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musharna

plant-genomics-mcp

batch_ensembl_plants_lookup_locus

Batch lookup of plant locus identifiers via Ensembl Plants API. Query up to 50 loci in one request to reduce API calls and improve efficiency.

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?

With no annotations, the description fully discloses behavioral traits: retries on 429/5xx via shared helper, Retry-After capped at 60s, error handling for missing loci landing in errors[] with [NotFoundError] prefix, and output shape matching the single-locus 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?

Three sentences, each providing essential information: purpose, output shape, and error/retry behavior. No superfluous content.

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, retries, errors) and no annotations, the description covers key aspects well. It references output shape but lacks details on rate limits beyond retry behavior. Overall sufficiently 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 value beyond the schema by explaining the results/error structure for the 'loci' parameter. The 'organism' parameter details are mostly covered by 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 clearly states it is a batch variant of ensembl_plants_lookup_locus, using the POST /lookup/id endpoint for up to 50 loci. It distinguishes from the single-locus sibling by mentioning the batch nature and HTTP round-trip efficiency.

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 when to use this tool (for batch lookups) and notes it is cheaper than parallel GETs. However, it does not explicitly state when not to use it or mention the single-locus alternative as a distinct use case.

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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