metabo-idmapper

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mapping_provenance

Recovers mapping provenance for metabolites: identifies what was mapped to KEGG/HMDB beyond the initial pass, documents unmapped entries with reasons, and separates exogenous kept vs xenobiotic excluded by origin.

Instructions

Recovery provenance for the report: what was mapped to KEGG / HMDB BEYOND the MetaboAnalyst 1st pass and by which logic, plus the unmapped (harmonized-name-tried, reason) and the two origin buckets. Writes kegg_recovered.tsv, hmdb_recovered.tsv, unmapped_harmonization.tsv, exogenous_kept.tsv (biological outside-host, KEPT + origin), and xenobiotic_excluded.tsv (non-biological contaminant, EXCLUDED + origin).

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": "mapping_provenance"
  }
}

Input Schema

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

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.0.1Jul 28, 2026

TDQS

B3.3/5.0

Behavior3/5

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

No annotations are present, so the description bears full responsibility for behavioral disclosure. It clearly states that the tool writes multiple TSV files, indicating a write operation. However, it does not mention permissions, reversibility, or side effects beyond file creation, which is acceptable given the file-writing nature.

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

Conciseness3/5

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

The description is a single, dense sentence that packs several key points (provenance, logic, unmapped, origin buckets) but becomes somewhat run-on. It could be more concise by splitting into bullet points or separate sentences for readability without losing content.

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

Completeness4/5

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

Given the complexity of the tool (multiple output files, detailed logic), the description provides a thorough overview of what is produced and the concept of provenance. However, it omits parameter explanations, which reduces completeness slightly. With no output schema, listing output files is valuable.

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?

The input schema has 0% description coverage, meaning the description does not explain the parameters 'export' and 'workdir'. The description focuses entirely on outputs and logic, leaving parameter semantics undefined. This forces agents to rely solely on the schema, which lacks 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 the tool's purpose: recovering provenance for KEGG/HMDB mappings beyond the initial pass, detailing logic, unmapped entries, and origin buckets. It lists specific output files, making the purpose concrete and distinct from sibling tools, which likely handle other aspects of metabolomics analysis.

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?

The description lacks explicit guidance on when to use this tool versus alternatives. It does not mention prerequisites, conditions, or when not to use it. The context is implied by the description but no direct usage recommendations are provided.

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