Skip to main content
Glama
musharna

plant-genomics-mcp

batch_kegg_pathways

Perform batch KEGG pathway lookups for up to 50 plant gene loci. Currently supports Arabidopsis thaliana only.

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?

No annotations provided, so description carries full burden. It explicitly discloses the organism limitation, explains the technical reason (cross-backend locus contract), and mentions the batch limit of 50. This goes beyond basic function to inform the agent of known constraints and error behavior.

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, highly concise, front-loaded with the core purpose. No superfluous information; every sentence serves a clear purpose.

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

Completeness5/5

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

Given the tool's moderate complexity (batch limit, organism restriction) and presence of an output schema, the description is complete. It covers the key behavioral aspects without needing elaboration on return values.

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% (only organism has description). The description adds value by reinforcing the maxItems for loci and explaining the organism limitation's root cause, which goes beyond what the schema provides.

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?

Description clearly states it's a batch version of kegg_pathways, up to 50 loci per call. Explicitly distinguishes from its sibling tool kegg_pathways by labeling it as batch version and specifying the limit.

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?

Clearly specifies when to use: for up to 50 loci, and only for arabidopsis_thaliana. Implicitly excludes other organisms by stating they raise an error. However, does not explicitly state alternatives (e.g., use kegg_pathways individually for non-ath organisms), leaving some room for ambiguity.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/musharna/plant-genomics-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server