文献引用整理与核验｜个人思维图谱小站

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assets/citation_checklist.md

Use this checklist to ensure your citations are accurate, complete, and properly formatted before final submission.

Pre-Submission Checklist

✓ Metadata Accuracy

All author names are correct and properly formatted
Article titles match the actual publication
Journal/conference names are complete (not abbreviated unless required)
Publication years are accurate
Volume and issue numbers are correct
Page ranges are accurate

✓ Required Fields

All @article entries have: author, title, journal, year
All @book entries have: author/editor, title, publisher, year
All @inproceedings entries have: author, title, booktitle, year
Modern papers (2000+) include DOI when available
All entries have unique citation keys

✓ DOI Verification

All DOIs are properly formatted (10.XXXX/...)
DOIs resolve correctly to the article
No DOI prefix in the BibTeX field (no "doi:" or "https://doi.org/")
Metadata from CrossRef matches your BibTeX entry
Run: python scripts/validate_citations.py references.bib --check-dois

✓ Formatting Consistency

Page ranges use double hyphen (--) not single (-)
No "pp." prefix in pages field
Author names use "and" separator (not semicolon or ampersand)
Capitalization protected in titles ({AlphaFold}, {CRISPR}, etc.)
Month names use standard abbreviations if included
Citation keys follow consistent format

✓ Duplicate Detection

No duplicate DOIs in bibliography
No duplicate citation keys
No near-duplicate titles
Preprints updated to published versions when available
Run: python scripts/validate_citations.py references.bib

✓ Special Characters

Accented characters properly formatted (e.g., {"u} for ü)
Mathematical symbols use LaTeX commands
Chemical formulas properly formatted
No unescaped special characters (%, &, $, #, etc.)

✓ BibTeX Syntax

All entries have balanced braces {}
Fields are separated by commas (a trailing comma is valid)
Valid entry types (@article, @book, etc.)
Run: python scripts/validate_citations.py references.bib

✓ File Organization

Bibliography sorted in logical order (by year, author, or key)
Consistent formatting throughout
No formatting inconsistencies between entries
Run: python scripts/format_bibtex.py references.bib --sort year

Automated Validation

Step 1: Format and Clean

python scripts/format_bibtex.py references.bib \
  --deduplicate \
  --sort year \
  --descending \
  --output clean_references.bib

What this does:

Removes duplicates
Standardizes formatting
Fixes common issues (page ranges, DOI format, etc.)
Sorts by year (newest first)

Step 2: Validate

python scripts/validate_citations.py clean_references.bib \
  --check-dois \
  --report validation_report.json \
  --verbose

What this does:

Checks required fields
Checks DOI registration; investigate doi_unverified warnings separately
Detects duplicates
Validates syntax
Generates detailed report

Step 3: Review Report

cat validation_report.json

Address any:

Errors: Must fix (missing fields, broken DOIs, syntax errors)
Warnings: Should fix (missing recommended fields, formatting issues)
Duplicates: Remove or consolidate

Step 4: Final Check

python scripts/validate_citations.py clean_references.bib --verbose

Goal: Zero errors, minimal warnings

Manual Review Checklist

Critical Citations (Top 10-20 Most Important)

For your most important citations, manually verify:

Visit DOI link and confirm it's the correct article
Check author names against the actual publication
Verify year matches publication date
Confirm journal/conference name is correct
Check that volume/pages match

Common Issues to Watch For

Missing Information:

No DOI for papers published after 2000
Missing volume or page numbers for journal articles
Missing publisher for books
Missing conference location for proceedings

Formatting Errors:

Single hyphen in page ranges (123-145 → 123--145)
Ampersands in author lists (Smith & Jones → Smith and Jones)
Unprotected acronyms in titles (DNA → {DNA})
DOI includes URL prefix (https://doi.org/10.xxx → 10.xxx)

Metadata Mismatches:

Author names differ from publication
Year is online-first instead of print publication
Journal name abbreviated when it should be full
Volume/issue numbers swapped

Duplicates:

Same paper cited with different citation keys
Preprint and published version both cited
Conference paper and journal version both cited

Field-Specific Checks

Biomedical Sciences

PubMed Central ID (PMCID) included when available
MeSH terms appropriate (if using)
Clinical trial registration number included (if applicable)
All references to treatments/drugs accurately cited

Computer Science

arXiv ID included for preprints
Conference proceedings properly cited (not just "NeurIPS")
Software/dataset citations include version numbers
GitHub links stable and permanent

