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musharna

plant-genomics-mcp

batch_kegg_pathways

Batch retrieve KEGG pathway annotations for up to 50 Arabidopsis thaliana gene loci in a single call. Supports only arabidopsis_thaliana in v1.1.0.

Instructions

Batch version of kegg_pathways. Up to 50 loci per call. v1.1.0: only arabidopsis_thaliana resolves — KEGG uses NCBI Entrez Gene IDs for other plants and our cross-backend locus contract can't produce those yet, so a non-ath organism= raises OrganismNotSupported before any HTTP fan-out.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
lociYes
organismNoPlant organism — only arabidopsis_thaliana is supported in v1.1.0; other plants raise OrganismNotSupported until an Entrez bridge landsarabidopsis_thaliana

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
toolYesThe batch tool name, e.g. batch_resolve_locus_to_uniprot
countYesNumber of loci in the input list
resultsYeslocus → per-locus result dict (same shape as the single-locus tool)
errorsYeslocus → '[ClassName] message' for PlantGenomicsError failures
Behavior4/5

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

Given no annotations, the description discloses important behaviors: only arabidopsis_thaliana resolves, other organisms raise an OrganismNotSupported error before API calls, and the maximum batch size. It provides technical reasoning and cost-saving behavior. However, it does not explicitly state read-only idempotency.

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 efficiently convey the batch nature, limit, and organism constraint. Every word adds value, and the most critical info (batch limit) is front-loaded. No waste.

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?

With an output schema present (context signal), return value details are not needed. The description covers the key constraints and error case for organism. However, it lacks information on partial failures within a batch and any other side effects, leaving some gaps for a batch tool.

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

Parameters4/5

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

Schema has 50% coverage (organism described, loci not). The description adds the loci max size (already in schema but reinforces) and organism restriction with technical context, which goes beyond the schema. However, loci format or expected identifiers are not detailed.

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 clearly states it is a 'Batch version of kegg_pathways' and specifies the batch limit of 50 loci. This distinguishes it from the single-locus sibling 'kegg_pathways', but the purpose is slightly dependent on knowing what the base tool does, making it not fully standalone.

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 multiple loci and warns about organism restrictions, but does not explicitly state when to use this tool versus alternatives like kegg_pathways. No when-not or explicit alternative guidance is provided, leaving the agent to infer context.

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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