Ensembl Xrefs Tools#

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

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

Available Tools#

Ensembl_get_cross_references (Type: EnsemblXrefsTool)#

Get external database cross-references for an Ensembl stable identifier with exact local offset p…

Ensembl_get_cross_references tool specification

Tool Information:

  • Name: Ensembl_get_cross_references

  • Type: EnsemblXrefsTool

  • Description: Get external database cross-references for an Ensembl stable identifier with exact local offset pagination over the complete Ensembl response. Supports an official external_db filter. Metadata exposes total_xrefs and next_offset; database_summary covers the full result while page_database_summary covers only returned xrefs.

Parameters:

  • ensembl_id (string) (required) Ensembl stable identifier. Can be gene (ENSG*), transcript (ENST*), or translation (ENSP*). Examples: ‘ENSG00000141510’ (TP53 gene), ‘ENST00000269305’ (TP53 canonical transcript).

  • external_db ([‘string’, ‘null’]) (optional) Optional: filter by external database name. Examples: ‘HGNC’, ‘EntrezGene’, ‘Uniprot_gn’, ‘MIM_GENE’, ‘Reactome_gene’, ‘GeneCards’. If not specified, returns all cross-references.

  • limit (integer) (optional) Maximum xrefs returned from the complete response (default 500).

  • offset (integer) (optional) Zero-based xref offset. Continue with metadata.next_offset.

Example Usage:

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

Ensembl_lookup_gene_by_symbol (Type: EnsemblXrefsTool)#

Look up Ensembl IDs for a gene symbol and species. The complete Ensembl response is exposed throu…

Ensembl_lookup_gene_by_symbol tool specification

Tool Information:

  • Name: Ensembl_lookup_gene_by_symbol

  • Type: EnsemblXrefsTool

  • Description: Look up Ensembl IDs for a gene symbol and species. The complete Ensembl response is exposed through local offset pagination with total_results and next_offset, instead of silently dropping matches after 50. An optional external_db filter is passed to Ensembl.

Parameters:

  • symbol (string) (required) Gene symbol to look up. Examples: ‘TP53’, ‘BRCA1’, ‘EGFR’, ‘BRAF’, ‘KRAS’.

  • species (string) (optional) Species name. Default: ‘human’. Examples: ‘human’, ‘mouse’, ‘rat’, ‘zebrafish’.

  • external_db ([‘string’, ‘null’]) (optional) Optional: filter by external database. Examples: ‘HGNC’, ‘EntrezGene’.

  • limit (integer) (optional) Maximum Ensembl IDs returned (default 50).

  • offset (integer) (optional) Zero-based result offset. Continue with metadata.next_offset.

Example Usage:

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