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by io.github.whiteknightonhorse
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NCBI Taxonomy Lineage

ncbi-eutils.taxonomy.lineage
Read-onlyIdempotent

Get the full taxonomic classification tree for one NCBI TaxID — every ancestor rank from domain/kingdom down to the organism itself (e.g. Eukaryota > Metazoa > Chordata > Mammalia > Carnivora > Felidae > Panthera > Panthera leo), plus scientific name, common name, and parent TaxID. Use ncbi-eutils.taxonomy_search first to find a tax_id. Data: eutils.ncbi.nlm.nih.gov, no auth required.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "tax_id": "<tax_id>"
    },
    "name": "ncbi-eutils.taxonomy.lineage"
  }
}

Input Schema

NameRequiredDescriptionDefault
tax_idYesNCBI Taxonomy ID (e.g. "9689" for Panthera leo), from ncbi-eutils.taxonomy_search results

Output Schema

NameRequiredDescriptionDefault
errorNoPresent only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
resultNoTool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already declare readOnly, idempotent, and non-destructive behavior. The description adds valuable context by naming the data source (eutils.ncbi.nlm.nih.gov), stating 'no auth required,' and clarifying that the output includes the full ancestor chain plus scientific name, common name, and parent TaxID.

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 sentences with no filler. The core behavior and example are front-loaded, followed by lookup guidance and source/auth information. Every sentence earns its place.

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 one-parameter read-only tool with a strong input schema, output schema, and comprehensive annotations, the description covers source, auth requirements, and prerequisite lookup. No material information needed to invoke it correctly is missing.

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?

The input schema has 100% coverage with a clear description, regex pattern, and worked example already present. The tool description mainly reinforces what the schema says, adding only the 'one tax ID' constraint and the search-first origin, which is minor additional value.

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 names a specific operation ('Get the full taxonomic classification tree'), a resource ('one NCBI TaxID'), and enumerates the returned fields with a concrete example. It clearly differentiates from the taxonomy_search sibling by framing that tool as the prerequisite lookup.

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 provides a clear prerequisite: 'Use ncbi-eutils.taxonomy_search first to find a tax_id.' It effectively communicates when this lineage tool is appropriate, though it does not explicitly contrast with the taxonomy.summary sibling or state when not to use this tool.

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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