Requirements
- Target platform
- OpenClaw
- Install method
- Manual import
- Extraction
- Extract archive
- Prerequisites
- OpenClaw
- Primary doc
- SKILL.md
Tencent SkillHub · Developer Tools
Pubmed Edirect
Search and retrieve literature from PubMed using NCBI's EDirect command-line tools. ⚠️ Advanced skill requiring manual installation.
skill openclawclawhub Free
Search and retrieve literature from PubMed using NCBI's EDirect command-line tools. ⚠️ Advanced skill requiring manual installation.
⬇ 0 downloads ★ 0 stars Unverified but indexed
Install for OpenClaw
Quick setup
- Download the package from Yavira.
- Extract the archive and review SKILL.md first.
- Import or place the package into your OpenClaw setup.
Package facts
- Download mode
- Yavira redirect
- Package format
- ZIP package
- Source platform
- Tencent SkillHub
- What's included
- ADVANCED.md, BASICS.md, EXAMPLES.md, INSTALL.md, OPENCLAW_INTEGRATION.md, REFERENCE.md
Validation
- Use the Yavira download entry.
- Review SKILL.md after the package is downloaded.
- Confirm the extracted package contains the expected setup assets.
Install with your agent
Agent handoff
Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.
- Download the package from Yavira.
- Extract it into a folder your agent can access.
- Paste one of the prompts below and point your agent at the extracted folder.
New install
I downloaded a skill package from Yavira. Read SKILL.md from the extracted folder and install it by following the included instructions. Tell me what you changed and call out any manual steps you could not complete.
Upgrade existing
I downloaded an updated skill package from Yavira. Read SKILL.md from the extracted folder, compare it with my current installation, and upgrade it while preserving any custom configuration unless the package docs explicitly say otherwise. Summarize what changed and any follow-up checks I should run.
Trust & source
Release facts
- Source
- Tencent SkillHub
- Verification
- Indexed source record
- Version
- 0.4.4
Provenance
- Publisher
- killgfat
- Source page
- View original listing
- Canonical URL
- Open canonical page
Documentation
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.gov domain) 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 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
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 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
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.
Category context
Code helpers, APIs, CLIs, browser automation, testing, and developer operations.
Source: Tencent SkillHub
Largest current source with strong distribution and engagement signals.
Package contents
Included in package
6 Docs
- ADVANCED.md
- BASICS.md
- EXAMPLES.md
- INSTALL.md
- OPENCLAW_INTEGRATION.md
- REFERENCE.md