Systematic Literature Review

Conduct rigorous, reproducible literature searches with verified citations.

When to Use

• •Conducting systematic literature review
• •Synthesizing knowledge on a topic
• •Writing the PLANNING phase literature review
• •Populating .research/literature/ directory
• •Updating manuscript/background.md
• •Meta-analysis or scoping reviews
• •Finding prior work on techniques

Core Workflow

1. PLAN         → Define question, scope, databases
2. SEARCH       → Systematic, documented searches
3. SCREEN       → Apply inclusion/exclusion criteria
4. EXTRACT      → Pull key data from sources
5. SYNTHESIZE   → Identify themes, patterns, gaps
6. VERIFY       → Validate all citations
7. DOCUMENT     → Create reproducible record

Phase 1: Planning

Define Research Question (PICO Framework)

For clinical/biomedical topics:

• •Population: Who is studied?
• •Intervention: What treatment/exposure?
• •Comparison: Versus what?
• •Outcome: What is measured?

Example: "What is the efficacy of CRISPR-Cas9 (I) for treating sickle cell disease (P) compared to standard care (C)?"

Develop Search Strategy

## Search Strategy for: [Topic]

### Core Concepts
1. [Primary concept] - synonyms: [alternative terms]
2. [Secondary concept] - synonyms: [alternative terms]
3. [Methodological aspect]

### Search Queries
- "[concept1] AND [concept2]"
- "[method] in [application domain]"
- "review [topic]" (for overview papers)

### Databases to Search
- [ ] PubMed (biomedical)
- [ ] bioRxiv (preprints)
- [ ] arXiv (computational, physics)
- [ ] Semantic Scholar (cross-disciplinary)
- [ ] OpenAlex (open access)
- [ ] Google Scholar (broad coverage)

### Inclusion Criteria
- Date range: [start] to [end]
- Languages: [list]
- Study types: [list]

### Exclusion Criteria
- [criterion 1]
- [criterion 2]

Phase 2: Systematic Search

Documenting Searches

For each database, record:

## Database: PubMed
- **Date searched**: YYYY-MM-DD
- **Date range**: [start] to [end]
- **Search string**: 

("CRISPR"[Title] OR "Cas9"[Title]) AND ("sickle cell"[MeSH] OR "SCD"[Title/Abstract])

- **Results**: N articles
- **Notes**: [any filter applied]

PubMed Search Tips

• •Use MeSH terms: "disease name"[MeSH]
• •Field tags: [Title], [Title/Abstract], [Author]
• •Boolean: AND, OR, NOT
• •Date filter: 2020:2024[Publication Date]
• •Article type: "Review"[Publication Type]

bioRxiv/medRxiv

• •Preprints - NOT peer-reviewed
• •Check if subsequently published
• •Note version and date

Semantic Scholar / OpenAlex

• •Good for citation networks
• •Cross-disciplinary coverage
• •Can find highly-cited papers

Phase 3: Screening

PRISMA Flow

Records identified (n = X)
├─ Duplicates removed (n = Y)
├─ Records screened (n = Z)
│  └─ Excluded by title/abstract (n = A)
├─ Full-text assessed (n = B)
│  └─ Excluded with reasons (n = C)
└─ Studies included (n = D)

Screening Checklist

For each paper:

• • Meets inclusion criteria
• • Doesn't meet exclusion criteria
• • Relevant to research question
• • Sufficient quality (peer-reviewed, appropriate methods)

Phase 4: Data Extraction

Extract from Each Source

1. •Metadata: Authors, year, journal, DOI
2. •Study design: Methods, population, sample size
3. •Key findings: Main results, effect sizes
4. •Limitations: Noted by authors
5. •Relevance: How it relates to your question
6. •Quality: Assessment of rigor

Literature Note Template

Create in .research/literature/[topic].md:

# Literature Review: [Topic]

Date: YYYY-MM-DD
Search strategy: [link to search doc]

## Summary
[2-3 sentence overview of the literature landscape]

## Key Themes

### Theme 1: [Name]
[Synthesis across multiple papers - NOT paper-by-paper]

Key points:
- Point 1 (Author1, Year; Author2, Year)
- Point 2 (Author3, Year)

### Theme 2: [Name]
...

## Gaps and Controversies
- [Gap 1]: Limited research on...
- [Controversy]: Conflicting results regarding...

## Key Papers

### Author (Year) - Title
- **DOI**: 10.xxxx/xxxxx
- **Main finding**: [One sentence]
- **Relevance**: [How it relates to your work]
- **Limitations**: [Key caveats]

## References
[BibTeX or formatted references]

Phase 5: Thematic Synthesis

Do This ✓

Organize by themes, not by paper:

Multiple delivery approaches have been investigated. Viral vectors 
(AAV) showed high efficiency (65-85%)¹⁻¹⁵ but raised immunogenicity 
concerns³,⁷. Lipid nanoparticles demonstrated lower efficiency 
(40-60%) but improved safety¹⁶⁻²³.

Don't Do This ✗

Paper-by-paper summary:

Smith (2020) found that viral vectors work well. Jones (2021) 
also used viral vectors. Wang (2022) tried nanoparticles...

Synthesis Template

## Thematic Synthesis

### Theme: [Name]

**Current understanding**: [Summary of what is known]

**Consensus areas**: [What most studies agree on]

**Controversies**: [Conflicting findings]

**Gaps**: [What's missing from the literature]

**Evidence quality**: [Overall assessment]

Phase 6: Citation Verification

CRITICAL: Verify All Citations

NEVER fabricate citations. Every claim must have a verifiable source.

Verification Checklist

For each citation:

• • DOI resolves correctly
• • Author names match
• • Year is correct
• • Title matches
• • Journal name correct

Citation Styles

APA (7th Edition)

Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Title of article. 
Journal Name, 22(4), 301-318. https://doi.org/10.xxx/yyy

Nature

Smith, J. D., Johnson, M. L. & Williams, K. R. Title of article. 
Nat. Rev. Drug Discov. 22, 301-318 (2023).

Vancouver

Smith JD, Johnson ML, Williams KR. Title of article. 
Nat Rev Drug Discov. 2023;22(4):301-18.

Phase 7: Documentation

Output Files

BibTeX Entry Template

@article{smith2023,
  author = {Smith, John D. and Johnson, Mary L. and Williams, Karen R.},
  title = {Title of the Article},
  journal = {Journal Name},
  year = {2023},
  volume = {22},
  number = {4},
  pages = {301--318},
  doi = {10.xxx/yyy},
  pmid = {12345678}
}

Integration with RA Workflow

PLANNING Phase Connection

Literature review is a gate for entering DEVELOPMENT:

• • At least one literature search completed → ✓ Creates .research/literature/ content
• • background.md has at least a rough draft → Uses literature synthesis

After Literature Review

1. •Update .research/literature/ with findings
2. •Draft sections in manuscript/background.md
3. •Add citations to .research/literature/*.bib
4. •Log activity in .research/logs/activity.md
5. •Update tasks.md with identified gaps

Connection to Other Skills

• •→ /write_background: Uses literature synthesis to draft background
• •→ /hypothesis_generation: Literature informs hypothesis development
• •← /deep_research: Alternative invocation for same functionality

Quality Checklist

Before completing a literature review:

• • Search strategy documented with all parameters
• • Multiple databases searched (minimum 3)
• • Inclusion/exclusion criteria clearly stated
• • PRISMA flow documented
• • Findings synthesized thematically (not paper-by-paper)
• • All DOIs verified
• • Citations formatted consistently
• • Gaps and controversies identified
• • Key papers annotated
• • BibTeX file created

Common Pitfalls