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musharna

plant-genomics-mcp

by musharna

Batch: GO Annotations

batch_locus_go_annotations
Read-onlyIdempotent

Batch query Gene Ontology annotations for up to 50 plant loci using UniProt and QuickGO, returning results with per-locus error handling.

Instructions

Batch variant of locus_go_annotations. Two-stage fanout — each locus is resolved to UniProt and then queried in QuickGO. Per-locus NotFoundError from either stage lands in errors[] with the typed prefix preserved. Capped at 50 loci.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
lociYesList of locus identifiers (1–50). Successes land in results[locus]; PlantGenomicsError failures in errors[locus].
limitNoMax annotations per locus from QuickGO (1–100, default 50)
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, openWorldHint, idempotentHint, and destructiveHint. The description adds significant behavioral detail: the two-stage fanout, per-locus error handling (NotFoundError into errors[] with typed prefix), and the 50-locus cap. This goes well beyond the 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?

The description is four sentences, each adding distinct information: purpose, process, error behavior, and cap. No unnecessary words; front-loaded with the most important information (batch variant).

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 complexity of a batch tool with a two-stage process, the description covers the key aspects. It mentions error handling and the cap. However, it could benefit from a brief note on when to prefer this over other batch tools or the single-locus version, though the tool name and sibling set provide some context.

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 description adds context about error handling for the 'loci' parameter (how errors are structured). It also clarifies the default for 'organism' and the range for 'limit'. This adds value beyond the schema descriptions.

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 locus_go_annotations, specifies the two-stage fanout (locus to UniProt to QuickGO), and includes a cap of 50 loci. This distinguishes it 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 implies use for multiple loci by being a batch variant, and mentions the cap of 50 loci. However, it does not explicitly state when not to use it or compare with other batch tools (e.g., batch_locus_literature) to avoid confusion.

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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