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Glama

get_taxonomy

Retrieve the complete GTDB taxonomic lineage for an organism, taxon, or genome ID, from domain through species. Use it to resolve names and inspect full classifications.

Instructions

Get the complete taxonomic lineage of an organism or taxon from GTDB. Returns the full classification from domain down to species level (d__Domain; p__Phylum; c__Class; o__Order; f__Family; g__Genus; s__Species).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameYesTaxon name or genome ID (e.g., 'Escherichia coli', 'Bacillus', 'GCF_000005845.2')

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

B3.4/5.0
Behavior3/5

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

No annotations are provided, so the description carries the full behavioral burden. It usefully discloses the return structure (d__; p__; c__; o__; f__; g__; s__ lineages), which compensates for the missing output schema, but says nothing about behavior for unknown/nonexistent taxa, name-matching rules, or whether ambiguous names resolve to multiple lineages.

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?

Two sentences, front-loaded with the core action and resource, and the parenthetical lineage format is a justified elaboration given the absence of an output schema. No filler.

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?

For a one-parameter, no-annotation tool with no output schema, the description adequately covers the return shape (lineage ranks). It falls short only on failure/edge behavior and sibling differentiation, which are minor gaps for this complexity level.

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% and includes concrete examples for the single 'name' parameter, so the schema does the heavy lifting. The description adds only the notion that name may be an organism or taxon, no format or resolution details beyond the schema examples.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb (Get) and resource (complete taxonomic lineage) plus the data source (GTDB), and specifies scope from domain to species. It is clear what the tool does, though it does not explicitly differentiate itself from the sibling get_taxon_summary or get_tree_path.

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 says what can be fetched but gives no explicit when-to-use guidance, no conditions distinguishing it from get_taxon_summary or get_tree_path, and no prerequisites or exclusions. Usage is only inferred from the purpose.

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