ref2pmid

name	ref2pmid
description	Use when converting reference citations or identifiers to PubMed IDs (PMIDs) using Entrez Direct utilities.
disable-model-invocation	true
user-invocable	true

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

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.