overall quality.

-

- **Key Questions:**

- - What is the central research question or hypothesis?

- - What are the main findings and conclusions?

- - Is the work scientifically sound and significant?

- - Is the work appropriate for the intended venue?

- - Are there any immediate major flaws that would preclude publication?

-

- **Output:** Brief summary (2-3 sentences) capturing the manuscript's essence and initial impression.

-

- ### Stage 2: Detailed Section-by-Section Review

-

- Conduct a thorough evaluation of each manuscript section, documenting specific concerns and strengths.

-

- #### Abstract and Title

- - **Accuracy:** Does the abstract accurately reflect the study's content and conclusions?

- - **Clarity:** Is the title specific, accurate, and informative?

- - **Completeness:** Are key findings and methods summarized appropriately?

- - **Accessibility:** Is the abstract comprehensible to a broad scientific audience?

-

- #### Introduction

- - **Context:** Is the background information adequate and current?

- - **Rationale:** Is the research question clearly motivated and justified?

- - **Novelty:** Is the work's originality and significance clearly articulated?

- - **Literature:** Are relevant prior studies appropriately cited?

- - **Objectives:** Are research aims/hypotheses clearly stated?

-

- #### Methods

- - **Reproducibility:** Can another researcher replicate the study from the description provided?

- - **Rigor:** Are the methods appropriate for addressing the research questions?

- - **Detail:** Are protocols, reagents, equipment, and parameters sufficiently described?

- - **Ethics:** Are ethical approvals, consent, and data handling properly documented?

- - **Statistics:** Are statistical methods appropriate, clearly described, and justified?

- - **Validation:** Are controls, replicates, and validation approaches adequate?

-

- **Critical elements to verify:**

- - Sample sizes and power calculations

- - Randomization and blinding procedures

- - Inclusion/exclusion criteria

- - Data collection protocols

- - Computational methods and software versions

- - Statistical tests and correction for multiple comparisons

- #### Results

- - **Presentation:** Are results presented logically and clearly?

- - **Figures/Tables:** Are visualizations appropriate, clear, and properly labeled?

- - **Statistics:** Are statistical results properly reported (effect sizes, confidence intervals, p-values)?

- - **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.

- **Required Process:**

- 1. Convert PDF to images using Python:

- ```bash

- python skills/scientific-slides/scripts/pdf_to_images.py presentation.pdf review/slide --dpi 150

- # Creates: review/slide-001.jpg, review/slide-002.jpg, etc.

- ```

- 2. Read and inspect EACH slide image file sequentially

- 3. Document issues with specific slide numbers

- 4. Provide feedback on visual formatting and content

- **Print when starting review:**

- ```

- [HH:MM:SS] PEER REVIEW: Presentation detected - converting to images for review

- [HH:MM:SS] PDF REVIEW: NEVER reading PDF directly - using image-based inspection

- #### Presentation-Specific Evaluation Criteria

-

- **Visual Design and Readability:**

- - [ ] Text is large enough (minimum 18pt, ideally 24pt+ for body text)

- - [ ] High contrast between text and background (4.5:1 minimum, 7:1 preferred)

- - [ ] Color scheme is professional and colorblind-accessible

- - [ ] Consistent visual design across all slides

- - [ ] White space is adequate (not cramped)

- - [ ] Fonts are clear and professional

-

- **Layout and Formatting (Check EVERY Slide Image):**

- - [ ] No text overflow or truncation at slide edges

- - [ ] No element overlaps (text over images, overlapping shapes)

- - [ ] Titles are consistently positioned

- - [ ] Content is properly aligned

- - [ ] Bullets and text are not cut off

- - [ ] Figures fit within slide boundaries

- - [ ] Captions and labels are visible and readable

-

- **Content Quality:**

- - [ ] One main idea per slide (not overloaded)

- - [ ] Minimal text (3-6 bullets per slide maximum)

- - [ ] Bullet points are concise (5-7 words each)

- - [ ] Figures are simplified and clear (not copy-pasted from papers)

- - [ ] Data visualizations have large, readable labels

- - [ ] Citations are present and properly formatted

- - [ ] Results/data slides dominate the presentation (40-50% of content)

- **Structure and Flow:**

- - [ ] Clear narrative arc (introduction → methods → results → discussion)

- - [ ] Logical progression between slides

- - [ ] Slide count appropriate for talk duration (~1 slide per minute)

- - [ ] Title slide includes authors, affiliation, date

- - [ ] Introduction cites relevant background literature (3-5 papers)

- - [ ] Discussion cites comparison papers (3-5 papers)

- - [ ] Conclusions slide summarizes key findings

- - [ ] Acknowledgments/funding slide at end

- **Scientific Content:**

- - [ ] Research question clearly stated

- - [ ] Methods adequately summarized (not excessive detail)

- - [ ] Results presented logically with clear visualizations

- - [ ] Statistical significance indicated appropriately

- - [ ] Conclusions supported by data shown

- - [ ] Limitations acknowledged where appropriate

- - [ ] Future directions or broader impact discussed

- **Common Presentation Issues to Flag:**

- **Critical Issues (Must Fix):**

- - Text overflow making content unreadable

- - Font sizes too small (<18pt)

- - Element overlaps obscuring data

- - Insufficient contrast (text hard to read)

- - Figures too complex or illegible

- - No citations (completely unsupported claims)

- - Slide count drastically mismatched to duration

- **Major Issues (Should Fix):**

- - Inconsistent design across slides

- - Too much text (walls of text, not bullets)

- - Poorly simplified figures (axis labels too small)

- - Cramped layout with insufficient white space

- - Missing key structural elements (no conclusion slide)

- - Poor color choices (not colorblind-safe)

- - Minimal results content (<30% of slides)

- **Minor Issues (Suggestions for Improvement):**

- - Could use more visuals/diagrams

- - Some slides slightly text-heavy

- - Minor alignment inconsistencies

- - Could benefit from more white space

- - Additional citations would strengthen claims

- - Color scheme could be more modern

- #### Review Report Format for Presentations

- **Summary Statement:**

- - Overall impression of presentation quality

- - Appropriateness for target audience and duration

- - Key strengths (visual design, content, clarity)

- - Key weaknesses (formatting issues, content gaps)

- - 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.

- ## Final Checklist

- Before finalizing the review, verify:

- - [ ] Summary statement clearly conveys overall assessment

- - [ ] Major concerns are clearly identified and justified

- - [ ] Suggested revisions are specific and actionable

- - [ ] Minor issues are noted but properly categorized

- - [ ] Statistical methods have been evaluated

- - [ ] Reproducibility and data availability assessed

- - [ ] Ethical considerations verified

- - [ ] Figures and tables evaluated for quality and integrity

- - [ ] Writing quality assessed

- - [ ] Tone is constructive and professional throughout

- - [ ] Review is thorough but proportionate to manuscript scope

- - [ ] Recommendation is consistent with identified issues