Citation Management

Citation Management

Overview

Manage citations systematically throughout the research and writing process. This skill provides tools and strategies for extracting accurate metadata from identifiers and bibliographic sources, validating citation information, cleaning duplicate references, and generating properly formatted BibTeX entries.

Critical for maintaining citation accuracy, avoiding reference errors, and ensuring reproducible research.

When to Use This Skill

Use this skill when:

• Resolving known or candidate papers from identifiers, titles, Google Scholar, or PubMed records
• Converting DOIs, PMIDs, or arXiv IDs to properly formatted BibTeX
• Extracting complete metadata for citations (authors, title, journal, year, etc.)
• Validating existing citations for accuracy
• Cleaning and formatting BibTeX files
• Checking citation counts for known papers in a specific field
• Verifying that citation information matches the actual publication
• Building a bibliography for a manuscript or thesis
• Checking for duplicate citations
• Ensuring consistent citation formatting

Core Workflow

Citation management follows a systematic process:

Phase 1: Citation Source Lookup

Goal: Locate exact source records for known references or tightly scoped citation candidates.

Google Scholar Search

Google Scholar provides the most comprehensive coverage across disciplines.

Basic Search:

# Search for papers on a topic
python scripts/search_google_scholar.py "CRISPR gene editing" \
  --limit 50 \
  --output results.json

# Search with year filter
python scripts/search_google_scholar.py "machine learning protein folding" \
  --year-start 2020 \
  --year-end 2024 \
  --limit 100 \
  --output ml_proteins.json

Advanced Search Strategies (see references/google_scholar_search.md):

• Use quotation marks for exact phrases: "deep learning"
• Search by author: author:LeCun
• Search in title: intitle:"neural networks"
• Exclude terms: machine learning -survey
• Find highly cited papers using sort options
• Filter by date ranges to get recent work

Best Practices:

• Use specific, targeted search terms
• Include key technical terms and acronyms
• Filter by recent years for fast-moving fields
• Check "Cited by" to find seminal papers
• Export top results for further analysis

PubMed Search

PubMed specializes in biomedical and life sciences literature (35+ million citations).

Basic Search:

# Search PubMed
python scripts/search_pubmed.py "Alzheimer's disease treatment" \
  --limit 100 \
  --output alzheimers.json

# Search with MeSH terms and filters
python scripts/search_pubmed.py \
  --query '"Alzheimer Disease"[MeSH] AND "Drug Therapy"[MeSH]' \
  --date-start 2020 \
  --date-end 2024 \
  --publication-types "Clinical Trial,Review" \
  --output alzheimers_trials.json

Advanced PubMed Queries (see references/pubmed_search.md):

• Use MeSH terms: "Diabetes Mellitus"[MeSH]
• Field tags: "cancer"[Title], "Smith J"[Author]
• Boolean operators: AND, OR, NOT
• Date filters: 2020:2024[Publication Date]
• Publication types: "Review"[Publication Type]
• Combine with E-utilities API for automation

Best Practices:

• Use MeSH Browser to find correct controlled vocabulary
• Construct complex queries in PubMed Advanced Search Builder first
• Include multiple synonyms with OR
• Retrieve PMIDs for easy metadata extraction
• Export to JSON or directly to BibTeX

Phase 2: Metadata Extraction

Goal: Convert paper identifiers (DOI, PMID, arXiv ID) to complete, accurate metadata.

Quick DOI to BibTeX Conversion

For single DOIs, use the quick conversion tool:

# Convert single DOI
python scripts/doi_to_bibtex.py 10.1038/s41586-021-03819-2

# Convert multiple DOIs from a file
python scripts/doi_to_bibtex.py --input dois.txt --output references.bib

# Different output formats
python scripts/doi_to_bibtex.py 10.1038/nature12345 --format json

Comprehensive Metadata Extraction

For DOIs, PMIDs, arXiv IDs, or URLs:

# Extract from DOI
python scripts/extract_metadata.py --doi 10.1038/s41586-021-03819-2

# Extract from PMID
python scripts/extract_metadata.py --pmid 34265844

# Extract from arXiv ID
python scripts/extract_metadata.py --arxiv 2103.14030

# Extract from URL
python scripts/extract_metadata.py --url "https://www.nature.com/articles/s41586-021-03819-2"

# Batch extraction from file (mixed identifiers)
python scripts/extract_metadata.py --input identifiers.txt --output citations.bib

