Ensembl Phenotype Tools#

Configuration File: ensembl_phenotype_tools.json Tool Type: Local Tools Count: 4

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

Available Tools#

EnsemblPheno_get_by_gene (Type: EnsemblPhenotypeTool)#

Get phenotype associations for a gene from Ensembl with limit/offset pagination and explicit tota…

EnsemblPheno_get_by_gene tool specification

Tool Information:

  • Name: EnsemblPheno_get_by_gene

  • Type: EnsemblPhenotypeTool

  • Description: Get phenotype associations for a gene from Ensembl with limit/offset pagination and explicit total/has_more metadata. Returns deduplicated diseases, traits, and clinical conditions from Cancer Gene Census, OMIM, ClinVar, NHGRI-EBI GWAS Catalog, Orphanet, and other sources. Example: TP53 currently has more than 400 associations and requires multiple pages.

Parameters:

  • species (string) (optional) Species name. Use ‘homo_sapiens’ for human. Default: ‘homo_sapiens’.

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

  • limit (integer) (optional) Maximum number of deduplicated phenotype associations to return in this page.

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

Example Usage:

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

EnsemblPheno_get_by_region (Type: EnsemblPhenotypeTool)#

Get phenotype associations for variants and genes in an Ensembl region with limit/offset paginati…

EnsemblPheno_get_by_region tool specification

Tool Information:

  • Name: EnsemblPheno_get_by_region

  • Type: EnsemblPhenotypeTool

  • Description: Get phenotype associations for variants and genes in an Ensembl region with limit/offset pagination and explicit total/has_more metadata. Returns deduplicated disease/trait associations from GWAS Catalog, ClinVar, Cancer Gene Census, and other sources. Even small well-studied regions can exceed 200 associations, so follow next_offset until has_more is false.

Parameters:

  • species (string) (optional) Species name. Use ‘homo_sapiens’ for human. Default: ‘homo_sapiens’.

  • region (string) (required) Genomic region in format ‘chromosome:start-end’. Example: ‘17:7661779-7687538’ for TP53, ‘17:43044295-43125482’ for BRCA1. Keep regions under 5Mb for reasonable response times.

  • feature_type ([‘string’, ‘null’]) (optional) Filter by feature type: ‘Variation’ (variants only), ‘Gene’ (genes only), ‘QTL’ (quantitative trait loci). Default: all types.

  • limit (integer) (optional) Maximum number of deduplicated phenotype associations to return in this page.

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

Example Usage:

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

EnsemblPheno_get_by_term (Type: EnsemblPhenotypeTool)#

Reverse phenotype lookup from the Ensembl REST API: given a trait/disease name or ontology access…

EnsemblPheno_get_by_term tool specification

Tool Information:

  • Name: EnsemblPheno_get_by_term

  • Type: EnsemblPhenotypeTool

  • Description: Reverse phenotype lookup from the Ensembl REST API: given a trait/disease name or ontology accession, return associated variants and genes with risk allele, p-value, beta, clinical significance, and source. Large result sets are paged with limit/offset; total_associations and next_offset make every association reachable.

Parameters:

  • species (string) (optional) Species name. Use ‘homo_sapiens’ for human. Default: ‘homo_sapiens’.

  • term ([‘string’, ‘null’]) (optional) Trait or disease name. Examples: ‘Alzheimer disease’, ‘Coronary artery disease’, ‘Type 2 diabetes mellitus’. If you pass an ontology accession (e.g. ‘EFO:0000249’) here it is auto-detected and routed correctly.

  • accession ([‘string’, ‘null’]) (optional) Ontology accession (EFO, HP, MONDO, Orphanet). Examples: ‘EFO:0000249’ (Alzheimer disease), ‘HP:0002511’ (Alzheimer disease phenotype), ‘MONDO:0004975’. Mutually exclusive with ‘term’.

  • limit (integer) (optional) Maximum associations per page.

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

Example Usage:

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

EnsemblPheno_get_by_variant (Type: EnsemblPhenotypeTool)#

Get phenotype associations for a specific variant (by rsID) from the Ensembl REST API. Returns tr…

EnsemblPheno_get_by_variant tool specification

Tool Information:

  • Name: EnsemblPheno_get_by_variant

  • Type: EnsemblPhenotypeTool

  • Description: Get phenotype associations for a specific variant (by rsID) from the Ensembl REST API. Returns traits, diseases, and phenotypes from sources such as the NHGRI-EBI GWAS catalog and ClinVar. Large result sets are paged with limit/offset; total_phenotypes and next_offset make every association reachable.

Parameters:

  • species (string) (optional) Species name. Use ‘homo_sapiens’ for human. Default: ‘homo_sapiens’.

  • variant_id (string) (required) Variant rsID. Examples: ‘rs429358’ (APOE e4), ‘rs7903146’ (TCF7L2 diabetes), ‘rs1801133’ (MTHFR).

  • limit (integer) (optional) Maximum phenotype associations per page.

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

Example Usage:

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