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musharna

plant-genomics-mcp

batch_bar_aiv_interactions

Retrieve regulatory and protein-protein interactions for up to 50 plant loci in parallel using BAR AIV, returning papers for Arabidopsis or partners for rice.

Instructions

Batch variant of bar_aiv_interactions. Fans out per-locus BAR AIV calls in parallel (up to 50 loci); all loci in a single call share the same organism. Each results[locus] is the full single-locus payload (kind=grn_papers for Arabidopsis with papers list, kind=ppi_predictions for rice with partners list).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
lociYesList of locus identifiers (1–50). Successes land in results[locus]; PlantGenomicsError failures in errors[locus].
organismNoarabidopsis_thaliana or oryza_sativa — slug, scientific/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?

With no annotations, the description carries full burden. It discloses parallel execution, locus limit, error handling (errors[locus]), and organism-dependent result structure (kind=grn_papers vs ppi_predictions). Lacks details on idempotency or rate limits, but covers key behaviors.

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 concise sentences with no waste. First sentence immediately clarifies batch nature, second details result shape. Front-loaded with key information.

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 (batch, parallel, organism-dependent outputs), the description covers purpose, limits, result structure, and error handling. Output schema exists, but the description adds extra context. Could be improved by mentioning concurrency behavior or retry, but still complete.

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%, but the description adds meaning: explains that all loci share the same organism and describes the result payload structure per locus (depending on organism). This goes beyond the schema.

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 explicitly identifies it as a batch variant of bar_aiv_interactions, stating it fans out per-locus calls in parallel (up to 50 loci) and shares organism. It clearly distinguishes 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?

It implies usage for multiple loci by calling itself a batch variant and mentions the 50-locus limit and shared organism. It doesn't explicitly state when not to use it, but the context is clear.

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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