Citation Management

Citation Management is a skill in K-Dense's Claude Scientific Writer (MIT) that handles the unglamorous part of research writing: finding papers, pulling accurate metadata, producing clean BibTeX, and checking the bibliography before you submit. Version 1.6 ships six Python scripts for that pipeline.

Key Features

• Search: search_google_scholar.py and search_pubmed.py query Google Scholar and PubMed (via NCBI E-utilities) and save results as JSON.
• Metadata extraction: doi_to_bibtex.py converts a single DOI, and extract_metadata.py handles DOIs, PMIDs, arXiv IDs, or URLs, singly or from a list. CrossRef is the primary source for DOIs.
• Mandatory enrichment: any @article missing volume, pages, or DOI after extraction must be filled by web search (through the Parallel web skill) or given a note explaining the gap.
• Formatting and validation: format_bibtex.py cleans and deduplicates a .bib file, and validate_citations.py checks completeness, venue conformance (for example --venue nature), and agreement with a LaTeX manuscript.
• Safety note: the skill tells agents to treat publisher metadata as untrusted input, pass it as argument lists rather than shell strings, and validate citation keys against ^[A-Za-z0-9]+$.

Use Cases

• Converting a reference list of DOIs and PMIDs into one consistent BibTeX file.
• Checking a thesis bibliography for duplicates, broken DOIs, and missing fields.
• Replacing preprints with their published journal versions before submission.

Pricing and Access

Free under MIT. CrossRef, doi.org, and arXiv are queried without credentials. Optional NCBI_EMAIL and NCBI_API_KEY identify you to NCBI and raise rate limits. OPENROUTER_API_KEY is only for optional diagrams.

Getting Started

1. Install the plugin in Claude Code: /plugin marketplace add https://github.com/K-Dense-AI/claude-scientific-writer, then /plugin install claude-scientific-writer.
2. pip install requests bibtexparser biopython (add scholarly for Google Scholar).
3. Try python scripts/doi_to_bibtex.py 10.1038/s41586-021-03819-2, then python scripts/validate_citations.py references.bib --report report.txt.

Limitation: Google Scholar has no official API, so its search relies on scraping libraries and can be rate-limited or blocked. Extracted metadata can still be wrong; the skill asks you to spot-check against the source.

Frequently Asked Questions

Does it replace Zotero?

No. It produces and cleans BibTeX; the skill's references describe exporting to Zotero via pyzotero rather than replacing a reference manager.

Can it check citations inside my paper?

Yes, validate_citations.py --manuscript paper.tex compares the .bib file with citations used in the LaTeX source.

Alternatives

• Literature Review Skill: the systematic search and synthesis this skill is designed to support.
• Research Lookup Skill: builds a verified reference packet, including a references.bib.
• Scholar Evaluation Skill: judges the quality of the work you cite.

Conclusion

Citation Management is a practical fit if you write in LaTeX and want scripted BibTeX extraction and validation inside Claude Code. It will not judge whether a source supports your claim; that check stays with you. More research skills are in the skills hub.