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, the complete chromosome karyotype with sizes, genebuild date, golden path length, and available coordinate system versions. Chromosomes are recognized from both Ensembl’s coord_system and karyotype fields, including assemblies whose regions are labeled primary_assembly. Essential for interpreting genomic coordinates and understanding assembly composition.

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 page through species available in the Ensembl database with their genome assembly info…

Ensembl_get_species_info tool specification

Tool Information:

  • Name: Ensembl_get_species_info

  • Type: EnsemblInfoTool

  • Description: Search and page through species available in the Ensembl database with their genome assembly information. Returns true total and filtered-match counts plus explicit pagination metadata, so broad queries do not silently stop at the first 50 species. Supports filtering by species name, common name, or taxonomy ID.

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.

  • limit (integer) (optional) Maximum matched species to return on this page.

  • offset (integer) (optional) Zero-based offset into the filtered species list.

Example Usage:

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