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musharna

plant-genomics-mcp

by musharna

BAR: eFP Expression

bar_efp_expression
Read-onlyIdempotent

Retrieve Arabidopsis natural-variation expression across 36 ecotypes, with per-replicate values, control samples, and geographic coordinates from BAR eFP world-map.

Instructions

Fetch BAR/eFP world-map natural-variation expression for an Arabidopsis locus. Wraps the world-eFP view at /microarray_gene_expression/world_efp/arabidopsis/{locus} — returns expression across ~36 ecotypes (Bay-0, Col-0, Cvi-1, Ler-2, ...) with per-replicate values, control samples, collection lat/lng, and a per-ecotype mean computed client-side. Arabidopsis only. BAR is keyless and a Global Core Biodata Resource (2023).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYesArabidopsis AGI locus, e.g. AT1G01010

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYes
speciesYes
ecotypesYes
probesetNoMicroarray probeset ID, uniform across ecotypes for one gene
source_urlYesBAR world-eFP endpoint URL for traceability
ecotype_countYesNumber of ecotype rows in `ecotypes`
Behavior4/5

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

Annotations already provide readOnlyHint, openWorldHint, idempotentHint, destructiveHint. The description adds behavioral details about the return structure (per-replicate values, control samples, lat/lng, mean) and the data source (wraps a specific endpoint). No contradictions with annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single paragraph with the main purpose front-loaded. It is concise but includes necessary context (resource details, data elements, scope). Every sentence adds value.

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?

Given the tool has only one parameter, good annotations, and an output schema (present but not shown), the description covers purpose, scope, data source, and return structure adequately. No gaps for an agent to select or invoke correctly.

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% with one parameter (locus) described as 'Arabidopsis AGI locus, e.g. AT1G01010'. The description adds context by specifying that it must be an Arabidopsis locus and provides an example, adding value 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?

Description clearly states it fetches world-map natural-variation expression data for an Arabidopsis locus from BAR/eFP, specifying the resource and what is returned (expression across ~36 ecotypes with per-replicate values, control samples, lat/lng, mean). This distinguishes it from sibling tools like bar_gene_summary or arabidopsis_natural_variation.

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 explicitly restricts usage to Arabidopsis and mentions BAR is keyless and a Global Core Biodata Resource, implying open access. However, it does not explicitly contrast with sibling tools or state when to prefer this over alternatives.

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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