Arrayexpress Tools

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

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

Available Tools

arrayexpress_get_experiment (Type: ArrayExpressRESTTool)

Get detailed information about a specific ArrayExpress experiment by its accession ID (E-GEOD, E-…

arrayexpress_get_experiment tool specification

Tool Information:

  • Name: arrayexpress_get_experiment

  • Type: ArrayExpressRESTTool

  • Description: Get detailed information about a specific ArrayExpress experiment by its accession ID (E-GEOD, E-MTAB, etc.). Returns complete experiment metadata including title, description, protocols, experimental design, and publication information from the original ArrayExpress database.

Parameters:

  • experiment_id (string) (required) ArrayExpress experiment ID (e.g., ‘E-MTAB-1234’)

Example Usage:

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

arrayexpress_get_experiment_files (Type: ArrayExpressRESTTool)

Get list of files associated with an ArrayExpress experiment. Returns file metadata including fil…

arrayexpress_get_experiment_files tool specification

Tool Information:

  • Name: arrayexpress_get_experiment_files

  • Type: ArrayExpressRESTTool

  • Description: Get list of files associated with an ArrayExpress experiment. Returns file metadata including file names, types, sizes, and download paths for raw data files, processed data files, and MAGE-TAB annotation files.

Parameters:

  • experiment_id (string) (required) ArrayExpress experiment ID

Example Usage:

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

arrayexpress_get_experiment_samples (Type: ArrayExpressRESTTool)

Get sample information for an ArrayExpress experiment. Returns sample metadata including sample n…

arrayexpress_get_experiment_samples tool specification

Tool Information:

  • Name: arrayexpress_get_experiment_samples

  • Type: ArrayExpressRESTTool

  • Description: Get sample information for an ArrayExpress experiment. Returns sample metadata including sample names, characteristics (e.g., organism part, developmental stage), experimental factors, and technical details from the original ArrayExpress MAGE-TAB annotations.

Parameters:

  • experiment_id (string) (required) ArrayExpress experiment ID

Example Usage:

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

arrayexpress_search_experiments (Type: ArrayExpressRESTTool)

Search ArrayExpress experiments - the original functional genomics database from EMBL-EBI. Search…

arrayexpress_search_experiments tool specification

Tool Information:

  • Name: arrayexpress_search_experiments

  • Type: ArrayExpressRESTTool

  • Description: Search ArrayExpress experiments - the original functional genomics database from EMBL-EBI. Searches microarray and RNA-seq experiments by keywords, species, or array platform. Returns experiment metadata including accession IDs (E-GEOD, E-MTAB), titles, descriptions, and study information. Note: Some newer ArrayExpress data is now hosted in BioStudies - use BioStudies tools if an accession is not found here.

Parameters:

  • keywords (string) (optional) Search keywords (e.g., disease name, tissue type, experimental condition)

  • species (string) (optional) Species name (e.g., ‘Homo sapiens’, ‘Mus musculus’)

  • array (string) (optional) Array platform name

  • limit (integer) (optional) Maximum number of results (default: 10, max: 100)

  • offset (integer) (optional) Offset for pagination (default: 0)

Example Usage:

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