{
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  "item": {
    "slug": "pubmed-edirect",
    "name": "Pubmed Edirect",
    "source": "tencent",
    "type": "skill",
    "category": "开发工具",
    "sourceUrl": "https://clawhub.ai/killgfat/pubmed-edirect",
    "canonicalUrl": "https://clawhub.ai/killgfat/pubmed-edirect",
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    "installMethod": "Manual import",
    "extraction": "Extract archive",
    "prerequisites": [
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    "packageFormat": "ZIP package",
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      "BASICS.md",
      "EXAMPLES.md",
      "INSTALL.md",
      "OPENCLAW_INTEGRATION.md",
      "REFERENCE.md"
    ],
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    "quickSetup": [
      "Download the package from Yavira.",
      "Extract the archive and review SKILL.md first.",
      "Import or place the package into your OpenClaw setup."
    ],
    "agentAssist": {
      "summary": "Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.",
      "steps": [
        "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."
      ],
      "prompts": [
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          "label": "New install",
          "body": "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."
        },
        {
          "label": "Upgrade existing",
          "body": "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."
        }
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      "recommendedAction": "download",
      "checkedAt": "2026-04-30T16:55:25.780Z",
      "expiresAt": "2026-05-07T16:55:25.780Z",
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        "redirectLocation": null,
        "bodySnippet": null
      },
      "scope": "source",
      "summary": "Source download looks usable.",
      "detail": "Yavira can redirect you to the upstream package for this source.",
      "primaryActionLabel": "Download for OpenClaw",
      "primaryActionHref": "/downloads/pubmed-edirect"
    },
    "validation": {
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        "Use the Yavira download entry.",
        "Review SKILL.md after the package is downloaded.",
        "Confirm the extracted package contains the expected setup assets."
      ],
      "postInstallChecks": [
        "Confirm the extracted package includes the expected docs or setup files.",
        "Validate the skill or prompts are available in your target agent workspace.",
        "Capture any manual follow-up steps the agent could not complete."
      ]
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    "downloadPageUrl": "https://openagent3.xyz/downloads/pubmed-edirect",
    "agentPageUrl": "https://openagent3.xyz/skills/pubmed-edirect/agent",
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    "briefUrl": "https://openagent3.xyz/skills/pubmed-edirect/agent.md"
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  "agentAssist": {
    "summary": "Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.",
    "steps": [
      "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."
    ],
    "prompts": [
      {
        "label": "New install",
        "body": "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."
      },
      {
        "label": "Upgrade existing",
        "body": "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."
      }
    ]
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  "documentation": {
    "source": "clawhub",
    "primaryDoc": "SKILL.md",
    "sections": [
      {
        "title": "PubMed EDirect Skill",
        "body": "Search and retrieve literature from PubMed using NCBI's EDirect command-line tools."
      },
      {
        "title": "⚠️ Security Advisory",
        "body": "Important: This skill requires installation of external command-line tools. The installation process involves:\n\nExternal script execution: Downloading and executing installation scripts from the official NCBI FTP server\nSystem modifications: Adding directories to your PATH environment variable\nPermission requirements: May require installation of Perl modules and dependencies\n\nBefore installation, you must:\n\nReview the installer script content after downloading\nConfirm the source is trustworthy (official ftp.ncbi.nlm.nih.gov domain)\nValidate in a test environment\nUnderstand all commands that will be executed"
      },
      {
        "title": "Overview",
        "body": "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.\n\nNote: 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."
