zotero-literature-verification

name	zotero-literature-verification
description	Complete workflow for verifying academic literature citations using Zotero MCP with full PDF reading and token management

Zotero Literature Verification

Complete workflow for verifying academic literature citations using Zotero MCP with 100% word-by-word PDF reading and token budget management.

Quick Start

When invoked with /zotero-literature-verification, guide the user through:

1. Token Budget Estimation - Calculate required tokens based on page count
2. PDF Extraction - Extract complete PDF text using PyMuPDF
3. Sequential Reading - Read every word from first to last page in chunks
4. Citation Verification - Verify citations with line numbers and exact quotes
5. Reference Generation - Generate ACM-formatted reference list from Zotero

Zero-Tolerance Protocol ⚠️

CRITICAL: When verifying citations, you MUST:

• ✅ Extract COMPLETE PDF text to /tmp
• ✅ Read EVERY word from first page to last page
• ✅ Record line numbers for all verified citations
• ✅ NEVER use keyword search as substitute for complete reading
• ✅ Monitor token usage after each paper

FORBIDDEN:

• ❌ Reading only Abstract and Conclusion
• ❌ Using grep/search without full text reading
• ❌ Skipping middle sections of papers
• ❌ Assuming content without reading

Token Budget Estimation

Formula: Pages × 700 + 1000 = Estimated Tokens

Papers	Pages	Est. Tokens	Safe?
1-2	10-20	~20k	✅ Safe
3-4	30-40	~50k	✅ Safe
5-6	50-90	~90k	✅ Safe
7+	100+	~140k+	⚠️ Split sessions

Token Zones:

• Safe: < 100k used (100k+ remaining)
• Caution: 100-150k used (50-100k remaining)
• Danger: > 150k used (< 50k remaining) → Pause and wait for user

Workflow

Step 1: Extract PDF

import fitz
doc = fitz.open('/Users/Zhuanz/Zotero/storage/XXXXXXXX/Paper.pdf')
text = '\n'.join([p.get_text() for p in doc])
with open('/tmp/paper_full.txt', 'w') as f:
    f.write(text)
print(f"✅ {doc.page_count} pages, {len(text)} chars")

Step 2: Read Sequentially

Read in chunks of 250-300 lines:

# Chunk 1: Lines 0-250 (Title, Abstract, Introduction)
Read("/tmp/paper_full.txt", offset=0, limit=250)

# Chunk 2: Lines 250-500 (Methods, early Results)
Read("/tmp/paper_full.txt", offset=250, limit=250)

# Chunk 3: Lines 500-750 (Results, Discussion)
Read("/tmp/paper_full.txt", offset=500, limit=250)

# Chunk 4: Lines 750-1000 (Conclusion, References)
Read("/tmp/paper_full.txt", offset=750, limit=250)

Step 3: Verify Citations

After complete reading, locate exact quotes:

# Find exact line number
grep -n "exact quoted phrase" /tmp/paper_full.txt

# Read context (±20 lines)
Read("/tmp/paper_full.txt", offset=436, limit=40)

Step 4: Get Metadata from Zotero

Use Zotero MCP tools:

• mcp__zotero__zotero_get_item_metadata - Get complete metadata
• mcp__zotero__zotero_search_items - Search by author/year/title
• mcp__zotero__zotero_get_item_fulltext - Get PDF text

Step 5: Generate Report

## Verification Report

| Paper | Pages | Status | Issues |
|-------|-------|--------|--------|
| Author 2025 | 15 | ✅ | Corrected: false attribution |
| Author 2024 | 19 | ✅ | None - accurate |

## References (ACM Format)

[Author Year] FirstName LastName, FirstName LastName. Year.
Title of Paper. In Proceedings of CONF (CONF 'YY), Vol. 19.
AAAI Press, Pages. DOI: https://doi.org/XX.XXXX/XXXXXXX

Token Management

Monitor after each paper:

if tokens_remaining < 50000:
    print("⚠️ WARNING: Less than 50k tokens remaining")
    print("Recommend: Save progress and continue in new session")

Real Performance (from 2026-02-05):

• 6 papers, 91 pages, 369,478 characters
• Token used: 113,000 / 200,000 (56.5%)
• Time: ~2 hours
• Result: 100% accurate verification

Emergency Procedures

Token Budget Exhausted (< 30k remaining)

# Save progress
cat > /tmp/verification_progress.txt << EOF
Completed: Paper1, Paper2, Paper3
Current: Paper4 (line 500/1200)
Pending: Paper5, Paper6
Token used: 150,000
EOF

# Report to user and STOP

Quality Checklist

Before claiming "verification complete":

• Read complete text (first page → last page)
• Located References section (proves completeness)
• Recorded line numbers for all citations
• Verified numerical data (N=X, p<0.05)
• Checked author's evaluation words
• Collected complete metadata from Zotero
• Generated ACM-formatted reference list
• Stayed within token budget

Dependencies

# Install PyMuPDF
pip install PyMuPDF

# Ensure Zotero is running with local API enabled
# Settings → Advanced → "Allow other applications to communicate with Zotero"

Documentation

• instructions.md - Complete workflow details
• QUICK_REFERENCE.md - Quick reference card
• example_workflow.py - Working example
• README.md - Project overview

Version History

• v2.0.0 (2026-02-05): Added token management, 6-paper verification workflow
• v1.0.0 (2026-02-02): Initial release