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yeyuan98

BioMCP

by yeyuan98
OverviewSchemaSourceRelated ServersDiscussionsAdmin
TypeScript
Remote

variant_get

Read-only

Retrieve detailed variant information by ID with core data always included; optionally request frequency, predictions, and clinical sections.

Instructions

Get detailed variant information with optional sections. Core data (id, gene, rsid, significance) is always returned at the top level. Use sections to request additional data. Response section keys mirror the requested section names: sections:["alphagenome_scores"] returns sections.alphagenome_scores — the legacy storage key (alphagenome) never appears in responses.

Input Schema

NameRequiredDescriptionDefault
idYesVariant ID (rsid e.g. rs113488022, HGVS e.g. NM_004333.4:c.1799T>A, ClinVar ID e.g. 13961 / clinvar_13961 / VCV0000013961). Multi-allelic rsIDs (one ClinVar allele per ALT, e.g. rs28934575): the top-level record is ONE allele, chosen by gnomad-availability — all alleles are returned under 'alleles' with a '_warning' naming the reflected allele; to select an exact allele use allele-qualified HGVS (e.g. NM_000546.5:c.733G>T), where the transcript version must match the indexed snpeff annotation (NM_000546.5 works; ClinVar's NM_000546.6 does not)
limitNo
sectionsNoSections to include: core, frequency, predictions, clinical, alphagenome_scores (currently unavailable — returns an error stub pending AlphaGenome gRPC reimplementation)

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.6.0-alpha.10
    • removedInput schema / additionalProperties
      Removed value: -false
  2. Changed1 schema field changedv1.6.0-alpha.7
    • addedInput schema / properties / id / minLength
      Added value: +1
  3. Changed1 schema field changedv1.6.0-alpha.3
    • changedInput schema / properties / id / description
      Previous value: -"Variant ID (rsid e.g. rs113488022, HGVS e.g. NM_004333.4:c.1799T>A, ClinVar ID e.g. 13961 / clinvar_13961 / VCV0000013961)"New value: +"Variant ID (rsid e.g. rs113488022, HGVS e.g. NM_004333.4:c.1799T>A, ClinVar ID e.g. 13961 / clinvar_13961 / VCV0000013961). Multi-allelic rsIDs (one ClinVar allele per ALT, e.g. rs28934575): the top-level record is ONE allele, chosen by gnomad-availability — all alleles are returned under 'alleles' with a '_warning' naming the reflected allele; to select an exact allele use allele-qualified HGVS (e.g. NM_000546.5:c.733G>T), where the transcript version must match the indexed snpeff annotation (NM_000546.5 works; ClinVar's NM_000546.6 does not)"
  4. Changed1 schema field changedv1.6.0-alpha.2
    • changedInput schema / properties / id / description
      Previous value: -"Variant ID (rsid, HGVS, or ClinVar ID)"New value: +"Variant ID (rsid e.g. rs113488022, HGVS e.g. NM_004333.4:c.1799T>A, ClinVar ID e.g. 13961 / clinvar_13961 / VCV0000013961)"
  5. Changed1 schema field changedv0.7.1
    • changedInput schema / properties / sections / description
      Previous value: -"Sections to include: core, frequency, predictions, clinical, alphagenome_scores"New value: +"Sections to include: core, frequency, predictions, clinical, alphagenome_scores (currently unavailable — returns an error stub pending AlphaGenome gRPC reimplementation)"
  6. First observedv0.1.8

TDQS

A3.7/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint and openWorldHint, and the description adds real behavioral payload beyond them: the guaranteed top-level core fields, the key-mirroring rule for response sections, and the guarantee that the legacy 'alphagenome' key never surfaces. It omits the failure mode of the alphagenome_scores section and what limit actually constrains, but the response-shape disclosure is valuable.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Purpose is front-loaded in the first sentence, followed by return-shape facts in a logical order with no filler. The final sentence on the legacy key is slightly niche but earns its place as an anti-confusion rule for agents parsing responses.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With no output schema, the description does the needed work of describing the return envelope (core fields at top level, section keys mirroring requests). Combined with the thorough id schema and the safety annotations, an agent has enough to call it; only the unexplained limit parameter and the unmentioned error stub keep it short of full completeness.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 67%: id and sections are richly documented in the schema itself, so the description's main contribution is the section-name-to-response-key mapping, which is genuinely additive. The limit parameter has no description anywhere, and the description doesn't explain what it limits in a single-variant lookup, leaving a real semantic gap.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb and resource ("Get detailed variant information") and clarifies that core fields are always returned while others are opt-in. It clearly reads as a detail-fetch counterpart to variant_search, though it never names that sibling explicitly to differentiate the two.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

"Use sections to request additional data" gives guidance on how to widen the response, which implies the default lightweight path. However, there is no explicit when-to-use condition versus variant_search, no prerequisite notes, and no warning that one of the listed sections fails.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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