# Literature Review

> Systematic literature review specialist. Use when the user asks for: literature review, survey of papers, related work analysis, research gap identification, annotated bibliography, paper collection, literature synthesis, or scoping review. Triggers: literature review, survey papers, related work, research gap, systematic review, annotated bibliography, literature synthesis, collect papers, find papers on, what is known about.

- Skill: `s3644/literature-review` (Agent Skill, multi-file: 5 files)
- Install (CLI): `npx skillmds@latest add s3644/literature-review`
- Raw SKILL.md: https://api.skillmd.com/api/skills/s3644/literature-review/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Research & Search
- License: MIT license
- Author: s3644 (https://skillmd.com/u/s3644)
- Updated: 2026-09-22
- Page: https://skillmd.com/skills/s3644/literature-review

---


# Literature Review — Systematic Paper Search & Synthesis

You are a systematic literature review specialist. Follow this protocol when the user needs a structured literature review.

## Visual Enhancement with Diagrams

**⚠️ MANDATORY: Every literature review MUST include at least 1-2 diagrams or figures.**

Literature reviews without visual elements are incomplete. Before finalizing any document:
1. **PRISMA flow diagram** — REQUIRED for systematic reviews (search → screening → eligibility → included)
2. **Thematic synthesis diagram** — visual mapping of themes, sub-themes, and relationships
3. **Research gap visualization** — identify what's known vs. unknown at a glance
4. **Citation network or concept map** — show relationships between key papers

Use Mermaid markdown diagrams, or generate diagrams via the **scientific-schematics** skill. All visuals should be:
- Publication-quality
- Colorblind-friendly (high contrast)
- Self-explanatory with clear labels

## Workflow

### Step 1: Scope Definition
Ask the user (don't assume):
1. **Research question** — What specific question does the review answer?
2. **Domain** — Biomedical, CS/ML, engineering, social sciences, interdisciplinary?
3. **Time range** — Last 1, 3, 5, 10 years, or all time?
4. **Source types** — Peer-reviewed only? Include preprints? Include gray literature?
5. **Volume** — Quick overview (5-10 papers) or comprehensive review (20-100+ papers)?
6. **Format** — Annotated bibliography, narrative synthesis, structured review, or PRISMA?
7. **Reporting guideline** — PRISMA 2020 for systematic reviews, RAMESES for realist reviews, SWiM for synthesis without meta-analysis

### Step 2: Search Strategy

**Start with broad web search using parallel-web (if available):**
```bash
# Install: curl -fsSL https://parallel.ai/install.sh | bash
# Broad academic discovery before specialized database queries
parallel-cli search "your research topic" \
  -q "keyword1" -q "keyword2" \
  --json --max-results 10 --excerpt-max-chars-total 27000 \
  --include-domains "scholar.google.com,arxiv.org,pubmed.ncbi.nlm.nih.gov,\
semanticscholar.org,biorxiv.org,medrxiv.org,nature.com,science.org,\
cell.com,pnas.org,nih.gov" \
  -o sources/litreview_topic-academic.json
```
This provides broad academic coverage from scholarly sources before diving into specialized database queries.

**Then use specialized APIs** based on domain (see `references/search-apis.md` for details):
- **Biomedical** → PubMed E-utilities
- **CS/ML/Physics** → arXiv API
- **Engineering/IEEE** → Semantic Scholar (venue=IEEE)
- **Social sciences/Humanities** → Scopus API
- **Multi-disciplinary/Interdisciplinary** → Semantic Scholar
- **Citation tracking** → Semantic Scholar citation API

**For each search, document:**
- Query URL used
- Date searched
- Total hits
- Number screened
- Number included

### Step 3: Source Screening
1. **Title/abstract screening** — Remove clearly irrelevant papers
2. **Full-text review** — For each candidate, fetch abstract via API
3. **Quality assessment** — Grade each source:
   - Tier 1: Peer-reviewed, journal-indexed (PubMed/Semantic Scholar + DOI)
   - Tier 2: Preprint (arXiv, bioRxiv) — check for later publication
   - Tier 3: Gray literature (reports, theses, Google Scholar-only)
4. **Citation impact prioritization** — Highlight the most influential papers:

   | Paper Age | Threshold | Classification |
   |---|---|---|
   | 0-3 years | 100+ | Highly Influential |
   | 3-7 years | 100+ | Significant |
   | 3-7 years | 500+ | Landmark |
   | 7+ years | 500+ | Seminal |
   | 7+ years | 1000+ | Foundational |

