How do I install the Archive Pubmed skill?

Run npx skillmds add vimalinx/archive-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 Archive Pubmed safe to use?

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

Which AI agents work with Archive 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 Archive Pubmed free to use?

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

Who published Archive Pubmed?

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

Archive Pubmed by vimalinx — Agent Skill

Name: Archive Pubmed
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

archive-pubmed

Quick Start

Command: archive-pubmed [download|verify|missing|index]
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/archive-pubmed
Full reference: See references/help.md for detailed documentation

When To Use This Tool

Maintain a local PubMed XML archive for offline literature search, text mining, or batch analysis.
Backfill missing baseline/update files after interrupted refreshes.
Verify downloaded gzip packages before rebuilding the search/posting layers.
Rebuild local PubMed postings after the archive content changes.

Common Patterns

# 1) Download new PubMed files and populate the local archive
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-pubmed

# 2) Check which PubMed packages are missing locally
archive-pubmed -missing

# 3) Rebuild the local PubMed search/posting structures
archive-pubmed -index

Recommended Workflow

Set EDIRECT_LOCAL_ARCHIVE and confirm the archive root is writable before starting.
Make sure the required helper commands for drive setup and versioned-record refresh are present.
Run archive-pubmed to download new files and populate the archive.
Use -verify or -missing if the refresh was interrupted or you suspect archive gaps.
Run -index only after the data files are stable, then inspect the timing summary before using the local archive with other EDirect tools.

Guardrails

--help and --version are not safe inspection switches; they still run archive setup and can emit real helper/env failures.
The script requires EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and pm-refresh.
-clean, -scrub, -scour, -erase, and -zap are destructive maintenance modes and must be run separately from -index.
Mixed-year archive states can force a cleanup path before reindexing; the script explicitly tells you to -zap or -scour in some stale-data scenarios.
-stem and -strict change how text is normalized and indexed, so record them in reproducible workflows.

---name: archive-pubmeddescription: Use when maintaining a local PubMed XML archive for offline literature search, indexing, or bulk processing.--- # archive-pubmed ## Quick Start - **Command**: `archive-pubmed [download|verify|missing|index]` - **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/archive-pubmed` - **Full reference**: See [references/help.md](references/help.md) for detailed documentation ## When To Use This Tool - Maintain a local PubMed XML archive for offline literature search, text mining, or batch analysis. - Backfill missing baseline/update files after interrupted refreshes. - Verify downloaded gzip packages before rebuilding the search/posting layers. - Rebuild local PubMed postings after the archive content changes. ## Common Patterns ```bash # 1) Download new PubMed files and populate the local archive export EDIRECT_LOCAL_ARCHIVE=/data/edirect archive-pubmed ``` ```bash # 2) Check which PubMed packages are missing locally archive-pubmed -missing ``` ```bash # 3) Rebuild the local PubMed search/posting structures archive-pubmed -index ``` ## Recommended Workflow 1. Set `EDIRECT_LOCAL_ARCHIVE` and confirm the archive root is writable before starting. 2. Make sure the required helper commands for drive setup and versioned-record refresh are present. 3. Run `archive-pubmed` to download new files and populate the archive. 4. Use `-verify` or `-missing` if the refresh was interrupted or you suspect archive gaps. 5. Run `-index` only after the data files are stable, then inspect the timing summary before using the local archive with other EDirect tools. ## Guardrails - `--help` and `--version` are not safe inspection switches; they still run archive setup and can emit real helper/env failures. - The script requires `EDIRECT_LOCAL_ARCHIVE`, `pm-setup`, `pm-prepare`, and `pm-refresh`. - `-clean`, `-scrub`, `-scour`, `-erase`, and `-zap` are destructive maintenance modes and must be run separately from `-index`. - Mixed-year archive states can force a cleanup path before reindexing; the script explicitly tells you to `-zap` or `-scour` in some stale-data scenarios. - `-stem` and `-strict` change how text is normalized and indexed, so record them in reproducible workflows.

Frequently asked questions