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musharna

plant-genomics-mcp

bar_efp_expression

Retrieve natural-variation expression data across 36 Arabidopsis ecotypes for a given locus, including per-replicate values and geographic coordinates.

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

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

With no annotations, the description carries the burden of disclosure. It reveals the tool wraps a specific endpoint, returns per-replicate values and lat/lng, and that the mean is computed client-side. This provides good behavioral context, though it omits response size or rate limits.

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 relatively concise but packed with details (ecotype list, data fields, endpoint URL). It is front-loaded with the core purpose. While not extremely terse, every sentence adds value without being overly verbose.

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 no annotations and an output schema exists, the description adequately explains the return content (ecotypes, replicates, lat/lng, mean) and scope (Arabidopsis only). It does not need to detail the output schema since that is separate, but covers the essential behavioral context for an agent to invoke the tool.

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?

The schema covers the single parameter 'locus' with a description and example. The tool description adds value by confirming the organism (Arabidopsis) and that the locus is an AGI identifier, which is not fully explicit in the schema. Schema coverage is 100%, so the baseline is 3; the extra context raises it to 4.

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 the tool fetches BAR/eFP world-map natural-variation expression for an Arabidopsis locus. It specifies the data type (expression across ~36 ecotypes) and the source endpoint, distinguishing it from sibling tools like bar_gene_summary or bar_aiv_interactions.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description notes the tool is 'Arabidopsis only' and mentions BAR is keyless, which implies usage context but does not explicitly state when to use this tool over siblings or provide when-not-to-use guidance. It could better differentiate from tools like bar_gene_summary.

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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