Systematic Review Screener

Source: https://github.com/aipoch/medical-research-skills

Systematic Review Screener

Automated abstract screening tool for systematic literature reviews with PRISMA workflow support.

Quick Check

Use this command to verify that the packaged script entry point can be parsed before deeper execution.

python -m py_compile scripts/main.py

Audit-Ready Commands

Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.

python -m py_compile scripts/main.py
python scripts/main.py --help
python scripts/main.py -h
python scripts/main.py --help

When to Use

• Use this skill when the task needs Automated abstract screening tool for systematic literature reviews with PRISMA workflow support.
• Use this skill for evidence insight tasks that require explicit assumptions, bounded scope, and a reproducible output format.
• Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence.

Workflow

1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
2. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
3. Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
4. Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

Overview

This skill screens academic abstracts against predefined inclusion/exclusion criteria, generating PRISMA-compliant outputs with decision rationale and confidence scores.

Technical Difficulty: High ⚠️ Manual verification recommended for final inclusion decisions.

Features

• Multi-format Input: PubMed MEDLINE, EndNote XML, CSV/TSV
• Criteria Matching: Configurable inclusion/exclusion rules
• Confidence Scoring: 0-100% confidence for each decision
• Conflict Detection: Flags abstracts requiring human review
• PRISMA Export: Flow diagram data and screening log
• Batch Processing: Handles large reference sets efficiently

Usage

Basic Screening

# Run with default settings
python scripts/main.py --input references.csv --criteria criteria.yaml

With PRISMA Export

python scripts/main.py --input references.xml --criteria criteria.yaml \
  --output results/ --prisma --format excel

Confidence Threshold

python scripts/main.py --input refs.txt --criteria criteria.yaml \
  --threshold 0.8 --conflict-only

Input Formats

1. CSV/TSV

Required columns: title, abstract (optional: authors, year, doi, pmid)

title,abstract,authors,year
title,abstract,authors,year

2. PubMed MEDLINE

Standard .txt export from PubMed search.

3. EndNote XML

Export from EndNote with abstracts included.

Criteria File (YAML)

See references/criteria_template.yaml for complete example:

study_type:
  include:
    - "randomized controlled trial"
    - "systematic review"
  exclude:
    - "case report"
    - "letter"
    - "editorial"

population:
  include_keywords:
    - "adults"
    - "elderly"
  exclude_keywords:
    - "pediatric"
    - "children"

intervention:
  required:
    - "drug therapy"
    - "medication"

language:
  allowed: ["English"]
  
year_range:
  min: 2010
  max: 2024

confidence_threshold: 0.75

Output Files

PRISMA Workflow Support

Generates structured data for PRISMA 2020 flow diagram:

{
  "identification": {
    "database_results": 1250,
    "register_results": 45,
    "other_sources": 12
  },
  "screening": {
    "records_screened": 1307,
    "records_excluded": 1150,
    "full_text_assessed": 157,
    "full_text_excluded": 89
  },
  "included": {
    "qualitative_synthesis": 68,
    "quantitative_synthesis": 42
  }
}

Configuration

Environment Variables

export SCREENING_THRESHOLD=0.75  # Default confidence threshold
export BATCH_SIZE=100             # Records per batch
export MAX_WORKERS=4              # Parallel processing workers

Command Line Options

Decision Algorithm

1. Keyword Matching: Exact and fuzzy keyword matching against title/abstract
2. Inclusion Scoring: Points for each inclusion criterion matched
3. Exclusion Check: Immediate exclusion if exclusion criterion detected
4. Confidence Calculation: Weighted score based on keyword presence and clarity
5. Conflict Flagging: Records with confidence < threshold flagged for manual review

Limitations

• Not for Final Decisions: Tool provides recommendations; human review required for inclusion
• Language Dependent: Optimized for English abstracts
• Structured Abstracts: Performs better on structured abstracts (Background/Methods/Results/Conclusion)
• Domain Specific: Criteria must be tailored to research question

References

• references/criteria_template.yaml - Complete criteria configuration example
• references/prisma_2020_checklist.pdf - PRISMA 2020 reporting guidelines
• references/sample_references.csv - Example input format

Version

Version: 1.0.0
Last Updated: 2026-02-05
Classification: Research Tool - Requires Human Verification

Risk Assessment

Security Checklist

• No hardcoded credentials or API keys
• No unauthorized file system access (../)
• Output does not expose sensitive information
• Prompt injection protections in place
• Input file paths validated (no ../ traversal)
• Output directory restricted to workspace
• Script execution in sandboxed environment
• Error messages sanitized (no stack traces exposed)
• Dependencies audited

Prerequisites

# Python dependencies
pip install -r requirements.txt

Evaluation Criteria

Success Metrics

• Successfully executes main functionality
• Output meets quality standards
• Handles edge cases gracefully
• Performance is acceptable

Test Cases

1. Basic Functionality: Standard input → Expected output
2. Edge Case: Invalid input → Graceful error handling
3. Performance: Large dataset → Acceptable processing time

Lifecycle Status

• Current Stage: Draft
• Next Review Date: 2026-03-06
• Known Issues: None
• Planned Improvements:
  • Performance optimization
  • Additional feature support

Output Requirements

Every final response should make these items explicit when they are relevant:

• Objective or requested deliverable
• Inputs used and assumptions introduced
• Workflow or decision path
• Core result, recommendation, or artifact
• Constraints, risks, caveats, or validation needs
• Unresolved items and next-step checks