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genomics-mcp

Official
by rewire-bio

get_features

Read-only

Retrieve genomic features overlapping a specified interval from indexed BED, GFF3, GTF, or bigBed files. Query by interval to get only relevant annotations.

Instructions

Features overlapping an interval from indexed BED/GFF3/GTF or bigBed. Not implemented in this build: returns error code 'unsupported' (E3, E5).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
fileYes
intervalYes
max_recordsNoLower the record limit.
feature_typesNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
dataNo
errorNoSet when status is error.
errorsNoPer-source failures in partial results.
limitsNo
statusYes
warningsNo
operationYes
provenanceNo
truncationNo
source_statusNo
schema_versionNo1

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.3/5.0
Behavior5/5

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

Annotations already indicate read-only and open-world hints, but the description adds crucial behavioral context: the tool is not implemented and returns error code 'unsupported' (E3, E5). This goes beyond the annotations and informs the agent that any call will fail, which is essential for correct selection.

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 sentences: the first front-loads the core purpose with format constraints, and the second adds the critical caveat that the tool is unimplemented. There is no redundant text; every word contributes essential information.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a tool that is not implemented, the description clearly communicates that it will fail, which is the most important fact. An output schema exists, so return details are not needed. However, the description does not explain what E3/E5 mean or suggest alternatives, leaving minor gaps.

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?

With schema description coverage at only 25%, the description needed to explain parameter meanings. It does add some value by specifying that the file must be an indexed BED/GFF3/GTF or bigBed and that results are features overlapping an interval. However, it does not describe max_records or feature_types, so it only partially compensates for the low schema coverage.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb-resource combination: returns features overlapping an interval, with explicit file type constraints (indexed BED/GFF3/GTF or bigBed). This clearly distinguishes it from sibling tools such as get_reads, get_variants, and get_coverage. The second sentence also clarifies it is not implemented, which further specifies its current status.

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

Usage Guidelines4/5

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

The description clearly states input requirements (indexed files, specific formats) and explicitly warns that the tool is not implemented in this build, so it should not be used as it will return error code 'unsupported'. However, it does not point to alternative tools for feature retrieval, leaving the agent to infer from sibling names.

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