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musharna

plant-genomics-mcp

by musharna

Batch: Resolve Locus → UniProt

batch_resolve_locus_to_uniprot
Read-onlyIdempotent

Batch resolve up to 50 plant locus identifiers to UniProtKB entries in parallel, retrieving protein metadata, gene names, organism, sequence length, and links.

Instructions

Batch variant of resolve_locus_to_uniprot. Fans out per-locus UniProtKB searches in parallel (up to 50 loci). Each results[locus] is the full single-locus record (primaryAccession + uniProtkbId + entryType + geneNames + organism + sequenceLength + web_url + …).

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 distinct loci queried, returned (== len(results) + len(errors)). The input list is de-duplicated first, so this is LOWER than the number of loci you sent if you sent a duplicate — that is de-duplication, not a dropped locus.
errorsYeslocus → '[ClassName] message' for PlantGenomicsError failures
resultsYeslocus → per-locus result dict (same shape as the single-locus tool)
Behavior5/5

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

Annotations already declare readOnlyHint, idempotentHint, and destructiveHint. The description adds valuable behavioral context: parallel fan-out, batch size limit of 50, and error handling per locus. This goes beyond annotations.

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 succinctly convey the tool's batch nature, parallelism, limits, and output structure. Every sentence is informative and well-placed.

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 and detailed annotations, the description fully covers the tool's purpose, behavior, limits, and result format. No critical gaps remain.

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% and each parameter has a schema description. The tool description adds no additional semantic information about parameters beyond what the schema already provides.

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 resolve_locus_to_uniprot, performing parallel searches for up to 50 loci. It explicitly distinguishes from the single-locus sibling by specifying batch behavior and result structure.

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 indicates it is a batch variant, implying use for multiple loci, but does not explicitly state when not to use or list alternatives among sibling batch tools. However, the context is clear given the sibling list.

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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