citation-management

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.

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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](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](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](references/core_workflow.md).

Phase 3: BibTeX Formatting

Produce clean, consistent entries. Entry types and required fields are in

[references/bibtex_formatting.md](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](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](references/core_workflow.md) and

[references/example_workflows.md](references/example_workflows.md).

Reference Files

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

Common Pitfalls to Avoid

1. Single source bias: Only using Google Scholar or PubMed

• Solution: Search multiple databases for comprehensive coverage

1. Accepting metadata blindly: Not verifying extracted information

• Solution: Spot-check extracted metadata against original sources

1. Ignoring DOI errors: Broken or incorrect DOIs in bibliography

• Solution: Run validation before final submission

1. Inconsistent formatting: Mixed citation key styles, formatting

• Solution: Use format_bibtex.py to standardize

1. Duplicate entries: Same paper cited multiple times with different keys

• Solution: Use duplicate detection in validation

1. 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.

1. Outdated preprints: Citing preprint when published version exists

• Solution: Check if preprints have been published, update to journal version

1. Special character issues: Broken LaTeX compilation due to characters

• Solution: Use proper escaping or Unicode in BibTeX

1. No validation before submission: Submitting with citation errors

• Solution: Always run validation as final check

1. 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:

1. Use literature-review for systematic search methodology
2. Use citation-management to extract and validate citations
3. Use literature-review to synthesize findings
4. 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:

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

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