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Get Marker Ortholog

get_marker_ortholog
Read-onlyIdempotent

Retrieve mouse-human ortholog mapping including human symbol, HGNC, NCBI Gene, Ensembl, OMIM, and GRCh38 coordinates. Accepts mouse or human gene identifiers.

Instructions

Return the mouse<->human ortholog mapping and cross-references for a marker: human symbol, HGNC id, NCBI Gene (human), Ensembl (human), OMIM gene id, and human GRCh38 coordinates. Accepts a mouse symbol/MGI id OR a human symbol/HGNC id (resolved to the mouse marker first). Signature: get_marker_ortholog(query, response_mode=).

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.
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
successNo
_metaNo
error_codeNo
messageNo
retryableNo
recovery_actionNo
fieldNo
allowed_valuesNo
hintNo
candidatesNo
mgi_idNo
mouse_symbolNo
match_typeNo
has_orthologNo
orthologNo
Behavior4/5

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

Annotations cover read-only, idempotent, non-destructive behavior. The description adds that query resolution happens from human to mouse first, and mentions the signature. No contradictions.

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 and a signature line, front-loaded with the main purpose. No redundancy, every word adds value.

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 two parameters, 100% schema coverage, and an output schema, the description fully explains inputs, behavior, and outputs. Suitable for an AI agent to use.

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

Parameters4/5

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

Schema coverage is 100% with good descriptions. The description adds nuance: it explains query accepts multiple types (symbols, IDs) and resolution order, which goes beyond schema.

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 returns mouse-human ortholog mapping and cross-references, listing specific fields (human symbol, HGNC id, NCBI Gene, Ensembl, OMIM, GRCh38 coordinates). It distinguishes from siblings like get_marker by focusing on orthologs.

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 specifies that the tool accepts mouse or human symbols/IDs and resolves to mouse first, providing clear input guidance. It does not explicitly state when not to use, but the purpose is well-defined.

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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