literature-review

foryourhealth111-pixel/Vibe-SkillsResearchReview advisedSnapshot 15a84ba662d3

Summary

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

SKILL.md

Literature Review

Overview

Conduct systematic, comprehensive literature reviews following rigorous academic methodology. Search multiple literature sources, synthesize findings thematically, verify citations for accuracy, and generate professional output documents in markdown and PDF formats.

When to Use This Skill

Use this skill when:

Conducting a systematic literature review for research or publication
Synthesizing current knowledge on a specific topic across multiple sources
Performing meta-analysis or scoping reviews
Writing the literature review section of a research paper or thesis
Investigating the state of the art in a research domain
Identifying research gaps and future directions
Requiring verified citations and professional formatting

Core Workflow

Literature reviews follow a structured, multi-phase workflow:

Phase 1: Planning and Scoping

Define Research Question: Use PICO framework (Population, Intervention, Comparison, Outcome) for clinical/biomedical reviews
- Example: "What is the efficacy of CRISPR-Cas9 (I) for treating sickle cell disease (P) compared to standard care (C)?"
Establish Scope and Objectives:
- Define clear, specific research questions
- Determine review type (narrative, systematic, scoping, meta-analysis)
- Set boundaries (time period, geographic scope, study types)
Develop Search Strategy:
- Identify 2-4 main concepts from research question

Multi-Database Search:

Select databases appropriate for the domain:

Biomedical & Life Sciences:
- Use PubMed/PMC for biomedical literature retrieval
- Include bioRxiv/medRxiv preprints when the review scope requires recent non-peer-reviewed evidence
- Use specialized biomedical databases for pathway, structure, variant, and target evidence when relevant
General Scientific Literature:
- Search arXiv via direct API (preprints in physics, math, CS, q-bio)
- Search Semantic Scholar via API (200M+ papers, cross-disciplinary)
- Use Google Scholar for comprehensive coverage (manual or careful scraping)
Specialized Databases:
- Include protein structure evidence when needed
- Include cancer genomics evidence when needed
- Include demographic, economic, or health statistics when needed
- Use specialized databases as appropriate for the domain
Document Search Parameters:
```
## Search Strategy

### Database: PubMed
- **Date searched**: 2024-10-25
- **Date range**: 2015-01-01 to 2024-10-25
- **Search string**:
```
("CRISPR"[Title] OR "Cas9"[Title]) AND ("sickle cell"[MeSH] OR "SCD"[Title/Abstract]) AND 2015:2024[Publication Date]
```
- **Results**: 247 articles
```
Repeat for each database searched.
Export and Aggregate Results:
- Export results in JSON format from each database
- Combine all results into a single file
- Use scripts/search_databases.py for post-processing:
```
python search_databases.py combined_results.json \
  --deduplicate \
  --format markdown \
  --output aggregated_results.md
```

Deduplication:
```
python search_databases.py results.json --deduplicate --output unique_results.json
```
- Removes duplicates by DOI (primary) or title (fallback)
- Document number of duplicates removed
Title Screening:
- Review all titles against inclusion/exclusion criteria
- Exclude obviously irrelevant studies
- Document number excluded at this stage
Abstract Screening:
- Read abstracts of remaining studies
- Apply inclusion/exclusion criteria rigorously
- Document reasons for exclusion
Full-Text Screening:
- Obtain full texts of remaining studies
- Conduct detailed review against all criteria
- Document specific reasons for exclusion
- Record final number of included studies

Create PRISMA Flow Diagram:

Initial search: n = X
├─ After deduplication: n = Y
├─ After title screening: n = Z
├─ After abstract screening: n = A
└─ Included in review: n = B

Create Review Document from template:

cp assets/review_template.md my_literature_review.md

Write Thematic Synthesis (NOT study-by-study summaries):

Organize Results section by themes or research questions
Synthesize findings across multiple studies within each theme
Compare and contrast different approaches and results
Identify consensus areas and points of controversy
Highlight the strongest evidence

Example structure:

#### 3.3.1 Theme: CRISPR Delivery Methods

Multiple delivery approaches have been investigated for therapeutic
gene editing. Viral vectors (AAV) were used in 15 studies^1-15^ and
showed high transduction efficiency (65-85%) but raised immunogenicity
concerns^3,7,12^. In contrast, lipid nanoparticles demonstrated lower
efficiency (40-60%) but improved safety profiles^16-23^.

