methodology-extractor

name	methodology-extractor
description	Batch extraction of experimental methods from multiple papers for protocol comparison
version	1.0.0
category	Research
tags	[]
author	AIPOCH
license	MIT
status	Draft
risk_level	Medium
skill_type	Tool/Script
owner	AIPOCH
reviewer
last_updated	2026-02-06

Methodology Extractor

Extract and compare experimental protocols across papers.

Use Cases

• Protocol optimization
• Methods comparison for systematic reviews
• Reproducibility assessment

Parameters

• paper_ids: List of papers to analyze
• method_type: Target method (e.g., "Western Blot", "qPCR")

Returns

• Comparison table of protocols
• Parameter variations across studies
• Best practice recommendations

Example

Input: 50 papers, method_type="Western Blot" Output: Table showing antibody concentrations, blocking conditions, wash times

Risk Assessment

Risk Indicator	Assessment	Level
Code Execution	Python/R scripts executed locally	Medium
Network Access	No external API calls	Low
File System Access	Read input files, write output files	Medium
Instruction Tampering	Standard prompt guidelines	Low
Data Exposure	Output files saved to workspace	Low

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

No additional Python packages required.

Evaluation Criteria

Success Metrics