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Get Phenotype Overview Grid

get_phenotype_overview
Read-onlyIdempotent

Retrieves a system-level phenotype overview for a gene, displaying top-level MP systems and their annotated terms. Use to identify affected systems, then drill down with get_marker_phenotypes.

Instructions

Return the gene page's 'Phenotype Overview' grid: for each top-level MP system annotated for the marker (adipose tissue, cardiovascular system, renal/urinary system, nervous system, neoplasm, vision/eye, ...), the distinct annotated MP terms rolled up via the MP ontology. Use this for the system-level overview, then get_marker_phenotypes(mp_system=) to drill into one system. Signature: get_phenotype_overview(query).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesA mouse marker symbol (current or synonym, case-insensitive), an MGI id (MGI:98968 or 98968), or a human gene symbol / HGNC id for the ortholog.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
successNo
_metaNo
error_codeNo
messageNo
retryableNo
recovery_actionNo
fieldNo
allowed_valuesNo
hintNo
candidatesNo
mgi_idNo
symbolNo
summaryNo
system_countNo
systemsNo
Behavior4/5

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

Annotations already declare readOnlyHint, destructiveHint, idempotentHint, openWorldHint. The description adds behavioral context about the output structure (grid with top-level systems and rolled-up terms). 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?

Two sentences: first explains what the tool returns, second gives usage guidance and the function signature. No unnecessary words; information is front-loaded.

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 tool returning a complex grid derived from ontology, the description adequately explains the output (top-level systems, rolled-up terms) and provides a usage pattern with its sibling. The presence of an output schema (not shown) supports completeness.

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 the parameter 'query' is well-documented in the schema with examples. The tool description does not add parameter details, which is acceptable since the schema is complete. Baseline 3 applies.

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 it returns the 'Phenotype Overview grid' for a marker, listing top-level MP systems and rolled-up terms. It distinguishes itself from the sibling tool get_marker_phenotypes by noting it provides a system-level overview rather than per-system details.

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 this tool (for system-level overview) and when to use an alternative (get_marker_phenotypes to drill into a specific system). The description provides clear context for selection.

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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