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musharna

plant-genomics-mcp

by musharna

Genomic Region → Features

ensembl_region_query
Read-onlyIdempotent

List genes, transcripts, CDS, or exons overlapping a genomic interval in Ensembl Plants. Provide region, start, and end to map QTL intervals without per-locus lookup.

Instructions

List features overlapping a genomic interval via Ensembl Plants /overlap/region. region is the seq-region name (chromosome / contig, e.g. '1'); start and end are 1-based inclusive. feature is one of gene / transcript / cds / exon (default gene). Answers 'what genes are in this QTL interval / assembly window' without a per-locus lookup. Ensembl caps the span — oversized regions error. ensembl_plants_assembly lists an organism's region names and their lengths; a region outside that list, or a start past its length, is an error here. Defaults to arabidopsis_thaliana; pass organism= for other species.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
endYes1-based inclusive end
startYes1-based start
regionYesseq-region name (chromosome / contig), e.g. '1' or 'Chr1'
featureNoFeature type to returngene
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countYesNumber of overlapping features returned
regionYesseq_region:start-end, e.g. 1:3000-10000
featureYesFeature type queried
featuresYesRaw Ensembl overlap records
organismYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.18.2

TDQS

A4.7/5.0
Behavior5/5

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

Annotations already declare readOnlyHint, openWorldHint, idempotentHint, and destructiveHint=false, so the safety profile is covered. The description adds valuable behavioral context beyond annotations: coordinate convention, Ensembl span caps causing errors, dependency on assembly region names, and default organism 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 dense and well-structured, front-loading the core operation, then coordinates, feature choices, use case, error behavior, and default organism in logical order. Every sentence contributes meaningful information without redundancy.

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

Completeness5/5

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

Despite being a moderately complex tool, the description covers the critical context: coordinate system, feature enum, default organism, error boundaries, and relationship to the assembly tool. The presence of an output schema removes the need to describe return values, so nothing essential is missing.

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 description coverage is 100%, so the schema fully documents each parameter. The description largely restates the schema's parameter meanings with examples ('1' or 'Chr1') and the feature default, but adds little semantic detail beyond what the schema already provides.

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?

Starts with a specific verb and resource ('List features overlapping a genomic interval via Ensembl Plants /overlap/region'), clearly stating the operation and scope. The phrase 'without a per-locus lookup' distinguishes it from sibling lookup tools, and the title reinforces the region-to-features purpose.

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

Usage Guidelines5/5

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

Explicitly describes the use case: answering 'what genes are in this QTL interval / assembly window'. It also names ensembl_plants_assembly as the way to discover valid region names and lengths, and notes error conditions that help an agent decide when this tool is appropriate.

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