Ensembl Phenotype Tools

Configuration File: ensembl_phenotype_tools.json Tool Type: Local Tools Count: 3

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 the Ensembl REST API. Returns diseases, traits, and cl…

EnsemblPheno_get_by_gene tool specification

Tool Information:

  • Name: EnsemblPheno_get_by_gene

  • Type: EnsemblPhenotypeTool

  • Description: Get phenotype associations for a gene from the Ensembl REST API. Returns diseases, traits, and clinical conditions linked to the gene, aggregated from multiple sources including Cancer Gene Census, OMIM, ClinVar, NHGRI-EBI GWAS catalog, and Orphanet. Each entry includes the phenotype description, data source, genomic location, and ontology accessions (EFO, HP, Orphanet). Example: BRCA1 returns 162 phenotype associations across multiple cancer types and other conditions.

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’.

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 all variants and genes in a genomic region from the Ensembl REST A…

EnsemblPheno_get_by_region tool specification

Tool Information:

  • Name: EnsemblPheno_get_by_region

  • Type: EnsemblPhenotypeTool

  • Description: Get phenotype associations for all variants and genes in a genomic region from the Ensembl REST API. Returns disease/trait associations from GWAS catalog, ClinVar, Cancer Gene Census, etc. for features overlapping the specified region. Useful for understanding the phenotypic landscape of a genomic interval, especially for interpreting GWAS loci or candidate regions. Example: TP53 region (chr17:7661779-7687538) returns phenotype associations from the NHGRI-EBI GWAS catalog.

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.

Example Usage:

query = {
    "name": "EnsemblPheno_get_by_region",
    "arguments": {
        "region": "example_value"
    }
}
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 associated with the variant from NHGRI-EBI GWAS catalog, ClinVar, and other sources. Includes risk alleles, beta coefficients/odds ratios, p-values, and study references. Example: rs429358 (APOE epsilon 4 variant) returns 1004 phenotype associations including Alzheimer disease, LDL cholesterol levels, and metabolite measurements.

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).

Example Usage:

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