Ensembl Overlap Tools#

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

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

Available Tools#

Ensembl_get_gene_overlapping_features (Type: EnsemblOverlapTool)#

Get features overlapping an Ensembl gene ID with limit/offset pagination and explicit total/has_m…

Ensembl_get_gene_overlapping_features tool specification

Tool Information:

  • Name: Ensembl_get_gene_overlapping_features

  • Type: EnsemblOverlapTool

  • Description: Get features overlapping an Ensembl gene ID with limit/offset pagination and explicit total/has_more metadata. Returns neighboring genes, transcripts, exons, regulatory elements, constrained elements, variants, and repeats selected by feature_types. Complex loci can contain thousands of records; follow next_offset until has_more is false.

Parameters:

  • gene_id (string) (required) Ensembl gene ID. Examples: ‘ENSG00000141510’ (TP53), ‘ENSG00000012048’ (BRCA1), ‘ENSG00000157764’ (BRAF).

  • feature_types (string) (optional) Comma-separated feature types. Options include ‘gene’, ‘transcript’, ‘exon’, ‘cds’, ‘regulatory’, ‘constrained’, ‘variation’, and ‘repeat’. Default: ‘gene’.

  • limit (integer) (optional) Maximum number of overlapping features to return in this page.

  • offset (integer) (optional) Zero-based feature offset. Use data.next_offset or metadata.next_offset for the next page.

Example Usage:

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

Ensembl_get_region_features (Type: EnsemblOverlapTool)#

Get genomic features overlapping a specified chromosomal region, including genes, transcripts, re…

Ensembl_get_region_features tool specification

Tool Information:

  • Name: Ensembl_get_region_features

  • Type: EnsemblOverlapTool

  • Description: Get genomic features overlapping a specified chromosomal region, including genes, transcripts, regulatory elements, and constrained elements. Results are paged with limit/offset; total_features and next_offset make every upstream feature reachable.

Parameters:

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

  • region (string) (required) Genomic region in format ‘chr:start-end’. Examples: ‘17:7661779-7687546’ (TP53), ‘7:140424943-140524564’ (BRAF), ‘13:32315086-32400266’ (BRCA2). Max region size ~5Mb.

  • feature_types (string) (optional) Comma-separated feature types to retrieve. Options: ‘gene’, ‘transcript’, ‘regulatory’, ‘constrained’, ‘variation’, ‘repeat’, ‘motif’. Default: ‘gene’. Example: ‘gene,regulatory,constrained’.

  • limit (integer) (optional) Maximum overlapping features per page.

  • offset (integer) (optional) Zero-based feature offset. Continue with data.next_offset while has_more is true.

Example Usage:

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