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rewire-bio

genomics-mcp

Official
by rewire-bio

lookup_gene

Read-only

Look up a gene to obtain its identifiers, transcripts, and source-attributed annotations from genomic reference databases. Filter by source and assembly to resolve versioned evidence.

Instructions

Gene identifiers, transcripts and source-attributed annotations. Not implemented in this build: returns error code 'unsupported' (E8).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
geneYes
includeNo
sourcesNoSource names; default all available.
assemblyNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
dataNo
errorNoSet when status is error.
errorsNoPer-source failures in partial results.
limitsNo
statusYes
warningsNo
operationYes
provenanceNo
truncationNo
source_statusNo
schema_versionNo1

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A3.5/5.0
Behavior5/5

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

The description explicitly discloses the tool's behavioral limitation: 'Not implemented in this build: returns error code 'unsupported' (E8).' This goes beyond the readOnlyHint and openWorldHint annotations, clearly telling the agent the call will fail. This is highly transparent.

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?

The description is extremely concise—two sentences with no filler. The primary purpose is front-loaded in the first sentence, and the critical caveat follows immediately. Every word earns its place.

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 tool that is not implemented, the description fully communicates the outcome (error code E8). It does not detail the intended return format, but since the tool cannot be used, the essential context is present. The description adequately covers the current behavior, though it omits details that would be relevant if the tool were functional.

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

Parameters1/5

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

Schema description coverage is only 25% (only the 'sources' parameter has a description). The tool description adds no information about the meaning or expected format of 'gene', 'include', or 'assembly'. With low coverage, the description should compensate but does not, leaving these parameters effectively undocumented.

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 what the tool provides: 'Gene identifiers, transcripts and source-attributed annotations.' This is a clear statement of the resource and scope, though it lacks an explicit verb (e.g., 'retrieve' or 'lookup'). The 'not implemented' notice further clarifies the current purpose is to return an error, which is transparent.

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

Usage Guidelines2/5

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

The description does not mention when to use this tool versus its siblings (e.g., lookup_variant, lookup_protein). It only states it is not implemented and returns an error, which implicitly discourages use but offers no alternative or decision guidance.

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