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 or conducting literature review, you MUST:

Reading Requirements (MANDATORY - NO EXCEPTIONS):

• ✅ Extract COMPLETE PDF text to /tmp
• ✅ Read EVERY SINGLE WORD from first page to last page
• ✅ Cover 100% of the document - NO skipping allowed
• ✅ Use sequential chunks to ensure complete coverage
• ✅ Verify completion by reading References section
• ✅ Track exact line numbers for all citations
• ✅ Monitor token usage after each paper

STRICTLY FORBIDDEN:

• ❌ Reading only Abstract, Introduction, and Conclusion
• ❌ Reading "representative sections" - MUST read ALL sections
• ❌ Using grep/search as substitute for complete reading
• ❌ Skipping methodology, results, or discussion sections
• ❌ Assuming content without actual reading
• ❌ Reading "key parts" and claiming completion
• ❌ Stopping after "getting the main idea"
• ❌ Any form of partial reading or summarization without full coverage

Reading Strategy (NON-NEGOTIABLE):

For ANY paper or document:

1. Extract full text to temporary file
2. Calculate total lines and plan chunk sizes (250-300 lines per chunk)
3. Read sequentially: lines 0-300, 300-600, 600-900, etc.
4. Continue until reaching the final line (References section)
5. Only after reaching final line may you claim "reading complete"
6. Record total lines read as proof of completion

Example for 1200-line paper:

• Chunk 1: Lines 0-300 ✓
• Chunk 2: Lines 300-600 ✓
• Chunk 3: Lines 600-900 ✓
• Chunk 4: Lines 900-1200 ✓
• Total: 1200/1200 lines (100%) ← This is the ONLY acceptable standard

Anti-Cheating Measures:

Self-Audit Before Claiming Completion:

• What is the total line count of this document?
• What is the last line number I read?
• Are these two numbers equal? (If NO, continue reading)
• Did I skip any sections between start and end?
• Can I quote from the middle sections (not just intro/conclusion)?

Penalty for Violation: If you discover you have not read 100% of a document:

1. Immediately acknowledge the error
2. Re-read the ENTIRE document from beginning
3. Update progress tracking to reflect honest completion status
4. Do NOT claim completion until 100% coverage achieved

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