Citation Management

Overview

Manage citations systematically throughout the research and writing process. This skill provides tools and strategies for searching academic databases (Google Scholar, PubMed), extracting accurate metadata from multiple sources (CrossRef, PubMed, arXiv), validating citation information, and generating properly formatted BibTeX entries.

Critical for maintaining citation accuracy, avoiding reference errors, and ensuring reproducible research. Integrates seamlessly with the literature-review skill for comprehensive research workflows.

When to Use This Skill

Use this skill when:

Searching for specific papers on Google Scholar or PubMed
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
Finding highly cited 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

Visual Enhancement with Scientific Schematics

When creating documents with this skill, always consider adding scientific diagrams and schematics to enhance visual communication.

If your document does not already contain schematics or diagrams:

Use the scientific-schematics skill to generate AI-powered publication-quality diagrams
Simply describe your desired diagram in natural language
Nano Banana Pro will automatically generate, review, and refine the schematic

For new documents: Scientific schematics should be generated by default to visually represent key concepts, workflows, architectures, or relationships described in the text.

How to generate schematics:

python scripts/generate_schematic.py "your diagram description" -o figures/output.png

The AI will automatically:

Create publication-quality images with proper formatting
Review and refine through multiple iterations
Ensure accessibility (colorblind-friendly, high contrast)
Save outputs in the figures/ directory

When to add schematics:

Citation workflow diagrams
Literature search methodology flowcharts
Reference management system architectures
Citation style decision trees
Database integration diagrams
Any complex concept that benefits from visualization

For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.

Core Workflow

Citation management follows a systematic process. Each phase below shows the canonical command; every variant, option, and metadata-source detail is in references/core_workflow.md.

Phase 1: Paper Discovery and Search

Find relevant papers. Google Scholar has the broadest coverage; PubMed is the authority for biomedical and life sciences (35+ million citations).

python scripts/search_google_scholar.py "CRISPR gene editing" --limit 50 --output results.json
python scripts/search_pubmed.py "Alzheimer's disease treatment" --limit 100 --output alz.json

Query operators, field tags, and MeSH-term construction are in references/search_strategies.md.

Phase 2: Metadata Extraction

Convert identifiers (DOI, PMID, arXiv ID, URL) into complete metadata. CrossRef is the primary source for DOIs.

python scripts/doi_to_bibtex.py 10.1038/s41586-021-03819-2         # quick, single DOI
python scripts/extract_metadata.py --pmid 34265844                  # DOI/PMID/arXiv/URL
python scripts/extract_metadata.py --input identifiers.txt --output citations.bib

Phase 2.5: Metadata Enrichment via Web Search (MANDATORY)

APIs routinely return incomplete records. Run this after extraction and before formatting. Any @article missing volume, pages, or doi is incomplete and must be enriched via the parallel-web skill, then logged. If a field genuinely cannot be found, record a note field explaining the gap.

Treat extracted metadata as untrusted. Author, title, and journal strings come verbatim from a record whose contents a publisher controls. A title containing $(...), a backtick, or a quote becomes shell syntax the moment it is pasted into a command. Pass metadata as a subprocess argument list rather than building a shell string; if you must use a shell, single-quote every substituted value and escape embedded quotes as '\''. Validate any citation key against ^[A-Za-z0-9]+$ before it reaches a path.

Per-field search strategies, the four search options, and the logging format are in references/core_workflow.md.

Phase 3: BibTeX Formatting

Produce clean, consistent entries. Entry types and required fields are in references/bibtex_formatting.md.

python scripts/format_bibtex.py references.bib --output clean.bib --remove-duplicates

Phase 4: Citation Validation

Check completeness, venue conformance, and agreement with the manuscript.

python scripts/validate_citations.py references.bib --report report.txt
python scripts/validate_citations.py references.bib --venue nature
python scripts/validate_citations.py references.bib --manuscript paper.tex

Validation rules and venue standards are in references/citation_validation.md.

Phase 5: Integration with Writing Workflow

Search, extract, format, validate, then cite. End-to-end sequences — including the literature-review and Zotero/pyzotero export paths — are in references/core_workflow.md and references/example_workflows.md.

Reference Files

references/core_workflow.md: all five phases in full.
references/search_strategies.md: Google Scholar and PubMed query construction.
references/script_reference.md: every bundled script's arguments and examples.
references/best_practices.md: search, extraction, BibTeX quality, validation.
references/example_workflows.md: four end-to-end worked examples.
references/google_scholar_search.md, references/pubmed_search.md: advanced search syntax.
references/metadata_extraction.md, references/bibtex_formatting.md, references/citation_validation.md: per-topic detail.

