claude-scientific-skills/scientific-thinking/literature-review/assets/review_template.md

# [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