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Biochemistry Archive MCP Server

Biochemistry Archive MCP Server

by AudreyZW
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

compare_compounds

Compare compounds side by side using ChEMBL IDs to view physicochemical properties and clinical phase, enabling rapid compound profiling.

Instructions

Physicochemical properties and clinical phase for compounds, side by side.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "chembl_ids": "<chembl_ids>"
    },
    "name": "compare_compounds"
  }
}

Input Schema

NameRequiredDescriptionDefault
chembl_idsYesChEMBL molecule ids

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

C2.9/5.0
Behavior2/5

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

No annotations are provided, so the description must carry behavioral disclosure. It says what data is returned but does not state that the operation is read-only, whether it has side effects, how missing or invalid ChEMBL IDs are handled, or any rate/limit behavior beyond the schema's maxItems.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

One sentence with no filler, but it omits the action verb and could be more front-loaded around comparison. Still appropriately sized for a simple tool.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The tool is simple with one parameter and has an output schema, so return values need not be explained. However, the description lacks usage guidance and behavioral context, leaving gaps for an agent choosing among compound-related siblings.

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 coverage is 100% and the single parameter is documented as 'ChEMBL molecule ids' with maxItems 25. The description adds no parameter-level meaning beyond 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?

States the resource (compounds) and the returned data (physicochemical properties and clinical phase) in a side-by-side comparison, but does not explicitly name the comparison verb or distinguish it from siblings like find_similar_compounds.

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 explicit when-to-use guidance, no alternatives, and no exclusions. The phrase 'side by side' implies comparing multiple compounds, but an agent must infer that from the name and schema.

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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