How do I install the Download Pubmed skill?

Run npx skillmds add vimalinx/download-pubmed in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Download Pubmed safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Download Pubmed?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Download Pubmed free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Download Pubmed?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Download Pubmed by vimalinx — Agent Skill

Name: Download Pubmed
Rating: 4.5 (4 reviews)
Author: vimalinx

File contents

download-pubmed

Quick Start

Command: download-pubmed [-ftp|-https] [section...]
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/download-pubmed
Full reference: See references/help.md

When To Use This Tool

Mirror PubMed XML baselines and daily update files into local storage.
Seed a local PubMed archive before running archive-pubmed, fetch-pubmed, or custom text-mining pipelines.
Refresh a PubMed mirror incrementally by targeting updatefiles after an initial baseline sync.

Common Patterns

# 1) Download the default PubMed mirror set: baseline + updatefiles
download-pubmed

# 2) Use HTTPS explicitly
download-pubmed -https

# 3) Download only one section
download-pubmed baseline
download-pubmed updatefiles

Recommended Workflow

Run this from a clean target directory because all downloaded .xml.gz files land in the current working directory.
Use the no-argument form once to fetch both baseline and updatefiles, or target sections explicitly when refreshing an existing mirror.
Let the wrapper finish its retry and validation cycle before deciding a file is broken.
Feed the validated archive into local indexing or parsing workflows instead of repeatedly querying PubMed live.

Guardrails

With no arguments, this command downloads both baseline and updatefiles, which is large.
The local wrapper validates XML payloads and deletes bad downloads before retrying, so interrupted runs can leave partial work that must be retried.
Output is written into the current directory; keep PubMed mirrors isolated from unrelated files.
This script does not expose a normal --help mode in practice, so rely on the captured reference rather than probing it with arbitrary flags.

---name: download-pubmeddescription: Use when you need to bulk-download PubMed baseline or update files from NCBI's FTP server for local offline analysis.--- # download-pubmed ## Quick Start - **Command:** `download-pubmed [-ftp|-https] [section...]` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/download-pubmed` - **Full reference:** See `references/help.md` ## When To Use This Tool - Mirror PubMed XML baselines and daily update files into local storage. - Seed a local PubMed archive before running `archive-pubmed`, `fetch-pubmed`, or custom text-mining pipelines. - Refresh a PubMed mirror incrementally by targeting `updatefiles` after an initial baseline sync. ## Common Patterns ```bash # 1) Download the default PubMed mirror set: baseline + updatefiles download-pubmed ``` ```bash # 2) Use HTTPS explicitly download-pubmed -https ``` ```bash # 3) Download only one section download-pubmed baseline download-pubmed updatefiles ``` ## Recommended Workflow 1. Run this from a clean target directory because all downloaded `.xml.gz` files land in the current working directory. 2. Use the no-argument form once to fetch both `baseline` and `updatefiles`, or target sections explicitly when refreshing an existing mirror. 3. Let the wrapper finish its retry and validation cycle before deciding a file is broken. 4. Feed the validated archive into local indexing or parsing workflows instead of repeatedly querying PubMed live. ## Guardrails - With no arguments, this command downloads both `baseline` and `updatefiles`, which is large. - The local wrapper validates XML payloads and deletes bad downloads before retrying, so interrupted runs can leave partial work that must be retried. - Output is written into the current directory; keep PubMed mirrors isolated from unrelated files. - This script does not expose a normal `--help` mode in practice, so rely on the captured reference rather than probing it with arbitrary flags.

Frequently asked questions