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) – use GxA_get_experiment_expression with an experiment_accession from the results and gene_id=<gene> to check whether a specific experiment actually has data for that gene. 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.

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. Caveat: the underlying GXA API does not expose per-experiment design/technology/contrasts/PubMed/assay-count data through this endpoint (confirmed live: those fields are always empty) – for that level of detail, visit the experiment’s page on https://www.ebi.ac.uk/gxa directly.

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 for differential expression EXPERIMENTS from EBI Expression Atlas by condition text and/or…

ExpressionAtlas_search_differential tool specification

Tool Information:

  • Name: ExpressionAtlas_search_differential

  • Type: ExpressionAtlasTool

  • Description: Search for differential expression EXPERIMENTS from EBI Expression Atlas by condition text and/or a gene mentioned in the experiment description. Supports disease-context expression analysis. Caveat: condition does real text filtering, but gene is a text-search coincidence (experiment descriptions rarely name individual genes) and does not return actual per-gene differential-expression values – treat gene-tagged results as a starting point for manual review, not a validated gene-specific result set.

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’)

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) by condition text and/or a …

ExpressionAtlas_search_experiments tool specification

Tool Information:

  • Name: ExpressionAtlas_search_experiments

  • Type: ExpressionAtlasTool

  • Description: Search all EBI Expression Atlas experiments (baseline + differential) by condition text and/or a gene mentioned in the experiment description. Returns experiment accessions, types, descriptions, and assay counts. Caveat: condition does real text filtering, but gene is a text-search coincidence (experiment descriptions rarely name individual genes), so a gene-only query effectively returns the unfiltered catalog – use to find relevant expression datasets, not 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’)

Example Usage:

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