pubmed-edirect - SKILL.md Agent Skill

name: pubmed-edirect description: Search and retrieve literature from PubMed using NCBI's EDirect command-line tools. metadata: { "openclaw": { "emoji": "🔬", "requires": { "anyBins": ["esearch", "efetch", "elink", "xtract"] }, "install": [ { "id": "edirect", "kind": "script", "bins": ["esearch", "efetch", "elink", "xtract", "einfo", "efilter"], "label": "Install EDirect (see INSTALL.md for details)", }, ], },

}

PubMed EDirect Skill

Search and retrieve literature from PubMed using NCBI's EDirect command-line tools.

Overview

This skill provides access to PubMed and other NCBI databases through the official EDirect (Entrez Direct) utilities. EDirect is a suite of programs that provide access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminals.

Note: This is a local installation skill – all tools run directly on your system without Docker or containerization. Follow the INSTALL.md guide for local setup.

Structure

The skill is organized into the following files:

INSTALL.md - Installation and configuration guide
BASICS.md - Basic usage and common commands
ADVANCED.md - Advanced techniques and complex queries
EXAMPLES.md - Practical usage examples
REFERENCE.md - Quick reference (field qualifiers, formats, etc.)
OPENCLAW_INTEGRATION.md - OpenClaw-specific usage guide
scripts/ - Useful bash scripts for common tasks

Quick Start

Install EDirect (see INSTALL.md)

Try a basic search:

esearch -db pubmed -query "CRISPR [TIAB]" | efetch -format abstract

Explore examples in EXAMPLES.md

Core Tools

The skill provides access to EDirect tools through OpenClaw's exec capability:

esearch - Search databases
efetch - Retrieve records
elink - Find related records
efilter - Filter results
xtract - Extract data from XML
einfo - Get database information

Databases Supported

EDirect supports numerous NCBI databases including:

pubmed - Biomedical literature
pmc - PubMed Central full-text articles
gene - Gene information
nuccore - Nucleotide sequences
protein - Protein sequences
mesh - Medical Subject Headings
And many more...

Key Features

Command-line access to NCBI databases
Pipeline architecture using Unix pipes
Structured data extraction with XML parsing
Batch processing capabilities
Cross-database linking between records

Getting Help

Use -help with any EDirect command: esearch -help
Consult the official documentation
Check troubleshooting in installation guide

Included Scripts

The scripts/ directory contains ready-to-use bash scripts:

`batch_fetch_abstracts.sh`

Fetch abstracts for a list of PMIDs with error handling and rate limiting.

./scripts/batch_fetch_abstracts.sh pmids.txt abstracts/ 0.5

`search_export_csv.sh`

Search PubMed and export results to CSV with metadata.

./scripts/search_export_csv.sh "CRISPR [TIAB]" 100 results.csv

`publication_trends.sh`

Analyze publication trends over time with visualization.

./scripts/publication_trends.sh "machine learning" 2010 2023 trends.csv

Notes

This skill requires EDirect to be installed and configured on your system. It provides command templates and examples that can be executed through OpenClaw's exec tool. For complex workflows, consider creating reusable shell scripts or using the included scripts.