Zotero Literature Verification

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

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