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musharna

plant-genomics-mcp

batch_locus_literature

Retrieve literature from Europe PMC for up to 50 plant loci in parallel, returning per-locus search results with hit counts and article details.

Instructions

Batch variant of locus_literature. Fans out per-locus Europe PMC searches in parallel (up to 50 loci). Each results[locus] is the full single-locus payload (query + hitCount + returned + hits[]).

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
sizeNoMax results per locus (1–25, default 10)

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 burden. Discloses parallel execution, loci limit, and result structure. Schema adds errors[locus] info. Missing rate limits or idempotency, but adequately transparent for batch context.

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 efficient sentences: first states purpose, second details output structure. No wasted words, good front-loading.

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?

Output schema exists, so return values are covered. Description explains batch behavior and parallel aspect. Lacks error handling depth beyond schema but sufficient for common use cases.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100% with descriptions for all parameters. Description adds context about output mapping (results[locus]), but parameter details are already in schema. Meets baseline with minor added value.

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?

Clearly states it's a batch variant of locus_literature, describes parallel fan-out per locus up to 50, and specifies the output structure (results[locus] with full payload). Distinguishes from sibling locus_literature.

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?

Explicitly connects to locus_literature and indicates batch usage for multiple loci. Mentions parallel processing and 50-loci limit, but lacks explicit when-not-to-use or alternative sibling 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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