Genomics MCP

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search_datasets

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Search genomics archives (EGA, ENA, ENCODE, GEO, NCBI) for studies and datasets using text queries, with optional organism, assembly, and record limit filters.

Instructions

Search one archive/catalog for studies or datasets by text query. Available for: ega, ena, encode, geo, ncbi_datasets.

Input Schema

TableJSON Schema

Name	Required	Description
`query`	Yes
`cursor`	No
`source`	Yes
`assembly`	No
`organism`	No
`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

B3/5.0

Behavior3/5

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

Annotations already establish readOnlyHint=true and openWorldHint=true, so the safety profile is covered. The description adds that the search is limited to one archive/catalog and lists valid sources, which is useful context beyond the annotations, but it does not describe pagination, rate limits, or result behavior.

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?

The description is two short sentences, front-loaded with the core action and followed by the source constraint. There is no filler or repetition, and every sentence contributes useful information.

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?

Given six parameters, low schema coverage, and no explicit routing guidance, the description is not complete enough. It covers the required query and source values, but omits how optional filters and pagination work and does not help an agent choose this tool over its 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 17%, so the description must compensate for missing parameter semantics. It clarifies the required query as text search and lists allowed source values, which is valuable. But it says nothing about cursor, assembly, organism, or max_records beyond the schema's minimal note, leaving most optional parameters undocumented.

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?

The description states a specific verb and resource: search one archive/catalog for studies or datasets by text query. It also enumerates valid source values (ega, ena, encode, geo, ncbi_datasets), which helps an agent understand scope. However, it does not clearly differentiate this tool from adjacent retrieval tools such as describe_dataset or list_sources.

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 description gives a source availability list, but no explicit guidance on when to use this tool versus alternatives like describe_dataset, list_sources, or list_files. It lacks when-not-to-use conditions and does not explain the role of optional filters or pagination.

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