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 all external database cross-references for an Ensembl stable identifier. Returns linked recor…

Ensembl_get_cross_references tool specification

Tool Information:

  • Name: Ensembl_get_cross_references

  • Type: EnsemblXrefsTool

  • Description: Get all external database cross-references for an Ensembl stable identifier. Returns linked records from HGNC, EntrezGene, UniProt, GeneCards, Reactome, MIM/OMIM, ArrayExpress, and other databases. Essential for mapping between Ensembl and other identifier systems, discovering related database entries, or building cross-database links for a gene. Can filter by specific external database. Example: ‘ENSG00000141510’ (TP53) returns 157 cross-references across 11 databases including HGNC:11998, EntrezGene:7157, GeneCards:TP53, MIM_GENE:191170, and Reactome pathways.

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.

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 gene IDs for a gene symbol across external databases. Given a gene symbol (e.g., …

Ensembl_lookup_gene_by_symbol tool specification

Tool Information:

  • Name: Ensembl_lookup_gene_by_symbol

  • Type: EnsemblXrefsTool

  • Description: Look up Ensembl gene IDs for a gene symbol across external databases. Given a gene symbol (e.g., ‘TP53’), returns all matching Ensembl gene and transcript IDs. Useful for converting gene symbols to Ensembl stable identifiers for use with other Ensembl APIs. Example: symbol ‘TP53’ in human returns ENSG00000141510 (gene) and related transcript/translation IDs; ‘BRCA1’ returns ENSG00000012048.

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’.

Example Usage:

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