plant-genomics-mcp

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BAR: Gene Summary

bar_gene_summary

Read-onlyIdempotent

Retrieve the BAR-curated ThaleMine summary and GAIA aliases for an Arabidopsis locus, including TAIR curator notes, Araport11 description, NCBI ID, and cross-database aliases.

Instructions

Fetch the BAR (Bio-Analytic Resource, U Toronto) merged ThaleMine + GAIA-aliases summary for an Arabidopsis locus. Returns the TAIR curator summary + Araport11 computational description from /thalemine/gene_information/ together with the NCBI Gene ID and cross-DB aliases (RefSeq, UniProt, TIGR locus-model IDs) from /gaia/aliases/. Arabidopsis only — ThaleMine carries taxon 3702 plus yeast/human for ortholog cross-reference. BAR is keyless and a Global Core Biodata Resource (2023); replaces the v0.9 subscription-gated tair_locus_info stub for the curator-summary use case.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`locus`	Yes	Arabidopsis AGI locus, e.g. AT1G01010

Output Schema

TableJSON Schema

Name	Required	Description
`agi`	No	AGI primary identifier echoed by ThaleMine, e.g. "AT1G01010"
`locus`	Yes
`symbol`	No	Gene symbol, e.g. "NAC001"
`aliases`	No	Cross-DB aliases from /gaia/aliases/ (RefSeq accessions, UniProt accessions, TIGR locus-model IDs, and TAIR aliases). Empty list if /gaia degraded.
`species`	Yes
`synonyms`	No	TAIR aliases (CSV from Gene.tairAliases, split on commas + stripped)
`full_name`	No	Gene name from ThaleMine
`source_url`	Yes	ThaleMine endpoint URL for traceability — a link for the client to open or fetch; no tool on this server dereferences it
`ncbi_gene_id`	No	NCBI Gene ID from /gaia/aliases/ — None if BAR has no NCBI cross-ref
`tair_locus_id`	No	TAIR locus ID from Gene.secondaryIdentifier, e.g. "locus:2200935"
`curator_summary`	No	Gene.tairCuratorSummary — the TAIR-curated functional summary prose
`brief_description`	No	Gene.briefDescription — short blurb (often same as full_name)
`tair_short_description`	No	Gene.tairShortDescription — TAIR-specific short description
`computational_description`	No	Gene.tairComputationalDescription — Araport11-sourced computed description

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv1.22.0Sep 24, 2026

changedOutput schema / properties / source_url / description

Previous value: -"ThaleMine endpoint URL for traceability"New value: +"ThaleMine endpoint URL for traceability — a link for the client to open or fetch; no tool on this server dereferences it"

First observedv1.8.0May 30, 2026

TDQS

A4.4/5.0

Behavior5/5

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

Beyond the annotations, the description adds valuable behavioral context: BAR is keyless, no subscription is needed, data comes from specific endpoints, and the underlying resource carries taxon 3702 plus yeast/human for ortholog cross-reference. This meaningfully supplements the readOnly/idempotent annotation hints.

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 front-loaded with the core action and return contents, and is dense but not bloated. The phrase 'Global Core Biodata Resource (2023)' is a credibility credential rather than operationally necessary detail, and 'keyless' plus the endpoint breakdown are the most valuable extras.

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?

For a one-parameter tool with an output schema, the description covers the input scope, data provenance, exact endpoints, returned fields, access model, and the intended replacement use case. Nothing essential is missing for an agent to call it correctly.

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?

The lone parameter 'locus' is already fully documented in the schema with the same Arabidopsis AGI locus format and example (AT1G01010). The description does not add new precision about accepted formats or edge cases, so the schema carries the weight here.

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 uses a specific verb and resource: 'Fetch the BAR ... merged ThaleMine + GAIA-aliases summary for an Arabidopsis locus.' It enumerates the returned content (TAIR curator summary, Araport11 description, NCBI Gene ID, cross-DB aliases) and explicitly distinguishes itself from the older tair_locus_info stub, making its role clear.

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 gives clear use context: it is for Arabidopsis locus curator summaries, excludes non-Arabidopsis use, and explicitly positions itself as replacing the subscription-gated tair_locus_info stub. It does not, however, contrast itself against other sibling locus/xref tools such as get_gene_xrefs or ensembl_plants_lookup_locus.

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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