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Resolve identifiers

resolve_entity
Read-onlyIdempotent

Map a name, alias or ambiguous identifier to exact species-qualified IDs before joining evidence. Returns candidates when ambiguous; a provider match score alone is not identity. Skip when you already hold an exact ID. e.g. {"entity":"gene","query":"LDL receptor","species":9606}

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": {
      "query": "<query>"
    },
    "name": "resolve_entity"
  }
}

Input Schema

NameRequiredDescriptionDefault
queryYesName, alias, symbol or identifier.
entityNo
speciesNoNCBI taxon ID; 9606 is human.
assemblyNoGenome build for coordinate IDs.

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. Added

TDQS

A4.4/5.0
Behavior4/5

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

Annotations already cover readOnly, idempotent, non-destructive and open-world behavior, so the description correctly spends its words elsewhere: it discloses that ambiguity yields multiple candidates and warns that 'a provider match score alone is not identity.' That ambiguity-handling caveat is real behavioral guidance not present in the annotations or schema.

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 dense sentences plus a one-line example, front-loaded with the core mapping action, then the ambiguity caveat, then the skip condition. No sentence restates the title or the schema.

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?

An output schema exists, so return values need not be described, and the description still flags candidate-returning ambiguity. With four parameters and an enum, the only unaddressed element is the genome-build parameter, a minor gap rather than a blocker.

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 75%, so the schema documents most parameters; the description adds meaning by stressing 'species-qualified' and by giving a concrete call shape ('entity=gene, query=LDL receptor, species=9606') that shows how entity and species combine. The 'assembly' parameter's role (coordinate IDs) is left entirely to the 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?

States a specific verb and resource ('Map a name, alias or ambiguous identifier to exact species-qualified IDs') and pins its role in the workflow ('before joining evidence'). That distinguishes it immediately from retrieval siblings like get_record or search_records, which return records rather than canonical identifiers.

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?

Gives an explicit exclusion ('Skip when you already hold an exact ID') and an implicit usage trigger (before joining evidence), which is the key decision point. It does not name a specific alternative sibling such as get_record, so the routing is strong but not fully spelled out.

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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