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Revise literature review template to enhance structure and clarity, including expanded sections for authors' affiliations, review types, and detailed methodology. Update abstract format to include background, objectives, methods, results, and conclusions. Introduce new subsections for protocol registration, quality assessment, and knowledge gaps, ensuring comprehensive guidance for systematic reviews.

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Vinayak Agarwal
2025-10-25 23:30:34 -07:00
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scientific-thinking/literature-review/assets/review_template.md
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# [Literature Review Title] # [Literature Review Title]
**Authors**: [Author Names] **Authors**: [Author Names and Affiliations]
**Date**: [Date] **Date**: [Date]
**Review Type**: [Narrative / Systematic / Scoping / Meta-Analysis] **Review Type**: [Narrative / Systematic / Scoping / Meta-Analysis / Umbrella Review]
**Review Protocol**: [PROSPERO ID if registered, or state "Not registered"]
**PRISMA Compliance**: [Yes/No/Partial - specify which guidelines]
--- ---
## Abstract ## Abstract
[150-250 word summary of the literature review including: **Background**: [Context and rationale]
- Background and context **Objectives**: [Primary and secondary objectives]
- Objective of the review **Methods**: [Databases, dates, selection criteria, quality assessment]
- Methods (databases searched, selection criteria) **Results**: [n studies included; key findings by theme]
- Key findings and themes **Conclusions**: [Main conclusions and implications]
- Conclusions and implications] **Registration**: [PROSPERO ID or "Not registered"]
**Keywords**: [5-8 keywords]
**Keywords**: [5-8 relevant keywords]
--- ---
@@ -42,28 +43,34 @@
## 2. Methodology ## 2. Methodology
### 2.1 Search Strategy ### 2.1 Protocol and Registration
**Databases Searched:** **Protocol**: [PROSPERO ID / OSF link / Not registered]
- [Database 1] (e.g., PubMed) **Deviations**: [Document any protocol deviations]
- [Database 2] (e.g., bioRxiv/medRxiv) **PRISMA**: [Checklist in Appendix B]
- [Database 3] (e.g., Semantic Scholar)
- [Additional databases as needed]
**Search Terms:** ### 2.2 Search Strategy
**Databases:** [PubMed, Scopus, Web of Science, bioRxiv, etc.]
**Supplementary:** [Citation chaining, grey literature, trial registries]
**Search String Example:**
``` ```
[Document exact search strings used] ("CRISPR"[Title/Abstract] OR "Cas9"[Title/Abstract]) AND
("disease"[MeSH Terms]) AND ("2015/01/01"[Date] : "2024/12/31"[Date])
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] **Dates:** [YYYY-MM-DD to YYYY-MM-DD] | **Executed:** [Date]
**Date of Search:** [Date when search was conducted] **Validation:** [Key papers used to test search strategy]
### 2.2 Inclusion and Exclusion Criteria ### 2.3 Tools and Software
**Screening:** [Rayyan, Covidence, ASReview]
**Analysis:** [VOSviewer, R, Python]
**Citation Management:** [Zotero, Mendeley, EndNote]
**AI Tools:** [Any AI-assisted tools used; document validation approach]
### 2.4 Inclusion and Exclusion Criteria
**Inclusion Criteria:** **Inclusion Criteria:**
- [Criterion 1: e.g., Published between 2015-2024] - [Criterion 1: e.g., Published between 2015-2024]
@@ -78,250 +85,328 @@ AND 2015:2024[Publication Date]
- [Criterion 3: e.g., Editorials and commentaries] - [Criterion 3: e.g., Editorials and commentaries]
- [Criterion 4: e.g., Duplicate publications] - [Criterion 4: e.g., Duplicate publications]
- [Criterion 5: e.g., Retracted articles] - [Criterion 5: e.g., Retracted articles]
- [Criterion 6: e.g., Studies with unavailable full text after author contact]
