metabo-idmapper

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backfill_hmdb

Bridges missing HMDB identifiers for entries with other IDs using BridgeDb to maximize HMDB coverage without altering existing assignments.

Instructions

Bridge missing HMDB for every non-excluded entry lacking an accepted HMDB, using its available ids (InChIKey/KEGG/ChEBI/PubChem) via BridgeDb in ONE batched call, then accept.

Reflects the run-2 finding that HMDB rides along with KEGG matching and is under-counted; this maximizes HMDB coverage. Does not touch KEGG assignments or the final_class/origin of KEGG-mapped or exogenous entries (HMDB is added as an extra xref); a structure-only entry that gains HMDB → HMDB-mapped. xenobiotic-excluded entries are skipped.

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": "backfill_hmdb"
  }
}

Input Schema

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

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.0.1Jul 28, 2026

TDQS

A3.9/5.0

Behavior4/5

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

With no annotations provided, the description bears full burden for behavioral transparency. It discloses that the operation is a single batched call, adds HMDB as an extra xref, does not modify KEGG assignments, and converts structure-only entries to HMDB-mapped. It does not cover potential side effects like rate limits, but the given details are sufficient for usage.

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 moderately concise and packs relevant information in two sentences. The first sentence is lengthy but captures the core functionality. The second provides context without redundancy. Slightly more brevity could be achieved, but it remains efficient.

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?

Given no output schema and a batch operation, the description explains the tool's effect and constraints well. However, it omits parameter semantics and does not specify the return value or confirmation. An agent would need to infer workdir from context. The description is adequate but not fully complete.

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?

The schema has no descriptions (0% coverage) and the description does not explain the two parameters ('db' and 'workdir'). The description mentions IDs used (InChIKey/KEGG/ChEBI/PubChem) but does not map these to parameters or clarify their values. This is a severe gap; an agent cannot determine what to provide for 'db' or 'workdir'.

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's action: bridging missing HMDB for entries lacking an accepted HMDB via BridgeDb in one batched call. It specifies the resource (HMDB), the verb (backfill/bridge), and the scope (non-excluded entries). It distinguishes from sibling tools like bridge_xref by focusing specifically on HMDB backfill.

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

Usage Guidelines5/5

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

The description provides explicit guidance on when to use the tool, including the motivation (run-2 finding about under-counted HMDB) and what it does not affect (KEGG assignments, final_class/origin of KEGG-mapped entries). It also states that xenobiotic-excluded entries are skipped, clarifying boundaries.

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