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Zhongwei Li
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skills/citation-management/assets/citation_checklist.md
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skills/citation-management/assets/citation_checklist.md
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# Citation Quality Checklist
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Use this checklist to ensure your citations are accurate, complete, and properly formatted before final submission.
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## Pre-Submission Checklist
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### ✓ Metadata Accuracy
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- [ ] All author names are correct and properly formatted
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- [ ] Article titles match the actual publication
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- [ ] Journal/conference names are complete (not abbreviated unless required)
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- [ ] Publication years are accurate
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- [ ] Volume and issue numbers are correct
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- [ ] Page ranges are accurate
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### ✓ Required Fields
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- [ ] All @article entries have: author, title, journal, year
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- [ ] All @book entries have: author/editor, title, publisher, year
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- [ ] All @inproceedings entries have: author, title, booktitle, year
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- [ ] Modern papers (2000+) include DOI when available
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- [ ] All entries have unique citation keys
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### ✓ DOI Verification
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- [ ] All DOIs are properly formatted (10.XXXX/...)
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- [ ] DOIs resolve correctly to the article
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- [ ] No DOI prefix in the BibTeX field (no "doi:" or "https://doi.org/")
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- [ ] Metadata from CrossRef matches your BibTeX entry
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- [ ] Run: `python scripts/validate_citations.py references.bib --check-dois`
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### ✓ Formatting Consistency
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- [ ] Page ranges use double hyphen (--) not single (-)
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- [ ] No "pp." prefix in pages field
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- [ ] Author names use "and" separator (not semicolon or ampersand)
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- [ ] Capitalization protected in titles ({AlphaFold}, {CRISPR}, etc.)
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- [ ] Month names use standard abbreviations if included
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- [ ] Citation keys follow consistent format
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### ✓ Duplicate Detection
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- [ ] No duplicate DOIs in bibliography
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- [ ] No duplicate citation keys
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- [ ] No near-duplicate titles
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- [ ] Preprints updated to published versions when available
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- [ ] Run: `python scripts/validate_citations.py references.bib`
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### ✓ Special Characters
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- [ ] Accented characters properly formatted (e.g., {\"u} for ü)
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- [ ] Mathematical symbols use LaTeX commands
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- [ ] Chemical formulas properly formatted
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- [ ] No unescaped special characters (%, &, $, #, etc.)
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### ✓ BibTeX Syntax
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- [ ] All entries have balanced braces {}
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- [ ] Fields separated by commas
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- [ ] No comma after last field in each entry
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- [ ] Valid entry types (@article, @book, etc.)
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- [ ] Run: `python scripts/validate_citations.py references.bib`
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### ✓ File Organization
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- [ ] Bibliography sorted in logical order (by year, author, or key)
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- [ ] Consistent formatting throughout
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- [ ] No formatting inconsistencies between entries
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- [ ] Run: `python scripts/format_bibtex.py references.bib --sort year`
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## Automated Validation
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### Step 1: Format and Clean
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```bash
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python scripts/format_bibtex.py references.bib \
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--deduplicate \
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--sort year \
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--descending \
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--output clean_references.bib
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```
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**What this does**:
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- Removes duplicates
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- Standardizes formatting
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- Fixes common issues (page ranges, DOI format, etc.)
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- Sorts by year (newest first)
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### Step 2: Validate
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```bash
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python scripts/validate_citations.py clean_references.bib \
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--check-dois \
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--report validation_report.json \
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--verbose
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```
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**What this does**:
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- Checks required fields
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- Verifies DOIs resolve
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- Detects duplicates
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- Validates syntax
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- Generates detailed report
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### Step 3: Review Report
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```bash
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cat validation_report.json
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```
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**Address any**:
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- **Errors**: Must fix (missing fields, broken DOIs, syntax errors)
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- **Warnings**: Should fix (missing recommended fields, formatting issues)
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- **Duplicates**: Remove or consolidate
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### Step 4: Final Check
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```bash
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python scripts/validate_citations.py clean_references.bib --verbose
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```
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**Goal**: Zero errors, minimal warnings
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## Manual Review Checklist
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### Critical Citations (Top 10-20 Most Important)
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For your most important citations, manually verify:
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- [ ] Visit DOI link and confirm it's the correct article
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- [ ] Check author names against the actual publication
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- [ ] Verify year matches publication date
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- [ ] Confirm journal/conference name is correct
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- [ ] Check that volume/pages match
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### Common Issues to Watch For
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**Missing Information**:
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- [ ] No DOI for papers published after 2000
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- [ ] Missing volume or page numbers for journal articles
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- [ ] Missing publisher for books
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- [ ] Missing conference location for proceedings
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**Formatting Errors**:
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- [ ] Single hyphen in page ranges (123-145 → 123--145)
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- [ ] Ampersands in author lists (Smith & Jones → Smith and Jones)
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- [ ] Unprotected acronyms in titles (DNA → {DNA})
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- [ ] DOI includes URL prefix (https://doi.org/10.xxx → 10.xxx)
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**Metadata Mismatches**:
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- [ ] Author names differ from publication
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- [ ] Year is online-first instead of print publication
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- [ ] Journal name abbreviated when it should be full
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- [ ] Volume/issue numbers swapped
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**Duplicates**:
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- [ ] Same paper cited with different citation keys
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- [ ] Preprint and published version both cited
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- [ ] Conference paper and journal version both cited
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## Field-Specific Checks
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### Biomedical Sciences
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- [ ] PubMed Central ID (PMCID) included when available
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- [ ] MeSH terms appropriate (if using)
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- [ ] Clinical trial registration number included (if applicable)
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- [ ] All references to treatments/drugs accurately cited
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### Computer Science
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- [ ] arXiv ID included for preprints
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- [ ] Conference proceedings properly cited (not just "NeurIPS")
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- [ ] Software/dataset citations include version numbers
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- [ ] GitHub links stable and permanent
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### General Sciences
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- [ ] Data availability statements properly cited
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- [ ] Retracted papers identified and removed
