Genomics MCP

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resolve_identifier

Read-only

Resolve gene, transcript, protein, or variant identifiers and flag ambiguous matches across genomic sources, so you can map queries to the correct reference.

Instructions

Resolve a gene/transcript/protein/variant identifier; reports ambiguity. Available for: default.

Input Schema

TableJSON Schema

Name	Required	Description
`sources`	No	Source names; default all available.
`assembly`	No
`identifier`	Yes
`target_types`	No

Output Schema

TableJSON Schema

Name	Required	Description	Default
`data`	No
`error`	No	Set when status is error.
`errors`	No	Per-source failures in partial results.
`limits`	No
`status`	Yes
`warnings`	No
`operation`	Yes
`provenance`	No
`truncation`	No
`source_status`	No
`schema_version`	No		1
`metadata_omitted`	No	Entries dropped from provenance/source_status/errors/warnings (or text shortened) to fit max_response_bytes. Absent when metadata is complete.

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv0.1.1Sep 28, 2026

addedOutput schema / properties / metadata_omitted

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": {
+        "type": "integer"
+      },
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Entries dropped from provenance/source_status/errors/warnings (or text shortened) to fit max_response_bytes. Absent when metadata is complete.",
+  "title": "Metadata Omitted"
+}

First observedv0.1.0Sep 24, 2026

TDQS

B3/5.0

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 one genuinely useful behavioral fact — that it 'reports ambiguity' rather than failing — but says nothing about resolution precedence, source selection behavior, or multi-match handling.

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?

Two tight clauses, front-loaded with the verb and resource; nothing is padded. The trailing 'Available for: default' reads as auto-generated boilerplate that adds no information but costs little.

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?

An output schema exists, so return values need not be explained. However, for a 4-parameter cross-entity resolver with 25% schema coverage and overlapping siblings, the description leaves the agent without enough to pick sources/assembly or to know how ambiguity is surfaced.

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%: 'sources' is documented but 'assembly', 'target_types', and 'identifier' lack schema descriptions. The description implies the accepted identifier types (mapping loosely to target_types) but never explains assembly selection or source scoping, so it does not compensate 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 ('Resolve a ... identifier') and names the identifier kinds it covers (gene/transcript/protein/variant), plus the behavioral outcome ('reports ambiguity'). It is clear but never distinguishes itself from siblings like lookup_gene, lookup_protein, or lookup_variant, which plausibly overlap.

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 only usage signal is the boilerplate 'Available for: default', which gives no context. There is no guidance on when to use this generic resolver versus the type-specific lookup_gene/lookup_protein/lookup_variant siblings, nor any prerequisite or exclusion.

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