PubMed EDirect Skill

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

⚠️ Security Advisory

Important: This skill requires installation of external command-line tools. The installation process involves:

1. External script execution: Downloading and executing installation scripts from the official NCBI FTP server

2. System modifications: Adding directories to your PATH environment variable

3. Permission requirements: May require installation of Perl modules and dependencies

Before installation, you must:

1. Review the installer script content after downloading

2. Confirm the source is trustworthy (official ftp.ncbi.nlm.nih.gov domain)

3. Validate in a test environment

4. Understand all commands that will be executed

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

1. Read the installation guide: Review INSTALL.md for secure installation steps

2. Manually install EDirect: ```bash

   Step 1: Download the script

   wget -q https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh

# Step 2: Review content (important for security) less install-edirect.sh

# Step 3: Execute installation ./install-edirect.sh ```

1. Verify installation: bash esearch -db pubmed -query "test" -retmax 1

2. Explore examples: Check 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

Security Best Practices

1. Script Review

# Always download first and review scripts
wget -q SOURCE_URL -O script.sh
less script.sh  # or cat script.sh | head -50

# Execute only after review
./script.sh

2. Environment Isolation

• Running in Docker containers provides isolation

• Use virtual machines for testing

• Set up dedicated user accounts

3. Least Privilege

• Do not run as root

• Set appropriate file permissions

• Use dedicated directories for data

4. Network Controls

• Configure firewall rules

• Use proxies for controlled access

• Monitor network traffic

Notes

Important: This skill requires manual installation and configuration. All installation steps require explicit user confirmation and execution.

This skill provides command-line access to NCBI databases through local installation of EDirect tools.