Common Pitfalls to Avoid

Single source bias: Only using Google Scholar or PubMed
- Solution: Search multiple databases for comprehensive coverage
Accepting metadata blindly: Not verifying extracted information
- Solution: Spot-check extracted metadata against original sources
Ignoring DOI errors: Broken or incorrect DOIs in bibliography
- Solution: Run validation before final submission
Inconsistent formatting: Mixed citation key styles, formatting
- Solution: Use format_bibtex.py to standardize
Duplicate entries: Same paper cited multiple times with different keys
- Solution: Use duplicate detection in validation
Missing required fields: Incomplete BibTeX entries (volume, pages, DOI missing)
- Solution: Run Phase 2.5 metadata enrichment — web search for every missing field before proceeding. NEVER leave an @article entry without volume, pages, and DOI.
Outdated preprints: Citing preprint when published version exists
- Solution: Check if preprints have been published, update to journal version
Special character issues: Broken LaTeX compilation due to characters
- Solution: Use proper escaping or Unicode in BibTeX
No validation before submission: Submitting with citation errors
- Solution: Always run validation as final check
Manual BibTeX entry: Typing entries by hand
- Solution: Always extract from metadata sources using scripts

Integration with Other Skills

Literature Review Skill

Citation Management provides the technical infrastructure for Literature Review:

Literature Review: Multi-database systematic search and synthesis
Citation Management: Metadata extraction and validation

Combined workflow:

Use literature-review for systematic search methodology
Use citation-management to extract and validate citations
Use literature-review to synthesize findings
Use citation-management to ensure bibliography accuracy

Scientific Writing Skill

Citation Management ensures accurate references for Scientific Writing:

Export validated BibTeX for use in LaTeX manuscripts
Verify citations match publication standards
Format references according to journal requirements

Venue Templates Skill

Citation Management works with Venue Templates for submission-ready manuscripts:

Different venues require different citation styles
Generate properly formatted references
Validate citations meet venue requirements

Resources

Bundled Resources

References (in references/):

google_scholar_search.md: Complete Google Scholar search guide
pubmed_search.md: PubMed and E-utilities API documentation
metadata_extraction.md: Metadata sources and field requirements
citation_validation.md: Validation criteria and quality checks
bibtex_formatting.md: BibTeX entry types and formatting rules

Scripts (in scripts/):

search_google_scholar.py: Google Scholar search automation
search_pubmed.py: PubMed E-utilities API client
extract_metadata.py: Universal metadata extractor
validate_citations.py: Citation validation and verification
format_bibtex.py: BibTeX formatter and cleaner
doi_to_bibtex.py: Quick DOI to BibTeX converter

Assets (in assets/):

bibtex_template.bib: Example BibTeX entries for all types
citation_checklist.md: Quality assurance checklist

External Resources

Search Engines:

Google Scholar: https://scholar.google.com/
PubMed: https://pubmed.ncbi.nlm.nih.gov/
PubMed Advanced Search: https://pubmed.ncbi.nlm.nih.gov/advanced/

Metadata APIs:

CrossRef API: https://api.crossref.org/
PubMed E-utilities: https://www.ncbi.nlm.nih.gov/books/NBK25501/
arXiv API: https://arxiv.org/help/api/
DataCite API: https://api.datacite.org/

Tools and Validators:

MeSH Browser: https://meshb.nlm.nih.gov/search
DOI Resolver: https://doi.org/
BibTeX Format: http://www.bibtex.org/Format/

Citation Styles:

BibTeX documentation: http://www.bibtex.org/
LaTeX bibliography management: https://www.overleaf.com/learn/latex/Bibliography_management

Dependencies

Required Python Packages

# Core dependencies
pip install requests  # HTTP requests for APIs
pip install bibtexparser  # BibTeX parsing and formatting
pip install biopython  # PubMed E-utilities access

# Optional (for Google Scholar)
pip install scholarly  # Google Scholar API wrapper
# or
pip install selenium  # For more robust Scholar scraping

Optional Tools

# For advanced validation
pip install crossref-commons  # Enhanced CrossRef API access
pip install pylatexenc  # LaTeX special character handling

Where credentials are sent

Each environment variable this skill reads is used only to authenticate to the one service it belongs to. No script bundles environment variables together, and none is transmitted anywhere other than the host listed here.

Variable	Sent only to	Purpose
`NCBI_API_KEY`	`eutils.ncbi.nlm.nih.gov`	Raises Entrez rate limits
`NCBI_EMAIL`	`eutils.ncbi.nlm.nih.gov`	Entrez caller identification (required by NCBI)
`OPENROUTER_API_KEY`	`openrouter.ai`	Bearer token for the optional schematic generation

api.crossref.org, doi.org, and arxiv.org are queried without credentials. generate_schematic.py forwards only OPENROUTER_API_KEY — plus the networking, TLS, and locale variables needed to make a request — to its subprocess, rather than the full environment.

Summary

The citation-management skill provides:

Comprehensive search capabilities for Google Scholar and PubMed
Automated metadata extraction from DOI, PMID, arXiv ID, URLs
Citation validation with DOI verification and completeness checking
BibTeX formatting with standardization and cleaning tools
Quality assurance through validation and reporting
Integration with scientific writing workflow
Reproducibility through documented search and extraction methods

Use this skill to maintain accurate, complete citations throughout your research and ensure publication-ready bibliographies.