⚠
High Risk:This skill has significant security concerns. Review the findings below before installing.

pubmed-edirect

⚠Caution·Scanned 2/18/2026

This skill provides command-line access to PubMed via EDirect with install instructions, examples, and shell scripts. It instructs running shell commands (e.g., exec -c '...', ./install-edirect.sh), downloads from ftp.ncbi.nlm.nih.gov, and directs storing NCBI_API_KEY in shell rc files.

from clawhub.ai·v5639713·59.2 KB·0 installs
Scanned from 0.3.0 at 5639713 · Transparency log ↗
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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

  1. Install EDirect (see INSTALL.md)
  2. Try a basic search: 
    esearch -db pubmed -query "CRISPR [TIAB]" | efetch -format abstract
  3. 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.