Genomics MCP

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lookup_protein

Read-only

Retrieve protein identity, function, and features from UniProt and cross-references by protein name to support genomic and functional annotation.

Instructions

Protein identity, function and features from UniProt and cross-references. Available for: default.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`protein`	Yes
`sources`	No	Source names; default all available.

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

C2.9/5.0

Behavior3/5

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

Annotations already declare readOnlyHint and openWorldHint. The description adds useful provenance context ('from UniProt and cross-references'), which goes slightly beyond the annotations, but it omits rate limits, authentication needs, and what 'cross-references' entails.

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?

The description is short and front-loads the core purpose. However, the second sentence 'Available for: default.' is cryptic and does not earn its place, while the useful first sentence could provide more precise scope.

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 format is covered, and annotations cover the safety profile. Still, the definition lacks usage guidance and does not explain the required protein input, leaving gaps for an agent choosing between multiple lookup tools.

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 coverage is 50%: 'sources' is documented in the schema, but the required 'protein' parameter has only a title and no description. The description does not explain accepted protein identifier formats or how 'sources' constrains cross-references, so it fails to compensate for the missing parameter detail.

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 lookup operation on proteins, including the data returned (identity, function, features) and the source domain (UniProt and cross-references). It distinguishes itself implicitly from lookup_gene and lookup_variant by resource, but does not explicitly contrast with close siblings like get_features or get_sequence.

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 explicit when-to-use guidance, no alternatives named, and no prerequisites or exclusions. The phrase 'Available for: default.' is not actionable usage guidance.

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