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musharna

plant-genomics-mcp

batch_bar_gene_summary

Retrieves gene summaries and aliases for up to 50 Arabidopsis loci in parallel from BAR ThaleMine and GAIA databases.

Instructions

Batch variant of bar_gene_summary. Fans out per-locus BAR ThaleMine + GAIA-aliases calls in parallel (up to 50 loci). Each results[locus] is the full single-locus payload (curator summary, computational description, NCBI Gene ID, cross-DB aliases). Arabidopsis only.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
lociYesList of locus identifiers (1–50). Successes land in results[locus]; PlantGenomicsError failures in errors[locus].

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
Behavior3/5

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

With no annotations, the description carries the burden. It mentions parallel fan-out and the result structure, but does not detail error handling beyond the schema's mention of PlantGenomicsError, or provide information about rate limits, idempotency, or cancellation 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?

The description is extremely concise: three sentences that cover purpose, scale, operation style, and result structure. No redundant information; every sentence is necessary.

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?

Given the output schema exists (not shown but referenced), the description adequately explains the result payload. It covers the batch nature, per-locus results, and scope (Arabidopsis only). It could mention the input schema's error structure more, but it's sufficient.

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?

The single parameter 'loci' has full schema coverage with a good description. The tool description adds meaning by specifying per-locus operation, the 50 limit, and the payload fields, which goes beyond the schema's description.

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's a batch variant of bar_gene_summary, specifies the fanned-out per-locus operation, up to 50 loci, and lists the payload contents (curator summary, computational description, NCBI Gene ID, cross-DB aliases). This distinguishes it from the single-locus bar_gene_summary and other batch tools like batch_atted_coexpression.

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 explicitly notes it's a batch variant, useful for multiple loci, with a limit of 50 and restriction to Arabidopsis. However, it does not explicitly state when not to use it or mention alternatives like bar_gene_summary for single loci.

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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