| name | ref |
| description | Manage academic references in CSL-JSON format. Add papers by DOI/PMID/ISBN/arXiv, search and list references, generate citations, manage full-text PDFs, and check for retractions. |
| allowed-tools | ["Bash","Read","Write","Edit","Glob","Grep"] |
ref — Reference Manager
A CLI tool for managing academic references using CSL-JSON as the single source of truth.
Quick Reference
| Task | Command |
|---|
| Add by DOI | ref add 10.1234/example |
| Add by PMID | ref add 12345678 |
| Add by ISBN | ref add 978-0-123456-78-9 |
| Add by arXiv | ref add 2301.12345 |
| Add from BibTeX | ref add references.bib |
| Add from RIS | ref add references.ris |
| Search | ref search "query" |
| List all | ref list |
| Show details | ref show <id> |
| Generate citation | ref cite <id> |
| Export | ref export <id> --output bibtex |
| Attach full-text | ref fulltext attach <id> paper.pdf |
| Fetch full-text | ref fulltext fetch <id> |
| Check retractions | ref check <id> |
| Remove | ref remove <id> |
| Update fields | ref update <id> --set "title=New Title" |
| Configure | ref config set <key> <value> |
Search Syntax
- Simple text:
ref search "machine learning"
- By author:
ref search "author:Smith"
- By year:
ref search "year:2024"
- By type:
ref search "type:article-journal"
- By tag:
ref search "tag:review"
- Combined:
ref search "author:Smith year:2024"
- Case-sensitive: prefix with
C/ (e.g., ref search "C/RNA")
Output Formats
Most commands support --output or --json flags:
--json — JSON output for programmatic use--output bibtex — BibTeX format--output yaml — YAML format
Full Help
Run ref --help for all commands and options.
Run ref <command> --help for command-specific help.
