metabo-idmapper

by Wooyoung-kim91

Overview Schema Source Related Servers Discussions Admin

Python

Local

structure_lookup

Converts metabolite names to PubChem CID, InChIKey, formula, and monoisotopic mass, attaching evidence.

Instructions

PubChem: name -> CID / InChIKey / formula / monoisotopic mass. Attaches evidence.

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": {
      "workdir": "<workdir>",
      "feature_id": "<feature_id>"
    },
    "name": "structure_lookup"
  }
}

Input Schema

Name	Required	Description	Default
`name`	No
`workdir`	Yes
`feature_id`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.0.1Jul 28, 2026

TDQS

C2.4/5.0

Behavior2/5

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

No annotations are supplied, so the description must fully convey behavioral traits. It states the output fields and mentions evidence attachment, but it omits details on side effects, authentication needs, rate limits, or whether modifications occur. The description is too minimal to fully inform an agent.

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?

The description is a single sentence that conveys the core purpose efficiently. However, it could benefit from being more structured (e.g., listing parameters) without losing conciseness.

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

Completeness1/5

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

Given no annotations, no output schema, 3 parameters with 0% schema coverage, and many sibling tools, the description is severely incomplete. It fails to explain the required parameters, output format, or how it differs from related tools like 'search_synonym' or 'exact_match'.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters1/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0%, so the description must explain parameters. It only mentions 'name' as input, but the schema includes two required parameters ('workdir' and 'feature_id') with no explanation. This leaves the agent unsure how to use those required parameters, making the description insufficient.

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 performs a PubChem lookup of chemical names to identifiers (CID, InChIKey, formula, monoisotopic mass) and attaches evidence. The verb and resource are clear, but it does not explicitly distinguish from siblings like 'search_synonym' or 'exact_match' which might also perform lookups.

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 does not mention prerequisites, contraindications, or alternative tools for different scenarios (e.g., searching by other identifiers).

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