| 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
esearch -db pubmed -query 'lycopene cyclase' | \
elink -related | \
elink -target protein
esearch -db pubmed -query 'Beadle GW [AUTH] AND Tatum EL [AUTH]' | \
elink -cited | \
efetch -format abstract
elink -db pubmed -id 19880848 -cmd prlinks
Recommended Workflow
- Start with a defined source database and record IDs.
- Decide whether you want same-database neighbors, cross-database links, or citation relations.
- Use
-cmd and -name to narrow the link mode when many link types exist.
- 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.
