Agent skill · data analytics · aiskillstore
extract-from-pdfs
This skill should be used when extracting structured data from scientific PDFs for systematic reviews, meta-analyses, or database creation. Use when working with collections of research papers that need to be converted into analyzable datasets with validation metrics.
Why this skill is useful
Adds a complete extraction pipeline with executable scripts for structured data extraction from scientific PDFs that aren't commonly available.
What it needs
Requires conda installed locally. Requires anthropic account access. About 4k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
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 Use when: Conducting systematic literature reviews requiring data extraction Building databases from scientific publications Converting PDF collections to structured datasets Validating extraction quality with ground truth metrics Comparing extraction approaches (different models, prompts) Do not use for: Single PDF summarization (use basic PDF reading instead) Full-text PDF search (use document search tools) PDF editing or manipulation Getting Started 1. Initial Setup Read the setup guide for installation and configuration: Key setup steps: Install dependencies: conda env create -f environment.yml Set API keys: export ANTHROPICAPIKEY='your-key' Optional: Install Ollama for free local filtering 2. Define Extraction Requirements Ask the user: Research domain and extraction goals How PDFs are organized (reference manager, directory, DOI list) Approximate collection size Preferred analysis environment (Python, R, etc.) Provide 2-3 example PDFs to analyze structure and design schema. 3. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/extract-from-pdfs