Genomics MCP

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inspect_locus

Read-only

Combine genomic data from multiple files at one locus and retrieve public evidence, with external annotation of private values only when allowed.

Instructions

Combine data from several files at one locus, plus public evidence. Values derived from private files are only sent to external sources if allow_external_annotation is true. Available for: default.

Input Schema

TableJSON Schema

Name	Required	Description
`files`	No
`interval`	Yes
`reference`	No
`max_records`	No	Lower the record limit.
`reference_sources`	No	Source names; default all available.
`allow_external_annotation`	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

B3.4/5.0

Behavior4/5

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

Annotations already cover read-only and open-world traits, but the description adds a non-obvious privacy gate: values derived from private files only leave the machine when allow_external_annotation is true. That is genuinely valuable behavioral context beyond the structured fields, though nothing is said about record capping or failure modes.

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 sentences, front-loaded with the core purpose and immediately followed by the caveat that governs whether the call is safe to make. 'Available for: default' adds little but costs almost nothing.

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 key privacy caveat is present. However, for a 6-parameter locus-aggregation tool the description omits operational essentials such as how multiple files/assemblies are reconciled and how max_records affects results.

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 coverage is only 33%, so the description is expected to compensate. It does explain the privacy meaning of allow_external_annotation (whose schema entry has no description), but leaves interval, files, reference, and max_records semantics to the schema, so it only partially fills the gap.

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 (combine) and resource (data from several files at one locus, plus public evidence), which clearly separates it from single-source siblings like get_variants or get_coverage. It does not explicitly name which siblings it overlaps or supersedes, so it stops short of a 5.

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 statement of when to use this versus alternatives such as get_features, get_variants, or get_coverage at the same locus – the aggregation intent is only implied by 'combine data from several files'. 'Available for: default' is operational metadata, not usage guidance.

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