Search and retrieve literature from PubMed using NCBI's EDirect command-line tools. ⚠️ Advanced skill requiring manual installation.
Real data. Real impact.
Growing
Developers
Per week
Open source
Skills give you superpowers. Install in 30 seconds.
Search and retrieve literature from PubMed using NCBI's EDirect command-line tools.
Important: This skill requires installation of external command-line tools. The installation process involves:
Before installation, you must:
ftp.ncbi.nlm.nih.govThis 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.
The skill is organized into the following files:
INSTALL.mdBASICS.mdADVANCED.mdEXAMPLES.mdREFERENCE.mdOPENCLAW_INTEGRATION.mdscripts/# Step 1: Download the script wget -q https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.shStep 2: Review content (important for security)
less install-edirect.sh
Step 3: Execute installation
./install-edirect.sh
esearch -db pubmed -query "test" -retmax 1
The skill provides access to EDirect tools through OpenClaw's
execesearchefetchelinkefilterxtracteinfoEDirect supports numerous NCBI databases including:
pubmedpmcgenenuccoreproteinmesh-helpesearch -helpThe
scripts/batch_fetch_abstracts.shFetch 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.shSearch PubMed and export results to CSV with metadata.
./scripts/search_export_csv.sh "CRISPR [TIAB]" 100 results.csv
publication_trends.shAnalyze publication trends over time with visualization.
./scripts/publication_trends.sh "machine learning" 2010 2023 trends.csv
# 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
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.
No automatic installation available. Please visit the source repository for installation instructions.
View Installation Instructions
1,500+ AI skills, agents & workflows. Install in 30 seconds. Part of the Torly.ai family.
© 2026 Torly.ai. All rights reserved.