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Search and retrieve literature from PubMed using NCBI's EDirect command-line tools. ⚠️ Advanced skill requiring manual installation.
기본적으로 소스를 먼저 확인하는 Prompt가 선택됩니다. 직접 명령으로 전환하거나 로컬 사본을 다운로드할 수도 있습니다.
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Codex 또는 Claude로 설치 이 Prompt를 복사해 Codex, Claude 또는 다른 어시스턴트에 붙여 넣으면 Skill 페이지를 검토하고 설치를 진행할 수 있습니다.
직접 명령은 검토 Prompt를 거치지 않습니다. 실행하기 전에 소스를 확인하세요.
npx skills add https://github.com/javimosch/open-claw-skills --skill pubmed-edirect명령은 한 줄로 유지됩니다. 복사하기 전에 가로로 스크롤해 전체 내용을 확인하세요.
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SOC 직업 분류 기준
SKILL.md 표시 중
| name | pubmed-edirect |
| description | Search and retrieve literature from PubMed using NCBI's EDirect command-line tools. ⚠️ Advanced skill requiring manual installation. |
| requires | {"bins":["esearch","efetch","elink","xtract","einfo","efilter"]} |
| install | [{"id":"edirect","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":"[Truncated]"},"env":["[Truncated]","[Truncated]"]}} |
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.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 1
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 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/ 0.5
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.