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yeyuan98

BioMCP

by yeyuan98
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TypeScript
Remote

variant_search

Read-only

Search human genomic variants by rsID, HGVS, gene, protein change, consequence, or ClinVar significance to retrieve matching annotations and clinical classifications.

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

NameRequiredDescriptionDefault
geneNoFilter by gene symbol (e.g., "BRAF"). Use together with hgvsp for protein change queries.
rsidNodbSNP rsID
hgvscNocDNA change — bare c. notation (e.g., c.1799T>A) or full HGVS (e.g., NM_004333.4:c.1799T>A)
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; echoed per row as cadd_phred so the filter is verifiable from each result
consequenceNoVariant consequence (e.g., missense, synonymous)
significanceNoClinVar significance category, matched exactly — records displayed as "Pathogenic/Likely pathogenic" match both pathogenic and likely_pathogenic; "Conflicting interpretations of pathogenicity" matches none of these
max_frequencyNoMaximum allele frequency (0-1)

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.6.0-alpha.10
    • removedInput schema / additionalProperties
      Removed value: -false
    • addedInput schema / properties / offset / maximum
      Added value: +9007199254740991
  2. Changed6 schema fields changedv1.6.0-alpha.7
    • addedInput schema / properties / gene / minLength
      Added value: +1
    • addedInput schema / properties / hgvsc / minLength
      Added value: +1
    • addedInput schema / properties / hgvsp / minLength
      Added value: +1
    • changedInput schema / properties / min_cadd / description
      Previous value: -"Minimum CADD score"New value: +"Minimum CADD score; echoed per row as cadd_phred so the filter is verifiable from each result"
    • addedInput schema / properties / query / minLength
      Added value: +1
    • addedInput schema / properties / rsid / minLength
      Added value: +1
  3. Changed2 schema fields changedv1.6.0-alpha.2
    • changedInput schema / properties / hgvsc / description
      Previous value: -"cDNA change"New value: +"cDNA change — bare c. notation (e.g., c.1799T>A) or full HGVS (e.g., NM_004333.4:c.1799T>A)"
    • addedInput schema / properties / significance / description
      Added value: +"ClinVar significance category, matched exactly — records displayed as \"Pathogenic/Likely pathogenic\" match both pathogenic and likely_pathogenic; \"Conflicting interpretations of pathogenicity\" matches none of these"
  4. First observedv0.1.8

TDQS

A3.6/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety profile is covered. The description adds no behavior beyond invocation syntax: it says nothing about how many results are returned by default, whether zero filters means a broad scan, or how the score/frequency filters interact. With annotations carrying the read-only signal, a 3 is appropriate.

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?

Front-loaded purpose sentence followed by a scannable four-bullet cheat sheet and a single prohibition. The bullets restate examples already present in the schema, which is mild redundancy, but every line is actionable and there is no filler.

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

Completeness3/5

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

Eleven parameters, all optional, no output schema, no required arguments. The description never says what happens when it is called with no filters at all, nor does it mention the limit cap of 50 that constrains result volume. For a wide, fully-optional search tool this leaves the agent guessing at default behavior.

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 description coverage is 100% and every property already carries an example, so the schema does the heavy lifting and the baseline is 3. The description's examples duplicate rather than extend the schema (rs113488022, NM_004333.4:c.1799T>A, BRAF/V600E all appear verbatim in property descriptions), adding reinforcement but no new semantics.

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 opening sentence gives a specific verb+resource ("Search for variants"), which implicitly separates it from the sibling variant_get (fetch-one) and the annotation tools variant_oncokb/variant_trials. It stops short of explicitly naming those siblings or stating what a result row contains, so an agent must infer the search-vs-fetch boundary from the verb alone.

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

Usage Guidelines4/5

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

The bulleted examples give concrete, per-mode invocation patterns (rsid, HGVS, gene+hgvsp, significance) and the closing sentence is an explicit anti-pattern rule: do not use compound free-text, use gene + hgvsp instead. That is strong when-to-use guidance, but it never routes the agent to alternatives (e.g. use variant_get once you have an exact ID) or states preconditions.

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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