How do I install the Archive Taxonomy skill?

Run npx skillmds add vimalinx/archive-taxonomy 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 Taxonomy 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 Taxonomy?

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 Taxonomy free to use?

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

Who published Archive Taxonomy?

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

Archive Taxonomy by vimalinx — Agent Skill

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

File contents

archive-taxonomy

Quick Start

Command: archive-taxonomy [daily|-index]
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/archive-taxonomy
Full reference: See references/help.md for detailed usage

When To Use This Tool

Build a local NCBI Taxonomy archive for offline taxon, lineage, and rank lookups.
Refresh taxonomy records after the upstream taxdump changes.
Rebuild postings so local EDirect searches can query taxonomy fields without going back to NCBI.
Use this when you want taxonomy data to live inside the same EDirect local-archive structure as other databases.

Common Patterns

# 1) Refresh the local taxonomy archive
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-taxonomy

# 2) Rebuild only the incremental index and invert layers
archive-taxonomy daily

# 3) Rebuild the full local taxonomy postings set
archive-taxonomy -index

Recommended Workflow

Set EDIRECT_LOCAL_ARCHIVE and confirm the archive root is writable.
Make sure the required EDirect helpers and local Go toolchain are available.
Run archive-taxonomy to download the taxdump and populate the local archive.
Follow with daily or -index as a separate command when you need refreshed search/posting layers.
Check the DAT, DWN, POP, IDX, INV, COL, MRG, and PST timing blocks before relying on the rebuilt archive.

Guardrails

--help and --version are not metadata-only; they still run real archive setup logic.
The script depends on EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and a working local go compiler.
Cleaning and indexing must be run as separate invocations.
The cleanup ladder (-clean, -scrub, -scour, -erase, -zap) is destructive and removes progressively more of the local taxonomy archive.
Default FTP mode may try Aspera-backed transfer; pick -https or -ftp explicitly if transport behavior matters.

---name: archive-taxonomydescription: Use when maintaining a local NCBI Taxonomy archive for offline lineage and taxon lookups in EDirect workflows.--- # archive-taxonomy ## Quick Start - **Command**: `archive-taxonomy [daily|-index]` - **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/archive-taxonomy` - **Full reference**: See [references/help.md](references/help.md) for detailed usage ## When To Use This Tool - Build a local NCBI Taxonomy archive for offline taxon, lineage, and rank lookups. - Refresh taxonomy records after the upstream taxdump changes. - Rebuild postings so local EDirect searches can query taxonomy fields without going back to NCBI. - Use this when you want taxonomy data to live inside the same EDirect local-archive structure as other databases. ## Common Patterns ```bash # 1) Refresh the local taxonomy archive export EDIRECT_LOCAL_ARCHIVE=/data/edirect archive-taxonomy ``` ```bash # 2) Rebuild only the incremental index and invert layers archive-taxonomy daily ``` ```bash # 3) Rebuild the full local taxonomy postings set archive-taxonomy -index ``` ## Recommended Workflow 1. Set `EDIRECT_LOCAL_ARCHIVE` and confirm the archive root is writable. 2. Make sure the required EDirect helpers and local Go toolchain are available. 3. Run `archive-taxonomy` to download the taxdump and populate the local archive. 4. Follow with `daily` or `-index` as a separate command when you need refreshed search/posting layers. 5. Check the `DAT`, `DWN`, `POP`, `IDX`, `INV`, `COL`, `MRG`, and `PST` timing blocks before relying on the rebuilt archive. ## Guardrails - `--help` and `--version` are not metadata-only; they still run real archive setup logic. - The script depends on `EDIRECT_LOCAL_ARCHIVE`, `pm-setup`, `pm-prepare`, and a working local `go` compiler. - Cleaning and indexing must be run as separate invocations. - The cleanup ladder (`-clean`, `-scrub`, `-scour`, `-erase`, `-zap`) is destructive and removes progressively more of the local taxonomy archive. - Default FTP mode may try Aspera-backed transfer; pick `-https` or `-ftp` explicitly if transport behavior matters.

Frequently asked questions