Genomics MCP

Official

by rewire-bio

Overview Schema Source Related Servers Discussions Admin

Python

Hybrid

get_sample_metadata

Read-only

Retrieve one sample's metadata and phenotype values exactly as supplied by EGA, ENA, ENCODE, GEO, or NCBI Datasets.

Instructions

Get one sample's metadata and phenotype values exactly as supplied by the source. Available for: ega, ena, encode, geo, ncbi_datasets.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`source`	Yes
`accession`	Yes

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

A3.5/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so safety and external reach are covered. The phrase 'exactly as supplied by the source' adds meaningful fidelity context (no normalization/reinterpretation), but no auth, rate-limit, or failure behavior is disclosed.

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 compact sentences: the purpose leads and the applicability constraint follows. No filler, no redundancy with the schema.

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?

The output schema exists, so return values need no explanation, and the source enumeration helps. However, for a two-required-parameter tool with zero schema descriptions, leaving 'accession' entirely unspecified is a real gap.

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

Parameters3/5

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

Schema description coverage is 0%, so the description must compensate. It partially does by enumerating accepted 'source' values, but the required 'accession' parameter is left completely undefined (format, identifier namespace, whether it must match the source).

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 and resource ('Get one sample's metadata and phenotype values'), scoped to a single sample, which implicitly separates it from list_samples and compare_samples. It stops short of naming any sibling explicitly, so the differentiation is inferable rather than stated.

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

Usage Guidelines3/5

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

The 'Available for: ega, ena, encode, geo, ncbi_datasets' line usefully constrains when this tool applies and enumerates valid source values, but there is no when-not guidance and no named alternative for retrieving metadata in bulk.

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