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** + +---