      },
      {
        "title": "Structure",
        "body": "The skill is organized into the following files:\n\nINSTALL.md - Installation and configuration guide\nBASICS.md - Basic usage and common commands\nADVANCED.md - Advanced techniques and complex queries\nEXAMPLES.md - Practical usage examples\nREFERENCE.md - Quick reference (field qualifiers, formats, etc.)\nOPENCLAW_INTEGRATION.md - OpenClaw-specific usage guide\nscripts/ - Useful bash scripts for common tasks"
      },
      {
        "title": "Quick Start",
        "body": "Read the installation guide: Review INSTALL.md for secure installation steps\nManually install EDirect:\n# Step 1: Download the script\nwget -q https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh\n\n# Step 2: Review content (important for security)\nless install-edirect.sh\n\n# Step 3: Execute installation\n./install-edirect.sh\n\n\nVerify installation:\nesearch -db pubmed -query \"test\" -retmax 1\n\n\nExplore examples: Check EXAMPLES.md"
      },
      {
        "title": "Core Tools",
        "body": "The skill provides access to EDirect tools through OpenClaw's exec capability:\n\nesearch - Search databases\nefetch - Retrieve records\nelink - Find related records\nefilter - Filter results\nxtract - Extract data from XML\neinfo - Get database information"
      },
      {
        "title": "Databases Supported",
        "body": "EDirect supports numerous NCBI databases including:\n\npubmed - Biomedical literature\npmc - PubMed Central full-text articles\ngene - Gene information\nnuccore - Nucleotide sequences\nprotein - Protein sequences\nmesh - Medical Subject Headings\nAnd many more..."
      },
      {
        "title": "Key Features",
        "body": "Command-line access to NCBI databases\nPipeline architecture using Unix pipes\nStructured data extraction with XML parsing\nBatch processing capabilities\nCross-database linking between records"
      },
      {
        "title": "Getting Help",
        "body": "Use -help with any EDirect command: esearch -help\nConsult the official documentation\nCheck troubleshooting in installation guide"
      },
      {
        "title": "Included Scripts",
        "body": "The scripts/ directory contains ready-to-use bash scripts:"
      },
      {
        "title": "batch_fetch_abstracts.sh",
        "body": "Fetch abstracts for a list of PMIDs with error handling and rate limiting.\n\n./scripts/batch_fetch_abstracts.sh pmids.txt abstracts/ 0.5"
      },
      {
        "title": "search_export_csv.sh",
        "body": "Search PubMed and export results to CSV with metadata.\n\n./scripts/search_export_csv.sh \"CRISPR [TIAB]\" 100 results.csv"
      },
      {
        "title": "publication_trends.sh",
        "body": "Analyze publication trends over time with visualization.\n\n./scripts/publication_trends.sh \"machine learning\" 2010 2023 trends.csv"
      },
      {
        "title": "1. Script Review",
        "body": "# Always download first and review scripts\nwget -q SOURCE_URL -O script.sh\nless script.sh  # or cat script.sh | head -50\n# Execute only after review\n./script.sh"
      },
      {
        "title": "2. Environment Isolation",
        "body": "Running in Docker containers provides isolation\nUse virtual machines for testing\nSet up dedicated user accounts"
      },
      {
        "title": "3. Least Privilege",
        "body": "Do not run as root\nSet appropriate file permissions\nUse dedicated directories for data"
      },
      {
        "title": "4. Network Controls",
        "body": "Configure firewall rules\nUse proxies for controlled access\nMonitor network traffic"
      },
      {
        "title": "Notes",
        "body": "Important: This skill requires manual installation and configuration. All installation steps require explicit user confirmation and execution.\n\nThis skill provides command-line access to NCBI databases through local installation of EDirect tools."
