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Citation Quality Checklist

scientific-skills/citation-management/assets/citation_checklist.md

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Citation Quality Checklist

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 separated by commas
  • No comma after last field in each entry
  • 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

bash
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

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

What this does:

  • Checks required fields
  • Verifies DOIs resolve
  • Detects duplicates
  • Validates syntax
  • Generates detailed report

Step 3: Review Report

bash
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

bash
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

  • ✓ 100% of entries have DOIs (for modern papers)
  • ✓ Zero validation errors
  • ✓ Zero missing required fields
  • ✓ Zero broken DOIs
  • ✓ Zero duplicates
  • ✓ Consistent formatting throughout
  • ✓ All citations manually spot-checked

Acceptable Bibliography

  • ✓ 90%+ of modern entries have DOIs
  • ✓ 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

bash
# 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

bash
# 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

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

Formatting Errors

bash
# 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

bash
# 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

bash
# 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

bash
# 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:

  1. Run format_bibtex.py --deduplicate
  2. Run validate_citations.py
  3. Fix all errors
  4. Compile successfully

Recommended:

  1. Format, deduplicate, and sort
  2. Validate with --check-dois
  3. Fix all errors and warnings
  4. Manually verify top citations
  5. Re-validate after fixes

Best Practice:

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

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