# Gene
Use gene commands to retrieve canonical metadata and targeted biological context.
## What the gene guide covers
- symbol-based retrieval,
- lightweight search,
- section expansion,
- JSON output for downstream systems.
## Search genes
Start with search when you are unsure of symbol spelling or aliases.
```bash
biomcp search gene -q BRAF --limit 5
```
Useful fields in search output typically include symbol, Entrez ID, and species.
## Get a gene record
```bash
biomcp get gene BRAF
```
The default gene view is concise and intended for orientation.
## Request deeper sections
BioMCP expands detail via positional sections.
Pathway view:
```bash
biomcp get gene BRAF pathways
```
Disease associations:
```bash
biomcp get gene BRAF diseases
```
Ontology terms:
```bash
biomcp get gene BRAF ontology
```
Protein summary:
```bash
biomcp get gene BRAF protein
```
GO terms and interactions:
```bash
biomcp get gene BRAF go interactions
```
CIViC evidence summary:
```bash
biomcp get gene BRAF civic
```
Multiple sections can be chained:
```bash
biomcp get gene BRAF pathways diseases
```
## Gene helper commands
```bash
biomcp gene trials BRAF --limit 5
biomcp gene drugs BRAF --limit 5
biomcp gene pathways BRAF
biomcp gene articles BRAF
biomcp gene definition BRAF
```
## Common workflows
### Clinical trial pivot
```bash
biomcp search trial -c melanoma --mutation "BRAF V600E" --limit 5
```
### Literature pivot
```bash
biomcp search article -g BRAF -d melanoma --limit 5
```
### Variant pivot
```bash
biomcp search variant -g BRAF --limit 5
```
## JSON mode
Use JSON for pipelines or agent post-processing.
```bash
biomcp --json get gene BRAF
```
## Error handling expectations
If a section name is unsupported, BioMCP returns an explicit unknown-section message
with hints about valid section names.
## Practical tips
- Keep section requests narrow for better focus.
- Start with one section, then add another only if needed.
- Use `search` first when symbol ambiguity is possible.
## Related guides
- [Variant](variant.md)
- [Article](article.md)
- [Trial](trial.md)
- [Protein](protein.md)
- [Progressive disclosure](../concepts/progressive-disclosure.md)
