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Augmented-Nature

Unofficial PubChem MCP Server

get_literature_references

Retrieve PubMed citations and scientific literature references for chemical compounds using PubChem Compound IDs to support research and verification.

Instructions

Get PubMed citations and scientific literature references

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID (CID)

Implementation Reference

  • src/index.ts:708-718 (registration)
    Tool registration in the tools array, including name, description, and input schema definition.
    {
      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'],
      },
    },
  • The main handler function that implements the logic for the get_literature_references tool. Currently a placeholder.
    private async handleGetLiteratureReferences(args: any) {
      return { content: [{ type: 'text', text: JSON.stringify({ message: 'Literature references not yet implemented', args }, null, 2) }] };
    }
  • src/index.ts:806-807 (registration)
    Dispatch case in the MCP request handler that routes calls to the specific tool handler.
    case 'get_literature_references':
      return await this.handleGetLiteratureReferences(args);
  • Input schema definition for validating arguments to the get_literature_references tool.
    inputSchema: {
      type: 'object',
      properties: {
        cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
      },
      required: ['cid'],
    },
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 the tool does but lacks details on permissions, rate limits, output format, or any constraints beyond the input parameter. For a read operation with no annotation coverage, this is insufficient.

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 with zero waste. It's front-loaded with the core purpose and appropriately sized for the tool's complexity, making it easy 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 lack of annotations and output schema, the description is incomplete. It doesn't explain what the tool returns (e.g., citation format, data structure) or any behavioral traits, leaving significant gaps for a tool that likely outputs complex literature data.

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 semantics beyond the input schema, which has 100% coverage for the single parameter 'cid'. The baseline score of 3 is appropriate since the schema fully documents the parameter, and the description doesn't compensate or add extra context about the CID usage.

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 resource ('PubMed citations and scientific literature references'), providing a specific purpose. However, it doesn't differentiate from sibling tools like 'get_external_references' or 'get_compound_info', which might also retrieve reference data, leaving some ambiguity about scope.

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 offers no guidance on when to use this tool versus alternatives. With many sibling tools available (e.g., 'get_external_references', 'search_patents'), there's no indication of context, prerequisites, or exclusions, leaving the agent to guess based on tool names 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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