Skip to main content
Glama
musharna

plant-genomics-mcp

bar_efp_expression

Retrieve natural-variation expression data for an Arabidopsis locus across 36 ecotypes, including per-replicate values, control samples, 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?

No annotations are provided, so the description must carry the full burden. It discloses the data returned: expression across ~36 ecotypes, per-replicate values, control samples, collection lat/lng, and a client-side mean. It also mentions the underlying endpoint. This provides sufficient behavioral insight for a read-only fetch tool, though it omits error conditions 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.

Conciseness5/5

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

The description is three sentences: the first clearly states the core purpose, the second details the output, and the third adds context about the resource. Every sentence earns its place, and the main action is front-loaded. It is efficient and informative without unnecessary words.

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 tool's moderate complexity and the existence of an output schema (not shown but indicated by context), the description adequately covers the key aspects: what data is returned and the organism. However, it does not mention pagination, max results, or error handling, which could be beneficial for completeness.

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 coverage is 100% (the only parameter 'locus' has a description in the schema). The description adds that the locus is an 'Arabidopsis AGI locus' (e.g., AT1G01010), which reinforces the organism constraint. However, this adds minimal value beyond the schema, so a baseline score of 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?

The description clearly states the tool's action with a specific verb-resource pair: 'Fetch BAR/eFP world-map natural-variation expression for an Arabidopsis locus.' It identifies the resource (BAR/eFP), data type (world-map natural-variation expression), and organism (Arabidopsis). This distinguishes it from sibling tools like bar_aiv_interactions, bar_gene_summary, and others that serve different data types.

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 provides clear context for usage by stating 'Arabidopsis only,' which implies the tool is not for other species. It also notes the resource is 'keyless,' suggesting no authentication is needed. However, it does not explicitly mention when to use this tool versus alternatives (e.g., other BAR tools) or provide direct exclusions.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/musharna/plant-genomics-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server