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metabolic.salvage_redundancy_check

Verifies that a genome-scale metabolic model detects known gene dependencies, acting as a positive control for model reliability.

Instructions

Fail-closed positive-control gate: is the GEM structurally capable of detecting a known dependency?

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
session_idYes
target_objectiveYes
positive_control_genesYes
Behavior2/5

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

With no annotations provided, the description carries the full burden. It only says the tool is a 'fail-closed positive-control gate' and checks structural capability. It does not explain what 'fail-closed' entails (e.g., returns false on failure?), what happens if the GEM is not capable, or any side effects. The behavioral disclosure is minimal.

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 with no redundancies, effectively front-loaded. However, being too concise sacrifices necessary detail. The sentence earns its place but leaves critical gaps.

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 three undocumented parameters, no output schema, and no annotations, the description is grossly incomplete. It does not specify return values, error conditions, or how to interpret results. A tool of this complexity demands far more context.

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 input schema has three required parameters with 0% description coverage. The description explains none of them: 'session_id', 'target_objective', and 'positive_control_genes' remain completely undefined. The agent cannot infer their meaning or format from the description.

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 'Fail-closed positive-control gate: is the GEM structurally capable of detecting a known dependency?' clearly states the tool's function (checking GEM capability) and uses domain-specific terminology that distinguishes it from siblings like 'metabolic.simulate' or 'metabolic.couple_and_test'. However, the jargon 'fail-closed positive-control gate' may be opaque to some AI agents, slightly reducing clarity.

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 provides no guidance on when to use this tool versus alternatives, nor does it mention prerequisites or exclusions. For example, there is no indication that this tool is a safety check before other analyses, or that it should not be used for validation beyond positive controls.

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

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