Zotero Management

Zotero Library Management

Systematic management of an academic literature library via Zotero.

When to Use

• User asks to add a paper to Zotero
• User asks to check their reading queue
• User wants to organize papers for a project
• User asks "what's in my library about X?"
• User asks to clean up or reorganize collections

Library Structure

Standard collection hierarchy:

00_Inbox           → Newly added, unprocessed papers
10_Active Projects → Papers actively being used in current work
20_Background      → General domain knowledge, surveys, textbooks
30_Reading Queue   → Papers to read, prioritized
40_Archive         → Completed projects, historical reference
90_Meta            → Templates, style guides, writing resources

Tag System

Use tags to cross-cut the collection hierarchy:

• Project tags: #Inception, #AI-Scientist-BioAge, #ChemRetro, #CAST
• Status tags: #to-read, #reading, #read, #summarized
• Priority tags: #urgent, #high, #low
• Type tags: #survey, #method, #benchmark, #position-paper

API Access

Two access modes:

| Mode | Endpoint | Capability | |------|----------|------------| | Local API | localhost:23119 | Read-only, fast, requires Zotero running | | Web API | api.zotero.org | Read-write, works always, needs API key |

# Check if Zotero is running locally
curl -s http://localhost:23119/api/users/0/items?limit=1

# Web API (read-write)
curl -s -H "Zotero-API-Key: $ZOTERO_API_KEY" \
  "https://api.zotero.org/users/$ZOTERO_USER_ID/items?limit=5"

Workflows

Adding a Paper

1. Find metadata: Get title, authors, year, venue, DOI/arXiv ID
2. Check for duplicates: Search existing library by title
3. Present summary to user: Don't auto-add — confirm first
4. Add to Zotero via Web API with:

• Correct item type (journalArticle, conferencePaper, preprint)
• All available metadata fields
• Collection: 30_Reading Queue (default) or user-specified
• Tags: project tag + #to-read

1. Attach notes: Source link (social media post, blog, etc.) as a note

Checking Reading Queue

# Get items in Reading Queue collection
curl -s -H "Zotero-API-Key: $ZOTERO_API_KEY" \
  "https://api.zotero.org/users/$ZOTERO_USER_ID/collections//items?limit=50"

Present as a prioritized list:

📚 Reading Queue (N papers)

🔴 Urgent:
1. [Paper Title] — added [date], tagged #Inception

🟡 High priority:
2. [Paper Title] — added [date], tagged #AI-Scientist-BioAge

⚪ Normal:
3. ...

After Reading a Paper

1. Move from 30_Reading Queue to 10_Active Projects or 20_Background
2. Update tag: #to-read → #read or #summarized
3. Add reading notes as a child note item
4. Link to project if relevant

Project Literature Setup

When starting a new project:

1. Create a project tag (e.g., #NewProject)
2. Do initial literature search (use literature-search skill)
3. Batch-add relevant papers to 30_Reading Queue with project tag
4. Prioritize: which papers must be read first?

Key Principles

1. Confirm before adding — always show summary, let user decide
2. Preserve provenance — record where you found the paper (social media link, search query)
3. One source of truth — Zotero is the canonical library; don't maintain parallel lists
4. Tags cross-cut collections — a paper can be in one collection but tagged for multiple projects
5. Regular maintenance — periodically review Inbox and Reading Queue for stale items

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: jxtse
• Source: jxtse/scientific-research-skills
• License: MIT

Install and usage instructions live in the source repository linked above.