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 want to inspect alias candidates. Known aliases that map to one canonical human gene can also be passed directly to get gene.

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. When MyGene.info returns genomic coordinates, BioMCP labels them with the GRCh38 genome build (Chromosome (GRCh38): ...) so coordinate consumers do not have to infer the reference. Its More: block keeps pathways, ontology, and diseases visible and now also surfaces funding as a direct follow-up from the base card.

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

Funding context (NIH Reporter grants mentioning the canonical symbol in the most recent 5 NIH fiscal years):

biomcp get gene ERBB2 funding

Diagnostic-test pivot (GTR tests for the gene):

biomcp get gene BRCA1 diagnostics

The diagnostics and funding sections are opt-in and are not included in biomcp get gene <symbol> all.

Gene-disease validity (ClinGen):

biomcp get gene BRAF clingen

When ClinGen validity rows are present, the gene card's See also: block promotes a recruiting-trial search keyed to the newest reviewed disease label already shown on the card, ahead of the generic gene pivots.

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

To add funding, request it explicitly:

biomcp get gene BRAF funding

Helper commands¶

biomcp gene trials BRAF --limit 5
biomcp gene trials SHANK3 --limit 5
biomcp gene drugs BRAF --limit 5
biomcp gene pathways BRAF
biomcp gene articles BRAF
biomcp gene definition BRAF

For CTGov, supported rare-disease genes such as SHANK3 reuse the shared trial plan so the search can include the associated condition expansion. Other genes and non-CTGov sources keep the literal gene trial search.

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.