biothings-mcp

biothings_get_genes

Fetch detailed information for multiple genes using a comma-separated list of Entrez or Ensembl IDs. Ideal when you know the exact identifiers.

Instructions

Fetch multiple genes by a comma-separated list of Entrez or Ensembl IDs.

    Retrieves detailed information for **multiple specific genes** in a single request using their exact known identifiers.
    **This is the preferred tool over `query_many_genes` for fetching multiple specific genes when you already know 
    their standard IDs (Entrez, Ensembl) and don't need complex search filters.**
    
    **Input Format:** Accepts a comma-separated list of gene IDs (Entrez or Ensembl).
    **Example:** `gene_ids=1017,1018` or `gene_ids=ENSG00000123374,ENSG00000134057`

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": {
      "gene_ids": "<gene_ids>"
    },
    "name": "biothings_get_genes"
  }
}

Input Schema

Name	Required	Default
`email`	No
`fields`	No	all
`species`	No
`gene_ids`	Yes

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.6Jun 26, 2026

TDQS

A3.8/5.0

Behavior3/5

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

With no annotations, the description carries the full burden. It states that the tool retrieves detailed information in a single request and provides input format examples, but it does not disclose error handling, limits on ID count, authentication needs, or output structure beyond 'detailed information'. The existence of an output schema is noted but not detailed.

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 short and front-loaded with the core purpose. It uses bold for emphasis and provides a clear example. A minor inefficiency: repeating the input format explanation could be streamlined.

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

Completeness2/5

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

Despite having an output schema and four parameters, the description only covers one parameter and omits details on output format, allowed values for 'fields', default behavior for 'species', and any constraints. This leaves the agent with insufficient context to use the tool correctly.

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

Parameters2/5

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

Schema description coverage is 0%, so the description must compensate. It only explains the 'gene_ids' parameter with format and examples. The 'email', 'fields', and 'species' parameters are completely undocumented, leaving significant ambiguity for the agent.

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 uses a specific verb ('fetch') and resource ('multiple genes'), and explicitly distinguishes itself from the sibling tool 'query_many_genes', making its purpose very clear.

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?

The description provides explicit guidance on when to use this tool ('when you already know their standard IDs and don't need complex search filters') and directly names the alternative tool ('query_many_genes').

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.