Metadata Sources (see references/metadata_extraction.md):

1. CrossRef API: Primary source for DOIs

   • Comprehensive metadata for journal articles
   • Publisher-provided information
   • Includes authors, title, journal, volume, pages, dates
   • Free, no API key required

2. PubMed E-utilities: Biomedical literature

   • Official NCBI metadata
   • Includes MeSH terms, abstracts
   • PMID and PMCID identifiers
   • Free, API key recommended for high volume

3. arXiv API: Preprints in physics, math, CS, q-bio

   • Complete metadata for preprints
   • Version tracking
   • Author affiliations
   • Free, open access

4. DataCite API: Research datasets, software, other resources

   • Metadata for non-traditional scholarly outputs
   • DOIs for datasets and code
   • Free access

What Gets Extracted:

• Required fields: author, title, year
• Journal articles: journal, volume, number, pages, DOI
• Books: publisher, ISBN, edition
• Conference papers: booktitle, conference location, pages
• Preprints: repository (arXiv, bioRxiv), preprint ID
• Additional: abstract, keywords, URL

Phase 3: BibTeX Formatting

Goal: Generate clean, properly formatted BibTeX entries.

Understanding BibTeX Entry Types

See references/bibtex_formatting.md for complete guide.

Common Entry Types:

• @article: Journal articles (most common)
• @book: Books
• @inproceedings: Conference papers
• @incollection: Book chapters
• @phdthesis: Dissertations
• @misc: Preprints, software, datasets

Required Fields by Type:

@article{citationkey,
  author  = {Last1, First1 and Last2, First2},
  title   = {Article Title},
  journal = {Journal Name},
  year    = {2024},
  volume  = {10},
  number  = {3},
  pages   = {123--145},
  doi     = {10.1234/example}
}

@inproceedings{citationkey,
  author    = {Last, First},
  title     = {Paper Title},
  booktitle = {Conference Name},
  year      = {2024},
  pages     = {1--10}
}

@book{citationkey,
  author    = {Last, First},
  title     = {Book Title},
  publisher = {Publisher Name},
  year      = {2024}
}

Formatting and Cleaning

Use the formatter to standardize BibTeX files:

# Format and clean BibTeX file
python scripts/format_bibtex.py references.bib \
  --output formatted_references.bib

# Sort entries by citation key
python scripts/format_bibtex.py references.bib \
  --sort key \
  --output sorted_references.bib

# Sort by year (newest first)
python scripts/format_bibtex.py references.bib \
  --sort year \
  --descending \
  --output sorted_references.bib

# Remove duplicates
python scripts/format_bibtex.py references.bib \
  --deduplicate \
  --output clean_references.bib

# Validate and report issues
python scripts/format_bibtex.py references.bib \
  --validate \
  --report validation_report.txt

Formatting Operations:

• Standardize field order
• Consistent indentation and spacing
• Proper capitalization in titles (protected with {})
• Standardized author name format
• Consistent citation key format
• Remove unnecessary fields
• Fix common errors (missing commas, braces)

Phase 4: Citation Validation

Goal: Verify all citations are accurate and complete.

Comprehensive Validation

# Validate BibTeX file
python scripts/validate_citations.py references.bib

# Validate and fix common issues
python scripts/validate_citations.py references.bib \
  --auto-fix \
  --output validated_references.bib

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

Validation Checks (see references/citation_validation.md):

1. DOI Verification:

   • DOI resolves correctly via doi.org
   • Metadata matches between BibTeX and CrossRef
   • No broken or invalid DOIs

2. Required Fields:

   • All required fields present for entry type
   • No empty or missing critical information
   • Author names properly formatted

3. Data Consistency:

   • Year is valid (4 digits, reasonable range)
   • Volume/number are numeric
   • Pages formatted correctly (e.g., 123--145)
   • URLs are accessible

4. Duplicate Detection:

   • Same DOI used multiple times
   • Similar titles (possible duplicates)
   • Same author/year/title combinations

5. Format Compliance:

   • Valid BibTeX syntax
   • Proper bracing and quoting
   • Citation keys are unique
   • Special characters handled correctly

Validation Output:

{
  "total_entries": 150,
  "valid_entries": 145,
  "errors": [
    {
      "citation_key": "Smith2023",
      "error_type": "missing_field",
      "field": "journal",
      "severity": "high"
    },
    {
      "citation_key": "Jones2022",
      "error_type": "invalid_doi",
      "doi": "10.1234/broken",
      "severity": "high"
    }
  ],
  "warnings": [
    {
      "citation_key": "Brown2021",
      "warning_type": "possible_duplicate",
      "duplicate_of": "Brown2021a",
      "severity": "medium"
    }
  ]
}

