Pubmed Edirect

Search and retrieve literature from PubMed using NCBI's EDirect command-line tools. ⚠️ Advanced skill requiring manual installation.

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
   

3. Verify installation:

   bash

   esearch -db pubmed -query "test" -retmax 1
   

4. 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.

bash

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

search_export_csv.sh

Search PubMed and export results to CSV with metadata.

bash

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

publication_trends.sh

Analyze publication trends over time with visualization.

bash

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

Security Best Practices

1. Script Review

bash

# 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.