biothings-mcp

biothings_query_taxons

Search taxa using Lucene queries with filters like scientific name, rank, or taxid. Returns taxon details and query metadata.

Instructions

Search taxa via Lucene query (e.g., scientific name, rank), returning taxon details and query metadata.

    Search for taxa using a query string with various filtering options.
    
    **Supported Query Features:**
    1. Simple Queries: "scientific_name:Homo sapiens", "common_name:human"
    2. Fielded Queries: "rank:species", "parent_taxid:9606", "has_gene:true"
    3. Range Queries: "taxid:[9606 TO 10090]", "lineage:>9606"
    4. Boolean Queries: "rank:species AND has_gene:true", "scientific_name:Homo* AND NOT rank:genus"
    5. Wildcard Queries: "scientific_name:Homo*", "common_name:*mouse*"

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": {
      "q": "<q>"
    },
    "name": "biothings_query_taxons"
  }
}

Input Schema

Name	Required	Default
`q`	Yes
`size`	No
`skip`	No
`sort`	No
`email`	No
`fields`	No	all

Output Schema

Name	Required	Description	Default
`hits`	Yes
`took`	No
`total`	No
`max_score`	No

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.6Jun 26, 2026

TDQS

B3.4/5.0

Behavior3/5

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

With no annotations, the description must disclose all behavioral traits. It describes query types but omits safety (read-only), rate limits, authentication needs, or error handling. The description is honest but incomplete for non-query behavior.

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?

The description is well-structured with headings and bullet points, front-loading the purpose. It is informative but could be slightly more concise by trimming redundant phrasing like 'Search for taxa using a query string with various filtering options.'

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given 6 parameters and an output schema, the description fails to document pagination (size, skip), sorting (sort), fields selection, or output structure beyond 'taxon details and query metadata.' This leaves the agent underinformed for effective invocation.

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

Parameters2/5

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

Schema description coverage is 0%, so the description must compensate. Only the 'q' parameter is explained with examples; 'size', 'skip', 'sort', 'email', and 'fields' are not described, leaving significant gaps in parameter understanding.

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 searches taxa via Lucene query, returning taxon details and metadata. It distinguishes from sibling tools like biothings_get_taxon (retrieval by ID) and biothings_query_many_taxons (batch query) by emphasizing query flexibility.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage for complex, fielded, or boolean queries but does not explicitly state when to use this tool vs alternatives (e.g., get_taxon for known IDs). No when-not guidance or exclusion criteria are provided.

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