A PRISMA 2020 systematic review and scoping review agent for Claude Code CLI. Covers the full review lifecycle: protocol development, search strategy, screening, data extraction, risk of bias assessment, evidence synthesis, and PRISMA-compliant reporting.
The agent follows a 1 agent + 4 forked sub-skills architecture. The orchestrating agent delegates each review phase to a specialized skill running in isolated (context: fork) context:
systematic-review-agent (orchestrator)
|
|-- sr-protocol-builder PICO/PCC, eligibility, search strategy, directory init
|-- sr-search-and-prompt PubMed/Scholar search, AI prompt generation, ingestion
|-- sr-screen-and-extract Screening decisions, data extraction, RoB assessment
|-- sr-synthesize-and-report Evidence tables, synthesis, PRISMA compliance, final report, audit
Each sub-skill receives a focused task, runs in its own context window, and returns results to the orchestrator. This keeps each phase within token limits while preserving methodological coherence across the full review.
- Claude Code CLI:
npm install -g @anthropic-ai/claude-code
# Copy agent definition
cp agents/systematic-review-agent.md ~/.claude/agents/
# Copy skills
cp -r skills/systematic-review-agent ~/.claude/skills/
cp -r skills/sr-protocol-builder ~/.claude/skills/
cp -r skills/sr-search-and-prompt ~/.claude/skills/
cp -r skills/sr-screen-and-extract ~/.claude/skills/
cp -r skills/sr-synthesize-and-report ~/.claude/skills/The agent integrates with the following optional skills when available:
| Skill | Purpose |
|---|---|
chain-of-verification |
Mandatory verification of all synthesis claims (--thorough mode) |
scientific-skills |
PubMed API (pubmed-database), ClinicalTrials.gov (clinicaltrials-database), citation verification (literature-review), PDF generation |
fetch-papers |
Open-access PDF retrieval via Unpaywall (free) |
/review init [topic] Initialize protocol and directory structure
/review search Execute searches and generate AI prompts
/review screen Run screening loop (title/abstract + full-text)
/review extract Run data extraction loop
/review synthesize Build evidence tables and final report
/review audit [path] Audit an existing review for PRISMA 2020 compliance
/review status Show PRISMA compliance and progress
/review checklist Display current PRISMA tracker
- PRISMA 2020 (27-item) and PRISMA-ScR (22-item) compliance tracking updated after every phase
- AI transparency reporting per PRISMA 2020 Items 8/9/11 and the emerging PRISMA-AI extension
- SWiM (Synthesis Without Meta-Analysis) 9-item checklist integration for narrative synthesis
14 reference documents bundled under skills/systematic-review-agent/references/:
- PRISMA 2020 checklist and Explanation & Elaboration
- PRISMA-ScR checklist with all 22 TipSheets
- PRISMA-P protocol checklist (17 items / 26 sub-items)
- PRISMA flow diagram guide (35-field data model, 4 variants)
- SWiM guideline for synthesis without meta-analysis
- Risk of bias tools (RoB 2, ROBINS-I, ROBINS-E, NOS, AMSTAR 2, QUADAS-2, PROBAST, QUIPS, and others)
- Search strategy guide (PubMed MeSH, Google Scholar, Embase, PRISMA-S, MECIR standards)
- GRADE certainty assessment (5 downgrade + 3 upgrade domains, SoF tables)
- Biomechanical review guide (BIOMECH_CHECKLIST, FE_CHECKLIST)
- AI prompt templates (Perplexity Pro, Elicit Pro, Gemini, Claude.ai)
- AI transparency requirements and disclosure framework
- 8 methodological decision trees (synthesis method, MA model, RoB tool, GRADE, reporting bias, heterogeneity, protocol deviations, review type selection)
9 project templates under skills/systematic-review-agent/assets/templates/:
- Review protocol (
REVIEW_PROTOCOL_TEMPLATE.md) - Review plan / paper checklist (
REVIEW_PLAN_TEMPLATE.md) - Data extraction form (
DATA_EXTRACTION_FORM_TEMPLATE.md) - Evidence table (
EVIDENCE_TABLE_TEMPLATE.md) - PRISMA flow diagram (
PRISMA_FLOW_TEMPLATE.md) - Screening log (
SCREENING_LOG_TEMPLATE.md) - AI usage log (
AI_USAGE_LOG_TEMPLATE.md) - Final report / manuscript (
FINAL_REPORT_TEMPLATE.md) - Review audit / compliance assessment (
REVIEW_AUDIT_TEMPLATE.md)
- Automated screening loop (
screening-loop.sh) for iterative paper-by-paper screening and extraction with fresh context per iteration - Deduplication by DOI/PMID across multiple search sources
- AI prompt generation for Perplexity Pro, Elicit Pro, Gemini, and Claude.ai web UIs
- Open-access PDF retrieval via Unpaywall integration
- Systematic reviews (intervention effectiveness)
- Scoping reviews
- Diagnostic test accuracy (DTA) reviews
- Prognostic factor reviews
- Prevalence/incidence reviews
- Prediction model reviews
- Etiological/risk factor reviews
- Biomechanical evidence reviews (cadaveric, finite element, animal model)
- Qualitative evidence synthesis (QES)
- Network meta-analysis (NMA)
- Umbrella reviews
- Living systematic reviews
- Rapid reviews
- Mixed methods reviews
8 structured decision trees for key methodological choice points:
- Synthesis method selection (meta-analysis vs. SWiM alternatives)
- Meta-analysis model selection (fixed-effect vs. random-effects)
- Risk of bias tool selection (by study design)
- GRADE certainty assessment (downgrading/upgrading)
- Reporting bias assessment (funnel plot, qualitative)
- Heterogeneity assessment (I-squared interpretation)
- Protocol deviation tracking
- Review type selection (SR vs. ScR vs. QES vs. umbrella vs. rapid)
- BIOMECH_CHECKLIST (6 domains) for cadaveric and mechanical testing studies
- FE_CHECKLIST (6 domains) for finite element modeling studies
- Adapted GRADE starting at Moderate for validated biomechanical studies
- Mixed-study synthesis guidance for combining clinical and engineering evidence
All reference files are indexed in skills/systematic-review-agent/references/INDEX.md. Key lookup paths:
| I need to... | Reference file |
|---|---|
| Track PRISMA compliance (SR) | prisma-2020-checklist.md |
| Track PRISMA compliance (ScR) | prisma-scr-checklist.md |
| Get item-by-item PRISMA guidance | prisma-ee-elaborations.md |
| Write a review protocol | prisma-p-checklist.md |
| Choose a risk of bias tool | risk-of-bias-tools.md or decision-trees.md |
| Build database search strings | search-strategy-guide.md |
| Rate certainty of evidence | quality-assessment-scales.md or decision-trees.md |
| Decide synthesis method | decision-trees.md and swim-guideline.md |
| Generate PRISMA flow diagram | prisma-flow-diagram-guide.md |
| Assess biomechanical studies | biomechanical-review-guide.md |
| Report AI tool use | prisma-ai-transparency.md |
This agent's methodology is informed by open-access and published standards including the Cochrane Handbook, PRISMA 2020, GRADE, and others. See ATTRIBUTION.md for the full bibliography.
This project is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) license.