Genenetwork Tools

Configuration File: genenetwork_tools.json Tool Type: Local Tools Count: 4

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

Available Tools

GeneNetwork_get_sample_data (Type: BaseRESTTool)

Get expression or phenotype values for a specific gene/trait across all samples in a GeneNetwork …

GeneNetwork_get_sample_data tool specification

Tool Information:

  • Name: GeneNetwork_get_sample_data

  • Type: BaseRESTTool

  • Description: Get expression or phenotype values for a specific gene/trait across all samples in a GeneNetwork dataset. Returns measurement values with standard errors for each inbred strain or individual in the genetic cross. Use this to find how a gene’s expression varies across strains, identify strain differences, or get data for QTL analysis. Dataset abbreviation and trait/probe ID must match the dataset.

Parameters:

  • dataset_name (string) (required) Dataset long abbreviation (e.g., ‘HC_M2_0606_P’ for BXD hippocampus, ‘BXDPublish’ for phenotypes). Obtain from GeneNetwork_list_datasets Long_Abbreviation field.

  • trait_name (string) (required) Probe/trait identifier within the dataset (e.g., ‘1436869_at’ for a microarray probe, ‘10001’ for a BXD phenotype trait). Must exist in the specified dataset.

Example Usage:

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

GeneNetwork_list_datasets (Type: BaseRESTTool)

List all datasets available for a specific genetic cross population in GeneNetwork. Datasets repr…

GeneNetwork_list_datasets tool specification

Tool Information:

  • Name: GeneNetwork_list_datasets

  • Type: BaseRESTTool

  • Description: List all datasets available for a specific genetic cross population in GeneNetwork. Datasets represent different tissues, time points, or measurement technologies for the population (e.g., ‘BXD Brain mRNA’, ‘BXD Liver Metabolites’, ‘BXD Phenotype’). Returns dataset names, abbreviations, data types, and timestamps. Use GeneNetwork_list_groups to find group names (e.g., ‘bxd’ for BXD cross).

Parameters:

  • group (string) (required) Genetic cross group name in lowercase (e.g., ‘bxd’, ‘bxh’, ‘hxb’, ‘bnlx-srjr-f2’). Obtain from GeneNetwork_list_groups.

Example Usage:

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

GeneNetwork_list_groups (Type: BaseRESTTool)

List genetic cross populations (groups) available in GeneNetwork for a given species. These group…

GeneNetwork_list_groups tool specification

Tool Information:

  • Name: GeneNetwork_list_groups

  • Type: BaseRESTTool

  • Description: List genetic cross populations (groups) available in GeneNetwork for a given species. These groups represent specific genetic crosses (e.g., BXD = C57BL/6J x DBA/2J recombinant inbred strains, BXH = BXH RI strains, HXB = Hybrid strains) used for QTL mapping and systems genetics. Each group can have hundreds of datasets measuring gene expression, metabolites, and phenotypes across the population. Returns group names, genetic types (riset, intercross, etc.), and IDs.

Parameters:

  • species (string) (required) Species short name (e.g., ‘mouse’, ‘rat’, ‘human’, ‘arabidopsis’). Get from GeneNetwork_list_species.

Example Usage:

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

GeneNetwork_list_species (Type: BaseRESTTool)

List all species available in GeneNetwork, the open systems genetics database for behavioral, neu…

GeneNetwork_list_species tool specification

Tool Information:

  • Name: GeneNetwork_list_species

  • Type: BaseRESTTool

  • Description: List all species available in GeneNetwork, the open systems genetics database for behavioral, neural, and physiological phenotypes. GeneNetwork contains genetic cross data for 13+ model organisms including mouse (BXD, BXH, AXB, etc.), rat, Arabidopsis, human, zebrafish, and barley. Returns species names and taxonomy IDs for use with other GeneNetwork tools.

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "GeneNetwork_list_species",
    "arguments": {
    }
}
result = tu.run(query)