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rewire-bio

genomics-mcp

Official
by rewire-bio

resolve_identifier

Read-only

Resolves gene, transcript, protein, or variant identifiers to their matching reference entries, reporting ambiguous matches. Handles source, assembly, and target type filters.

Instructions

Resolve a gene/transcript/protein/variant identifier; reports ambiguity. Not implemented in this build: returns error code 'unsupported' (E8).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sourcesNoSource names; default all available.
assemblyNo
identifierYes
target_typesNo

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

B3.3/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true. The description adds two important behavioral facts: it reports ambiguity and it returns error code 'unsupported' (E8) in this build. This goes beyond the annotations and is crucial for an agent to avoid wasting a call. No contradiction exists.

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?

Two sentences with no extraneous content. The main purpose is stated first, followed immediately by the critical caveat. Every word earns its place.

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?

Given the tool is not implemented, the description tells the agent it will fail, which is essential. However, parameter semantics are missing, and no alternative tools are suggested. The output schema exists but its content is not provided here. The description is adequate for a non-functional tool but not fully complete.

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

Parameters2/5

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

Schema description coverage is only 25% (only 'sources' has a description). The description does not explain any parameters, though it hints at identifier types. It does not clarify 'assembly' or 'target_types' semantics, so it fails to compensate for the low schema coverage.

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 clearly states a specific action ('Resolve') on a defined resource ('gene/transcript/protein/variant identifier') and mentions the behavioral trait of reporting ambiguity. However, it does not explicitly differentiate from sibling lookup tools such as lookup_gene or lookup_variant, so it is clear but not distinguished.

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?

No guidance is given on when to use this tool versus alternatives. The only usage-related information is the warning that it is not implemented, but it does not direct the agent to an alternative tool or specify conditions for selection. Thus, there is no effective usage guidance.

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