### 2.3 Study Selection Process ### 2.5 Study Selection
**PRISMA Flow Diagram:** **Reviewers:** [n independent reviewers] | **Conflict resolution:** [Method]
**Inter-rater reliability:** [Cohen's kappa = X]
**PRISMA Flow:**
``` ```
Initial database search: n = [X] Records identified: n=[X] → Deduplicated: n=[Y] →
├─ After deduplication: n = [Y] Title/abstract screened: n=[Y] → Full-text assessed: n=[Z] → Included: n=[N]
├─ 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:** **Exclusion reasons:** [List with counts]
- [Reason 1]: n = [X]
- [Reason 2]: n = [Y]
- [Reason 3]: n = [Z]
### 2.4 Data Extraction ### 2.6 Data Extraction
[Describe what data was extracted from each study: study design, sample size, methods, key findings, limitations, etc.] **Method:** [Standardized form (Appendix E); pilot-tested on n studies]
**Extractors:** [n independent] | **Verification:** [Double-checked]
### 2.5 Quality Assessment **Items:** Study ID, design, population, interventions/exposures, outcomes, statistics, funding, COI, bias domains
[Describe quality assessment methods used:] **Missing data:** [Author contact protocol]
- **Tool used**: [e.g., Cochrane Risk of Bias, Newcastle-Ottawa Scale, AMSTAR 2]
- **Quality ratings**: [Describe how studies were rated] ### 2.7 Quality Assessment
- **Quality distribution**: [Summary of quality across included studies]
**Tool:** [Cochrane RoB 2.0 / ROBINS-I / Newcastle-Ottawa / AMSTAR 2 / JBI]
**Method:** [2 independent reviewers; third for conflicts]
**Rating:** [Low/Moderate/High risk of bias]
**Publication bias:** [Funnel plots, Egger's test - if meta-analysis]
### 2.8 Synthesis and Analysis
**Approach:** [Narrative / Meta-analysis / Both]
**Statistics** (if meta-analysis): Effect measures, heterogeneity (I², τ²), sensitivity analyses, subgroups
**Software:** [RevMan, R, Stata]
**Certainty:** [GRADE framework; factors: bias, inconsistency, indirectness, imprecision]
--- ---
## 3. Results ## 3. Results
### 3.1 Search Results Overview ### 3.1 Study Selection
- **Total studies identified**: [n] **Summary:** [X records → Y deduplicated → Z full-text → N included (M in meta-analysis)]
- **Studies included in review**: [n] **Study types:** [RCTs: n=X, Observational: n=Y, Reviews: n=Z]
- **Study types**: [Breakdown by study type] **Years:** [Range; peak year]
- **Publication years**: [Distribution] **Geography:** [Countries represented]
- **Countries/regions**: [Geographic distribution if relevant] **Source:** [Peer-reviewed: n=X, Preprints: n=Y]
### 3.2 Study Characteristics ### 3.2 Bibliometric Overview
[Table summarizing key characteristics of included studies] [Optional: Trends, journal distribution, author networks, citations, keywords - if analyzed with VOSviewer or similar]
### 3.3 Study Characteristics
| Study | Year | Design | Sample Size | Key Methods | Main Findings | Quality | | Study | Year | Design | Sample Size | Key Methods | Main Findings | Quality |
|-------|------|--------|-------------|-------------|---------------|---------| |-------|------|--------|-------------|-------------|---------------|---------|
| First Author et al. | 2023 | [Type] | n=[X] | [Methods] | [Brief findings] | [High/Moderate/Low] | | First Author et al. | 2023 | [Type] | n=[X] | [Methods] | [Brief findings] | [Low/Mod/High RoB] |
| [Add rows for each study] | | | | | | |
### 3.3 Thematic Analysis **Quality:** Low RoB: n=X ([%]); Moderate: n=Y ([%]); High: n=Z ([%])
[Organize findings by themes or research questions. Do NOT simply summarize each paper sequentially. Instead, synthesize across studies.] ### 3.4 Thematic Synthesis
#### 3.3.1 Theme 1: [Major Theme or Research Question] [Organize by themes, NOT study-by-study. Synthesize across studies to identify consensus, controversies, and gaps.]
