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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.

biomcp search gene BRAF --limit 5

Useful fields in search output typically include symbol, Entrez ID, and species.

Get a gene record

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:

biomcp get gene BRAF pathways

Disease associations:

biomcp get gene BRAF diseases

Ontology terms:

biomcp get gene BRAF ontology

Protein summary:

biomcp get gene BRAF protein

GO terms and interactions:

biomcp get gene BRAF go interactions

CIViC evidence summary:

biomcp get gene BRAF civic

Tissue expression (GTEx):

biomcp get gene BRAF expression

Druggability profile (DGIdb):

biomcp get gene BRAF druggability

Gene-disease validity (ClinGen):

biomcp get gene BRAF clingen

Multiple sections can be chained:

biomcp get gene BRAF pathways diseases

Gene helper commands

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

biomcp search trial -c melanoma --mutation "BRAF V600E" --limit 5

Literature pivot

biomcp search article -g BRAF -d melanoma --limit 5

Variant pivot

biomcp search variant -g BRAF --limit 5

JSON mode

Use JSON for pipelines or agent post-processing.

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