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40_Archive → Completed projects, historical reference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
- Find metadata: Get title, authors, year, venue, DOI/arXiv ID
- Check for duplicates: Search existing library by title
- Present summary to user: Don't auto-add — confirm first
- 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
- 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/<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
- Move from
30_Reading Queue to 10_Active Projects or 20_Background
- Update tag:
#to-read → #read or #summarized
- Add reading notes as a child note item
- Link to project if relevant
Project Literature Setup
When starting a new project:
- Create a project tag (e.g.,
#NewProject)
- Do initial literature search (use literature-search skill)
- Batch-add relevant papers to
30_Reading Queue with project tag
- Prioritize: which papers must be read first?
Key Principles
- Confirm before adding — always show summary, let user decide
- Preserve provenance — record where you found the paper (social media link, search query)
- One source of truth — Zotero is the canonical library; don't maintain parallel lists
- Tags cross-cut collections — a paper can be in one collection but tagged for multiple projects
- Regular maintenance — periodically review Inbox and Reading Queue for stale items
1---2name: zotero-management3description: 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.4---56# Zotero Library Management78Systematic management of an academic literature library via Zotero.910## When to Use1112- User asks to add a paper to Zotero13- User asks to check their reading queue14- User wants to organize papers for a project15- User asks "what's in my library about X?"16- User asks to clean up or reorganize collections1718## Library Structure1920Standard collection hierarchy:2122```2300_Inbox → Newly added, unprocessed papers2410_Active Projects → Papers actively being used in current work2520_Background → General domain knowledge, surveys, textbooks2630_Reading Queue → Papers to read, prioritized2740_Archive → Completed projects, historical reference2890_Meta → Templates, style guides, writing resources29```3031## Tag System3233Use tags to cross-cut the collection hierarchy:3435- **Project tags**: `#Inception`, `#AI-Scientist-BioAge`, `#ChemRetro`, `#CAST`36- **Status tags**: `#to-read`, `#reading`, `#read`, `#summarized`37- **Priority tags**: `#urgent`, `#high`, `#low`38- **Type tags**: `#survey`, `#method`, `#benchmark`, `#position-paper`3940## API Access4142Two access modes:4344| Mode | Endpoint | Capability |45|------|----------|------------|46| **Local API** | `localhost:23119` | Read-only, fast, requires Zotero running |47| **Web API** | `api.zotero.org` | Read-write, works always, needs API key |4849```bash50# Check if Zotero is running locally51curl -s http://localhost:23119/api/users/0/items?limit=15253# Web API (read-write)54curl -s -H "Zotero-API-Key: $ZOTERO_API_KEY" \55 "https://api.zotero.org/users/$ZOTERO_USER_ID/items?limit=5"56```5758## Workflows5960### Adding a Paper61621. **Find metadata**: Get title, authors, year, venue, DOI/arXiv ID632. **Check for duplicates**: Search existing library by title643. **Present summary to user**: Don't auto-add — confirm first654. **Add to Zotero** via Web API with:66 - Correct item type (journalArticle, conferencePaper, preprint)67 - All available metadata fields68 - Collection: `30_Reading Queue` (default) or user-specified69 - Tags: project tag + `#to-read`705. **Attach notes**: Source link (social media post, blog, etc.) as a note7172### Checking Reading Queue7374```bash75# Get items in Reading Queue collection76curl -s -H "Zotero-API-Key: $ZOTERO_API_KEY" \77 "https://api.zotero.org/users/$ZOTERO_USER_ID/collections/<COLLECTION_KEY>/items?limit=50"78```7980Present as a prioritized list:81```82📚 Reading Queue (N papers)8384🔴 Urgent:851. [Paper Title] — added [date], tagged #Inception8687🟡 High priority:882. [Paper Title] — added [date], tagged #AI-Scientist-BioAge8990⚪ Normal:913. ...92```9394### After Reading a Paper95961. Move from `30_Reading Queue` to `10_Active Projects` or `20_Background`972. Update tag: `#to-read` → `#read` or `#summarized`983. Add reading notes as a child note item994. Link to project if relevant100101### Project Literature Setup102103When starting a new project:1041. Create a project tag (e.g., `#NewProject`)1052. Do initial literature search (use literature-search skill)1063. Batch-add relevant papers to `30_Reading Queue` with project tag1074. Prioritize: which papers must be read first?108109## Key Principles1101111. **Confirm before adding** — always show summary, let user decide1122. **Preserve provenance** — record where you found the paper (social media link, search query)1133. **One source of truth** — Zotero is the canonical library; don't maintain parallel lists1144. **Tags cross-cut collections** — a paper can be in one collection but tagged for multiple projects1155. **Regular maintenance** — periodically review Inbox and Reading Queue for stale items
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