[Synthesize findings across multiple studies related to this theme. Compare and contrast different approaches and results. Identify consensus and controversies.] #### 3.4.1 Theme 1: [Title]
**Key Findings:** **Findings:** [Synthesis of key findings from multiple studies]
- [Finding 1 supported by Studies X, Y, Z] **Supporting studies:** [X, Y, Z]
- [Finding 2 with contradictory evidence from Studies A vs. B] **Contradictory evidence:** [If any]
- [Finding 3 with emerging evidence from Studies C, D] **Certainty:** [GRADE rating if applicable]
**Example Studies:** ### 3.5 Methodological Approaches
**Study A (First Author et al., Year)**: [Brief description of methods and findings relevant to this theme]^1^ **Common methods:** [Method 1 (n studies), Method 2 (n studies)]
**Emerging techniques:** [New approaches observed]
**Methodological quality:** [Overall assessment]
**Study B (Second Author et al., Year)**: [Brief description showing contrast or support]^2^ ### 3.6 Meta-Analysis Results
[Continue for each relevant study] [Include only if conducting meta-analysis]
#### 3.3.2 Theme 2: [Second Major Theme] **Effect estimates:** [Primary/secondary outcomes with 95% CI, p-values]
**Heterogeneity:** [I²=X%, τ²=Y, interpretation]
**Subgroups & sensitivity:** [Key findings from analyses]
**Publication bias:** [Funnel plot, Egger's p=X]
**Forest plots:** [Include for primary outcomes]
[Follow same structure as Theme 1] ### 3.7 Knowledge Gaps
#### 3.3.3 Theme 3: [Third Major Theme] **Knowledge:** [Unanswered research questions]
**Methodological:** [Study design/measurement issues]
[Continue for all major themes identified] **Translational:** [Research-to-practice gaps]
**Populations:** [Underrepresented groups/contexts]
### 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. Discussion
### 4.1 Summary of Main Findings ### 4.1 Main Findings
[Provide a high-level synthesis of the most important findings from your review. What are the key takeaways?] [Synthesize key findings by research question]
**Principal findings:** [Top 3-5 takeaways]
**Consensus:** [Where studies agree]
**Controversy:** [Conflicting results]
### 4.2 Interpretation and Implications ### 4.2 Interpretation and Implications
[Interpret the findings in context. What do they mean for the field? How do they advance our understanding?] **Context:** [How findings advance/challenge current understanding]
**Mechanisms:** [Potential explanations for observed patterns]
**Clinical/Practical Implications:** **Implications for:**
[How might these findings impact practice or application?] - **Practice:** [Actionable recommendations]
- **Policy:** [If relevant]
**Research Implications:** - **Research:** [Theoretical, methodological, priority directions]
[What do these findings mean for future research directions?]
### 4.3 Strengths and Limitations ### 4.3 Strengths and Limitations
**Strengths of This Review:** **Strengths:** [Comprehensive search, rigorous methods, large evidence base, transparency]
- [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:** **Limitations:**
- [Limitation 1: e.g., Publication bias may be present] - Search/selection: [Language bias, database coverage, grey literature, publication bias]
- [Limitation 2: e.g., Heterogeneity in study designs] - Methodological: [Heterogeneity, study quality]
- [Limitation 3: e.g., Limited to English-language publications] - Temporal: [Rapid evolution, search cutoff date]
- [Limitation 4: e.g., Rapid field evolution; recent work may be missed]
**Impact:** [How limitations affect conclusions]
### 4.4 Comparison with Previous Reviews ### 4.4 Comparison with Previous Reviews
[If relevant, compare your findings with previous literature reviews on similar topics. What's new or different?] [If relevant: How does this review update/differ from prior reviews?]
