APIbase

Look Up Gene by Symbol

science.ensembl.gene_lookup

Read-onlyIdempotent

Look up any gene by symbol across 300+ vertebrate and non-vertebrate species to retrieve Ensembl gene ID, coordinates, biotype, description, and transcript details.

Instructions

Look up a gene by symbol (e.g. "BRCA1", "TP53") in any of 300+ vertebrate and non-vertebrate species. Returns Ensembl gene ID, genomic coordinates, biotype, description, and (optionally) the full list of transcripts with their coordinates. Data: rest.ensembl.org (EMBL-EBI / Wellcome Sanger Institute), no auth required.

Input Schema

Name	Required	Description
`expand`	No	Include the list of transcripts for this gene in the response. Default: true
`symbol`	Yes	Gene symbol to look up (e.g. "BRCA1", "TP53", "EGFR")
`species`	Yes	Species name in Ensembl format — scientific snake_case (e.g. "homo_sapiens", "mus_musculus") or common alias (e.g. "human", "mouse")

Output Schema

Name	Required	Description	Default
`error`	No	Present only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
`result`	No	Tool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.

Schema Changelog

Changes observed during successful MCP inspections.

Addedv2.2.0Oct 29, 2026

TDQS

A4.3/5.0

Behavior4/5

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

Annotations already cover the read-only, idempotent, non-destructive safety profile. The description adds contextual behavior beyond annotations: 'no auth required', the specific data source (rest.ensembl.org), and the optional transcript list behavior tied to the expand parameter. No contradiction 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?

Three sentences with no filler: the first states the core action, the second lists return fields, the third gives data provenance and auth status. Every sentence earns its place.

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 read-only lookup with an output schema and full parameter documentation, the description covers all necessary invocation context: species scope, return values, optional transcript expansion, data source, and auth. Nothing essential is missing.

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%, so the schema already documents all three parameters with examples. The description adds marginal value by restating symbol examples and mentioning the optional transcripts, but it does not systematically add meaning beyond the schema. Baseline 3 is appropriate.

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 opens with a specific verb and resource ('Look up a gene by symbol'), names example symbols, and lists exact return fields (Ensembl gene ID, coordinates, biotype, description, transcripts). This clearly distinguishes it from sibling tools like science.ensembl.sequence_region and other science.* lookups.

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 gives clear context: use it for symbol-based gene lookup across 300+ species, and notes the data source. However, it does not explicitly mention when not to use it or name alternatives such as mygene.genes.symbol, leaving some routing to the agent's inference.

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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