plant-genomics-mcp

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Resolve Locus → UniProt

resolve_locus_to_uniprot

Read-onlyIdempotent

Map a plant locus to its canonical UniProtKB record. Prefers reviewed Swiss-Prot entries, falls back to TrEMBL for non-model organisms, and returns accession, gene names, and a link.

Instructions

Resolve a plant locus to its canonical UniProtKB record. Prefers reviewed (Swiss-Prot) entries; falls back to unreviewed (TrEMBL) when no curated record exists (common for non-Arabidopsis plants). organism accepts a canonical slug, scientific/common name, or NCBI taxid (default arabidopsis_thaliana; e.g. oryza_sativa, zea_mays). A gene symbol answers only when it names one locus; a symbol shared by several loci (ARF1) is InvalidArguments listing them. Returns primaryAccession, uniProtkbId, entryType, recommendedName, geneNames, organism, taxonId, sequenceLength, web_url (a link for the client to open; no tool on this server retrieves it). This is the protein-side entry point — pair with InterPro / AlphaFold / Reactome / structural-bio tools.

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
`taxonId`	No	NCBI taxonomy ID
`web_url`	No	Browser URL for the UniProt entry — a link for the client to open or fetch; no tool on this server dereferences it
`organism`	No	Scientific name
`reviewed`	Yes	True if Swiss-Prot (curated)
`entryType`	Yes	e.g. 'UniProtKB reviewed (Swiss-Prot)' or '... (TrEMBL)'
`geneNames`	No	Gene symbols, e.g. ['NAC001']
`locus_query`	Yes	The locus identifier the user asked about
`uniProtkbId`	Yes	UniProtKB ID, e.g. NAC1_ARATH
`sequenceLength`	No	Protein length in residues
`recommendedName`	No	Recommended protein name
`primaryAccession`	Yes	UniProt accession, e.g. Q0WV96
`upstream_version`	No	UniProt release that produced THIS record, as stated by the upstream's own header (e.g. '2026_02'). null means UniProt 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.

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv1.22.0Sep 24, 2026

changedOutput schema / properties / web_url / description

Previous value: -"Browser URL for the UniProt entry"New value: +"Browser URL for the UniProt entry — a link for the client to open or fetch; no tool on this server dereferences it"

Changed1 schema field changedv1.20.0Jul 28, 2026

addedOutput schema / properties / upstream_version

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "UniProt release that produced THIS record, as stated by the upstream's own header (e.g. '2026_02'). null means UniProt 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

A4.7/5.0

Behavior5/5

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

The annotations already mark the tool as read-only, idempotent, and non-destructive. The description adds valuable behavior beyond this: reviewed-entry preference, TrEMBL fallback behavior, InvalidArguments behavior for ambiguous gene symbols, and the note that web_url is for client opening only and no server tool retrieves it. No contradiction with 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?

The description is compact and information-dense, with the primary purpose front-loaded. Every sentence earns its place: preference behavior, parameter formats, ambiguity handling, output fields, and integration guidance are all covered 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?

Given the output schema exists and annotations cover the safety profile, the description is complete. It covers input formats, default behavior, failure mode for ambiguous symbols, output highlights, and guidance on how the result link should be used. Nothing essential for correct invocation is missing.

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%, so the baseline is 3. The description adds meaningful semantics by explaining that locus can also be a gene symbol but only when unambiguous, and by enriching organism with defaults and concrete examples like oryza_sativa and zea_mays. This goes beyond the schema's per-parameter descriptions.

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?

States a specific action and resource: 'Resolve a plant locus to its canonical UniProtKB record' with explicit preference behavior for Swiss-Prot vs TrEMBL. The phrase 'protein-side entry point' further distinguishes this tool from the many locus/annotation siblings in the list.

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 frames this as the protein-side entry point and suggests pairing with InterPro, AlphaFold, Reactome, and structural-bio tools. It does not explicitly state when to use this over the batch sibling or the many other locus tools, but the singular/batch split and protein-side framing provide clear enough context.

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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