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🦀 ClawHub

Pubmed Edirect

by @killgfat

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

Versionv0.4.4
Downloads3,473
Stars⭐ 4
#research#legal
TERMINAL
clawhub install pubmed-edirect

📖 About This Skill

name: pubmed-edirect description: Search and retrieve literature from PubMed using NCBI's EDirect command-line tools. ⚠️ Advanced skill requiring manual installation. requires: bins: - esearch - efetch - elink - xtract - einfo - efilter install: - id: edirect kind: manual label: Manual Installation Required - Review INSTALL.md docs: https://www.ncbi.nlm.nih.gov/books/NBK179288/ note: "⚠️ User must manually download and review official installer script" security_level: elevated metadata: openclaw: emoji: 🔬 category: advanced security_level: elevated requires: bins: - esearch - efetch - elink - xtract - einfo - efilter env: - name: NCBI_API_KEY optional: true description: NCBI API key for increased rate limits (10 requests/sec vs 3 requests/sec) - name: NCBI_EMAIL optional: true description: Email address to identify yourself to NCBI

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: 

       # 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: 
       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.

    ./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.

    💡 Examples

    1. Read the installation guide: Review INSTALL.md for secure installation steps 2. Manually install EDirect: 

       # 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: 
       esearch -db pubmed -query "test" -retmax 1
    4. Explore examples: Check EXAMPLES.md

    📋 Tips & Best Practices

    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.