Bar Tools#

Configuration File: bar_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the bar_tools.json configuration file.

Available Tools#

BAR_get_gene_info (Type: BARTool)#

Get plant gene annotation from the BAR (Bio-Analytic Resource for Plant Biology, a Global Core Bi…

BAR_get_gene_info tool specification

Tool Information:

  • Name: BAR_get_gene_info

  • Type: BARTool

  • Description: Get plant gene annotation from the BAR (Bio-Analytic Resource for Plant Biology, a Global Core Biodata Resource): genomic position, strand, aliases, and functional annotation. Example: gene_id=’AT1G01010’ (species=’arabidopsis’, the default) returns NAC domain protein 1’s Chr1 coordinates and aliases ANAC001/NAC001/NTL10. Distinct from ToolUniverse’s plant_reactome tools, which cover pathways, not per-gene annotation.

Parameters:

  • gene_id (string) (required) Gene locus identifier, e.g. ‘AT1G01010’ (Arabidopsis).

  • species ([‘string’, ‘null’]) (optional) Species, e.g. ‘arabidopsis’ (default).

Example Usage:

query = {
    "name": "BAR_get_gene_info",
    "arguments": {
        "gene_id": "example_value"
    }
}
result = tu.run(query)

BAR_get_rnaseq_expression (Type: BARTool)#

Get RNA-seq gene expression data from the BAR (Bio-Analytic Resource for Plant Biology). database…

BAR_get_rnaseq_expression tool specification

Tool Information:

  • Name: BAR_get_rnaseq_expression

  • Type: BARTool

  • Description: Get RNA-seq gene expression data from the BAR (Bio-Analytic Resource for Plant Biology). database=’single_cell’ (the default) returns per-cluster mean expression across replicates from single-cell atlases – a data type no other ToolUniverse plant tool exposes. Example: gene_id=’At1g01010’ returns its mean expression value in each of dozens of single-cell clusters.

Parameters:

  • gene_id (string) (required) Gene locus identifier, e.g. ‘At1g01010’ (Arabidopsis).

  • species ([‘string’, ‘null’]) (optional) Species, e.g. ‘arabidopsis’ (default).

  • database ([‘string’, ‘null’]) (optional) RNA-seq dataset, e.g. ‘single_cell’ (default).

Example Usage:

query = {
    "name": "BAR_get_rnaseq_expression",
    "arguments": {
        "gene_id": "example_value"
    }
}
result = tu.run(query)