metabo-idmapper

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gem_crosswalk

Maps metabolite identifiers from KEGG, HMDB, or ChEBI to Mouse-GEM MAM species for metabolic model flux input. Identifies and flags IDs not found in the GEM.

Instructions

Map accepted KEGG/HMDB/ChEBI ids to Mouse-GEM MAM species (flux input). Sets gem_mam + gem_cause ('id-gap' when it has ids but the GEM lacks the xref).

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>"
    },
    "name": "gem_crosswalk"
  }
}

Input Schema

Name	Required	Description	Default
`workdir`	Yes
`model_path`	No
`feature_ids`	No

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.0.1Jul 28, 2026

TDQS

A3.6/5.0

Behavior3/5

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

The description discloses that the tool sets 'gem_mam' and 'gem_cause' fields and explains the 'id-gap' condition. However, with no annotations, it omits other behavioral traits such as auth needs, rate limits, or side effects. The core behavior is clarified but not fully transparent.

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?

Two sentences, zero waste. The first sentence front-loads the primary purpose, the second adds a key behavioral detail. Every word earns its place.

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 core mapping logic and field setting are explained, but given the absence of output schema and annotations, the description lacks details on return values, prerequisites (e.g., model_path), and side effects. For a state-setting tool, more completion is needed.

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

Parameters2/5

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

Schema description coverage is 0%, and the description vaguely hints that 'feature_ids' are the IDs to map but does not explain 'workdir' or 'model_path'. This provides minimal additional meaning beyond the raw schema, failing to compensate for the lack of schema descriptions.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states it maps KEGG/HMDB/ChEBI IDs to Mouse-GEM MAM species for flux input, using a specific verb ('Map') and resource ('accepted...ids to Mouse-GEM MAM species'). This distinguishes it from sibling tools like bridge_xref or exact_match, which likely handle different mapping scenarios.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage for flux input mapping from specific databases, but lacks explicit guidance on when to avoid this tool or prefer alternatives like bridge_xref. No exclusion criteria or context are provided.

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