biothings-mcp

biothings_get_chems

Fetch multiple chemical compounds by providing a comma-separated list of IDs, such as InChIKeys or PubChem CIDs, to retrieve their data in one request.

Instructions

Fetch multiple chemical compounds by a comma-separated list of IDs.

    Retrieves information for multiple chemical compounds in a single request.
    
    **Input Format:** Accepts comma-separated list of chemical IDs in various formats:
    - InChIKeys: "KTUFNOKKBVMGRW-UHFFFAOYSA-N,XEFQLINVKFYRCS-UHFFFAOYSA-N"
    - PubChem CIDs: "5793,5281"
    - Mixed formats: "KTUFNOKKBVMGRW-UHFFFAOYSA-N,5281"

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": {
      "chem_ids": "<chem_ids>"
    },
    "name": "biothings_get_chems"
  }
}

Input Schema

Name	Required	Default
`email`	No
`fields`	No	all
`chem_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

A3.6/5.0

Behavior3/5

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

No annotations are provided, so the description carries the burden. It indicates a read operation (fetch) but does not disclose what happens with invalid IDs, rate limits, or authentication needs.

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 relatively concise with a clear structure including an Input Format subsection. However, it contains slight redundancy ('Retrieves information' repeats the purpose).

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

Completeness3/5

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

Despite an existing output schema, the description lacks guidance on optional parameters (email, fields) and does not mention pagination or response shape. It is adequate but incomplete.

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 coverage is 0%. The description adds meaningful context for chem_ids (formats, examples) but does not explain email or fields parameters, nor their possible values.

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 clearly states the tool fetches multiple chemical compounds by a comma-separated list of IDs. It distinguishes from biothings_get_chem (singular) and provides specific input format examples.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies use when you have a list of IDs but does not explicitly contrast with alternative tools like biothings_query_chems or provide conditions for when not to use it.

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