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Zotero

manage Zotero libraries and citations

Published by OpenAI Updated May 5
Covers Research Writing Knowledge Management Codex Zotero

Description

Use Zotero Desktop from Codex to enable/probe the local API, search a local Zotero library, list items/collections/tags, export BibTeX, insert citation keys into LaTeX or Markdown drafts, read indexed full text when requested, and import BibTeX/RIS records into Zotero through the connector server. Use when the user mentions Zotero, citations, references.bib, BibTeX export, local Zotero API, localhost:23119, or adding citations from a Zotero library.

SKILL.md

Zotero

Use this skill to operate a user's local Zotero Desktop library from Codex.

Core helper:

python3 <plugin-root>/skills/zotero/scripts/zotero.py <command>

Resolve <plugin-root> by going two directories up from this SKILL.md file.

The helper is stdlib-only and follows the repo convention of running plugin Python helpers with python3 / #!/usr/bin/env python3; it does not require Codex-specific runtime discovery.

Fast starts

Check readiness in one command:

python3 <plugin-root>/skills/zotero/scripts/zotero.py status --json

Enable the local API and restart Zotero if needed:

python3 <plugin-root>/skills/zotero/scripts/zotero.py enable --restart

Search and export citation data:

python3 <plugin-root>/skills/zotero/scripts/zotero.py search "transformer" --json
python3 <plugin-root>/skills/zotero/scripts/zotero.py export-bibtex --out references.bib

Insert a citation from Zotero into a draft and keep references.bib in sync:

python3 <plugin-root>/skills/zotero/scripts/zotero.py cite --query "Attention Is All You Need" --tex paper.tex --bib references.bib --marker '<cite>'

Workflow

  1. Start with status --json. Do not rediscover prefs, ports, or profile paths manually unless the helper fails.
  2. If local_api_enabled_pref is false, run enable --restart when the user asked you to operate Zotero. This updates Zotero's local preference and restarts Zotero so port 23119 comes up.
  3. Use read-only local API commands for normal work:
    • inventory for item/collection/tag summaries.
    • search <query> for papers/items.
    • export-bibtex or sync-bib for .bib files.
    • cite for inserting a citation into a draft.
  4. Only retrieve attachment file URLs or full text when the user asks for PDFs, attachment paths, or full-text content.
  5. Treat Zotero library writes as explicit write actions. Before import-bibtex, import-ris, or connector save commands, confirm the exact record/source and destination unless the user's prompt already explicitly asked to add/import it.

Common commands

# Readiness and route map
python3 <plugin-root>/skills/zotero/scripts/zotero.py status --json
python3 <plugin-root>/skills/zotero/scripts/zotero.py probe --json

# Library inventory
python3 <plugin-root>/skills/zotero/scripts/zotero.py inventory
python3 <plugin-root>/skills/zotero/scripts/zotero.py collections
python3 <plugin-root>/skills/zotero/scripts/zotero.py tags

# Search and export
python3 <plugin-root>/skills/zotero/scripts/zotero.py search "BERT"
python3 <plugin-root>/skills/zotero/scripts/zotero.py export-bibtex --out references.bib
python3 <plugin-root>/skills/zotero/scripts/zotero.py export-bibtex --item-key PXW99EKT
python3 <plugin-root>/skills/zotero/scripts/zotero.py citations --style apa --json

# Draft editing
python3 <plugin-root>/skills/zotero/scripts/zotero.py cite --item-key PXW99EKT --tex paper.tex --bib references.bib --marker '<cite>'
python3 <plugin-root>/skills/zotero/scripts/zotero.py cite --query "BERT" --markdown notes.md --bib references.bib --marker '<cite>'

# Attachments and full text; use only on request
python3 <plugin-root>/skills/zotero/scripts/zotero.py children PXW99EKT --json
python3 <plugin-root>/skills/zotero/scripts/zotero.py fulltext 2JAZS9U8 --out attention-fulltext.txt
python3 <plugin-root>/skills/zotero/scripts/zotero.py file-url 2JAZS9U8

# Writes to Zotero; confirm first unless explicitly requested
python3 <plugin-root>/skills/zotero/scripts/zotero.py selected-target --json
python3 <plugin-root>/skills/zotero/scripts/zotero.py import-bibtex --file new-reference.bib --yes
python3 <plugin-root>/skills/zotero/scripts/zotero.py import-ris --file new-reference.ris --yes

Output standards

  • For inventory/search, return title, creators, year, Zotero item key, and BibTeX key when available.
  • Explain the two-key distinction when relevant: Zotero item keys like PXW99EKT are not the same as exported BibTeX keys like vaswani_attention_2023.
  • For .bib export, return the absolute output path and entry count.
  • For draft citation insertion, report the edited file, inserted citation key, and updated .bib path.
  • For blockers, name the exact gate: Zotero app missing, local API disabled, port closed, connector unavailable, no matching item, or write not confirmed.

Route details

Read references/local-api-routes.md only when you need endpoint details beyond the helper commands.

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