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

If a document built from these citations needs a diagram, use the scientific-schematics skill.

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. Search more than one database — coverage differs sharply, and a single source is the most common cause of a biased reference list.

# OpenAlex: multidisciplinary REST API; optional OPENALEX_API_KEY for account quota
python scripts/search_openalex.py "CRISPR gene editing" --limit 50 --output results.json

# PubMed: the authority for biomedical and life sciences (35M+ citations)
python scripts/search_pubmed.py "Alzheimer's disease treatment" --limit 100 --output alz.json

# Google Scholar: broadest reach, but scraped -- rate-limited and prone to blocking
python scripts/search_google_scholar.py "CRISPR gene editing" --limit 50 --output scholar.json

Prefer OpenAlex or PubMed as the primary source. Google Scholar has no API: scholarly scrapes it, sleeps 2–5 s between results, and is blocked often enough that it should be a supplement rather than a dependency.

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

Phase 2: Metadata Extraction

Convert identifiers (DOI, PMID, PMCID, 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/PMCID/arXiv/URL
python scripts/extract_metadata.py --input identifiers.txt --output citations.bib

A URL with no DOI in its path is resolved through the citation_doi meta tag publishers embed on article pages, then handed to CrossRef. Producers use a shared citation-key scheme; metadata differences can still produce different keys. Confirm duplicates by DOI and bibliographic identity.

Phase 2.5: Metadata Enrichment via Web Search (MANDATORY)

APIs routinely return incomplete records. Run this after extraction and before formatting. Investigate missing bibliographic fields against the publisher record and log each source. Online-first articles may have no volume/pages yet; some use an article number or have no DOI. Preserve the actual publication state, use the style-appropriate article-number field, and never invent pages, volume, or DOI. Record unavailable/not-applicable fields in the audit log; add a rendered note only when useful to the reader or required by the citation style.

Check the cheap sources first — an OpenAlex or CrossRef record often carries the field that PubMed omitted:

python scripts/search_openalex.py "<exact title>" --limit 1

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

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