Skip to main content
Glama
berntpopp
by berntpopp

Get Taxon

get_taxon
Read-onlyIdempotent

Resolve an organism in the UniProt taxonomy by providing a numeric NCBI taxon ID or scientific/common name. Returns the direct parent, rank, and optional lineage for taxon ID queries.

Instructions

Resolve an organism in the UniProt taxonomy. Pass a numeric NCBI taxon id (e.g. 9606) for full detail (scientific/common name, rank, the DIRECT parent, and an optional ordered lineage from species up to root), or a scientific/common name to get candidate taxon ids. Use the resolved taxon id with find_proteins(organism_taxon=...). Name matches are ranked best-first (an exact scientific/common-name hit leads, tagged match_quality:'exact'), so matches[0] and next_commands point at the right organism. Numeric-id and common-organism-name lookups are fast (~0 ms for common names); an uncommon name triggers a multi-second taxonomy scan. Signature: get_taxon(taxon, include_lineage=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
taxonYesNCBI taxon id (digits) or a scientific/common name.
include_lineageNoInclude the ancestor lineage (id lookups only).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
successNo
_metaNo
error_codeNo
messageNo
retryableNo
recovery_actionNo
fieldNo
allowed_valuesNo
hintNo
taxon_idNo
scientific_nameNo
common_nameNo
rankNo
parent_taxon_idNo
lineageNo
queryNo
match_countNo
matchesNo
Behavior5/5

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

Annotations already indicate read-only, idempotent, and open-world. The description adds: exact match quality tagging ('exact'), ranked name matches, lineage inclusion only for id lookups, and performance characteristics. No contradictions 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?

Approximately 120 words, well-structured with clear sections: purpose, usage guidance, performance notes, and signature. Every sentence adds unique value 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?

For a 2-parameter tool with output schema, the description covers behavioral aspects (output details for each input type), performance, and integration with sibling tools. No gaps remain; completeness is high.

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

Parameters5/5

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

Schema coverage is 100% with descriptions for both parameters. The description adds context: taxon parameter can be numeric id or name with example, and include_lineage only works for id lookups. This enriches understanding beyond schema.

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 clearly states the tool resolves organisms in UniProt taxonomy, distinguishing it from sibling tools like find_proteins. It specifies two modes: numeric NCBI taxon id for full detail (scientific/common name, rank, parent, optional lineage) and name for candidate ids, with an example (9606). This is specific and actionable.

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 guides when to use: 'Use the resolved taxon id with find_proteins(organism_taxon=...).' It also warns about performance differences: numeric-id and common names are fast (~0 ms), uncommon names trigger a multi-second scan. This helps the agent decide based on input type.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/berntpopp/uniprot-link'

If you have feedback or need assistance with the MCP directory API, please join our Discord server