pubmed-edirectSearch and retrieve literature from PubMed using NCBI's EDirect command-line tools. ⚠️ Advanced skill requiring manual installation.
Install via ClawdBot CLI:
clawdbot install killgfat/pubmed-edirectSearch 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.gov domain)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.
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
# 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
esearch -db pubmed -query "test" -retmax 1The 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 informationEDirect supports numerous NCBI databases including:
pubmed - Biomedical literaturepmc - PubMed Central full-text articlesgene - Gene informationnuccore - Nucleotide sequencesprotein - Protein sequencesmesh - Medical Subject Headings-help with any EDirect command: esearch -helpThe scripts/ directory contains ready-to-use bash 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/ 0.5search_export_csv.shSearch PubMed and export results to CSV with metadata.
./scripts/search_export_csv.sh "CRISPR [TIAB]" 100 results.csvpublication_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.shImportant: 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.
Generated Mar 1, 2026
Researchers can use this skill to systematically search PubMed for relevant studies, retrieve abstracts, and export results for analysis. It supports batch processing of queries, enabling comprehensive literature reviews in fields like biomedicine or public health.
Pharma companies can leverage EDirect to monitor recent publications on drug targets, gene interactions, or clinical trials. The skill allows automated data extraction to track trends and inform R&D decisions, enhancing efficiency in drug development pipelines.
Healthcare analysts can query PubMed for epidemiological studies or treatment outcomes to support evidence-based practices. By integrating with scripts, they can generate reports on disease trends or treatment efficacy for hospital or policy use.
Biotech firms can use this skill to gather competitive intelligence by searching for patents, gene sequences, or publication metrics. It facilitates analysis of research landscapes to identify opportunities or assess market gaps.
Educational institutions can automate retrieval of up-to-date medical literature for curriculum development or student resources. The skill helps compile relevant articles and abstracts to support teaching materials in medical or nursing programs.
Offer a service where users pay a monthly fee for access to enhanced PubMed search tools, automated report generation, and data visualization. Revenue comes from subscriptions tailored to academic or corporate clients needing regular literature updates.
Provide consulting services to help organizations integrate EDirect into their workflows, such as setting up custom scripts or training staff. Revenue is generated through project-based fees or ongoing support contracts for specialized use cases.
Sell curated datasets extracted from PubMed, such as publication trends or gene-disease associations, to clients in pharma or biotech. Revenue streams include one-time purchases or licensing fees for access to processed, structured data.
💬 Integration Tip
Ensure users have basic command-line proficiency and review security practices before installation; integrate with existing data pipelines using the provided scripts for automation.
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