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Augmented-Nature

PubChem MCP Server

get_literature_references

Retrieve PubMed citations and scientific literature references by inputting a PubChem Compound ID (CID) for comprehensive research insights.

Instructions

Get PubMed citations and scientific literature references

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID (CID)

Implementation Reference

  • The main execution handler for the 'get_literature_references' tool. It currently returns a placeholder response indicating the feature is not yet implemented.
    private async handleGetLiteratureReferences(args: any) {
      return { content: [{ type: 'text', text: JSON.stringify({ message: 'Literature references not yet implemented', args }, null, 2) }] };
    }
  • Input schema definition for the tool, specifying the expected 'cid' parameter.
    inputSchema: {
      type: 'object',
      properties: {
        cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
      },
      required: ['cid'],
    },
  • src/index.ts:708-718 (registration)
    Registration of the tool in the ListTools response, defining name, description, and schema.
    {
      name: 'get_literature_references',
      description: 'Get PubMed citations and scientific literature references',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },
  • src/index.ts:806-807 (registration)
    Switch case in the CallToolRequest handler that dispatches to the specific tool handler.
    case 'get_literature_references':
      return await this.handleGetLiteratureReferences(args);
Behavior2/5

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

With no annotations provided, the description carries full burden but offers minimal behavioral insight. It states what the tool returns (PubMed citations/literature references) but doesn't disclose format, pagination, rate limits, authentication needs, or whether it's a read-only operation. For a tool with zero annotation coverage, this is inadequate.

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 extremely concise (one short phrase) with zero wasted words. It's front-loaded with the core purpose. Every word earns its place.

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, no output schema, and a single parameter, the description is incomplete. It doesn't explain what format the references come in, how many are returned, whether there are limitations, or what happens with invalid CIDs. For a tool that presumably returns structured data, more context is needed.

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% (the single parameter 'cid' is well-described in the schema as 'PubChem Compound ID (CID)'). The description doesn't add any parameter information beyond what's in the schema, so baseline 3 is appropriate.

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: 'Get PubMed citations and scientific literature references' specifies the action (get) and resource (PubMed citations/literature references). It distinguishes from many siblings focused on molecular analysis, but doesn't explicitly differentiate from 'get_external_references' which might overlap.

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. The description doesn't mention prerequisites, constraints, or when to choose this over other reference-related tools like 'get_external_references' or 'search_patents'.

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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