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- [ ] Preprints checked for published versions
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- [ ] Supplementary materials referenced if critical
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## Final Pre-Submission Steps
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### 1 Week Before Submission
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- [ ] Run full validation with DOI checking
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- [ ] Fix all errors and critical warnings
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- [ ] Manually verify top 10-20 most important citations
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- [ ] Check for any retracted papers
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### 3 Days Before Submission
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- [ ] Re-run validation after any manual edits
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- [ ] Ensure all in-text citations have corresponding bibliography entries
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- [ ] Ensure all bibliography entries are cited in text
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- [ ] Check citation style matches journal requirements
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### 1 Day Before Submission
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- [ ] Final validation check
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- [ ] LaTeX compilation successful with no warnings
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- [ ] PDF renders all citations correctly
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- [ ] Bibliography appears in correct format
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- [ ] No placeholder citations (Smith et al. XXXX)
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### Submission Day
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- [ ] One final validation run
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- [ ] No last-minute edits without re-validation
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- [ ] Bibliography file included in submission package
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- [ ] Figures/tables referenced in text match bibliography
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## Quality Metrics
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### Excellent Bibliography
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- ✓ 100% of entries have DOIs (for modern papers)
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- ✓ Zero validation errors
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- ✓ Zero missing required fields
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- ✓ Zero broken DOIs
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- ✓ Zero duplicates
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- ✓ Consistent formatting throughout
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- ✓ All citations manually spot-checked
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### Acceptable Bibliography
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- ✓ 90%+ of modern entries have DOIs
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- ✓ Zero high-severity errors
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- ✓ Minor warnings only (e.g., missing recommended fields)
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- ✓ Key citations manually verified
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- ✓ Compilation succeeds without errors
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### Needs Improvement
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- ✗ Missing DOIs for recent papers
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- ✗ High-severity validation errors
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- ✗ Broken or incorrect DOIs
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- ✗ Duplicate entries
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- ✗ Inconsistent formatting
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- ✗ Compilation warnings or errors
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## Emergency Fixes
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If you discover issues at the last minute:
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### Broken DOI
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```bash
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# Find correct DOI
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# Option 1: Search CrossRef
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# https://www.crossref.org/
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# Option 2: Search on publisher website
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# Option 3: Google Scholar
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# Re-extract metadata
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python scripts/extract_metadata.py --doi CORRECT_DOI
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```
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### Missing Information
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```bash
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# Extract from DOI
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python scripts/extract_metadata.py --doi 10.xxxx/yyyy
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# Or from PMID (biomedical)
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python scripts/extract_metadata.py --pmid 12345678
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# Or from arXiv
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python scripts/extract_metadata.py --arxiv 2103.12345
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```
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### Duplicate Entries
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```bash
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# Auto-remove duplicates
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python scripts/format_bibtex.py references.bib \
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--deduplicate \
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--output fixed_references.bib
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```
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### Formatting Errors
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```bash
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# Auto-fix common issues
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python scripts/format_bibtex.py references.bib \
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--output fixed_references.bib
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# Then validate
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python scripts/validate_citations.py fixed_references.bib
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```
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## Long-Term Best Practices
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### During Research
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- [ ] Add citations to bibliography file as you find them
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- [ ] Extract metadata immediately using DOI
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- [ ] Validate after every 10-20 additions
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- [ ] Keep bibliography file under version control
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### During Writing
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- [ ] Cite as you write
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- [ ] Use consistent citation keys
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- [ ] Don't delay adding references
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- [ ] Validate weekly
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### Before Submission
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- [ ] Allow 2-3 days for citation cleanup
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- [ ] Don't wait until the last day
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- [ ] Automate what you can
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- [ ] Manually verify critical citations
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## Tool Quick Reference
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### Extract Metadata
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```bash
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# From DOI
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python scripts/doi_to_bibtex.py 10.1038/nature12345
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# From multiple sources
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python scripts/extract_metadata.py \
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--doi 10.1038/nature12345 \
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--pmid 12345678 \
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--arxiv 2103.12345 \
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--output references.bib
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```
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### Validate
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```bash
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# Basic validation
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python scripts/validate_citations.py references.bib
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# With DOI checking (slow but thorough)
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python scripts/validate_citations.py references.bib --check-dois
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# Generate report
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python scripts/validate_citations.py references.bib \
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--report validation.json \
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--verbose
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```
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### Format and Clean
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```bash
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# Format and fix issues
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python scripts/format_bibtex.py references.bib
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# Remove duplicates and sort
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python scripts/format_bibtex.py references.bib \
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--deduplicate \
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--sort year \
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--descending \
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--output clean_refs.bib
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```
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## Summary
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**Minimum Requirements**:
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1. Run `format_bibtex.py --deduplicate`
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2. Run `validate_citations.py`
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3. Fix all errors
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4. Compile successfully
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**Recommended**:
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1. Format, deduplicate, and sort
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2. Validate with `--check-dois`
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3. Fix all errors and warnings
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4. Manually verify top citations
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5. Re-validate after fixes
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**Best Practice**:
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1. Validate throughout research process
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2. Use automated tools consistently
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3. Keep bibliography clean and organized
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4. Document any special cases
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5. Final validation 1-3 days before submission
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**Remember**: Citation errors reflect poorly on your scholarship. Taking time to ensure accuracy is worthwhile!
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