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claude-scientific-skills/scientific-thinking/literature-review/assets/review_template.md
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[Literature Review Title]

Authors: [Author Names] Date: [Date] Review Type: [Narrative / Systematic / Scoping / Meta-Analysis]


Abstract

[150-250 word summary of the literature review including:

  • Background and context
  • Objective of the review
  • Methods (databases searched, selection criteria)
  • Key findings and themes
  • Conclusions and implications]

Keywords: [5-8 relevant keywords]


1. Introduction

1.1 Background and Context

[Provide background information on the topic. Establish why this literature review is important and timely. Discuss the broader context and current state of knowledge.]

1.2 Scope and Objectives

[Clearly define the scope of the review and state the specific objectives. What questions will this review address?]

Primary Research Questions:

  1. [Research question 1]
  2. [Research question 2]
  3. [Research question 3]

1.3 Significance

[Explain the significance of this review. Why is it important to synthesize this literature now? What gaps does it fill?]


2. Methodology

2.1 Search Strategy

Databases Searched:

  • [Database 1] (e.g., PubMed)
  • [Database 2] (e.g., bioRxiv/medRxiv)
  • [Database 3] (e.g., Semantic Scholar)
  • [Additional databases as needed]

Search Terms:

[Document exact search strings used]

Example:
("CRISPR"[Title] OR "Cas9"[Title] OR "gene editing"[Title/Abstract])
AND ("disease name"[MeSH] OR "related term"[Title/Abstract])
AND 2015:2024[Publication Date]

Search Date: [Date range: YYYY-MM-DD to YYYY-MM-DD] Date of Search: [Date when search was conducted]

2.2 Inclusion and Exclusion Criteria

Inclusion Criteria:

  • [Criterion 1: e.g., Published between 2015-2024]
  • [Criterion 2: e.g., Peer-reviewed articles and preprints]
  • [Criterion 3: e.g., English language]
  • [Criterion 4: e.g., Human or animal studies]
  • [Criterion 5: e.g., Original research or systematic reviews]

Exclusion Criteria:

  • [Criterion 1: e.g., Case reports with n<5]
  • [Criterion 2: e.g., Conference abstracts without full text]
  • [Criterion 3: e.g., Editorials and commentaries]
  • [Criterion 4: e.g., Duplicate publications]
  • [Criterion 5: e.g., Retracted articles]

2.3 Study Selection Process

PRISMA Flow Diagram:

Initial database search: n = [X]
├─ After deduplication: n = [Y]
├─ Title screening
│  ├─ Included: n = [Z]
│  └─ Excluded: n = [Y-Z]
├─ Abstract screening
│  ├─ Included: n = [A]
│  └─ Excluded: n = [Z-A]
└─ Full-text screening
   ├─ Included in review: n = [B]
   └─ Excluded: n = [A-B]

Reasons for Exclusion at Full-Text Stage:

  • [Reason 1]: n = [X]
  • [Reason 2]: n = [Y]
  • [Reason 3]: n = [Z]

2.4 Data Extraction

[Describe what data was extracted from each study: study design, sample size, methods, key findings, limitations, etc.]

2.5 Quality Assessment

[Describe quality assessment methods used:]

  • Tool used: [e.g., Cochrane Risk of Bias, Newcastle-Ottawa Scale, AMSTAR 2]
  • Quality ratings: [Describe how studies were rated]
  • Quality distribution: [Summary of quality across included studies]

3. Results

3.1 Search Results Overview

  • Total studies identified: [n]
  • Studies included in review: [n]
  • Study types: [Breakdown by study type]
  • Publication years: [Distribution]
  • Countries/regions: [Geographic distribution if relevant]

3.2 Study Characteristics

[Table summarizing key characteristics of included studies]

Study Year Design Sample Size Key Methods Main Findings Quality
First Author et al. 2023 [Type] n=[X] [Methods] [Brief findings] [High/Moderate/Low]
[Add rows for each study]

3.3 Thematic Analysis

[Organize findings by themes or research questions. Do NOT simply summarize each paper sequentially. Instead, synthesize across studies.]

3.3.1 Theme 1: [Major Theme or Research Question]

[Synthesize findings across multiple studies related to this theme. Compare and contrast different approaches and results. Identify consensus and controversies.]

Key Findings:

  • [Finding 1 supported by Studies X, Y, Z]
  • [Finding 2 with contradictory evidence from Studies A vs. B]
  • [Finding 3 with emerging evidence from Studies C, D]

Example Studies:

Study A (First Author et al., Year): [Brief description of methods and findings relevant to this theme]^1^

Study B (Second Author et al., Year): [Brief description showing contrast or support]^2^

[Continue for each relevant study]

3.3.2 Theme 2: [Second Major Theme]

[Follow same structure as Theme 1]

3.3.3 Theme 3: [Third Major Theme]

[Continue for all major themes identified]

3.4 Methodological Approaches

[Summarize the methods used across studies. What techniques are most common? What novel approaches have emerged?]

