Ensembl Info Tools

Configuration File: ensembl_info_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

Ensembl_get_assembly_info (Type: EnsemblInfoTool)

Get genome assembly metadata for a species from the Ensembl REST API. Returns assembly name, acce…

Ensembl_get_assembly_info tool specification

Tool Information:

  • Name: Ensembl_get_assembly_info

  • Type: EnsemblInfoTool

  • Description: Get genome assembly metadata for a species from the Ensembl REST API. Returns assembly name, accession, version history, chromosome karyotype with sizes, genebuild date, golden path length, and available coordinate system versions. Essential for interpreting genomic coordinates and understanding assembly composition. Example: ‘homo_sapiens’ returns GRCh38.p14, assembly date 2013-12, genebuild May 2025, 194 top-level regions, karyotype chromosomes 1-22 plus X and Y.

Parameters:

  • species (string) (required) Ensembl species name (lowercase with underscores). Examples: ‘homo_sapiens’ (human), ‘mus_musculus’ (mouse), ‘danio_rerio’ (zebrafish), ‘drosophila_melanogaster’ (fruit fly), ‘saccharomyces_cerevisiae’ (yeast).

Example Usage:

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

Ensembl_get_species_info (Type: EnsemblInfoTool)

Search and list species available in the Ensembl database with their genome assembly information….

Ensembl_get_species_info tool specification

Tool Information:

  • Name: Ensembl_get_species_info

  • Type: EnsemblInfoTool

  • Description: Search and list species available in the Ensembl database with their genome assembly information. Returns species name, common name, taxonomy ID, current assembly version, and Ensembl division. Supports filtering by species name, common name, or taxonomy ID. Useful for discovering which genomes are available and their assembly versions before querying other Ensembl endpoints. Example: searching ‘mouse’ returns Mus musculus (taxon 10090, assembly GRCm39) plus related species.

Parameters:

  • search (string) (optional) Search term to filter species. Can be a species name (‘mus_musculus’), common name (‘mouse’), display name (‘Mouse’), or taxonomy ID (‘10090’). Leave empty to list all 348+ species.

Example Usage:

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