metabo-idmapper

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bridge_xref

Map metabolite identifiers across KEGG, HMDB, ChEBI, PubChem, and InChIKey in batch, attaching cross-referenced IDs to user-specified feature entries using BridgeDb.

Instructions

Promote ids across systems via BridgeDb (batch; DB loads once).

Each query: {id, source, targets:[...], feature_id?}. source/target in {kegg,hmdb,chebi,pubchem,inchikey}. If feature_id + workdir are given, bridged ids are attached to that entry as a 'bridgedb' candidate.

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>",
      "queries": "<queries>"
    },
    "name": "bridge_xref"
  }
}

Input Schema

Name	Required	Description	Default
`db`	No
`queries`	Yes
`workdir`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.0.1Jul 28, 2026

TDQS

B3.4/5.0

Behavior3/5

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

With no annotations, the description carries full burden. It mentions batch processing, one-time DB load, and side effect of attaching candidates when feature_id and workdir are provided. However, it omits error conditions, performance, or what happens without feature_id.

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 concise with key points front-loaded. It uses bullet-like structure for query format, but could be slightly more organized. No extra verbiage.

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?

For a tool with 3 params, no output schema, and no annotations, the description covers the main use case but lacks details on return values, error handling, and limitations. It's adequate but not comprehensive.

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 0%, so description must compensate. It explains the 'queries' parameter structure and valid source/target values, and ties 'workdir' to condition. But the 'db' parameter is entirely undocumented, leaving a gap.

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 the tool promotes IDs across systems using BridgeDb in batch mode, which is a specific verb-resource pairing. This distinguishes it from siblings like structure_lookup or exact_match by focusing on cross-referencing IDs.

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 guidance on when to use this tool versus alternatives among 19 siblings. The description implies use for batch ID mapping across specific databases, but lacks when-not-tos or comparisons.

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