Genomics MCP

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list_sources

Read-only

Enumerate genomic data and reference sources, showing their status and supported operations, to identify which can be queried.

Instructions

List data and reference sources, their state and supported operations.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`kind`	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

B3/5.0

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 is covered. The description adds that results carry state and supported operations per source, which is useful context, but it says nothing about permissions, pagination, or result size for a read across external sources.

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?

A single sentence with no filler, and the resource plus returned attributes are front-loaded. It is arguably under-specified rather than padded, but structurally it is clean.

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 values need not be described, and the read-only annotations cover safety. However, for a tool whose only parameter is an undocumented enum filter, the description leaves the primary narrowing mechanism invisible, which is a real gap for an agent deciding how to call it.

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 0% and the single 'kind' parameter is never mentioned. The enum values (archive, catalog, reference, storage, local) are left entirely unexplained, so the caller cannot know that results can be filtered by source kind, even though 'reference' hints at one of them.

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 clear verb (List) and resource (data and reference sources) and even previews what comes back (state, supported operations). It does not differentiate itself from siblings like list_samples or list_files, which also enumerate resources, so the purpose is clear but not uniquely scoped.

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 no when-to-use guidance, no prerequisites, and names no alternative among the many sibling list/search tools. An agent must infer that this is the discovery step for sources rather than samples or files.

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