- name
- pubmed-edirect
- description
- Search and retrieve literature from PubMed using NCBI's EDirect command-line tools. ⚠️ Advanced skill requiring manual installation.
- requires
- bins
- install
- 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
- env
- optional
- true
- description
- NCBI API key for increased rate limits (10 requests/sec vs 3 requests/sec)
- 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:
- External script execution: Downloading and executing installation scripts from the official NCBI FTP server
- System modifications: Adding directories to your PATH environment variable
- Permission requirements: May require installation of Perl modules and dependencies
Before installation, you must:
- Review the installer script content after downloading
- Confirm the source is trustworthy (official
ftp.ncbi.nlm.nih.govdomain) - Validate in a test environment
- 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 guideBASICS.md- Basic usage and common commandsADVANCED.md- Advanced techniques and complex queriesEXAMPLES.md- Practical usage examplesREFERENCE.md- Quick reference (field qualifiers, formats, etc.)OPENCLAW_INTEGRATION.md- OpenClaw-specific usage guidescripts/- Useful bash scripts for common tasks
Quick Start
- Read the installation guide: Review INSTALL.md for secure installation steps
- 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- Verify installation:
esearch -db pubmed -query "test" -retmax 1- Explore examples: Check EXAMPLES.md
Core Tools
The skill provides access to EDirect tools through OpenClaw's exec capability:
esearch- Search databasesefetch- Retrieve recordselink- Find related recordsefilter- Filter resultsxtract- Extract data from XMLeinfo- Get database information
Databases Supported
EDirect supports numerous NCBI databases including:
pubmed- Biomedical literaturepmc- PubMed Central full-text articlesgene- Gene informationnuccore- Nucleotide sequencesprotein- Protein sequencesmesh- 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
-helpwith 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/ 0.5search_export_csv.sh
Search PubMed and export results to CSV with metadata.
./scripts/search_export_csv.sh "CRISPR [TIAB]" 100 results.csvpublication_trends.sh
Analyze publication trends over time with visualization.
./scripts/publication_trends.sh "machine learning" 2010 2023 trends.csvSecurity 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.sh2. 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.