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Augmented-Nature

Unofficial PubChem MCP Server

get_assay_info

Retrieve detailed bioassay data from PubChem using the Assay ID to access experimental protocols, results, and chemical activity information.

Instructions

Get detailed information for a specific bioassay by AID

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
aidYesPubChem Assay ID (AID)

Implementation Reference

  • The handler function that implements the core logic of the 'get_assay_info' tool. It makes an API call to PubChem's assay endpoint using the provided AID and returns the formatted JSON response or throws an error.
    private async handleGetAssayInfo(args: any) {
      try {
        const response = await this.apiClient.get(`/assay/aid/${args.aid}/JSON`);
        return {
          content: [
            {
              type: 'text',
              text: JSON.stringify(response.data, null, 2),
            },
          ],
        };
      } catch (error) {
        throw new McpError(
          ErrorCode.InternalError,
          `Failed to get assay info: ${error instanceof Error ? error.message : 'Unknown error'}`
        );
      }
    }
  • The input schema definition for the 'get_assay_info' tool, specifying that it requires a numeric 'aid' parameter (PubChem Assay ID).
    inputSchema: {
      type: 'object',
      properties: {
        aid: { type: 'number', description: 'PubChem Assay ID (AID)' },
      },
      required: ['aid'],
    },
  • src/index.ts:589-599 (registration)
    The tool registration entry in the MCP tools list, defining the name, description, and input schema for 'get_assay_info'.
    {
      name: 'get_assay_info',
      description: 'Get detailed information for a specific bioassay by AID',
      inputSchema: {
        type: 'object',
        properties: {
          aid: { type: 'number', description: 'PubChem Assay ID (AID)' },
        },
        required: ['aid'],
      },
    },
  • src/index.ts:782-783 (registration)
    The switch case in the request handler that dispatches calls to 'get_assay_info' to the appropriate handler method.
    case 'get_assay_info':
      return await this.handleGetAssayInfo(args);
Behavior2/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It states it 'Get detailed information,' implying a read-only operation, but doesn't specify what 'detailed information' includes, potential rate limits, authentication needs, or error handling. This is a significant gap for a tool with no annotation coverage.

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 directly states the tool's purpose without unnecessary words. It is appropriately sized and front-loaded, making it easy for an agent to parse quickly.

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?

Given the complexity of bioassay data, no annotations, and no output schema, the description is incomplete. It doesn't explain what 'detailed information' entails, such as assay metadata, results, or related compounds, leaving the agent uncertain about the tool's output and full capabilities.

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 input schema has 100% description coverage, with the 'aid' parameter clearly documented as 'PubChem Assay ID (AID).' The description adds no additional meaning beyond this, such as format examples or constraints, so it meets the baseline for high schema coverage without compensating value.

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 action ('Get detailed information') and resource ('for a specific bioassay by AID'), making the purpose understandable. However, it doesn't explicitly differentiate from sibling tools like 'search_bioassays' or 'get_compound_bioactivities', which could provide related information, so it doesn't reach the highest 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, such as needing a specific AID, or compare it to siblings like 'search_bioassays' for broader queries or 'get_compound_bioactivities' for compound-focused data, leaving the agent without usage context.

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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