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pubmed-search-mcp

by u9401066
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Python
Remote

search_clinvar

Read-onlyIdempotent

Search ClinVar for clinical variants to determine clinical significance, disease associations, and pathogenicity classifications.

Instructions

Search ClinVar for clinical variants.

═══════════════════════════════════════════════════════════════ USE CASES: ═══════════════════════════════════════════════════════════════

  • Look up clinical significance of genetic variants

  • Find variants associated with diseases

  • Research gene-disease associations

  • Get variant pathogenicity classifications

Args: query: Gene name, variant, or disease condition limit: Maximum results (1-50)

Returns: JSON with variant records including significance and conditions

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
queryYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed8 schema fields changedv0.7.2
    • addedInput schema / additionalProperties
      Added value: +false
    • removedInput schema / properties / limit / anyOf
      Removed value: -[
-  {
-    "type": "integer"
-  },
-  {
-    "type": "string"
-  }
-]
    • addedInput schema / properties / limit / maximum
      Added value: +50
    • addedInput schema / properties / limit / minimum
      Added value: +1
    • addedInput schema / properties / limit / type
      Added value: +"integer"
    • addedInput schema / properties / query / maxLength
      Added value: +500
    • addedInput schema / properties / query / minLength
      Added value: +1
    • changedOutput schema / (root)
      Previous value: -{
-  "properties": {
-    "result": {
-      "title": "Result",
-      "type": "string"
-    }
-  },
-  "required": [
-    "result"
-  ],
-  "title": "search_clinvarOutput",
-  "type": "object"
-}New value: +null
  2. First observedv0.5.16

TDQS

A3.7/5.0
Behavior3/5

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

Annotations already declare readOnly, idempotent, openWorld, and non-destructive, so safety is covered. The description adds the return shape ('JSON with variant records including significance and conditions'), which is useful since there is no output schema, but it discloses no rate limits, pagination, or scoping behavior.

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

Conciseness3/5

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

The first line is well front-loaded, but the box-drawing banner section for USE CASES consumes vertical space without adding semantic content. The Args/Returns structure is efficient, but overall it is bulkier than needed.

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?

For a 2-parameter read tool with no output schema, the description covers purpose, accepted query forms, the limit bound, and the return content. It lacks pagination/ordering notes, but nothing critical to calling it correctly is missing.

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

Parameters4/5

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

Schema description coverage is 0%, so the description must carry the load. It documents 'query' as accepting a gene name, variant, or disease condition (a real semantic addition the schema omits) and clarifies 'limit' as maximum results, compensating well for the coverage 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?

States a specific verb+resource: 'Search ClinVar for clinical variants.' The ClinVar domain distinguishes it from the many literature/gene/compound siblings, though it doesn't explicitly say how it differs from search_gene or search_compound.

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 USE CASES block gives four concrete scenarios (clinical significance lookup, disease-associated variants, gene-disease associations, pathogenicity classification), which is clear context for when to reach for it. It offers no explicit exclusions or named sibling alternatives, so it falls short of a 5.

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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