elink

name	elink
description	Use when you need to navigate relationships between records in NCBI Entrez databases, find related articles, track citations, or link records across different databases such as PubMed to Protein.
disable-model-invocation	true
user-invocable	true

elink

Quick Start

• Command: elink
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/elink
• Full reference: See references/help.md for complete options and examples

When To Use This Tool

• Traverse relationships between Entrez records after you already have IDs.
• Jump from PubMed to linked genes, proteins, assemblies, or other database objects.
• Follow citations with -cited or -cites.
• Discover which link types exist before building a larger EDirect workflow.

Common Patterns

# 1) Find related PubMed records, then linked proteins
esearch -db pubmed -query 'lycopene cyclase' | \
  elink -related | \
  elink -target protein

# 2) Follow citation links
esearch -db pubmed -query 'Beadle GW [AUTH] AND Tatum EL [AUTH]' | \
  elink -cited | \
  efetch -format abstract

# 3) Inspect a specific link provider URL
elink -db pubmed -id 19880848 -cmd prlinks

Recommended Workflow

1. Start with a defined source database and record IDs.
2. Decide whether you want same-database neighbors, cross-database links, or citation relations.
3. Use -cmd and -name to narrow the link mode when many link types exist.
4. Feed the linked IDs into efetch, esummary, or xtract rather than reading raw XML by eye.

Guardrails

• elink needs valid database names and IDs from Entrez, not arbitrary external identifiers.
• -related, -target, -cited, and -cites solve different problems; pick the right one before chaining.
• Use -name when multiple link relationships exist between the same databases.
• Link traversal is network-dependent and can fail independently of your local pipeline logic.