ref

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.