Genenetwork Ext Tools

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

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

Available Tools

GeneNetwork_get_dataset_info (Type: BaseRESTTool)

Get metadata about a specific GeneNetwork dataset including its full name, data type, data scale,…

GeneNetwork_get_dataset_info tool specification

Tool Information:

  • Name: GeneNetwork_get_dataset_info

  • Type: BaseRESTTool

  • Description: Get metadata about a specific GeneNetwork dataset including its full name, data type, data scale, tissue, and public access status. Returns information about expression profiling datasets from genetic crosses (BXD, LXS, etc.) covering various tissues and platforms. Use GeneNetwork_list_datasets to find available dataset names first.

Parameters:

  • dataset_name (string) (required) Dataset name/abbreviation. Examples: ‘HC_M2_0606_P’ (Hippocampus Consortium M430v2), ‘BR_M2_1106_R’ (Brain mRNA).

Example Usage:

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

GeneNetwork_get_trait_info (Type: BaseRESTTool)

Get detailed information about a specific trait (probe/gene) in a GeneNetwork dataset. Returns tr…

GeneNetwork_get_trait_info tool specification

Tool Information:

  • Name: GeneNetwork_get_trait_info

  • Type: BaseRESTTool

  • Description: Get detailed information about a specific trait (probe/gene) in a GeneNetwork dataset. Returns trait metadata including gene symbol, description, chromosome, megabase position, mean expression value, linkage statistics (LRS score, locus), additive effect, and p-value. Requires a dataset name and trait name (probe ID). Use GeneNetwork_list_datasets to find available datasets and their names. Common datasets include BXD hippocampus, liver, and brain expression arrays.

Parameters:

  • dataset_name (string) (required) Dataset name/abbreviation. Examples: ‘HC_M2_0606_P’ (Hippocampus Consortium M430v2), ‘BR_M2_1106_R’ (Brain mRNA).

  • trait_name (string) (required) Trait/probe identifier. Examples: ‘1436869_at’ (Shh probe), ‘1457211_at’, ‘1418701_at’. These are microarray probe IDs for expression datasets.

Example Usage:

query = {
    "name": "GeneNetwork_get_trait_info",
    "arguments": {
        "dataset_name": "example_value",
        "trait_name": "example_value"
    }
}
result = tu.run(query)