### 4.5 Future Research Directions ### 4.5 Future Research
[Based on identified gaps and your analysis, propose specific future research directions:] **Priority questions:**
1. [Question] - Rationale, suggested approach, expected impact
2. [Question] - Rationale, suggested approach, expected impact
3. [Question] - Rationale, suggested approach, expected impact
1. **Direction 1**: [Specific research direction with rationale] **Recommendations:** [Methodological improvements, understudied populations, emerging technologies]
2. **Direction 2**: [Specific research direction with rationale]
3. **Direction 3**: [Specific research direction with rationale]
--- ---
## 5. Conclusions ## 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.] [Concise conclusions addressing research questions]
**Key Conclusions:** 1. [Conclusion directly addressing primary research question]
1. [Conclusion 1] 2. [Key finding conclusion]
2. [Conclusion 2] 3. [Gap/future direction conclusion]
3. [Conclusion 3]
**Evidence certainty:** [High/Moderate/Low/Very Low]
**Translation readiness:** [Ready / Needs more research / Preliminary]
--- ---
## 6. References ## 6. Declarations
[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.] ### Author Contributions
[CRediT taxonomy: Author 1 - Conceptualization, Methodology, Writing; Author 2 - Analysis, Review; etc.]
### Format Options: ### Funding
[Grant details with numbers] OR [No funding received]
**APA Style:** ### Conflicts of Interest
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 [Author-specific declarations] OR [None]
**Nature Style:** ### Data Availability
1. First Author, A. A., Second Author, B. B. & Third Author, C. C. Title of article. *J. Name* **volume**, pages (year). **Protocol:** [PROSPERO/OSF ID or "Not registered"]
**Data/Code:** [Repository URL/DOI or "Available upon request"]
**Materials:** [Search strategies (Appendix A), PRISMA checklist (Appendix B), extraction form (Appendix E)]
**Vancouver Style:** ### Acknowledgments
1. First Author AA, Second Author BB, Third Author CC. Title of article. Abbreviated Journal Name. Year;volume(issue):pages. [Contributors not meeting authorship criteria, librarians, patient involvement]
--- ---
## Appendices ## 7. References
### Appendix A: Detailed Search Strings [Use consistent style: APA / Nature / Vancouver]
[Provide complete, reproducible search strings for each database] **Format examples:**
**Database: PubMed** APA: Author, A. A., & Author, B. B. (Year). Title. *Journal*, *volume*(issue), pages. https://doi.org/xx.xxxx
Nature: Author, A. A. & Author, B. B. Title. *J. Name* **volume**, pages (year).
Vancouver: Author AA, Author BB. Title. J Abbrev. Year;volume(issue):pages. doi:xx.xxxx
1. [First reference]
2. [Second reference]
3. [Continue...]
---
## 8. Appendices
### Appendix A: Search Strings
**PubMed** (Date: YYYY-MM-DD; Results: n)
``` ```
[Exact search string with all operators and filters] [Complete search string with operators and MeSH terms]
``` ```
**Database: bioRxiv** [Repeat for each database: Scopus, Web of Science, bioRxiv, etc.]
### Appendix B: PRISMA Checklist
| Section | Item | Reported? | Page |
|---------|------|-----------|------|
| Title | Identify as systematic review | Yes/No | # |
| Abstract | Structured summary | Yes/No | # |
| Methods | Eligibility, sources, search, selection, data, quality | Yes/No | # |
