gh-k-dense-ai-claude-scientific-writer-claude-scientific-writer/skills/citation-management/assets/citation_checklist.md

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

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
• Verifies DOIs resolve
• 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

• ✓ 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

# 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:

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!