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Augmented-Nature

PubChem MCP Server

get_toxicity_info

Retrieve toxicity details such as LD50, carcinogenicity, and mutagenicity for chemical compounds using the PubChem Compound ID (CID) from the PubChem MCP Server.

Instructions

Get toxicity data including LD50, carcinogenicity, and mutagenicity

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID (CID)

Implementation Reference

  • The handler function that executes the 'get_toxicity_info' tool logic. Currently a placeholder that returns a 'not yet implemented' message.
    private async handleGetToxicityInfo(args: any) {
      return { content: [{ type: 'text', text: JSON.stringify({ message: 'Toxicity info not yet implemented', args }, null, 2) }] };
    }
  • Input schema defining the expected parameters (cid) for the tool.
    inputSchema: {
      type: 'object',
      properties: {
        cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
      },
      required: ['cid'],
    },
  • src/index.ts:650-660 (registration)
    Tool definition and registration in the server's tools array, including name, description, and schema.
    {
      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)
    Switch case in the request handler that dispatches 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. It states what data is retrieved but doesn't describe how the tool behaves: e.g., whether it returns structured data, error handling for invalid CIDs, rate limits, or authentication needs. For a read operation with no annotation coverage, this leaves significant gaps in understanding operational traits.

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?

The description is a single, efficient sentence that front-loads the core purpose without unnecessary words. Every part ('Get toxicity data including LD50, carcinogenicity, and mutagenicity') directly contributes to understanding the tool's function, making it highly concise and well-structured.

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 has one parameter with full schema coverage and no output schema, the description is minimally adequate. It specifies the data types returned but lacks details on output format, error cases, or behavioral context. For a simple lookup tool, this is passable but leaves room for improvement in completeness, especially without annotations.

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%, with the single parameter 'cid' fully documented in the schema as 'PubChem Compound ID (CID)'. The description adds no additional parameter semantics beyond implying that toxicity data is fetched for the given CID. This meets the baseline score of 3 since the schema adequately covers parameter details.

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 verb ('Get') and the resource ('toxicity data'), specifying the types of data included (LD50, carcinogenicity, mutagenicity). It distinguishes this from general compound info tools like 'get_compound_info' by focusing on toxicity. However, it doesn't explicitly differentiate from 'get_safety_data' which might overlap, preventing a perfect score.

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 (e.g., needing a CID), exclusions, or comparisons to sibling tools like 'get_safety_data' or 'predict_admet_properties' that might handle related toxicity or safety aspects. Usage is implied only by the tool name and description.

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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