How do I install the Ref2pmid skill?

Run npx skillmds add vimalinx/ref2pmid 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 Ref2pmid safe to use?

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Which AI agents work with Ref2pmid?

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 Ref2pmid free to use?

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

Who published Ref2pmid?

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

Ref2pmid by vimalinx — Agent Skill

Name: Ref2pmid
Rating: 4.5 (4 reviews)
Author: vimalinx

File contents

ref2pmid

Tiny EDirect wrapper around transmute -r2p. It maps citation-style XML or similar reference payloads to PMIDs, but it is only a stdin transformer and does not expose its own help text.

Quick Start

Command: ref2pmid
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/ref2pmid
Actual implementation: a one-line shell wrapper calling transmute -r2p "$@"

When To Use This Tool

Converting bibliographic references to PubMed IDs
Part of the Entrez Direct (EDirect) bioconda package for NCBI database queries
Turning citation XML streams into PMID-enriched output for later EDirect steps

Common Patterns

# 1) Convert a citation XML stream to PMIDs
cat citations.xml | ref2pmid

# 2) Source-comment example using explicit matching options
cat uniprot_citations.xml | ref2pmid -options remote,strict

# 3) Continue into downstream EDirect processing
cat citations.xml | ref2pmid | efetch -db pubmed -format xml

Recommended Workflow

Start from a real citation-oriented XML stream rather than free-form text.
Pipe that stream into ref2pmid.
If you need stricter or remote matching behavior, pass options through to the underlying transmute layer.
Feed the resulting PMIDs into later EDirect commands or save them for audit.

Guardrails

ref2pmid has no standalone help/version implementation. In local tests, -help and -version both fell through to transmute and failed because no stdin was supplied.
Because the wrapper is literally transmute -r2p "$@", any extra flags are passed straight through to transmute.
The tool expects input from stdin or a transmute-compatible file path; calling it empty is not a metadata-safe operation.

---name: ref2pmiddescription: Use when converting reference citations or identifiers to PubMed IDs (PMIDs) using Entrez Direct utilities.--- # ref2pmid Tiny EDirect wrapper around `transmute -r2p`. It maps citation-style XML or similar reference payloads to PMIDs, but it is only a stdin transformer and does not expose its own help text. ## Quick Start - **Command:** `ref2pmid` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/ref2pmid` - **Actual implementation:** a one-line shell wrapper calling `transmute -r2p "$@"` ## When To Use This Tool - Converting bibliographic references to PubMed IDs - Part of the Entrez Direct (EDirect) bioconda package for NCBI database queries - Turning citation XML streams into PMID-enriched output for later EDirect steps ## Common Patterns ```bash # 1) Convert a citation XML stream to PMIDs cat citations.xml | ref2pmid ``` ```bash # 2) Source-comment example using explicit matching options cat uniprot_citations.xml | ref2pmid -options remote,strict ``` ```bash # 3) Continue into downstream EDirect processing cat citations.xml | ref2pmid | efetch -db pubmed -format xml ``` ## Recommended Workflow 1. Start from a real citation-oriented XML stream rather than free-form text. 2. Pipe that stream into `ref2pmid`. 3. If you need stricter or remote matching behavior, pass options through to the underlying `transmute` layer. 4. Feed the resulting PMIDs into later EDirect commands or save them for audit. ## Guardrails - `ref2pmid` has no standalone help/version implementation. In local tests, `-help` and `-version` both fell through to `transmute` and failed because no stdin was supplied. - Because the wrapper is literally `transmute -r2p "$@"`, any extra flags are passed straight through to `transmute`. - The tool expects input from stdin or a `transmute`-compatible file path; calling it empty is not a metadata-safe operation.

Frequently asked questions