How do I install the Archive Nlmnlp skill?

Run npx skillmds add vimalinx/archive-nlmnlp 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 Nlmnlp safe to use?

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Which AI agents work with Archive Nlmnlp?

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 Nlmnlp free to use?

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

Who published Archive Nlmnlp?

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

Archive Nlmnlp by vimalinx — Agent Skill

Name: Archive Nlmnlp
Rating: 4.5 (4 reviews)
Author: vimalinx

File contents

archive-nlmnlp

Quick Start

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

When To Use This Tool

Build a local PubMed concept archive backed by PubTator Central, GeneRIF, and gene metadata files.
Support offline lookup of chemical, disease, gene, synonym, and GeneRIF-derived postings in EDirect workflows.
Refresh the archive after upstream concept files change, then rebuild postings in the usual EDirect layout.
Use this instead of stitching together the PubTator and GeneRIF files manually.

Common Patterns

# 1) Refresh the local NLM NLP extras and archive over HTTPS
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-nlmnlp -https

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

# 3) Rebuild merged postings for downstream local searching
archive-nlmnlp -index

Recommended Workflow

Set EDIRECT_LOCAL_ARCHIVE and confirm the archive root exists and is writable.
Make sure pm-setup, pm-prepare, and the local Go toolchain are available.
Run archive-nlmnlp or archive-nlmnlp -https to stage the latest PubTator / GeneRIF support files.
Follow with daily or -index as a separate command when you need refreshed postings.
Check the DWN, IDX, INV, MRG, and PST timing blocks to confirm each stage actually ran.

Guardrails

--help and --version are not safe inspection switches; they still trigger archive setup and prerequisite checks.
The script depends on EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and a local go compiler.
Default transport may try the FTP / Aspera path; use -https or -ftp explicitly if you need predictable transfer behavior.
Cleaning and indexing must be run separately.
The cleanup aliases remove scratch data, so do not use them casually on a populated archive.

---name: archive-nlmnlpdescription: Use when maintaining a local NLM NLP concept archive over PubMed for offline chemical, disease, gene, or GeneRIF lookups.--- # archive-nlmnlp ## Quick Start - **Command**: `archive-nlmnlp [daily|-index]` - **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/archive-nlmnlp` - **Full reference**: See [references/help.md](references/help.md) for complete documentation ## When To Use This Tool - Build a local PubMed concept archive backed by PubTator Central, GeneRIF, and gene metadata files. - Support offline lookup of chemical, disease, gene, synonym, and GeneRIF-derived postings in EDirect workflows. - Refresh the archive after upstream concept files change, then rebuild postings in the usual EDirect layout. - Use this instead of stitching together the PubTator and GeneRIF files manually. ## Common Patterns ```bash # 1) Refresh the local NLM NLP extras and archive over HTTPS export EDIRECT_LOCAL_ARCHIVE=/data/edirect archive-nlmnlp -https ``` ```bash # 2) Rebuild only the incremental index and invert layers archive-nlmnlp daily ``` ```bash # 3) Rebuild merged postings for downstream local searching archive-nlmnlp -index ``` ## Recommended Workflow 1. Set `EDIRECT_LOCAL_ARCHIVE` and confirm the archive root exists and is writable. 2. Make sure `pm-setup`, `pm-prepare`, and the local Go toolchain are available. 3. Run `archive-nlmnlp` or `archive-nlmnlp -https` to stage the latest PubTator / GeneRIF support files. 4. Follow with `daily` or `-index` as a separate command when you need refreshed postings. 5. Check the `DWN`, `IDX`, `INV`, `MRG`, and `PST` timing blocks to confirm each stage actually ran. ## Guardrails - `--help` and `--version` are not safe inspection switches; they still trigger archive setup and prerequisite checks. - The script depends on `EDIRECT_LOCAL_ARCHIVE`, `pm-setup`, `pm-prepare`, and a local `go` compiler. - Default transport may try the FTP / Aspera path; use `-https` or `-ftp` explicitly if you need predictable transfer behavior. - Cleaning and indexing must be run separately. - The cleanup aliases remove scratch data, so do not use them casually on a populated archive.

Frequently asked questions