General Sciences

Data availability statements properly cited
Retracted papers identified and removed
Preprints checked for published versions
Supplementary materials referenced if critical

Final Pre-Submission Steps

1 Week Before Submission

Run full validation with DOI checking
Fix all errors and critical warnings
Manually verify top 10-20 most important citations
Check for any retracted papers

3 Days Before Submission

Re-run validation after any manual edits
Ensure all in-text citations have corresponding bibliography entries
Ensure all bibliography entries are cited in text
Check citation style matches journal requirements

1 Day Before Submission

Final validation check
LaTeX compilation successful with no warnings
PDF renders all citations correctly
Bibliography appears in correct format
No placeholder citations (Smith et al. XXXX)

Submission Day

One final validation run
No last-minute edits without re-validation
Bibliography file included in submission package
Figures/tables referenced in text match bibliography

Quality Metrics

Excellent Bibliography

✓ Assigned DOIs included; DOI-less publications explicitly verified
✓ Zero validation errors
✓ Zero missing required fields
✓ Zero broken DOIs
✓ Zero duplicates
✓ Consistent formatting throughout
✓ All citations manually spot-checked

Acceptable Bibliography

✓ Available DOI metadata checked against authoritative records
✓ Zero high-severity errors
✓ Minor warnings only (e.g., missing recommended fields)
✓ Key citations manually verified
✓ Compilation succeeds without errors

Needs Improvement

✗ Missing DOIs for recent papers
✗ High-severity validation errors
✗ Broken or incorrect DOIs
✗ Duplicate entries
✗ Inconsistent formatting
✗ Compilation warnings or errors

Emergency Fixes

If you discover issues at the last minute:

Broken DOI

# Find correct DOI
# Option 1: Search CrossRef
# https://www.crossref.org/

# Option 2: Search on publisher website
# Option 3: Google Scholar

# Re-extract metadata
python scripts/extract_metadata.py --doi CORRECT_DOI

Missing Information

# Extract from DOI
python scripts/extract_metadata.py --doi 10.xxxx/yyyy

# Or from PMID (biomedical)
python scripts/extract_metadata.py --pmid 12345678

# Or from arXiv
python scripts/extract_metadata.py --arxiv 2103.12345

Duplicate Entries

# Auto-remove duplicates
python scripts/format_bibtex.py references.bib \
  --deduplicate \
  --output fixed_references.bib

Formatting Errors

# Auto-fix common issues
python scripts/format_bibtex.py references.bib \
  --output fixed_references.bib

# Then validate
python scripts/validate_citations.py fixed_references.bib

Long-Term Best Practices

During Research

Add citations to bibliography file as you find them
Extract metadata immediately using DOI
Validate after every 10-20 additions
Keep bibliography file under version control

During Writing

Cite as you write
Use consistent citation keys
Don't delay adding references
Validate weekly

Before Submission

Allow 2-3 days for citation cleanup
Don't wait until the last day
Automate what you can
Manually verify critical citations

Tool Quick Reference

Extract Metadata

# From DOI
python scripts/doi_to_bibtex.py 10.1038/nature12345

# From multiple sources
python scripts/extract_metadata.py \
  --doi 10.1038/nature12345 \
  --pmid 12345678 \
  --arxiv 2103.12345 \
  --output references.bib

Validate

# Basic validation
python scripts/validate_citations.py references.bib

# With DOI checking (slow but thorough)
python scripts/validate_citations.py references.bib --check-dois

# Generate report
python scripts/validate_citations.py references.bib \
  --report validation.json \
  --verbose

Format and Clean

# Format and fix issues
python scripts/format_bibtex.py references.bib

# Remove duplicates and sort
python scripts/format_bibtex.py references.bib \
  --deduplicate \
  --sort year \
  --descending \
  --output clean_refs.bib

Summary

Minimum Requirements:

Run format_bibtex.py --deduplicate
Run validate_citations.py
Fix all errors
Compile successfully

Recommended:

Format, deduplicate, and sort
Validate with --check-dois
Fix all errors and warnings
Manually verify top citations
Re-validate after fixes

Best Practice:

Validate throughout research process
Use automated tools consistently
Keep bibliography clean and organized
Document any special cases
Final validation 1-3 days before submission

Remember: Citation errors reflect poorly on your scholarship. Taking time to ensure accuracy is worthwhile!