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yeyuan98

BioMCP

by yeyuan98
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TypeScript
Remote

variant_search

Read-only

Search genomic variants by rsID, HGVS, gene, or protein change. Filter results by ClinVar significance, consequence, allele frequency, or CADD score to find relevant variant annotations.

Instructions

Search for variants. Use structured parameters for best results:

  • rsid: e.g. query="rs113488022"

  • HGVS: e.g. query="NM_004333.4:c.1799T>A"

  • Gene filter: e.g. gene="BRAF" with hgvsp="V600E" or consequence="missense"

  • ClinVar significance: e.g. significance="pathogenic" Do NOT use compound free-text like "BRAF V600E" — use separate gene and hgvsp parameters instead.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
geneNoFilter by gene symbol (e.g., "BRAF"). Use together with hgvsp for protein change queries.
rsidNodbSNP rsID
hgvscNocDNA change
hgvspNoProtein change (e.g., V600E). Use with gene parameter for compound queries.
limitNoMaximum results
queryNoVariant query (rsid or HGVS notation). Avoid compound queries like "BRAF V600E" — use gene + hgvsp parameters instead.
offsetNoResult offset
min_caddNoMinimum CADD score
consequenceNoVariant consequence (e.g., missense, synonymous)
significanceNo
max_frequencyNoMaximum allele frequency (0-1)

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.8

TDQS

A4.7/5.0
Behavior4/5

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

Annotations indicate readOnlyHint=true and openWorldHint=true. The description adds behavior beyond annotations by explaining correct query patterns and discouraging compound queries. No contradictions, but does not elaborate on response format or pagination.

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

Conciseness5/5

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

Concise single paragraph with bullet-like structure. Efficiently conveys purpose, examples, and warnings. No extraneous information; every sentence adds value.

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?

Given 11 optional parameters and no output schema, the description covers main search types and warnings. It could mention pagination (limit/offset) or result format, but those are in schema. Sufficient for a search tool.

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

Parameters5/5

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

Schema coverage is 91% with descriptions, but the description adds significant value by providing concrete examples (e.g., 'query="NM_004333.4:c.1799T>A"'), showing how to combine gene and hgvsp, and emphasizing the prohibition of compound free-text.

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

Purpose5/5

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

The description clearly states 'Search for variants' and provides specific examples of valid queries (rsid, HGVS, gene filter, ClinVar significance). It differentiates from sibling tools like variant_get by focusing on search with structured parameters.

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

Usage Guidelines5/5

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

Explicit guidelines on when to use structured parameters vs. compound free-text, with examples and a direct warning against using 'BRAF V600E' as free-text. Provides clear context for proper usage.

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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