Expression Atlas Tools#

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

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

Available Tools#

ExpressionAtlas_get_baseline (Type: ExpressionAtlasTool)#

List baseline gene expression experiments in EBI Expression Atlas for a given species. The gene…

ExpressionAtlas_get_baseline tool specification

Tool Information:

  • Name: ExpressionAtlas_get_baseline

  • Type: ExpressionAtlasTool

  • Description: List baseline gene expression experiments in EBI Expression Atlas for a given species. The gene argument is used to label the request and suggest a follow-up call, but does NOT filter the returned experiment list (the underlying API has no reliable way to filter experiments by gene). Do NOT use GxA_get_experiment_expression’s gene_id filter to check whether a specific experiment has data for a gene – that endpoint only returns a small default sample of the experiment’s genes (verified live: ~29 of 9,570 for E-MTAB-2836) and silently ignores gene-filter parameters, so a miss there is not evidence of absence. For a reliable per-gene baseline expression check, use GTEx_get_expression_summary (human tissues, verified working) or HPA_get_rna_expression_in_specific_tissues instead. Results use recoverable offset pagination: continue with next_offset while has_more is true. Complements GTEx and HPA. No API key needed.

Parameters:

  • gene (string) (required) Gene symbol (e.g., ‘TP53’, ‘WDR7’) or Ensembl ID (e.g., ‘ENSG00000141510’)

  • species (string) (optional) Species name (default: ‘homo sapiens’). Also supports ‘mus musculus’, ‘rattus norvegicus’, etc.

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of experiments to return (default 50, max 500). Compare with the total reported in the response to see how many exist.

  • offset ([‘integer’, ‘null’]) (optional) Zero-based index of the first experiment to return, for paging through results beyond the first page (e.g. offset=50 returns 51-100). Default: 0.

Example Usage:

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

ExpressionAtlas_get_experiment (Type: ExpressionAtlasTool)#

Get metadata for a specific Expression Atlas experiment by accession (e.g., E-MTAB-2836): accessi…

ExpressionAtlas_get_experiment tool specification

Tool Information:

  • Name: ExpressionAtlas_get_experiment

  • Type: ExpressionAtlasTool

  • Description: Get metadata for a specific Expression Atlas experiment by accession (e.g., E-MTAB-2836): accession, type, species, and description/URLs. The experiment’s design comes back in assay_groups: one entry per condition with its factor value, ontology term, replicate count and full sample properties (FACTOR = varied, SAMPLE = held fixed), plus factors, assay_group_count and an assay_count summed from the replicates. Caveat: GXA leaves experimentalFactors, technologyType, contrasts, numberOfAssays, pubmedIds and lastUpdate null on its own experiment object (confirmed live), so technology, contrasts, pubmed_ids and last_update are usually empty; for those, visit the experiment’s page on https://www.ebi.ac.uk/gxa directly. This tool returns metadata and design only; for the per-gene expression values use GxA_get_experiment_expression, which reports them with their unit. An accession Expression Atlas does not hold returns status=error with error_details.type=’NotFound’, not a successful empty result.

Parameters:

  • accession (string) (required) Expression Atlas experiment accession (e.g., ‘E-MTAB-2836’, ‘E-GEOD-26284’)

Example Usage:

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

ExpressionAtlas_search_differential (Type: ExpressionAtlasTool)#

Search differential-expression EXPERIMENTS from EBI Expression Atlas with recoverable offset pagi…

ExpressionAtlas_search_differential tool specification

Tool Information:

  • Name: ExpressionAtlas_search_differential

  • Type: ExpressionAtlasTool

  • Description: Search differential-expression EXPERIMENTS from EBI Expression Atlas with recoverable offset pagination; continue with next_offset while has_more is true. condition does real text filtering, but gene is only a text-search coincidence and does not return validated per-gene differential-expression values.

Parameters:

  • gene (string) (optional) Gene symbol or Ensembl ID (e.g., ‘TP53’, ‘ENSG00000141510’)

  • condition (string) (optional) Condition/disease to filter by (e.g., ‘cancer’, ‘inflammation’, ‘breast’)

  • species (string) (optional) Species name (default: ‘homo sapiens’)

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of experiments to return (default 50, max 500). Compare with the total reported in the response to see how many exist.

  • offset ([‘integer’, ‘null’]) (optional) Zero-based index of the first experiment to return, for paging through results beyond the first page (e.g. offset=50 returns 51-100). Default: 0.

Example Usage:

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

ExpressionAtlas_search_experiments (Type: ExpressionAtlasTool)#

Search all EBI Expression Atlas experiments (baseline + differential) with recoverable offset pag…

ExpressionAtlas_search_experiments tool specification

Tool Information:

  • Name: ExpressionAtlas_search_experiments

  • Type: ExpressionAtlasTool

  • Description: Search all EBI Expression Atlas experiments (baseline + differential) with recoverable offset pagination; continue with next_offset while has_more is true. condition does real text filtering, but gene is only a text-search coincidence, so use this to find datasets rather than as a validated per-gene result set.

Parameters:

  • gene (string) (optional) Gene symbol or Ensembl ID

  • condition (string) (optional) Biological condition or tissue (e.g., ‘brain’, ‘cancer’, ‘kidney’)

  • species (string) (optional) Species name (optional, e.g., ‘homo sapiens’)

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of experiments to return (default 50, max 500). Compare with the total reported in the response to see how many exist.

  • offset ([‘integer’, ‘null’]) (optional) Zero-based index of the first experiment to return, for paging through results beyond the first page (e.g. offset=50 returns 51-100). Default: 0.

Example Usage:

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