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musharna

plant-genomics-mcp

batch_phytozome_lookup_locus

Batch lookup up to 50 plant locus identifiers in parallel via Phytozome BioMart, returning per-locus gene metadata including organism, chromosome, coordinates, and description.

Instructions

Batch variant of phytozome_lookup_locus. Fans out per-locus BioMart queries in parallel (up to 50 loci). Each results[locus] is the full single-locus row (organism_name, gene_name, chromosome, start/end/strand, description).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
lociYesList of locus identifiers (1–50). Successes land in results[locus]; PlantGenomicsError failures in errors[locus].
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_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 are provided, so the description carries the full burden. It discloses parallelism, a limit of 50 loci, and the structure of successes and failures. However, it does not mention potential side effects, rate limits, or authentication needs.

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 with no wasted words. The first sentence conveys the core purpose, and the second adds key details about parallelism and result structure.

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 is complete for a batch tool given the output schema exists and sibling tools are listed. It covers parallelism, limits, and result fields, though error format details could be slightly expanded.

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 coverage is 100% with adequate parameter descriptions. The description adds value by explaining the output structure (results[locus] and errors[locus]), which helps understand parameter usage. It compensates for the format of responses beyond 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 variant of phytozome_lookup_locus that fans out per-locus BioMart queries in parallel, and describes the result structure. This distinguishes it from the single-locus sibling tool and provides specific verb and resource.

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 implies use for multiple loci (batch) and names the single-locus variant as sibling. However, it does not explicitly state when not to use or provide alternative tools for other scenarios.

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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