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musharna

plant-genomics-mcp

batch_phytozome_lookup_locus

Perform parallel batch lookups of up to 50 Phytozome locus identifiers, retrieving gene metadata including organism, chromosome, coordinates, and description per locus.

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 provided, so description carries full burden. It discloses parallel execution, a limit of 50 loci, and the result structure including error handling (successes in results[locus], failures in errors[locus]). This is transparent but lacks details on rate limits or authentication.

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 concise sentences: first defines the tool's core functionality, second details the output format. No unnecessary words.

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 that an output schema exists, the description adequately covers the tool's behavior: parallelism, limit, and result structure. It is complete for a batch variant tool with minimal complexity.

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%. The description adds value for the 'loci' parameter by explaining how results and errors are stored, which goes beyond the schema description. The 'organism' parameter is not further elaborated.

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 for up to 50 loci, and it specifies the output structure. This distinguishes it from the single-locus sibling.

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 but does not explicitly state when to use this vs the single-locus tool or provide exclusions/alternatives. Guidance is minimal.

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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