uniprot-mcp-server

uniprot-mcp-server: get taxonomy

uniprot_get_taxonomy

Read-onlyIdempotent

Resolve a taxonomy record by NCBI taxon ID (e.g. 9606) or scientific name (e.g. "Homo sapiens") — provide exactly one. Returns the scientific and common name, mnemonic, rank, parent, and the full lineage. Set include_children to also fetch immediate child taxa (a separate lookup — not inline on the record) in pages of 100 with the total child count; when more remain, pass the returned cursor to fetch the next page. Use this to turn an organism name into the taxon ID that uniprot_search_proteins (organism_id) and uniprot_get_proteome (taxon_id) expect.

Input Schema

TableJSON Schema

Name	Required	Description
`name`	No	Organism scientific name, e.g. "Homo sapiens". Provide this OR taxon_id, not both. Matched against the scientific name.
`cursor`	No	Forward-pagination cursor from a prior children page, for the next page of the same taxon; a cursor issued for another taxon is rejected. Only meaningful with include_children.
`taxon_id`	No	NCBI taxonomy ID, e.g. 9606. Provide this OR name, not both.
`include_children`	No	When true, also fetch a page of up to 100 immediate child taxa via a follow-up search. Defaults to false.

Output Schema

TableJSON Schema

Name	Required	Description
`cap`	No	The page size that was applied, when more remain.
`error`	No	Present when the call failed. Absent on success.
`shown`	No	Number of children on this page, when more remain.
`taxon`	No	The taxonomy record.
`cursor`	No	Forward cursor for the next children page. Absent on the last page.
`notice`	No	Paging guidance when more children remain — the total and how to continue.
`lineage`	No	Full lineage from root to the taxon's near ancestor.
`children`	No	One page of immediate children (up to 100). Present only when include_children is true.
`truncated`	No	True when more children remain past this page — fetch them with cursor.
`childCount`	No	Number of immediate children on this page (when include_children is true).
`totalChildren`	No	Total immediate children of the taxon across all pages (when include_children is true).

Schema Changelog

Changes observed during successful MCP inspections.

Changed12 schema fields changedOct 14, 2026

addedInput schema / properties / cursor

Added value: +{
+  "description": "Forward-pagination cursor from a prior children page, for the next page of the same taxon; a cursor issued for another taxon is rejected. Only meaningful with include_children.",
+  "type": "string"
+}

changedInput schema / properties / include_children / description

Previous value: -"When true, also fetch the immediate child taxa via a follow-up search. Defaults to false."New value: +"When true, also fetch a page of up to 100 immediate child taxa via a follow-up search. Defaults to false."

addedOutput schema / properties / cap

Added value: +{
+  "description": "The page size that was applied, when more remain.",
+  "type": "number"
+}

changedOutput schema / properties / childCount / description

Previous value: -"Number of immediate children returned (when include_children is true)."New value: +"Number of immediate children on this page (when include_children is true)."

changedOutput schema / properties / children / description

Previous value: -"Immediate children. Present only when include_children is true."New value: +"One page of immediate children (up to 100). Present only when include_children is true."

addedOutput schema / properties / cursor

Added value: +{
+  "description": "Forward cursor for the next children page. Absent on the last page.",
+  "type": "string"
+}

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `missing_identifier`: Neither taxon_id nor name was provided. `conflicting_identifier`: Both taxon_id and name were provided. `not_found`: The taxon ID or name did not resolve to a record. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `missing_identifier`: Neither taxon_id nor name was provided. `conflicting_identifier`: Both taxon_id and name were provided. `not_found`: The taxon ID or name did not resolve to a record. `invalid_cursor`: The cursor was issued for another taxon, is malformed, or UniProt could not continue from it. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "missing_identifier",
-  "conflicting_identifier",
-  "not_found"
-]New value: +[
+  "missing_identifier",
+  "conflicting_identifier",
+  "not_found",
+  "invalid_cursor"
+]

addedOutput schema / properties / notice

Added value: +{
+  "description": "Paging guidance when more children remain — the total and how to continue.",
+  "type": "string"
+}

addedOutput schema / properties / shown

Added value: +{
+  "description": "Number of children on this page, when more remain.",
+  "type": "number"
+}

addedOutput schema / properties / totalChildren

Added value: +{
+  "description": "Total immediate children of the taxon across all pages (when include_children is true).",
+  "type": "number"
+}

addedOutput schema / properties / truncated

Added value: +{
+  "description": "True when more children remain past this page — fetch them with cursor.",
+  "type": "boolean"
+}

First observedAug 22, 2026

TDQS

A4.6/5.0

Behavior4/5

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

Annotations cover the safety profile (readOnly, idempotent, openWorld), and the description adds genuinely non-obvious behavior: children are fetched via a separate follow-up lookup rather than inline, results are paged at 100 with a total count, and a cursor is scoped to its originating taxon. It stops short of describing failure modes for an unmatched name.

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?

Dense but front-loaded: identifier forms first, then child-fetch paging, then the cross-tool routing. Every sentence carries information; only the return-field enumeration is arguably redundant given the output schema exists.

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?

All four parameters, the mutual-exclusion rule, the child-pagination flow, and downstream usage are covered, and an output schema is present so return values need not be re-explained. Nothing an agent needs to call it correctly 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, but the description adds meaning the schema does not: 'provide exactly one' of name/taxon_id even though the schema marks nothing required, and it clarifies the pagination contract for cursor/include_children.

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?

Specific verb + resource ('Resolve a taxonomy record') with the two accepted identifier forms spelled out and examples given. It is unambiguously distinct from siblings like uniprot_get_entry or uniprot_search_proteins.

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?

Ends with an explicit routing statement: use this to convert an organism name into the taxon ID that uniprot_search_proteins (organism_id) and uniprot_get_proteome (taxon_id) expect. It also states the 'provide exactly one' precondition, so both when-to-use and constraints are covered.

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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