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Reference Management Skill

Save and manage biomedical references by PMID with PubMed API and citation formatting.

11|4|Updated Nov 25, 2025
Search Tags:#pdf#bibliography#mcp#citation#pubmed#reference-management#foam
One-click install
npx skills add https://github.com/u9401066/med-paper-assistant --skill reference-management-skill
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: Reference Management Skill
Source: https://github.com/u9401066/med-paper-assistant/tree/main/vscode-extension/skills/reference-management
Command: npx skills add https://github.com/u9401066/med-paper-assistant --skill reference-management-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Reduces the friction of saving, deduplicating, reading, and formatting biomedical references by providing direct PubMed-backed storage, local search, PDF reading, and citation formatting tied to research projects.

Core Features & Use Cases

  • Direct PubMed saving: Prefer save_reference_mcp(pmid) to pull verified metadata from the pubmed-search API and persist it to a project.
  • Fallback and validation: Accepts agent-provided article metadata via save_reference(article) when the API is unavailable and checks for existing PMIDs to avoid duplicates.
  • Reference management tools: List saved references, search local references, retrieve formatted citation strings, set citation styles (Vancouver/APA/etc.), and rebuild Foam wikilink aliases for note integration.
  • PDF and notes support: Read downloaded full text with character limits and attach concise agent_notes that summarize relevance, methods, and key findings for downstream drafting tasks.
  • Use case: After a PubMed search, select key articles to save into a project, add structured agent notes about relevance, and generate a formatted reference list for manuscript export.

Quick Start

Save the PubMed article with PMID 12345678 into the current project and include an agent note summarizing relevance and key findings.

Frequently Asked Questions about Reference Management Skill

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

FAQPage Schema
How do I save PubMed references by PMID into my research project?▼

Save PubMed references by PMID using the save_reference_mcp(pmid) function, which pulls verified metadata from the PubMed API and persists it to project-scoped storage. If the PubMed API is unavailable, you can use save_reference(article) with agent-provided metadata as a fallback.

What is the best way to format biomedical citations for a manuscript?▼

Format biomedical citations for manuscripts by setting a citation style like Vancouver or APA, then retrieving formatted citation strings from saved references. The reference management workflow generates a formatted reference list ready for export.

Can I read downloaded PDF full text and add notes to saved references?▼

Yes, you can read downloaded PDF full text with character limits and attach concise agent_notes summarizing relevance, methods, and key findings. These notes are saved with the reference for downstream drafting tasks.

Does reference management work with Foam wikilinks?▼

Yes, reference management supports Foam wikilink rebuilding for note integration. You can rebuild Foam wikilink aliases to connect saved references seamlessly with your Foam knowledge base.

How do I check if a PubMed reference already exists in my project?▼

Check for existing PubMed references by verifying PMIDs during the save process. The reference management system checks for existing PMIDs to avoid duplicates and supports listing and searching locally saved references within project scopes.

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