      }
    ],
    "body": "PubMed EDirect Skill\n\nSearch and retrieve literature from PubMed using NCBI's EDirect command-line tools.\n\n⚠️ Security Advisory\n\nImportant: This skill requires installation of external command-line tools. The installation process involves:\n\nExternal script execution: Downloading and executing installation scripts from the official NCBI FTP server\nSystem modifications: Adding directories to your PATH environment variable\nPermission requirements: May require installation of Perl modules and dependencies\n\nBefore installation, you must:\n\nReview the installer script content after downloading\nConfirm the source is trustworthy (official ftp.ncbi.nlm.nih.gov domain)\nValidate in a test environment\nUnderstand all commands that will be executed\nOverview\n\nThis 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.\n\nNote: 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.\n\nStructure\n\nThe skill is organized into the following files:\n\nINSTALL.md - Installation and configuration guide\nBASICS.md - Basic usage and common commands\nADVANCED.md - Advanced techniques and complex queries\nEXAMPLES.md - Practical usage examples\nREFERENCE.md - Quick reference (field qualifiers, formats, etc.)\nOPENCLAW_INTEGRATION.md - OpenClaw-specific usage guide\nscripts/ - Useful bash scripts for common tasks\nQuick Start\nRead the installation guide: Review INSTALL.md for secure installation steps\nManually install EDirect:\n# Step 1: Download the script\nwget -q https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh\n\n# Step 2: Review content (important for security)\nless install-edirect.sh\n\n# Step 3: Execute installation\n./install-edirect.sh\n\nVerify installation:\nesearch -db pubmed -query \"test\" -retmax 1\n\nExplore examples: Check EXAMPLES.md\nCore Tools\n\nThe skill provides access to EDirect tools through OpenClaw's exec capability:\n\nesearch - Search databases\nefetch - Retrieve records\nelink - Find related records\nefilter - Filter results\nxtract - Extract data from XML\neinfo - Get database information\nDatabases Supported\n\nEDirect supports numerous NCBI databases including:\n\npubmed - Biomedical literature\npmc - PubMed Central full-text articles\ngene - Gene information\nnuccore - Nucleotide sequences\nprotein - Protein sequences\nmesh - Medical Subject Headings\nAnd many more...\nKey Features\nCommand-line access to NCBI databases\nPipeline architecture using Unix pipes\nStructured data extraction with XML parsing\nBatch processing capabilities\nCross-database linking between records\nGetting Help\nUse -help with any EDirect command: esearch -help\nConsult the official documentation\nCheck troubleshooting in installation guide\nIncluded Scripts\n\nThe scripts/ directory contains ready-to-use bash scripts:\n\nbatch_fetch_abstracts.sh\n\nFetch abstracts for a list of PMIDs with error handling and rate limiting.\n\n./scripts/batch_fetch_abstracts.sh pmids.txt abstracts/ 0.5\n\nsearch_export_csv.sh\n\nSearch PubMed and export results to CSV with metadata.\n\n./scripts/search_export_csv.sh \"CRISPR [TIAB]\" 100 results.csv\n\npublication_trends.sh\n\nAnalyze publication trends over time with visualization.\n\n./scripts/publication_trends.sh \"machine learning\" 2010 2023 trends.csv\n\nSecurity Best Practices\n1. Script Review\n# Always download first and review scripts\nwget -q SOURCE_URL -O script.sh\nless script.sh  # or cat script.sh | head -50\n# Execute only after review\n./script.sh\n\n2. Environment Isolation\nRunning in Docker containers provides isolation\nUse virtual machines for testing\nSet up dedicated user accounts\n3. Least Privilege\nDo not run as root\nSet appropriate file permissions\nUse dedicated directories for data\n4. Network Controls\nConfigure firewall rules\nUse proxies for controlled access\nMonitor network traffic\nNotes\n\nImportant: This skill requires manual installation and configuration. All installation steps require explicit user confirmation and execution.\n\nThis skill provides command-line access to NCBI databases through local installation of EDirect tools."
  },
  "trust": {
    "sourceLabel": "tencent",
    "provenanceUrl": "https://clawhub.ai/killgfat/pubmed-edirect",
    "publisherUrl": "https://clawhub.ai/killgfat/pubmed-edirect",
    "owner": "killgfat",
    "version": "0.4.4",
    "license": null,
    "verificationStatus": "Indexed source record"
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    "downloadUrl": "https://openagent3.xyz/downloads/pubmed-edirect",
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