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pubmed-cli

Search PubMed from the terminal and retrieve article metadata, citations, and MeSH terms as structured JSON.

88|16|Updated Feb 12, 2026
Search Tags:#research#cli#json#pubmed#mesh#literature-search#citation-network
One-click install
npx skills add https://github.com/drpedapati/sciclaw --skill pubmed-cli
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubmed-cli
Source: https://github.com/drpedapati/sciclaw/tree/main/skills/pubmed-cli
Command: npx skills add https://github.com/drpedapati/sciclaw --skill pubmed-cli

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

PubMed CLI brings PubMed searches, article metadata retrieval, citation graph traversal, and MeSH lookups to the terminal, enabling reproducible literature workflows with a lean, script-friendly interface.

Core Features & Use Cases

  • Search PubMed with Boolean/MeSH queries from the command line and return structured JSON.
  • Fetch article details by PMID (title, abstract, authors, DOI, MeSH terms) and export citations in RIS if needed.
  • Traverse citation networks with cited-by and references, discover related papers with relevance scores, and look up MeSH terms.
  • Build reproducible literature review workflows by combining search, fetch, references, and related queries.

Quick Start

Run pubmed search "ALS" and fetch details for the top results to bootstrap a literature review.

Frequently Asked Questions about pubmed-cli

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

FAQPage Schema
How do I search PubMed and export structured JSON from the terminal?▼

You can search PubMed using Boolean and MeSH queries from the terminal to retrieve article metadata, citations, and MeSH terms, with results output as structured JSON suitable for downstream agents.

Can I traverse citation networks and find related papers using PubMed metadata?▼

PubMed metadata allows you to traverse citation networks by fetching cited-by and references data, discover related papers with relevance scores, and look up associated MeSH terms for literature analysis.

How do I fetch article details and export RIS citations using a PubMed PMID?▼

Fetch article details like title, abstract, authors, DOI, and MeSH terms by PMID, and optionally export citations in RIS format to build reproducible literature review workflows.

What is the best way to build reproducible literature review workflows with PubMed searches?▼

Build reproducible literature review workflows by combining PubMed search, article fetching, references traversal, and related queries within a lean, script-friendly terminal interface.

Does PubMed CLI require any specific dependencies or API keys to retrieve MeSH terms?▼

PubMed CLI requires PubMed access to function, but operates with no external dependencies, allowing you to retrieve MeSH terms and article metadata directly from the terminal.

Can I generate a knowledge graph from PubMed citation networks using JSON output?▼

PubMed citation network traversal outputs structured JSON, enabling you to generate knowledge graphs and support end-to-end workflows from query to cited-by and references analysis.

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