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get_external_references

Retrieve links to external chemical databases like ChEMBL, DrugBank, and KEGG for PubChem compounds to access additional research data and cross-reference chemical information.

Instructions

Get links to external databases (ChEMBL, DrugBank, KEGG, etc.)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID (CID)

Implementation Reference

  • The main handler function for the 'get_external_references' tool. It currently serves as a placeholder, returning a message that the feature is not yet implemented.
    private async handleGetExternalReferences(args: any) {
      return { content: [{ type: 'text', text: JSON.stringify({ message: 'External references not yet implemented', args }, null, 2) }] };
    }
  • src/index.ts:685-695 (registration)
    Tool registration in the setTools call, including name, description, and input schema definition.
    {
      name: 'get_external_references',
      description: 'Get links to external databases (ChEMBL, DrugBank, KEGG, etc.)',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },
  • Input schema definition for the tool, specifying the required 'cid' parameter.
    inputSchema: {
      type: 'object',
      properties: {
        cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
      },
      required: ['cid'],
    },
  • src/index.ts:802-803 (registration)
    Dispatcher switch case that routes calls to the specific handler function.
    case 'get_external_references':
      return await this.handleGetExternalReferences(args);
Behavior2/5

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

With no annotations, the description carries full burden but lacks behavioral details. It doesn't specify if this is a read-only operation, potential rate limits, authentication needs, or what the output format looks like (e.g., list of URLs, structured data). The description is minimal and doesn't compensate for the absence of annotations.

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 with no wasted words. It directly states what the tool does and provides relevant examples, making it easy to scan and understand 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 no annotations and no output schema, the description is incomplete for a tool that likely returns structured external reference data. It doesn't explain return values, error conditions, or behavioral traits, leaving significant gaps for an AI agent to understand how to use it effectively in context with many sibling tools.

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%, so the schema fully documents the 'cid' parameter as a PubChem Compound ID. The description adds no additional parameter semantics beyond implying external database links are retrieved for a compound, which is already inferred from the tool name and schema. Baseline 3 is appropriate as the schema handles parameter documentation.

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 links') and resource ('external databases'), specifying examples like ChEMBL, DrugBank, and KEGG. It distinguishes this tool from siblings that focus on properties, bioactivities, or searches, though it doesn't explicitly contrast with 'get_literature_references' or 'get_assay_info' for related external data.

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?

No guidance is provided on when to use this tool versus alternatives. It doesn't mention prerequisites, such as needing a PubChem CID, or differentiate from siblings like 'get_literature_references' for external academic links or 'get_assay_info' for database-specific assay data.

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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