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citation-management

Search academic databases and generate validated BibTeX citations from DOIs, PMIDs, and arXiv IDs.

Updated Oct 7, 2022
Search Tags:#bibliography#citations#metadata extraction#bibtex#pubmed#doi#google scholar
One-click install
npx skills add https://github.com/tamagusko/linux-cfg --skill citation-management-tamagusko
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: citation-management
Source: https://github.com/tamagusko/linux-cfg/tree/main/dotfiles/claude/skills/citation-management
Command: npx skills add https://github.com/tamagusko/linux-cfg --skill citation-management-tamagusko

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve? Building accurate bibliographies for research papers requires manually searching databases, copying metadata, and formatting BibTeX entries, which introduces errors like broken DOIs, missing fields, and duplicate entries that can delay or embarrass a submission. ## Core Features & Use Cases - Academic Search: Query Google Scholar and PubMed with advanced filters (MeSH terms, date ranges, publication types) and export results to JSON or BibTeX. - Metadata Extraction: Convert DOIs, PMIDs, arXiv IDs, or article URLs into complete BibTeX entries using the CrossRef, PubMed E-utilities, and arXiv APIs. - Validation and Formatting: Verify DOIs resolve, check required fields, detect duplicates, and standardize BibTeX formatting with automated fix-up. - Use Case: While writing a manuscript, you collect 50 DOIs from your notes. Run the extraction script to build references.bib, deduplicate and sort it, then validate every DOI before submission. ## Quick Start Ask the assistant to convert a list of DOIs into a validated, deduplicated BibTeX bibliography file for your manuscript.

Frequently Asked Questions about citation-management

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I convert a DOI to BibTeX format?▼

Run the doi_to_bibtex.py script with one or more DOIs, or pass a text file of DOIs via --input. It queries the CrossRef content negotiation API and outputs ready-to-use BibTeX entries to stdout or a file.

How do I search PubMed from the command line?▼

Use the search_pubmed.py script with a query string supporting MeSH terms, field tags, and Boolean operators. It uses the NCBI E-utilities API and can filter by date range and publication type, exporting results to JSON or BibTeX.

Can I extract citation metadata from an arXiv ID or PMID?▼

Yes, the extract_metadata.py script accepts DOIs, PMIDs, arXiv IDs, and article URLs. It automatically detects the identifier type and queries the appropriate API (CrossRef, PubMed, or arXiv) to build a complete BibTeX entry.

How do I check a BibTeX file for broken DOIs and duplicates?▼

Run validate_citations.py on your .bib file to verify DOI resolution, required fields, and duplicate entries. Use --auto-fix to correct common issues and --report to generate a detailed JSON validation report.

Does the PubMed search require an API key?▼

No API key is required, but providing an email via the NCBI_EMAIL environment variable is recommended, and an NCBI_API_KEY increases rate limits for high-volume queries. Without them, requests still work at the default throttled rate.

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