Extract Structured Data from Scientific PDFs

Purpose

Extract standardized, structured data from scientific PDF literature using Claude's vision capabilities. Transform PDF collections into validated databases ready for statistical analysis in Python, R, or other frameworks.

Core capabilities:

• Organize metadata from BibTeX, RIS, directories, or DOI lists
• Filter papers by abstract using Claude (Haiku/Sonnet) or local models (Ollama)
• Extract structured data from PDFs with customizable schemas
• Repair and validate JSON outputs automatically
• Enrich with external databases (GBIF, WFO, GeoNames, PubChem, NCBI)
• Calculate precision/recall metrics for quality assurance
• Export to Python, R, CSV, Excel, or SQLite

When to Use This Skill