From af246ac5624ba5e9497ee52c84220bc09da57f4b Mon Sep 17 00:00:00 2001 From: Vinayak Agarwal Date: Sat, 25 Oct 2025 23:30:34 -0700 Subject: [PATCH] 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. --- .../assets/review_template.md | 437 +++++++++++------- 1 file changed, 261 insertions(+), 176 deletions(-) diff --git a/scientific-thinking/literature-review/assets/review_template.md b/scientific-thinking/literature-review/assets/review_template.md index c6c4478..601325b 100644 --- a/scientific-thinking/literature-review/assets/review_template.md +++ b/scientific-thinking/literature-review/assets/review_template.md @@ -1,21 +1,22 @@ # [Literature Review Title] -**Authors**: [Author Names] +**Authors**: [Author Names and Affiliations] **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 -[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] +**Background**: [Context and rationale] +**Objectives**: [Primary and secondary objectives] +**Methods**: [Databases, dates, selection criteria, quality assessment] +**Results**: [n studies included; key findings by theme] +**Conclusions**: [Main conclusions and implications] +**Registration**: [PROSPERO ID or "Not registered"] +**Keywords**: [5-8 keywords] --- @@ -42,28 +43,34 @@ ## 2. Methodology -### 2.1 Search Strategy +### 2.1 Protocol and Registration -**Databases Searched:** -- [Database 1] (e.g., PubMed) -- [Database 2] (e.g., bioRxiv/medRxiv) -- [Database 3] (e.g., Semantic Scholar) -- [Additional databases as needed] +**Protocol**: [PROSPERO ID / OSF link / Not registered] +**Deviations**: [Document any protocol deviations] +**PRISMA**: [Checklist in Appendix B] -**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] - -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] +("CRISPR"[Title/Abstract] OR "Cas9"[Title/Abstract]) AND +("disease"[MeSH Terms]) AND ("2015/01/01"[Date] : "2024/12/31"[Date]) ``` -**Search Date:** [Date range: YYYY-MM-DD to YYYY-MM-DD] -**Date of Search:** [Date when search was conducted] +**Dates:** [YYYY-MM-DD to YYYY-MM-DD] | **Executed:** [Date] +**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:** - [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 4: e.g., Duplicate publications] - [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] -├─ 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] +Records identified: n=[X] → Deduplicated: n=[Y] → +Title/abstract screened: n=[Y] → Full-text assessed: n=[Z] → Included: n=[N] ``` -**Reasons for Exclusion at Full-Text Stage:** -- [Reason 1]: n = [X] -- [Reason 2]: n = [Y] -- [Reason 3]: n = [Z] +**Exclusion reasons:** [List with counts] -### 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:] -- **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] +**Missing data:** [Author contact protocol] + +### 2.7 Quality Assessment + +**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 -### 3.1 Search Results Overview +### 3.1 Study Selection -- **Total studies identified**: [n] -- **Studies included in review**: [n] -- **Study types**: [Breakdown by study type] -- **Publication years**: [Distribution] -- **Countries/regions**: [Geographic distribution if relevant] +**Summary:** [X records → Y deduplicated → Z full-text → N included (M in meta-analysis)] +**Study types:** [RCTs: n=X, Observational: n=Y, Reviews: n=Z] +**Years:** [Range; peak year] +**Geography:** [Countries represented] +**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 | |-------|------|--------|-------------|-------------|---------------|---------| -| First Author et al. | 2023 | [Type] | n=[X] | [Methods] | [Brief findings] | [High/Moderate/Low] | -| [Add rows for each study] | | | | | | | +| First Author et al. | 2023 | [Type] | n=[X] | [Methods] | [Brief findings] | [Low/Mod/High RoB] | -### 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:** -- [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] +**Findings:** [Synthesis of key findings from multiple studies] +**Supporting studies:** [X, Y, Z] +**Contradictory evidence:** [If any] +**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] - -[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] +**Knowledge:** [Unanswered research questions] +**Methodological:** [Study design/measurement issues] +**Translational:** [Research-to-practice gaps] +**Populations:** [Underrepresented groups/contexts] --- ## 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 -[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:** -[How might these findings impact practice or application?] - -**Research Implications:** -[What do these findings mean for future research directions?] +**Implications for:** +- **Practice:** [Actionable recommendations] +- **Policy:** [If relevant] +- **Research:** [Theoretical, methodological, priority 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] +**Strengths:** [Comprehensive search, rigorous methods, large evidence base, transparency] **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] +- Search/selection: [Language bias, database coverage, grey literature, publication bias] +- Methodological: [Heterogeneity, study quality] +- Temporal: [Rapid evolution, search cutoff date] + +**Impact:** [How limitations affect conclusions] ### 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] -2. **Direction 2**: [Specific research direction with rationale] -3. **Direction 3**: [Specific research direction with rationale] +**Recommendations:** [Methodological improvements, understudied populations, emerging technologies] --- ## 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 1] -2. [Conclusion 2] -3. [Conclusion 3] +1. [Conclusion directly addressing primary research question] +2. [Key finding conclusion] +3. [Gap/future direction conclusion] + +**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:** -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 +### Conflicts of Interest +[Author-specific declarations] OR [None] -**Nature Style:** -1. First Author, A. A., Second Author, B. B. & Third Author, C. C. Title of article. *J. Name* **volume**, pages (year). +### Data Availability +**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:** -1. First Author AA, Second Author BB, Third Author CC. Title of article. Abbreviated Journal Name. Year;volume(issue):pages. +### Acknowledgments +[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 | -|-------|------|---------------------| -| Author et al. | Year | [Reason] | +### Appendix G: Author Contacts -### 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] +| Study | Contact Date | Response | Data Received | +|-------|--------------|----------|---------------| +| Author et al. | YYYY-MM-DD | Yes/No | Yes/No/Partial | --- -## Supplementary Materials +## 9. Supplementary Materials -[If applicable, list supplementary files:] -- Supplementary Table 1: [Description] -- Supplementary Figure 1: [Description] -- Supplementary Data: [Description] +[If applicable] + +**Tables:** S1 (Full study characteristics), S2 (Quality scores), S3 (Subgroups), S4 (Sensitivity) +**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 -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 +**Review type adaptations:** +- Systematic Review: Use all sections +- Meta-Analysis: Include sections 3.6, Appendix F +- Narrative Review: May omit some methodology detail +- Scoping Review: Follow PRISMA-ScR, may omit quality assessment + +**Key principles:** +1. Remove all [bracketed placeholders] +2. Follow PRISMA 2020 guidelines +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** + +---