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musharna

plant-genomics-mcp

batch_bar_gene_summary

Retrieve gene summaries and aliases for up to 50 Arabidopsis loci in parallel, integrating data from BAR ThaleMine and GAIA.

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
Behavior4/5

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

With no annotations provided, the description carries the full burden. It discloses parallel execution (up to 50 loci), success/error placement in results and errors respectively, and that errors are of type PlantGenomicsError. This is good behavioral transparency beyond just 'batch operation'.

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 sentences: first announces the batch variant, second explains parallel execution and limit, third lists payload fields and organism restriction. Every sentence adds critical information; no redundancy.

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 presence of an output schema, the description does not need to detail return values. It covers purpose, usage scope, parallelism, limit, error handling, payload content, and organism restriction. For a single-parameter batch tool, this is fully adequate.

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%, and the schema already provides a description for the 'loci' parameter. The description adds value by explaining the parallel behavior, the 1-50 range, and the success/error structure. This goes beyond the schema's basic 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 is a batch variant of bar_gene_summary, explains it fans out per-locus calls in parallel, lists the fields in the payload (curator summary, computational description, NCBI Gene ID, cross-DB aliases), and restricts to Arabidopsis only. This effectively distinguishes it from the single-locus sibling bar_gene_summary.

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?

By labeling itself as a 'batch variant' of bar_gene_summary, it implies use when summarizing multiple loci. It specifies a 1-50 limit. While it does not explicitly state when not to use or name alternatives, the sibling context (bar_gene_summary for single locus) provides clear guidance.

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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