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plant-genomics-mcp

by musharna
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Python
Remote

Batch: ATTED-II Coexpression

batch_atted_coexpression
Read-onlyIdempotent

Retrieve ATTED-II co-expression data for up to 50 gene loci across seven plant species, including Arabidopsis, soybean, rice, tomato, and maize.

Instructions

Batch version of atted_coexpression. Up to 50 loci per call. Covers: arabidopsis_thaliana, glycine_max, medicago_truncatula, oryza_sativa, solanum_lycopersicum, vitis_vinifera, zea_mays. Any other organism raises OrganismNotSupported before any request (both the single and batch forms).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
lociYes
top_nNo
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)

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.22.0
    • addedInput schema / properties / loci / minItems
      Added value: +1
  2. Changed1 schema field changedv1.19.4
    • changedOutput schema / properties / count / description
      Previous value: -"Number of loci in the input list"New value: +"Number 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."
  3. First observedv1.8.0

TDQS

A3.8/5.0
Behavior4/5

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

Annotations already declare read-only, open-world, idempotent, and non-destructive behavior, so the bar is lower. The description adds concrete behavioral details: the 50-locus cap and early OrganismNotSupported error for unsupported organisms, which go beyond what annotations provide.

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 short sentences with no filler. Key constraints are front-loaded, and each sentence adds useful information: batch nature, capacity, supported organisms, and error behavior.

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 and simple wrapper semantics, the description covers batch capacity, supported organisms, and failure mode. It could more explicitly state when to choose this over the single atted_coexpression, but the batch naming and sibling context make that reasonably clear.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is only 33%, so the description must compensate. It adds the supported organism list and the 50-locus cap, but the cap is already in schema maxItems and it says nothing about top_n, leaving a core parameter's meaning undocumented.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States it is the batch version of atted_coexpression, with a concrete batch limit of 50 loci and a list of supported organisms. This distinguishes it from the single-locus sibling, though it never explicitly states the action (e.g., 'retrieves coexpression data').

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?

Gives explicit batch capacity (up to 50 loci), enumerates supported organisms, and states that unsupported organisms raise OrganismNotSupported before any request. It implies use for batch queries but does not explicitly contrast with the single atted_coexpression tool or other batch siblings.

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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