# Elink

> 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.

- Skill: `vimalinx/elink` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add vimalinx/elink`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/elink/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: vimalinx (https://skillmd.com/u/vimalinx)
- Updated: 2026-08-19
- Page: https://skillmd.com/skills/vimalinx/elink

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# elink

## Quick Start
- **Command:** `elink`
- **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/elink`
- **Full reference:** See [references/help.md](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

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

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

```bash
# 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.