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resolve_gene

Resolve ambiguous gene symbols, aliases, or accessions to canonical gene entities with cross-references and a match audit trail. Use taxon, chromosome, and locus type hints for accurate disambiguation.

Instructions

Resolve an ambiguous gene symbol, alias, or accession to an authoritative entity.

Args: query: Gene symbol (e.g. TP53), alias (e.g. HER2, p53), or accession. taxon_id: NCBI Taxonomy ID (default: 9606 for human). chromosome: Optional chromosome hint for disambiguation (e.g. '17' or 'chr17'). locus_type: Optional biotype hint (e.g. 'protein-coding', 'pseudogene').

Returns: JSON string containing the resolved canonical gene entity, cross-references, and match audit trail.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYes
taxon_idNo
chromosomeNo
locus_typeNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4/5.0
Behavior3/5

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

With no annotations, the description carries the full burden of disclosing behavior. It does explain the return format (JSON string with canonical entity, cross-references, and match audit trail), but it does not describe what happens on no match, multiple ambiguous hits, or whether the operation is read-only. This is a moderate gap for an otherwise straightforward lookup tool.

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 front-loaded with the purpose sentence, followed by a compact Args list and Returns line. Every sentence adds useful information and there is no filler, though the structure is slightly verbose with the docstring-style sections.

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

Completeness4/5

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

Given the tool's moderate complexity, all four parameters are documented and an output schema is present, so return structure is already covered. The description lacks explicit error/edge-case behavior and sibling differentiation, but it is otherwise complete enough for an agent to call it correctly.

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

Parameters5/5

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

Schema description coverage is 0%, yet the description fully compensates by adding meaning to every parameter: query examples (TP53, HER2, p53), default taxon_id with human-specific context, chromosome format examples, and locus_type biotype examples. Each parameter is more actionable than the bare schema types provide.

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 opening sentence uses a specific verb ('Resolve') and states the exact resource and ambiguity condition: gene symbols, aliases, or accessions are mapped to an authoritative entity. This clearly differentiates the tool from batch_resolve_genes (single vs batch) and get_protein_info (resolution vs protein information).

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 when a query is ambiguous and needs authoritative resolution, and it hints at optional disambiguation arguments. However, it does not explicitly state when to prefer batch_resolve_genes for multiple queries or when get_protein_info would be more appropriate, so the guidance is implied rather than explicit.

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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