Elink

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.