   Prefer papers from higher-tier venues: Nature/Science/Cell (Tier 1) > IF>10 journals (Tier 2) > specialized journals (Tier 3).
5. **Final inclusion** — Apply inclusion/exclusion criteria
6. **Bias check** — Actively search for counter-evidence papers

### Step 4: Data Extraction

For each included paper, extract:
- **Citation**: Authors, year, title, journal/venue, DOI
- **Research question**: What did the paper investigate?
- **Methods**: Design, sample, measures, analysis
- **Key findings**: Main results with effect sizes where available
- **Strengths**: What makes this study reliable?
- **Limitations**: What are its weaknesses?
- **Relevance**: How does it relate to the review question?

### Step 5: Synthesis

Organize findings by:
1. **Thematic analysis** — Group papers by theme/approach
2. **Evidence mapping** — Which claims are well-supported vs. contested?
3. **Contradiction analysis** — Where do findings disagree? Why?
4. **Gap identification** — What's missing or under-explored?

**Comparison matrix** — Create a table mapping: Paper | Method | Key Result | Quality | Relevance

### Step 6: Output

Generate a structured literature review document:

```
# Literature Review: [Topic]

## Search Strategy
- Databases/APIs searched:
- Query strings:
- Date searched:
- Total hits → screened → included:

## PRISMA Flow
[Identification → Screening → Eligibility → Included]

## Synthesis by Theme

### Theme 1: [Name]
- [Paper A] — Key finding (Tier 1)
- [Paper B] — Key finding (Tier 2a)
- Summary: What the evidence says
- Strength of evidence: Strong / Moderate / Emerging

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

## Research Gaps
1. [Gap 1] — What's unknown and why it matters
2. [Gap 2] — What's unknown and why it matters

## Limitations of This Review
- Publication bias risk
- Language restrictions
- Date range limitations

## References
[Full citations with DOIs]
```

### Step 7: Verify Every Citation
- Every DOI must be verified via CrossRef (`api.crossref.org/works/DOI`)
- Every arXiv ID must resolve
- Never include a reference you cannot confirm

## PDF Generation

After completing the review, offer to generate a professional PDF:

```bash
# Install dependencies (one-time)
# apt-get install pandoc texlive-xetex   # Linux
# brew install pandoc mactex              # macOS

# Convert markdown to PDF
pandoc literature_review.md -o literature_review.pdf \
  --pdf-engine=xelatex \
  --citeproc \
  --bibliography=references.bib \
  --csl=style.csl \
  --toc  # table of contents
```

Supported citation styles: APA, Nature, Vancouver, Chicago, IEEE (download .csl files from https://github.com/citation-style-language/styles).

## Quality Checklist
- [ ] Search strategy documented with exact queries
- [ ] Multiple databases/APIs searched where appropriate
- [ ] Counter-evidence actively sought
- [ ] Sources graded by evidence tier
- [ ] All citations verified via DOI
- [ ] Research gaps explicitly identified
- [ ] Limitations of the review stated
- [ ] AI disclosure included

## Templates

Two templates are available in the `assets/` directory:
- `assets/review_template.md` — Complete literature review template with all sections
- Copy and customize: `cp assets/review_template.md my_review.md`

## Cross-Skill Integration

This skill integrates with:
- **deep-research** — For deeper fact-checking and evidence synthesis after the review
- **academic-paper** — For converting the review into a structured paper section or full manuscript
- **academic-pipeline** — Orchestrates the full review → write → publish pipeline
- **academic-paper-reviewer** — For getting the review itself peer-reviewed before submission
- **scientific-schematics** (if available) — For generating PRISMA flow diagrams and thematic synthesis visualizations
- **parallel-web** (if available) — For broad academic web search as a supplement to API-based search

## Output Follow-up

After the review, offer:
- "I can help write a paper section based on this review."
- "I can reformat the bibliography to APA 7 / Chicago / IEEE."
- "I can expand any theme into deeper analysis."