APIbase

Batch Fetch Multiple Genes

mygene.genes.batch

Read-onlyIdempotent

Retrieve annotation data for up to 1000 NCBI Entrez or Ensembl gene IDs in one request, returning symbols, coordinates, pathways, and related fields to enrich gene lists.

Instructions

Retrieve annotation data for up to 1000 genes in a single request by providing a comma-separated list of NCBI Entrez Gene IDs or Ensembl gene IDs. Returns the same fields as mygene.genes.info for each gene: symbol, name, gene type, taxon, summary, Ensembl IDs, UniProt accession, genomic coordinates, and pathway memberships. Ideal for enriching gene lists from RNA-seq experiments, GWAS results, or drug target panels. Mix of NCBI Entrez and Ensembl IDs is supported in the same request.

Input Schema

Name	Required	Description	Default
`ids`	Yes	Comma-separated list of NCBI Entrez Gene IDs or Ensembl gene IDs to retrieve in one request (e.g. "1017,1018,1019" for CDK2/CDK3/CDK4, or "ENSG00000123374,ENSG00000012048"). Maximum 1000 IDs per call.
`fields`	No	Comma-separated fields to return for each gene. Default: symbol, name, taxid, entrezgene, type_of_gene, summary, ensembl, uniprot, alias, genomic_pos, pathway. Limit fields to reduce response size for large batches.

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

A4.4/5.0

Behavior4/5

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

Annotations already establish read-only, idempotent, non-destructive behavior, so the bar is lower. The description adds meaningful behavioral context: the 1000-gene batch limit, support for mixing Entrez and Ensembl IDs, and return-field parity with mygene.genes.info. It does not discuss missing-ID handling or error cases, but the output schema covers return structure and the annotations cover safety.

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 action and input format, and the follow-up sentences add use cases and ID-mixing support. The returned-field list is useful but partially redundant with the schema's default `fields` description, so it is efficient rather than maximally lean.

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 batched, read-only gene lookup with an output schema, the description covers everything an agent needs to select and invoke it correctly: input ID types, maximum batch size, supported mixing, returned fields, and appropriate use cases. There are no critical gaps.

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 description coverage is 100%, so the baseline is 3. The description adds extra meaning beyond the schema by explicitly stating that mixing NCBI Entrez and Ensembl IDs in the same request is supported and by tying the fields parameter to the exact output of mygene.genes.info. This is modest but real added value.

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 states a specific verb ('Retrieve'), a clear resource ('annotation data for genes'), and the exact input mechanism ('comma-separated list of NCBI Entrez Gene IDs or Ensembl gene IDs'). It also distinguishes itself from the sibling mygene.genes.info by noting it returns the same fields in batch form, so an agent can tell them apart immediately.

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 usage context with concrete examples ('enriching gene lists from RNA-seq experiments, GWAS results, or drug target panels') and implies the batch-vs-single distinction through 'up to 1000 genes in a single request.' It does not explicitly say 'for a single gene use mygene.genes.info' or 'use search when you don't have IDs', so it stops short of full exclusion guidance.

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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