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Search Mammalian Phenotype Terms

search_phenotype_terms
Read-onlyIdempotent

Search mammalian phenotype terms by free-text query to retrieve MP IDs, names, and definitions. Use to resolve a phenotype description for further queries.

Instructions

Free-text search over Mammalian Phenotype (MP) term names and definitions (FTS, relevance-ranked). Returns {mp_id, name, definition, score} plus a truncation contract {total, returned, limit, truncated} (widen step in next_commands when truncated). Use this to resolve a phenotype description to an MP id, then find_markers_by_phenotype or get_mp_term. Signature: search_phenotype_terms(query, limit=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesFree-text phenotype query (e.g. 'small kidney').
limitNoMax hits (default 25).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
successNo
_metaNo
error_codeNo
messageNo
retryableNo
recovery_actionNo
fieldNo
allowed_valuesNo
hintNo
candidatesNo
queryNo
totalNo
returnedNo
limitNo
truncatedNo
resultsNo
Behavior4/5

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

Annotations already provide read-only, idempotent hints. The description adds behavioral details (FTS, relevance-ranked, truncation contract with next_commands) that help the agent understand result handling, going beyond the 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?

Three sentences plus a signature. No wasted words; information is front-loaded and efficiently presented.

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?

Given the simple nature of the tool, rich annotations, and presence of an output schema, the description covers purpose, return structure, truncation, and next steps. Complete for effective agent use.

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 coverage is 100%, so baseline is 3. The description repeats schema info (e.g., 'free-text phenotype query (e.g. 'small kidney')') but does not add new meaning beyond what's in the parameter descriptions.

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?

Clearly states a free-text search over Mammalian Phenotype terms, specifying FTS and relevance ranking. Differentiates from sibling tools like find_markers_by_phenotype and get_mp_term by explicitly stating the use case: resolving a phenotype description to an MP id.

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 tells when to use the tool ('resolve a phenotype description to an MP id') and what to do next ('then find_markers_by_phenotype or get_mp_term'). Provides clear workflow context.

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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