Zotero Management

---
name: zotero-management
description: >
  Manages a Zotero academic reference library through both the local API
  (localhost:23119, read-only) and the Web API (api.zotero.org, read-write),
  using a structured collection hierarchy (Inbox / Active Projects /
  Background / Reading Queue / Archive / Meta) plus project, status, priority,
  and type tags. Handles adding papers with full metadata, deduplication,
  attaching provenance notes, moving items between collections, updating tags
  after reading, listing the prioritized reading queue, and setting up the
  literature scaffold for a new project. Use when the user asks to add /
  save / file / organize a paper in Zotero, check / list / clean up the
  reading queue, move papers between collections, tag papers for a project,
  query their library ("what do I have on X?"), or set up Zotero for a new
  research project.
---

# 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40_Archive         → Completed projects, historical reference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 |

```bash
# 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`
5. **Attach notes**: Source link (social media post, blog, etc.) as a note

### Checking Reading Queue

```bash
# Get items in Reading Queue collection
curl -s -H "Zotero-API-Key: $ZOTERO_API_KEY" \
  "https://api.zotero.org/users/$ZOTERO_USER_ID/collections/<COLLECTION_KEY>/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