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mcp MCP server · A · ToolBench

mcp

GWAS Catalog Model Context Protocol (MCP) server providing access to curated results from the GWAS Catalog, a database of published human genome-wide association (GWAS) studies

2026-07-28+STREAMABLE_HTTP3 tools

81/100

Definition Quality83

Protocol Readiness75

SupportabilityNot measured-

Spec posture

Inferred effective spec 2026-07-28+·current baseline 2026-07-28

Static source inference · medium confidence · detected: Logging

Deprecated protocol patterns detected

Summary

Three well-structured read-only tools with comprehensive input schemas and clear descriptions. All tools have detailed parameter definitions with type constraints (patterns, enums, min/max). Descriptions are action-oriented and explain query capabilities. Output schemas are documented via ToolResponse wrapper with pagination and suggestions. Naming follows verb_noun convention (get_*). Main gaps: no error handling guidance in descriptions, no per-parameter descriptions visible in schema (only in code comments), and no tool annotations (readOnlyHint, idempotentHint) declared in MCP registration.

Tools (3)

gwascatalog_get_associationsread onlysource verified83/100

Returns: SNP-trait association records. Query by: association ID, trait, gene, variant, study accession, PubMed ID

gwascatalog_get_studiesread onlysource verified83/100

Returns: GWAS study metadata. Query by: study accession, trait, gene, ancestry, cohort, PubMed ID

gwascatalog_get_traitsread onlysource verified83/100

Returns: EFO trait metadata. Query by: EFO ID, trait name, mapped gene, PubMed ID, URI

Issues (5)

MEDIUMrecovery-guide ↗

Tool descriptions lack error recovery guidance. No mention of what to do if a query returns no results, how to broaden searches, or when to try alternative parameters.

gwascatalog_get_traitsgwascatalog_get_studiesgwascatalog_get_associations

MEDIUMtool-annotations ↗

Tool annotations (readOnlyHint, idempotentHint) not declared in MCP tool registration. While tools are read-only, explicit annotations enable agents to reason about safety and retry semantics.

gwascatalog_get_traitsgwascatalog_get_studiesgwascatalog_get_associations

MEDIUMtool-description ↗

Parameter descriptions exist in code but may not be fully visible in JSON Schema. Verify all 30+ parameters have inline descriptions in the schema definition, not just in comments.

gwascatalog_get_traitsgwascatalog_get_studiesgwascatalog_get_associations

Recommendations

Add explicit tool annotations to MCP registration: readOnlyHint=true and idempotentHint=true for all three tools. This enables agents to safely retry without side-effect concerns.
Enhance tool descriptions with recovery guidance: 'If no results, try: (1) removing filters to broaden search, (2) using gwascatalog_get_traits to explore EFO terms first, (3) checking PubMed ID format (8-12 digits).'
Document output schema in each tool description: 'Returns ToolResponse with: data (array of results), pagination (page, total_results, truncated), suggestions (actionable next steps for empty/truncated results).'
Verify all 30+ parameters have descriptions in the JSON Schema definition itself (not just code comments). Ensure descriptions include format hints: 'EFO ID format: EFO_0001060 or MONDO_0005180' and 'Gene symbol: uppercase HGNC symbol (e.g., ISG20, HLA-DRA).'
Add pagination guidance to descriptions: 'Results are paginated (default 10 per page, max 50). Use page parameter (0-indexed) to fetch additional results. Truncated flag indicates more results available.'

Spec posture evidence

Inferred effective spec: 2026-07-28+.

Relies on Logging (deprecated) - log to stderr or use OpenTelemetry

Score history

Overall score trend

First recorded score · v2 rubric

81/100

Scored	Grade	Overall	Spec posture	Rubric
2026-09-23	A	81	2026-07-28+	v2