lit-synthesizer - Synthesize PubMed and bioRxiv literature into reports.
Searches PubMed and bioRxiv to synthesize literature into markdown reports, create citation graphs, and generate reproducibility bundles.
Tags
Updated: 2026-09-24Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Search PubMed via NCBI E-utilities
- Search bioRxiv via Europe PMC
- Synthesize recurring abstract themes
- Build node-edge citation graph
- Export reproducibility bundle
- Generate structured Markdown report
Inputs
- Search query string
- Output directory path
Outputs
- Markdown synthesis report
- Structured JSON paper dataset
- JSON citation graph
- CSV paper list table
- Reproducibility bundle
Requirements
- Python >= 3.11
- biopython >= 1.83
- Linux or macOS
- Network access for API queries