Unofficial PubChem MCP Server

compare_activity_profiles

Analyze and compare bioactivity profiles across multiple chemical compounds using PubChem data to identify similarities and differences in biological effects.

Instructions

Compare bioactivity profiles across multiple compounds

Input Schema

TableJSON Schema

Name	Required	Description	Default
`cids`	Yes	Array of PubChem CIDs (2-50)
`activity_type`	No	Specific activity type for comparison (optional)

Implementation Reference

src/index.ts:1156-1158 (handler)

Handler function that executes the tool logic. Currently a placeholder returning a 'not yet implemented' message with input args.

private async handleCompareActivityProfiles(args: any) {
  return { content: [{ type: 'text', text: JSON.stringify({ message: 'Activity profile comparison not yet implemented', args }, null, 2) }] };
}

src/index.ts:626-636 (schema)

Input schema definition for the tool, defining parameters: cids (array of numbers, 2-50) and optional activity_type (string).

  name: 'compare_activity_profiles',
  description: 'Compare bioactivity profiles across multiple compounds',
  inputSchema: {
    type: 'object',
    properties: {
      cids: { type: 'array', items: { type: 'number' }, description: 'Array of PubChem CIDs (2-50)', minItems: 2, maxItems: 50 },
      activity_type: { type: 'string', description: 'Specific activity type for comparison (optional)' },
    },
    required: ['cids'],
  },
},

src/index.ts:788-789 (registration)
Registration in the switch statement that routes tool calls named 'compare_activity_profiles' to the corresponding handler.
```
case 'compare_activity_profiles':
  return await this.handleCompareActivityProfiles(args);
```

Schema Changelog

Changes observed during successful MCP inspections.

First observedAug 15, 2025

TDQS

C2.9/5.0

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 but offers minimal information. It implies a read-only comparison operation but doesn't specify output format, performance characteristics, rate limits, or error conditions. For a tool with 2 parameters and no output schema, this leaves significant gaps in understanding how it behaves.

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's appropriately sized for a tool with clear parameters and no complex behavioral nuances to explain.

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 tool's complexity (comparing multiple compounds), lack of annotations, and absence of an output schema, the description is insufficiently complete. It doesn't explain what the comparison yields (e.g., similarity scores, visualizations, or structured data), which is critical for an agent to understand the tool's utility and integrate results into workflows.

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 already documents both parameters thoroughly. The description adds no additional parameter semantics beyond what's in the schema (e.g., it doesn't explain what 'bioactivity profiles' consist of or how the comparison is performed). This meets the baseline expectation when schema coverage is high.

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 as comparing bioactivity profiles across compounds, specifying both the action (compare) and the resource (bioactivity profiles). It distinguishes from siblings like 'get_compound_bioactivities' (which retrieves rather than compares) and 'search_bioassays' (which searches rather than compares profiles), though it doesn't explicitly name these alternatives.

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, appropriate contexts, or exclusions, leaving the agent to infer usage from the purpose alone. For example, it doesn't clarify if this is for exploratory analysis versus targeted comparison.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.