Common Methods:

  • [Method 1]: Used in [n] studies [cite relevant studies]
  • [Method 2]: Used in [n] studies [cite relevant studies]

Emerging Techniques:

  • [New technique 1]: [Description and studies using it]
  • [New technique 2]: [Description and studies using it]

3.5 Gaps in Current Knowledge

[Identify what's missing from the current literature based on your analysis:]

  1. Gap 1: [Description of knowledge gap]
  2. Gap 2: [Description of methodological gap]
  3. Gap 3: [Description of translational gap]

4. Discussion

4.1 Summary of Main Findings

[Provide a high-level synthesis of the most important findings from your review. What are the key takeaways?]

4.2 Interpretation and Implications

[Interpret the findings in context. What do they mean for the field? How do they advance our understanding?]

Clinical/Practical Implications: [How might these findings impact practice or application?]

Research Implications: [What do these findings mean for future research directions?]

4.3 Strengths and Limitations

Strengths of This Review:

  • [Strength 1: e.g., Comprehensive multi-database search]
  • [Strength 2: e.g., Rigorous quality assessment]
  • [Strength 3: e.g., Large number of included studies]

Limitations:

  • [Limitation 1: e.g., Publication bias may be present]
  • [Limitation 2: e.g., Heterogeneity in study designs]
  • [Limitation 3: e.g., Limited to English-language publications]
  • [Limitation 4: e.g., Rapid field evolution; recent work may be missed]

4.4 Comparison with Previous Reviews

[If relevant, compare your findings with previous literature reviews on similar topics. What's new or different?]

4.5 Future Research Directions

[Based on identified gaps and your analysis, propose specific future research directions:]

  1. Direction 1: [Specific research direction with rationale]
  2. Direction 2: [Specific research direction with rationale]
  3. Direction 3: [Specific research direction with rationale]

5. Conclusions

[Provide clear, concise conclusions that directly address your research questions. Summarize the state of knowledge and emphasize the most important insights from your review.]

Key Conclusions:

  1. [Conclusion 1]
  2. [Conclusion 2]
  3. [Conclusion 3]

6. References

[List all references cited in the review. Use consistent formatting throughout. All DOIs should be verified using the verify_citations.py script before final submission.]

Format Options:

APA Style:

  1. First Author, A. A., Second Author, B. B., & Third Author, C. C. (Year). Title of article. Journal Name, volume(issue), pages. https://doi.org/xx.xxxx/yyyyy

Nature Style:

  1. First Author, A. A., Second Author, B. B. & Third Author, C. C. Title of article. J. Name volume, pages (year).

Vancouver Style:

  1. First Author AA, Second Author BB, Third Author CC. Title of article. Abbreviated Journal Name. Year;volume(issue):pages.

Appendices

Appendix A: Detailed Search Strings

[Provide complete, reproducible search strings for each database]

Database: PubMed

[Exact search string with all operators and filters]

Database: bioRxiv

[Exact search string]

[Continue for all databases]

Appendix B: Excluded Studies

[Optional: List studies excluded at full-text stage with reasons]

Study Year Reason for Exclusion
Author et al. Year [Reason]

Appendix C: Quality Assessment Details

[Optional: Detailed quality assessment scores for each included study]

Study Criterion 1 Criterion 2 Criterion 3 Overall Quality
Study 1 [Score] [Score] [Score] [High/Moderate/Low]

Appendix D: Data Extraction Form

[Optional: Template or example of data extraction form used]


Supplementary Materials

[If applicable, list supplementary files:]

  • Supplementary Table 1: [Description]
  • Supplementary Figure 1: [Description]
  • Supplementary Data: [Description]

Citation Verification Status: [✓ All citations verified with verify_citations.py]

Review Completion Date: [Date]

Last Updated: [Date]


Notes for Using This Template

  1. Remove all bracketed placeholders and replace with your content
  2. Verify all DOIs using the verify_citations.py script
  3. Follow PRISMA guidelines for systematic reviews when applicable
  4. Maintain consistent citation style throughout (choose one: APA, Nature, Vancouver, etc.)
  5. Use the thematic organization approach rather than study-by-study summaries
  6. Include specific numbers in your methodology and results sections
  7. Be objective and critical in your analysis
  8. Document everything for reproducibility
  9. Generate PDF using generate_pdf.py when complete
  10. Delete this Notes section from your final review