Xenbase Tools#

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

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

Available Tools#

Xenbase_get_gene (Type: XenbaseTool)#

Get detailed Xenopus gene information from Xenbase via the Alliance of Genome Resources. Returns …

Xenbase_get_gene tool specification

Tool Information:

  • Name: Xenbase_get_gene

  • Type: XenbaseTool

  • Description: Get detailed Xenopus gene information from Xenbase via the Alliance of Genome Resources. Returns gene symbol, name, synopsis, genomic location, synonyms, cross-references, and species details. Supports both Xenopus tropicalis and Xenopus laevis genes. Gene IDs use Xenbase format (e.g., ‘XB-GENE-484286’ or ‘Xenbase:XB-GENE-484286’).

Parameters:

  • gene_id (string) (required) Xenbase gene ID. Can be with or without ‘Xenbase:’ prefix. Examples: ‘XB-GENE-484286’ (tp53, X. tropicalis), ‘XB-GENE-6252168’ (tp53.L, X. laevis), ‘XB-GENE-487192’ (pax6, X. tropicalis).

Example Usage:

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

Xenbase_search_genes (Type: XenbaseTool)#

Search for Xenopus (frog) genes in Xenbase via the Alliance of Genome Resources API. Returns gene…

Xenbase_search_genes tool specification

Tool Information:

  • Name: Xenbase_search_genes

  • Type: XenbaseTool

  • Description: Search for Xenopus (frog) genes in Xenbase via the Alliance of Genome Resources API. Returns gene IDs, symbols, names, species, every upstream synonym, and synonyms_count for both Xenopus tropicalis and Xenopus laevis; aliases are not limited to the former five-item prefix. Optionally filter by species (tropicalis or laevis). Useful for finding and disambiguating amphibian homologs of human disease genes.

Parameters:

  • query (string) (required) Gene symbol or name to search. Examples: ‘tp53’, ‘pax6’, ‘sox2’, ‘bmp4’, ‘wnt3a’, ‘fgf8’.

  • species (string) (optional) Optional species filter: ‘tropicalis’ for X. tropicalis, ‘laevis’ for X. laevis. Leave empty for both species.

  • limit (integer) (optional) Maximum number of results to return. Default: 10.

Example Usage:

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