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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

When UniProt exposes legacy protein names, the protein section includes an Also known as: line with alternative full names and short names from UniProt. When UniProt exposes alternative products, the same section also includes an Isoforms (N) line with isoform names and the displayed isoform length when that length is available from the base UniProt record.

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

Protein tissue expression and localization (Human Protein Atlas):

biomcp get gene BRAF hpa

Druggability profile (DGIdb interactions plus OpenTargets tractability and safety):

biomcp get gene BRAF druggability

Gene-disease validity (ClinGen):

biomcp get gene BRAF clingen

Constraint metrics (gnomAD):

biomcp get gene BRAF constraint

Multiple sections can be chained:

biomcp get gene BRAF pathways diseases

All supported sections:

biomcp get gene BRAF all

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

Error handling expectations

If a section name is unsupported, BioMCP returns an explicit unknown-section message with hints about valid section names.

JSON mode

Use JSON for pipelines or agent post-processing.

biomcp --json get gene BRAF

biomcp --json get gene BRAF druggability includes DGIdb interaction fields plus OpenTargets tractability[] modality summaries and safety_liabilities[] event summaries.

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.