Genomics MCP

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list_samples

Read-only

Fetch sample records for a study or dataset by source and accession from EGA, ENA, ENCODE, GEO, or NCBI Datasets, with cursor and record limits.

Instructions

List samples of a study/dataset as supplied by the source. Available for: ega, ena, encode, geo, ncbi_datasets.

Input Schema

TableJSON Schema

Name	Required	Description
`cursor`	No
`source`	Yes
`accession`	Yes
`max_records`	No	Lower the record limit.

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

B3.2/5.0

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 and network profile is covered. The description's 'as supplied by the source' hints that results are raw/unmodified from the upstream repository, but adds no detail on pagination, auth, or rate limits beyond that.

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 short, front-loaded sentences with no filler; the source enumeration is the most actionable part. Slightly terse for a multi-source, paginated listing tool, but nothing is wasted.

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 presence of an output schema means return values need not be described, and the source list is helpful. Still, with three of four parameters undocumented and no routing guidance among many siblings, the definition is only minimally complete for the tool's complexity.

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% (just 'Lower the record limit.' on max_records), so source, accession, and cursor are undocumented in the schema. The description compensates only indirectly by naming the valid source values, and says nothing about cursor or accession semantics.

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 ('List samples of a study/dataset') with the scoping qualifier 'as supplied by the source'. However, it does not differentiate from near-siblings such as get_sample_metadata or compare_samples, so an agent must infer which sample-oriented tool is appropriate.

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?

'Available for: ega, ena, encode, geo, ncbi_datasets' gives the applicable source domains, which is useful context. But there is no when-to-use vs when-not guidance relative to the many sibling tools (e.g. get_sample_metadata, list_files), leaving usage implied only.

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