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 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_term (Type: EnsemblPhenotypeTool)

Reverse phenotype lookup from the Ensembl REST API: given a trait/disease NAME (e.g. ‘Alzheimer d…

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 (e.g. ‘Alzheimer disease’) OR an ontology accession (EFO/HP/MONDO, e.g. ‘EFO:0000249’, ‘HP:0002511’), return ALL associated variants and genes with their risk allele, p-value, beta, clinical significance, and source (NHGRI-EBI GWAS catalog, ClinVar, dbGaP, etc.). This is the inverse of the gene/region/variant -> phenotype tools: it starts from a phenotype and finds the underlying genetics. Provide the query under ‘term’ (name) or ‘accession’ (ontology ID); an ontology-looking value passed as ‘term’ is auto-routed to the accession endpoint. Example: ‘Alzheimer disease’ returns 4450 records (e.g. rs201377759 in APP); ‘EFO:0000249’ returns 3111 records (e.g. rs7810606 in EPHA1, GWAS p=4e-11). Up to 500 associations are returned.

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’.

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 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)