pubmed-literature-miner

Biomedical literature mining using PubMed/MEDLINE for systematic review support

509 stars

Best use case

pubmed-literature-miner is best used when you need a repeatable AI agent workflow instead of a one-off prompt.

Biomedical literature mining using PubMed/MEDLINE for systematic review support

Teams using pubmed-literature-miner should expect a more consistent output, faster repeated execution, less prompt rewriting.

When to use this skill

You want a reusable workflow that can be run more than once with consistent structure.

When not to use this skill

You only need a quick one-off answer and do not need a reusable workflow.
You cannot install or maintain the underlying files, dependencies, or repository context.

Installation

Claude Code / Cursor / Codex

$curl -o ~/.claude/skills/pubmed-literature-miner/SKILL.md --create-dirs "https://raw.githubusercontent.com/a5c-ai/babysitter/main/library/specializations/domains/science/scientific-discovery/skills/pubmed-literature-miner/SKILL.md"

Manual Installation

Download SKILL.md from GitHub
Place it in .claude/skills/pubmed-literature-miner/SKILL.md inside your project
Restart your AI agent — it will auto-discover the skill

How pubmed-literature-miner Compares

Feature / Agent	pubmed-literature-miner	Standard Approach
Platform Support	Not specified	Limited / Varies
Context Awareness	High	Baseline
Installation Complexity	Unknown	N/A

Frequently Asked Questions

What does this skill do?

Biomedical literature mining using PubMed/MEDLINE for systematic review support

Where can I find the source code?

You can find the source code on GitHub using the link provided at the top of the page.

SKILL.md Source

# PubMed Literature Miner

## Purpose

Provides biomedical literature mining capabilities using PubMed/MEDLINE for systematic review support and PICO framework analysis.

## Capabilities

- MeSH term-based search
- PICO element extraction
- Abstract screening automation
- Citation deduplication
- PRISMA flow diagram data generation
- Full-text retrieval coordination

## Usage Guidelines

1. **MeSH Terms**: Use controlled vocabulary for precise searches
2. **PICO Framework**: Structure searches around population, intervention, comparison, outcome
3. **Screening**: Apply inclusion/exclusion criteria systematically
4. **PRISMA Compliance**: Generate required flow diagram data

## Tools/Libraries

- Biopython
- PyMed
- NCBI E-utilities

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