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musharna

plant-genomics-mcp

batch_resolve_locus_to_uniprot

Resolve up to 50 plant locus identifiers to detailed UniProtKB records in parallel. Maps each locus to primary accession, gene names, organism, sequence length, and more.

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 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 are provided, so the description carries full burden. It discloses parallel processing, per-locus results, and error handling (successes in results, failures in errors). Additional details like rate limits or side effects are absent but not critical for this tool.

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, no extraneous words, front-loaded with key purpose and behavior. Efficiently conveys all necessary information.

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 output schema presence, the description adequately explains result fields, parallelism, error handling, and limits. Complete for a batch tool with clear annotations coverage.

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 both parameters. The description adds context about the result structure and error handling but largely duplicates schema information. Baseline 3 is appropriate.

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?

Description clearly states it is a batch variant of resolve_locus_to_uniprot, specifies the action (parallel searches up to 50 loci), and describes the result structure. It distinguishes itself from the single-locus sibling tool.

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 clearly implies usage for batch resolution of multiple loci, mentions parallel execution and the 50-locus limit. However, it does not explicitly state when to avoid using it or provide alternatives beyond the single-locus variant.

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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