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BioMCP

by yeyuan98
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TypeScript
Remote

ensembl_lookup

Read-only

Resolve a gene symbol or Ensembl ID to stable identifiers, canonical transcript, and genomic coordinates across any Ensembl species; set expand=true to return all transcripts with protein IDs.

Instructions

Resolve a gene in Ensembl terms for ANY Ensembl species (356 available): stable ID (ENSG…), symbol↔ID mapping, versioned identifier, canonical transcript, and coordinates on the current assembly (GRCh38 human, GRCm39 mouse, …). With expand=true, returns all transcripts with translation/protein IDs.

Accepts an HGNC symbol (BRAF) or Ensembl gene ID (ENSG00000157764, versioned or bare — versions are resolved to the current record). Species accepts scientific names or aliases ('homo_sapiens'/'human', 'mus_musculus'/'mouse'). For rich human gene annotation (summary, pathways, drugs, diseases) use gene_get instead — this tool is the identifier/structure authority.

Input Schema

NameRequiredDescriptionDefault
expandNoInclude all transcripts with translation/protein IDs
speciesNoSpecies name or alias — 'human' (default), 'mouse', 'mus_musculus', 'rat', …human
gene_or_idYesHGNC symbol (BRAF) or Ensembl gene ID (ENSG00000157764, versioned or bare)

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.6.0-alpha.10
    • removedInput schema / additionalProperties
      Removed value: -false
  2. Changed1 schema field changedv1.6.0-alpha.7
    • addedInput schema / properties / gene_or_id / minLength
      Added value: +1
  3. Addedv0.7.1

TDQS

A4.6/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety profile is covered. The description adds meaningful behavior: 356 species, versioned IDs resolved to the current record, and expand returning all transcripts with translation/protein IDs. It does not describe error or ambiguity handling, so it falls short of the richest behavioral disclosure.

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 tightly written sentences, front-loaded with the core purpose, then input/species behavior, then the sibling-tool boundary. Parenthetical examples earn their place and no sentence is redundant.

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?

With no output schema, the description still explains the key return content: stable ID, symbol↔ID mapping, canonical transcript, coordinates, and expanded transcripts with protein IDs. It is complete enough to call correctly, though it could say more about response shape or edge-case behavior.

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%, so the baseline is 3; the schema already explains gene_or_id, species, and expand. The description still adds semantic value by clarifying that versioned and bare IDs are resolved to the current record and by giving species aliases across the 356-species scope.

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?

Uses a specific verb and resource: 'Resolve a gene in Ensembl terms', then enumerates stable ID, symbol↔ID mapping, versioned identifiers, canonical transcript, and coordinates. It explicitly distinguishes itself from gene_get, so an agent can select it without opening sibling schemas.

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?

States the exact use case (ANY Ensembl species), accepted inputs, species aliases, and the effect of expand=true. It also names the alternative gene_get for rich human annotation, making the boundary between the two tools 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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