| Results | Selection, characteristics, risk of bias, syntheses | Yes/No | # |
| Discussion | Interpretation, limitations, conclusions | Yes/No | # |
| Other | Registration, support, conflicts, availability | Yes/No | # |
### Appendix C: Excluded Studies
| Study | Year | Reason | Category |
|-------|------|--------|----------|
| Author et al. | Year | [Reason] | [Wrong population/outcome/design/etc.] |
**Summary:** Wrong population (n=X), Wrong outcome (n=Y), etc.
### Appendix D: Quality Assessment
**Tool:** [Cochrane RoB 2.0 / ROBINS-I / Newcastle-Ottawa / etc.]
| Study | Domain 1 | Domain 2 | Domain 3 | Overall |
|-------|----------|----------|----------|---------|
| Study 1 | Low | Low | Some concerns | Low |
| Study 2 | [Score] | [Score] | [Score] | [Overall] |
### Appendix E: Data Extraction Form
``` ```
[Exact search string] STUDY: Author______ Year______ DOI______
DESIGN: □RCT □Cohort □Case-Control □Cross-sectional □Other______
POPULATION: n=_____ Age_____ Setting_____
INTERVENTION/EXPOSURE: _____
OUTCOMES: Primary_____ Secondary_____
RESULTS: Effect size_____ 95%CI_____ p=_____
QUALITY: □Low □Moderate □High RoB
FUNDING/COI: _____
``` ```
[Continue for all databases] ### Appendix F: Meta-Analysis Details
### Appendix B: Excluded Studies [Only if meta-analysis performed]
[Optional: List studies excluded at full-text stage with reasons] **Software:** [R 4.x.x with meta/metafor packages / RevMan / Stata]
**Model:** [Random-effects; justification]
**Code:** [Link to repository]
**Sensitivity analyses:** [Details]
| Study | Year | Reason for Exclusion | ### Appendix G: Author Contacts
|-------|------|---------------------|
| Author et al. | Year | [Reason] |
### Appendix C: Quality Assessment Details | Study | Contact Date | Response | Data Received |
|-------|--------------|----------|---------------|
[Optional: Detailed quality assessment scores for each included study] | Author et al. | YYYY-MM-DD | Yes/No | Yes/No/Partial |
| 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 ## 9. Supplementary Materials
[If applicable, list supplementary files:] [If applicable]
- Supplementary Table 1: [Description]
- Supplementary Figure 1: [Description] **Tables:** S1 (Full study characteristics), S2 (Quality scores), S3 (Subgroups), S4 (Sensitivity)
- Supplementary Data: [Description] **Figures:** S1 (PRISMA diagram), S2 (Risk of bias), S3 (Funnel plot), S4 (Forest plots), S5 (Networks)
**Data:** S1 (Extraction file), S2 (Search results), S3 (Analysis code), S4 (PRISMA checklist)
**Repository:** [OSF/GitHub/Zenodo URL with DOI]
--- ---
**Citation Verification Status**: [✓ All citations verified with verify_citations.py] ## Review Metadata
**Review Completion Date**: [Date] **Registration:** [Registry] ID: [Number] (Date: YYYY-MM-DD)
**Search dates:** Initial: [Date]; Updated: [Date]
**Version:** [1.0] | **Last updated:** [Date]
**Last Updated**: [Date] **Quality checks:**
- [ ] Citations verified with verify_citations.py
- [ ] PRISMA checklist completed
- [ ] Search reproducible
- [ ] Independent data verification
- [ ] Code peer-reviewed
- [ ] All authors approved
--- ---
## Notes for Using This Template ## Usage Notes
1. **Remove all bracketed placeholders** and replace with your content **Review type adaptations:**
2. **Verify all DOIs** using the verify_citations.py script - Systematic Review: Use all sections
3. **Follow PRISMA guidelines** for systematic reviews when applicable - Meta-Analysis: Include sections 3.6, Appendix F
4. **Maintain consistent citation style** throughout (choose one: APA, Nature, Vancouver, etc.) - Narrative Review: May omit some methodology detail
5. **Use the thematic organization** approach rather than study-by-study summaries - Scoping Review: Follow PRISMA-ScR, may omit quality assessment
6. **Include specific numbers** in your methodology and results sections
7. **Be objective and critical** in your analysis **Key principles:**
8. **Document everything** for reproducibility 1. Remove all [bracketed placeholders]
9. **Generate PDF** using generate_pdf.py when complete 2. Follow PRISMA 2020 guidelines
10. **Delete this Notes section** from your final review 3. Pre-register when feasible (PROSPERO/OSF)
4. Use thematic synthesis, not study-by-study
5. Be transparent and reproducible
6. Verify all DOIs before submission
7. Make data/code openly available
**Common pitfalls to avoid:**
- Don't list studies - synthesize them
- Don't cherry-pick results
- Don't ignore limitations
- Don't overstate conclusions
- Don't skip publication bias assessment
**Resources:**
- PRISMA 2020: http://prisma-statement.org/
- PROSPERO: https://www.crd.york.ac.uk/prospero/
- Cochrane Handbook: https://training.cochrane.org/handbook
- GRADE: https://www.gradeworkinggroup.org/
**DELETE THIS SECTION FROM YOUR FINAL REVIEW**
---