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musharna

plant-genomics-mcp

by musharna

Batch: KEGG Pathways

batch_kegg_pathways
Read-onlyIdempotent

Batch retrieve KEGG pathway annotations for up to 50 gene loci. Currently supports Arabidopsis thaliana.

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 distinct loci queried, returned (== len(results) + len(errors)). The input list is de-duplicated first, so this is LOWER than the number of loci you sent if you sent a duplicate — that is de-duplication, not a dropped locus.
errorsYeslocus → '[ClassName] message' for PlantGenomicsError failures
resultsYeslocus → per-locus result dict (same shape as the single-locus tool)
Behavior4/5

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

Annotations already indicate readOnly, idempotent, and non-destructive behavior. The description adds important behavioral constraints: batch size limit and organism support limitation, including that other organisms raise OrganismNotSupported.

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, concise and front-loaded with the purpose. Every sentence adds value: batch nature, limit, and version-specific constraint.

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?

The description covers essential aspects: batch behavior, limits, and organism constraint. With output schema present, return values are handled. It could mention when to prefer batch over single, but the version note adds useful context.

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 description coverage is 50% (organism parameter described in schema, loci not). The tool description adds meaning for both: 'Up to 50 loci per call' for loci and clarifies organism limitation beyond schema text. It provides valuable context that complements the schema.

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 it is a batch version of kegg_pathways with a limit of 50 loci, and it specifies the organism constraint. It distinguishes itself from the single-version sibling by being a batch tool.

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

Usage Guidelines4/5

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

The description provides clear usage context: up to 50 loci per call and organism limitation (only arabidopsis_thaliana supported). It implies when to use batch vs. single but does not explicitly contrast them.

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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