Skip to main content
Glama
musharna

plant-genomics-mcp

by musharna
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

Batch: KEGG Pathways

batch_kegg_pathways
Read-onlyIdempotent

Retrieve KEGG pathway annotations for up to 50 plant loci per call, covering Arabidopsis, brachypodium, soybean, barley, rice, poplar, and maize.

Instructions

Batch version of kegg_pathways. Up to 50 loci per call. Covers: arabidopsis_thaliana, brachypodium_distachyon, glycine_max, hordeum_vulgare, oryza_sativa, populus_trichocarpa, zea_mays. Any other organism raises OrganismNotSupported before any request (both the single and batch forms).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
lociYes
organismNoPlant organism — accepts canonical slug, scientific or common name, or NCBI taxid; see the tool description for which KEGG coversarabidopsis_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)

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.22.0
    • addedInput schema / properties / loci / minItems
      Added value: +1
    • changedInput schema / properties / organism / description
      Previous value: -"Plant organism — only arabidopsis_thaliana is supported in v1.1.0; other plants raise OrganismNotSupported until an Entrez bridge lands"New value: +"Plant organism — accepts canonical slug, scientific or common name, or NCBI taxid; see the tool description for which KEGG covers"
  2. Changed1 schema field changedv1.19.4
    • changedOutput schema / properties / count / description
      Previous value: -"Number of loci in the input list"New value: +"Number 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."
  3. First observedv1.8.0

TDQS

A4/5.0
Behavior4/5

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

Annotations already indicate read-only, idempotent, and non-destructive behavior. The description adds valuable traits: the 50-loci cap and the pre-request validation that raises OrganismNotSupported for unsupported organisms. This goes beyond annotations without contradicting them.

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?

Three concise sentences, each carrying essential information: batch nature, limit, supported organisms, and error behavior. The content is front-loaded and there is no redundancy or filler.

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?

For a read-only batch tool with an output schema and safety annotations, the description covers the key operational details: batch limit, organism coverage, and error handling. It does not explain what the loci parameter should contain, but that may be inferred from the sibling kegg_pathways tool. Overall, the description is sufficient for an agent to call the tool correctly.

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

Parameters3/5

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

The schema covers the organism parameter with a description, but the loci parameter has no schema description, and the tool description does not clarify what loci should be (e.g., gene IDs, locus identifiers). The description does add the list of supported organisms and the error behavior, but it only partially compensates for the undocumented loci parameter.

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 identifies the tool as the 'Batch version of kegg_pathways', which clearly indicates its purpose as a batched pathway lookup. It specifies the batch limit (50 loci) and enumerates supported organisms, differentiating it from the single-locus sibling and other batch tools. However, it never explicitly states that it returns KEGG pathways for the given loci, relying on the sibling's implied functionality.

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?

It implies usage for multiple loci via the 'batch version' phrasing and sets clear limits. It also explicitly warns that unsupported organisms raise an error before any request, guiding the agent to validate organisms upfront. It does not name alternatives or explicitly state when not to use it, but the context is sufficient.

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

Deploy Server

Other Tools