Bgee Tools

Configuration File: bgee_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

Bgee_get_gene_expression (Type: BgeeTool)

Get expression data for a gene across tissues and organs from the Bgee database. Returns where a …

Bgee_get_gene_expression tool specification

Tool Information:

  • Name: Bgee_get_gene_expression

  • Type: BgeeTool

  • Description: Get expression data for a gene across tissues and organs from the Bgee database. Returns where a gene is expressed with expression scores, confidence levels, and quality ratings. Supports RNA-Seq, Affymetrix, EST, and in situ hybridization data types. Requires both an Ensembl gene ID and NCBI taxonomy ID. Example: ENSG00000141510 (TP53) with species 9606 (human) returns expression across 145+ tissues including ventricular zone (score 95.11), ganglionic eminence, and monocytes.

Parameters:

  • gene_id (string) (required) Ensembl gene ID. Examples: ‘ENSG00000141510’ (human TP53), ‘ENSMUSG00000059552’ (mouse Trp53), ‘ENSDARG00000115148’ (zebrafish tp53).

  • species_id (string) (required) NCBI taxonomy ID for the species. Examples: ‘9606’ (human), ‘10090’ (mouse), ‘7955’ (zebrafish), ‘7227’ (fruit fly).

Example Usage:

query = {
    "name": "Bgee_get_gene_expression",
    "arguments": {
        "gene_id": "example_value",
        "species_id": "example_value"
    }
}
result = tu.run(query)

Bgee_list_species (Type: BgeeTool)

List all species available in the Bgee gene expression database. Returns species with taxonomy ID…

Bgee_list_species tool specification

Tool Information:

  • Name: Bgee_list_species

  • Type: BgeeTool

  • Description: List all species available in the Bgee gene expression database. Returns species with taxonomy IDs, genome versions, and common names. Bgee currently covers 29+ animal species including major model organisms (human, mouse, zebrafish, fruit fly, C. elegans, rat) and additional vertebrates and invertebrates. Useful for discovering which species are available before querying gene expression data.

Parameters:

No parameters required.

Example Usage:

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

Bgee_search_genes (Type: BgeeTool)

Search for genes in the Bgee comparative gene expression database across 29+ animal species. Bgee…

Bgee_search_genes tool specification

Tool Information:

  • Name: Bgee_search_genes

  • Type: BgeeTool

  • Description: Search for genes in the Bgee comparative gene expression database across 29+ animal species. Bgee integrates RNA-Seq, Affymetrix, EST, and in situ hybridization data to provide curated expression calls. Search by gene symbol, name, or description. Returns matching genes with species information, biotype, and expression summaries. Example: searching ‘TP53’ returns tumor protein p53 across human, mouse, zebrafish, and other model organisms.

Parameters:

  • query (string) (required) Gene name, symbol, or description to search for. Examples: ‘TP53’, ‘insulin’, ‘BRCA1’, ‘sonic hedgehog’.

Example Usage:

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