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musharna

plant-genomics-mcp

batch_ensembl_plants_lookup_locus

Look up up to 50 plant locus identifiers in a single HTTP request using Ensembl Plants, reducing latency compared to individual lookups.

Instructions

Batch variant of ensembl_plants_lookup_locus. Uses Ensembl's native POST /lookup/id endpoint — one HTTP round-trip for up to 50 loci, materially cheaper than N parallel GETs. Successes in results[] with the same shape as the single-locus tool. Retries 429/5xx via the shared _http helper (Retry-After capped at 60 s). Misses (loci with no record) still land in errors[] with the [NotFoundError] prefix; the whole batch only fails when the retry budget is exhausted.

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
Behavior5/5

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

Discloses retry behavior for 429/5xx with capped Retry-After, error handling (NotFoundError in errors[]), and that batch only fails after retry exhaustion. No annotations provided, so description fully carries transparency burden.

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?

Three sentences covering identity, benefit, shape, and error handling. Every sentence adds value, no redundancy.

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?

With output schema present, description covers purpose, behavior, error handling, batch limits, and distinguishes from sibling. No gaps given the tool's complexity and context.

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 100%; description adds minor context (same shape as single-locus) but not significant beyond schema. 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?

Clearly identifies as a batch variant of ensembl_plants_lookup_locus, specifies it uses POST /lookup/id endpoint for up to 50 loci, and distinguishes from the single-locus sibling by highlighting cost savings.

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?

States batch is cheaper for multiple loci due to one round-trip, implying use when loci count > 1. Does not explicitly exclude single-locus use but strongly suggests it via sibling tool existence.

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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