plant-genomics-mcp

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Ensembl Plants: Locus Metadata

ensembl_plants_lookup_locus

Read-onlyIdempotent

Retrieve gene metadata for a plant locus identifier from Ensembl Plants. Specify an organism such as rice or maize to get records for species beyond Arabidopsis.

Instructions

Fetch metadata for a plant locus identifier from Ensembl Plants. Defaults to arabidopsis_thaliana; pass organism= for other plant species (oryza_sativa, zea_mays, ...). Locus is the TAIR-style identifier (e.g. AT1G01010 for Arabidopsis NAC001).

Input Schema

TableJSON Schema

Name	Required	Description	Default
`locus`	Yes	e.g. AT1G01010 (Arabidopsis), Os01g0100100 (rice)
`organism`	No	Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid	arabidopsis_thaliana

Output Schema

TableJSON Schema

Name	Required	Description
`id`	Yes	Locus identifier, e.g. AT1G01010
`end`	No
`start`	No
`source`	No
`strand`	No	1 forward, -1 reverse
`biotype`	No	protein_coding, lncRNA, miRNA, ...
`db_type`	No	Usually "core"
`organism`	Yes	Plant organism canonical slug, e.g. arabidopsis_thaliana
`logic_name`	No	Source annotation pipeline
`description`	No
`object_type`	No	Usually "Gene"
`display_name`	No	Human-readable gene symbol
`assembly_name`	No	e.g. TAIR10
`seq_region_name`	No	Chromosome / contig name
`upstream_version`	No	Ensembl Plants release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='ensembl_plants') reports the release its own endpoint calls current at query time, or why there is none. null means Ensembl Plants did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered.
`canonical_transcript`	No

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv1.27.0Sep 27, 2026

changedOutput schema / properties / upstream_version / description

Previous value: -"Ensembl Plants release that produced THIS response, — always null today: this backend states no release on its responses. null means Ensembl Plants did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered."New value: +"Ensembl Plants release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='ensembl_plants') reports the release its own endpoint calls current at query time, or why there is none. null means Ensembl Plants did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered."

Changed1 schema field changedv1.22.0Sep 24, 2026

addedOutput schema / properties / upstream_version

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Ensembl Plants release that produced THIS response, — always null today: this backend states no release on its responses. null means Ensembl Plants did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered.",
+  "title": "Upstream Version"
+}

First observedv1.8.0May 30, 2026

TDQS

A3.8/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true, idempotentHint=true, and destructiveHint=false, so the safety profile is covered. The description adds the default organism and identifier format, which is useful context but not a behavioral trait beyond what annotations provide. It does not describe error behavior or edge cases, but that is not required given the annotations.

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?

Three concise sentences that front-load the core purpose, then add the default and identifier format. There is no redundancy or filler, and every sentence contributes to correct usage.

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?

With an output schema present, the description need not explain return values. It covers the primary usage (fetch metadata), the default organism, and the identifier format. It doesn't mention potential limitations (e.g., which species are supported beyond the examples), but the examples and default give enough guidance for a typical call. The lack of sibling differentiation is a minor gap given the tool's simple purpose.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100% for both parameters, so the baseline is 3. The description adds value by explaining the TAIR-style identifier with a concrete example (AT1G01010) and clarifying that organism defaults to arabidopsis_thaliana. This enriches the schema descriptions with practical usage context.

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 clear verb ('Fetch metadata') and a specific resource ('plant locus identifier from Ensembl Plants'). It also provides an example identifier and distinguishes the data source from similar tools like TAIR or Phytozome, making its purpose unambiguous.

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 explains the default organism and how to change it, but it never states when to prefer this tool over the many sibling tools (e.g., tair_locus_info, phytozome_lookup_locus). There is no explicit when-to-use or when-not-to-use guidance, so an agent must infer the appropriate context from the data source alone.

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

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