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Augmented-Nature

Unofficial PubChem MCP Server

get_toxicity_info

Retrieve toxicity data for chemical compounds including LD50, carcinogenicity, and mutagenicity from PubChem to assess safety and health risks.

Instructions

Get toxicity data including LD50, carcinogenicity, and mutagenicity

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID (CID)

Implementation Reference

  • The main handler function that implements the logic for the get_toxicity_info tool. It currently serves as a placeholder indicating the feature is not yet implemented.
    private async handleGetToxicityInfo(args: any) {
      return { content: [{ type: 'text', text: JSON.stringify({ message: 'Toxicity info not yet implemented', args }, null, 2) }] };
    }
  • The tool definition object containing the schema for input validation, description, and name used for MCP tool registration.
    {
      name: 'get_toxicity_info',
      description: 'Get toxicity data including LD50, carcinogenicity, and mutagenicity',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },
  • src/index.ts:794-795 (registration)
    The case statement in the central request handler switch that routes calls to the specific tool handler.
    case 'get_toxicity_info':
      return await this.handleGetToxicityInfo(args);
Behavior2/5

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

No annotations are provided, so the description carries the full burden of behavioral disclosure. While 'Get' implies a read-only operation, the description doesn't specify whether this requires authentication, has rate limits, returns structured or unstructured data, or handles errors. For a tool with no annotation coverage, this leaves significant behavioral gaps unaddressed.

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 a single, efficient sentence that states the core purpose without unnecessary words. It's appropriately sized for a simple lookup tool and front-loads the key information. However, it could be slightly more structured by separating the tool's purpose from the data types returned.

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?

Given the tool's moderate complexity (toxicity data retrieval), lack of annotations, and absence of an output schema, the description is minimally adequate but incomplete. It covers what data is returned but not the format, scope, or limitations. For a tool with no structured behavioral hints, more context about response structure and constraints would be beneficial.

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?

The description adds no parameter-specific information beyond what's already in the schema (which has 100% coverage). It doesn't explain what 'cid' represents in context, provide examples of valid values, or clarify the relationship between CID and toxicity data. Since schema coverage is high, the baseline score of 3 is appropriate, but the description doesn't enhance parameter understanding.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's purpose with a specific verb ('Get') and resource ('toxicity data'), and lists the types of data returned (LD50, carcinogenicity, mutagenicity). It distinguishes itself from siblings like 'get_safety_data' by focusing specifically on toxicity metrics rather than general safety information. However, it doesn't explicitly contrast with other similar tools like 'get_compound_properties' or 'predict_admet_properties'.

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

Usage Guidelines2/5

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

The description provides no guidance on when to use this tool versus alternatives. It doesn't mention prerequisites (like needing a PubChem CID), compare it to similar tools (like 'get_safety_data' or 'get_compound_properties'), or indicate when other tools might be more appropriate. The agent must infer usage from the tool name and description alone.

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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