Genomics MCP

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lookup_gene

Read-only

Retrieve gene identifiers, transcripts, and source-attributed annotations for a specified gene; optionally filter results by source and assembly.

Instructions

Gene identifiers, transcripts and source-attributed annotations. Available for: default.

Input Schema

TableJSON Schema

Name	Required	Description
`gene`	Yes
`include`	No
`sources`	No	Source names; default all available.
`assembly`	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

C2.4/5.0

Behavior2/5

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 by structured data. The description adds nothing beyond that — no auth requirements, no coverage/rate notes, no explanation of what 'source-attributed' means operationally or what happens when a gene is absent.

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?

It is short and the content-bearing fragment comes first, but the second fragment ('Available for: default') consumes space without conveying usable information. Brevity here reflects under-specification rather than disciplined conciseness.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

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 described, but with four parameters at 25% coverage and no usage context, an agent lacks enough to call this correctly. The definition is incomplete for a tool embedded among many similar lookup_* siblings.

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'), and the description does not compensate: it never explains what 'gene' accepts (symbol, ID, accession?), what 'include' selects, or what 'assembly' should be. 'Source-attributed' faintly gestures at the sources parameter but gives no format or allowed values.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose3/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description names the resources involved (gene identifiers, transcripts, source-attributed annotations) but is a noun fragment with no verb, so the action (retrieve) is only implied. It does loosely distinguish itself from lookup_variant/lookup_protein by naming gene-centric data, but an agent must infer the actual operation.

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?

There is no when-to-use guidance, no prerequisites, and no mention of the obvious alternatives such as resolve_identifier or lookup_variant. The phrase 'Available for: default' is opaque and does not tell the agent which context or assembly selects this tool.

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