Critical Analysis:
- Evaluate methodological strengths and limitations across studies
- Assess quality and consistency of evidence
- Identify knowledge gaps and methodological gaps
- Note areas requiring future research
Write Discussion:
- Interpret findings in broader context
- Discuss clinical, practical, or research implications
- Acknowledge limitations of the review itself
- Compare with previous reviews if applicable
- Propose specific future research directions

Verify All DOIs:
```
python scripts/verify_citations.py my_literature_review.md
```
This script:
- Extracts all DOIs from the document
- Verifies each DOI resolves correctly
- Retrieves metadata from CrossRef
- Generates verification report
- Outputs properly formatted citations
Review Verification Report:
- Check for any failed DOIs
- Verify author names, titles, and publication details match
- Correct any errors in the original document
- Re-run verification until all citations pass
Format Citations Consistently:
- Choose one citation style and use throughout (see references/citation_styles.md)
- Common styles: APA, Nature, Vancouver, Chicago, IEEE
- Use verification script output to format citations correctly
- Ensure in-text citations match reference list format

Generate PDF:
```
python scripts/generate_pdf.py my_literature_review.md \
  --citation-style apa \
  --output my_review.pdf
```
Options:
- --citation-style: apa, nature, chicago, vancouver, ieee
- --no-toc: Disable table of contents
- --no-numbers: Disable section numbering
- --check-deps: Check if pandoc/xelatex are installed
Review Final Output:
- Check PDF formatting and layout
- Verify all sections are present
- Ensure citations render correctly
- Check that figures/tables appear properly
- Verify table of contents is accurate
Quality Checklist:
- All DOIs verified with verify_citations.py
- Citations formatted consistently
- PRISMA flow diagram included (for systematic reviews)
- Search methodology fully documented
- Inclusion/exclusion criteria clearly stated
- Results organized thematically (not study-by-study)
- Quality assessment completed
- Limitations acknowledged
- References complete and accurate
- PDF generates without errors

# Search PubMed
pubmed search "CRISPR gene editing" --limit 100

# Search with filters
# Use PubMed Advanced Search Builder to construct complex queries
# Then execute via PubMed/Entrez-compatible access

search biorxiv "CRISPR sickle cell" --limit 50

# Example search categories:
# q-bio.QM (Quantitative Methods)
# q-bio.GN (Genomics)
# q-bio.MN (Molecular Networks)
# cs.LG (Machine Learning)
# stat.ML (Machine Learning Statistics)

# Search format: category AND terms
search_query = "cat:q-bio.QM AND ti:\"single cell sequencing\""

Paper Age	Citation Threshold	Classification
0-3 years	20+ citations	Noteworthy
0-3 years	100+ citations	Highly Influential
3-7 years	100+ citations	Significant
3-7 years	500+ citations	Landmark Paper
7+ years	500+ citations	Seminal Work
7+ years	1000+ citations	Foundational

# 1. Create review document from template
cp assets/review_template.md crispr_sickle_cell_review.md

# 2. Search multiple literature sources
# - Use PubMed for curated biomedical literature
# - Include bioRxiv/medRxiv preprints when recent non-peer-reviewed evidence matters
# - Use direct API access for arXiv, Semantic Scholar
# - Export results in JSON format

# 3. Aggregate and process results
python scripts/search_databases.py combined_results.json \
  --deduplicate \
  --rank citations \
  --year-start 2015 \
  --year-end 2024 \
  --format markdown \
  --output search_results.md \
  --summary

# 4. Screen results and extract data
# - Manually screen titles, abstracts, full texts
# - Extract key data into the review document
# - Organize by themes

# 5. Write the review following template structure
# - Introduction with clear objectives
# - Detailed methodology section
# - Results organized thematically
# - Critical discussion
# - Clear conclusions

# 6. Verify all citations
python scripts/verify_citations.py crispr_sickle_cell_review.md

# Review the citation report
cat crispr_sickle_cell_review_citation_report.json

# Fix any failed citations and re-verify
python scripts/verify_citations.py crispr_sickle_cell_review.md

# 7. Generate professional PDF
python scripts/generate_pdf.py crispr_sickle_cell_review.md \
  --citation-style nature \
  --output crispr_sickle_cell_review.pdf

# 8. Review final PDF and markdown outputs

pip install requests  # For citation verification

# For PDF generation
brew install pandoc  # macOS
apt-get install pandoc  # Linux

# For LaTeX (PDF generation)
brew install --cask mactex  # macOS
apt-get install texlive-xetex  # Linux

python scripts/generate_pdf.py --check-deps

literature-review

Summary

Literature Review

Overview

When to Use This Skill

Core Workflow

Phase 1: Planning and Scoping

Phase 2: Systematic Literature Search

Phase 3: Screening and Selection

Phase 4: Data Extraction and Quality Assessment

Phase 5: Synthesis and Analysis

Phase 6: Citation Verification

Phase 7: Document Generation

Database-Specific Search Guidance

PubMed / PubMed Central

bioRxiv / medRxiv

arXiv

Semantic Scholar

Specialized Biomedical Databases

Citation Chaining

Citation Style Guide

APA (7th Edition)

Nature

Vancouver

Prioritizing High-Impact Papers (CRITICAL)

Citation Count Thresholds

Journal and Venue Tiers

Author Reputation Assessment

Identifying Seminal Papers

Best Practices

Search Strategy

Screening and Selection

Screening and Selection

Synthesis

Quality and Reproducibility

Writing

Common Pitfalls to Avoid

Example Workflow

Resources

Bundled Resources

External Resources

Dependencies

Required Python Packages

Required System Tools

Summary

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