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musharna

plant-genomics-mcp

by musharna

Batch: STRING Interactions

batch_string_interactions
Read-onlyIdempotent

Retrieve protein-protein interactions for up to 50 plant gene loci or accessions in a single call using STRING-DB.

Instructions

Batch version of string_interactions. Up to 50 inputs per call.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana
loci_or_accessionsYes

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)
Behavior3/5

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

Annotations already declare readOnlyHint, openWorldHint, idempotentHint, and destructiveHint. The description adds no additional behavioral context beyond 'Up to 50 inputs per call,' which is already in the schema. No contradictions.

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 filler, front-loaded with key information about batch nature and capacity.

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 output schema exists and annotations cover safety, the description provides the essential batch limit and links to the parent tool. Could mention how results are returned or any processing specifics, but sufficient for a simple batch wrapper.

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 description coverage is only 33% (organism has description). The description adds value by noting the 50-input limit, which relates to loci_or_accessions, but does not elaborate on limit or organism parameters. 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?

The description clearly states it's a batch version of string_interactions, specifying the resource and the batch limit (up to 50 inputs). This distinguishes it from its single-input sibling.

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 when multiple inputs need processing, and the sibling list includes string_interactions as the alternative. However, it does not explicitly state when not to use or provide detailed context.

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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