Phase 5: Integration with Writing Workflow

Building References for Manuscripts

Complete workflow for creating a bibliography:

# 1. Search for papers on your topic
python scripts/search_pubmed.py \
  '"CRISPR-Cas Systems"[MeSH] AND "Gene Editing"[MeSH]' \
  --date-start 2020 \
  --limit 200 \
  --output crispr_papers.json

# 2. Extract DOIs from search results and convert to BibTeX
python scripts/extract_metadata.py \
  --input crispr_papers.json \
  --output crispr_refs.bib

# 3. Add specific papers by DOI
python scripts/doi_to_bibtex.py 10.1038/nature12345 >> crispr_refs.bib
python scripts/doi_to_bibtex.py 10.1126/science.abcd1234 >> crispr_refs.bib

# 4. Format and clean the BibTeX file
python scripts/format_bibtex.py crispr_refs.bib \
  --deduplicate \
  --sort year \
  --descending \
  --output references.bib

# 5. Validate all citations
python scripts/validate_citations.py references.bib \
  --auto-fix \
  --report validation.json \
  --output final_references.bib

# 6. Review validation report and fix any remaining issues
cat validation.json

# 7. Use in your LaTeX document
# \bibliography{final_references}

Citation Validation In Review Documents

When a review document already exists, use this skill for the technical citation layer:

1. Extract all cited identifiers and bibliography records
2. Validate metadata against DOI, PMID, arXiv, CrossRef, or PubMed sources
3. Normalize BibTeX keys and citation style fields
4. Verify the final bibliography before manuscript build or submission

# After completing literature review
# Verify all citations in the review document
python scripts/validate_citations.py my_review_references.bib --report review_validation.json

# Format for specific citation style if needed
python scripts/format_bibtex.py my_review_references.bib \
  --style nature \
  --output formatted_refs.bib

Search Strategies

Google Scholar Best Practices

Finding Seminal and High-Impact Papers (CRITICAL):

Always prioritize papers based on citation count, venue quality, and author reputation:

Citation Count Thresholds:

Venue Quality Tiers:

• Tier 1 (Prefer): Nature, Science, Cell, NEJM, Lancet, JAMA, PNAS
• Tier 2 (High Priority): Impact Factor >10, top conferences (NeurIPS, ICML, ICLR)
• Tier 3 (Good): Specialized journals (IF 5-10)
• Tier 4 (Sparingly): Lower-impact peer-reviewed venues

Author Reputation Indicators:

• Senior researchers with h-index >40
• Multiple publications in Tier-1 venues
• Leadership at recognized institutions
• Awards and editorial positions

Search Strategies for High-Impact Papers:

• Sort by citation count (most cited first)
• Look for review articles from Tier-1 journals for overview
• Check "Cited by" for impact assessment and recent follow-up work
• Use citation alerts for tracking new citations to key papers
• Filter by top venues using source:Nature or source:Science
• Search for papers by known field leaders using author:LastName

Advanced Operators (full list in references/google_scholar_search.md):

"exact phrase"           # Exact phrase matching
author:lastname          # Search by author
intitle:keyword          # Search in title only
source:journal           # Search specific journal
-exclude                 # Exclude terms
OR                       # Alternative terms
2020..2024              # Year range

Example Searches:

# Find recent reviews on a topic
"CRISPR" intitle:review 2023..2024

# Find papers by specific author on topic
author:Church "synthetic biology"

# Find highly cited foundational work
"deep learning" 2012..2015 sort:citations

# Exclude surveys and focus on methods
"protein folding" -survey -review intitle:method

PubMed Best Practices

Using MeSH Terms: MeSH (Medical Subject Headings) provides controlled vocabulary for precise searching.

1. Find MeSH terms at https://meshb.nlm.nih.gov/search
2. Use in queries: "Diabetes Mellitus, Type 2"[MeSH]
3. Combine with keywords for comprehensive coverage

Field Tags:

[Title]              # Search in title only
[Title/Abstract]     # Search in title or abstract
[Author]             # Search by author name
[Journal]            # Search specific journal
[Publication Date]   # Date range
[Publication Type]   # Article type
[MeSH]              # MeSH term

Building Complex Queries:

# Clinical trials on diabetes treatment published recently
"Diabetes Mellitus, Type 2"[MeSH] AND "Drug Therapy"[MeSH] 
AND "Clinical Trial"[Publication Type] AND 2020:2024[Publication Date]

# Reviews on CRISPR in specific journal
"CRISPR-Cas Systems"[MeSH] AND "Nature"[Journal] AND "Review"[Publication Type]

# Specific author's recent work
"Smith AB"[Author] AND cancer[Title/Abstract] AND 2022:2024[Publication Date]

E-utilities for Automation: The scripts use NCBI E-utilities API for programmatic access:

• ESearch: Search and retrieve PMIDs
• EFetch: Retrieve full metadata
• ESummary: Get summary information
• ELink: Find related articles

See references/pubmed_search.md for complete API documentation.

Tools and Scripts

search_google_scholar.py

Search Google Scholar and export results.

Features:

• Automated searching with rate limiting
• Pagination support
• Year range filtering
• Export to JSON or BibTeX
• Citation count information

Usage:

# Basic search
python scripts/search_google_scholar.py "quantum computing"

# Advanced search with filters
python scripts/search_google_scholar.py "quantum computing" \
  --year-start 2020 \
  --year-end 2024 \
  --limit 100 \
  --sort-by citations \
  --output quantum_papers.json

# Export directly to BibTeX
python scripts/search_google_scholar.py "machine learning" \
  --limit 50 \
  --format bibtex \
  --output ml_papers.bib

search_pubmed.py

Search PubMed using E-utilities API.

Features:

• Complex query support (MeSH, field tags, Boolean)
• Date range filtering
• Publication type filtering
• Batch retrieval with metadata
• Export to JSON or BibTeX

Usage:

# Simple keyword search
python scripts/search_pubmed.py "CRISPR gene editing"

# Complex query with filters
python scripts/search_pubmed.py \
  --query '"CRISPR-Cas Systems"[MeSH] AND "therapeutic"[Title/Abstract]' \
  --date-start 2020-01-01 \
  --date-end 2024-12-31 \
  --publication-types "Clinical Trial,Review" \
  --limit 200 \
  --output crispr_therapeutic.json

# Export to BibTeX
python scripts/search_pubmed.py "Alzheimer's disease" \
  --limit 100 \
  --format bibtex \
  --output alzheimers.bib

extract_metadata.py

Extract complete metadata from paper identifiers.

Features:

• Supports DOI, PMID, arXiv ID, URL
• Queries CrossRef, PubMed, arXiv APIs
• Handles multiple identifier types
• Batch processing
• Multiple output formats

Usage:

# Single DOI
python scripts/extract_metadata.py --doi 10.1038/s41586-021-03819-2

# Single PMID
python scripts/extract_metadata.py --pmid 34265844

# Single arXiv ID
python scripts/extract_metadata.py --arxiv 2103.14030

# From URL
python scripts/extract_metadata.py \
  --url "https://www.nature.com/articles/s41586-021-03819-2"

# Batch processing (file with one identifier per line)
python scripts/extract_metadata.py \
  --input paper_ids.txt \
  --output references.bib

# Different output formats
python scripts/extract_metadata.py \
  --doi 10.1038/nature12345 \
  --format json  # or bibtex, yaml

validate_citations.py

Validate BibTeX entries for accuracy and completeness.

Features:

• DOI verification via doi.org and CrossRef
• Required field checking
• Duplicate detection
• Format validation
• Auto-fix common issues
• Detailed reporting

Usage:

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

# With auto-fix
python scripts/validate_citations.py references.bib \
  --auto-fix \
  --output fixed_references.bib

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

# Only check DOIs
python scripts/validate_citations.py references.bib \
  --check-dois-only

format_bibtex.py

Format and clean BibTeX files.

Features:

• Standardize formatting
• Sort entries (by key, year, author)
• Remove duplicates
• Validate syntax
• Fix common errors
• Enforce citation key conventions

Usage:

# Basic formatting
python scripts/format_bibtex.py references.bib

# Sort by year (newest first)
python scripts/format_bibtex.py references.bib \
  --sort year \
  --descending \
  --output sorted_refs.bib

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

# Complete cleanup
python scripts/format_bibtex.py references.bib \
  --deduplicate \
  --sort year \
  --validate \
  --auto-fix \
  --output final_refs.bib