Gwas Tools

Configuration File: gwas_tools.json Tool Type: Local Tools Count: 13

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

Available Tools

GWAS_search_associations_by_gene (Type: GWASGeneSearch)

Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).

GWAS_search_associations_by_gene tool specification

Tool Information:

  • Name: GWAS_search_associations_by_gene

  • Type: GWASGeneSearch

  • Description: Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).

Parameters:

  • gene_name (string) (required) Gene symbol (e.g., BRCA1).

  • size (integer) (optional) Max associations to return.

Example Usage:

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

gwas_get_association_by_id (Type: GWASAssociationByID)

Get a specific GWAS association by its unique identifier.

gwas_get_association_by_id tool specification

Tool Information:

  • Name: gwas_get_association_by_id

  • Type: GWASAssociationByID

  • Description: Get a specific GWAS association by its unique identifier.

Parameters:

  • association_id (string) (required) GWAS association identifier

Example Usage:

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

gwas_get_associations_for_snp (Type: GWASAssociationsForSNP)

Get all associations for a specific SNP with optional sorting.

gwas_get_associations_for_snp tool specification

Tool Information:

  • Name: gwas_get_associations_for_snp

  • Type: GWASAssociationsForSNP

  • Description: Get all associations for a specific SNP with optional sorting.

Parameters:

  • rs_id (string) (required) dbSNP rs identifier

  • sort (string) (optional) Sort field (e.g., ‘p_value’, ‘or_value’)

  • direction (string) (optional) Sort direction (‘asc’ or ‘desc’)

  • size (integer) (optional) Number of results to return per page

  • page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_get_associations_for_study (Type: GWASAssociationsForStudy)

Get all associations for a specific study, sorted by p-value.

gwas_get_associations_for_study tool specification

Tool Information:

  • Name: gwas_get_associations_for_study

  • Type: GWASAssociationsForStudy

  • Description: Get all associations for a specific study, sorted by p-value.

Parameters:

  • accession_id (string) (required) Study accession identifier

  • size (integer) (optional) Number of results to return per page

  • page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_get_associations_for_trait (Type: GWASAssociationsForTrait)

Get all associations for a specific trait, sorted by p-value (most significant first).

gwas_get_associations_for_trait tool specification

Tool Information:

  • Name: gwas_get_associations_for_trait

  • Type: GWASAssociationsForTrait

  • Description: Get all associations for a specific trait, sorted by p-value (most significant first).

Parameters:

  • disease_trait (string) (optional) Disease or trait name for text-based search (e.g., ‘diabetes’, ‘hypertension’)

  • efo_uri (string) (optional) Full EFO ontology URI (e.g., ‘http://www.ebi.ac.uk/efo/EFO_0001645’)

  • efo_id (string) (optional) EFO/OBA term ID (e.g., ‘EFO_0001645’, ‘OBA_2050062’). Recommended for reliable trait filtering.

  • efo_trait (string) (optional) Exact EFO trait label. Use when you know the canonical trait string.

  • size (integer) (optional) Number of results to return per page

  • page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_get_snp_by_id (Type: GWASSNPByID)

Get a specific GWAS SNP by its rs ID.

gwas_get_snp_by_id tool specification

Tool Information:

  • Name: gwas_get_snp_by_id

  • Type: GWASSNPByID

  • Description: Get a specific GWAS SNP by its rs ID.

Parameters:

  • rs_id (string) (required) dbSNP rs identifier

Example Usage:

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

gwas_get_snps_for_gene (Type: GWASSNPsForGene)

Get all GWAS Catalog SNPs mapped to a specific gene by gene name (e.g., ‘BRCA1’, ‘TP53’). Returns…

gwas_get_snps_for_gene tool specification

Tool Information:

  • Name: gwas_get_snps_for_gene

  • Type: GWASSNPsForGene

  • Description: Get all GWAS Catalog SNPs mapped to a specific gene by gene name (e.g., ‘BRCA1’, ‘TP53’). Returns variant details including rs IDs, chromosomal positions, and functional annotations. Use this when you want to find all catalogued variants within or near a specific gene.

Parameters:

  • mapped_gene (string) (required) Gene name or symbol

  • size (integer) (optional) Number of results to return per page

  • page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_get_studies_for_trait (Type: GWASStudiesForTrait)

Get studies for a specific trait with optional filters for cohort, GxE interactions, and summary …

gwas_get_studies_for_trait tool specification

Tool Information:

  • Name: gwas_get_studies_for_trait

  • Type: GWASStudiesForTrait

  • Description: Get studies for a specific trait with optional filters for cohort, GxE interactions, and summary statistics.

Parameters:

  • disease_trait (string) (optional) Disease or trait name for text-based search (e.g., ‘diabetes’, ‘alzheimer disease’)

  • efo_uri (string) (optional) Full EFO ontology URI (e.g., ‘http://www.ebi.ac.uk/efo/EFO_0001645’)

  • efo_id (string) (optional) EFO/OBA term ID (e.g., ‘EFO_0001645’, ‘OBA_2050062’). Recommended for reliable trait filtering.

  • efo_trait (string) (optional) Exact EFO trait label. Use when you know the canonical trait string.

  • cohort (string) (optional) Cohort name (e.g., ‘UKB’ for UK Biobank)

  • gxe (boolean) (optional) Filter for Gene-by-Environment interaction studies

  • full_pvalue_set (boolean) (optional) Filter for studies with full summary statistics

  • size (integer) (optional) Number of results to return per page

  • page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_get_study_by_id (Type: GWASStudyByID)

Get a specific GWAS study by its unique identifier.

gwas_get_study_by_id tool specification

Tool Information:

  • Name: gwas_get_study_by_id

  • Type: GWASStudyByID

  • Description: Get a specific GWAS study by its unique identifier.

Parameters:

  • study_id (string) (required) GWAS study identifier

Example Usage:

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

gwas_get_variants_for_trait (Type: GWASVariantsForTrait)

Search the GWAS Catalog for all genetic variants (SNPs) linked to a specific disease or trait. Ac…

gwas_get_variants_for_trait tool specification

Tool Information:

  • Name: gwas_get_variants_for_trait

  • Type: GWASVariantsForTrait

  • Description: Search the GWAS Catalog for all genetic variants (SNPs) linked to a specific disease or trait. Accepts free-text disease/trait names (e.g., ‘diabetes’, ‘breast cancer’), EFO ontology IDs, or EFO trait labels. Returns variant details including rsIDs, p-values, mapped genes, and genomic locations. This is the best tool for finding all GWAS variants for a disease when you do NOT already have a specific variant ID.

Parameters:

  • disease_trait (string) (optional) Disease or trait name for text-based search (e.g., ‘diabetes’, ‘breast cancer’)

  • efo_uri (string) (optional) Full EFO ontology URI (e.g., ‘http://www.ebi.ac.uk/efo/EFO_0001645’)

  • efo_id (string) (optional) EFO/OBA term ID (e.g., ‘EFO_0001645’, ‘OBA_2050062’). Recommended for reliable trait filtering.

  • efo_trait (string) (optional) Exact EFO trait label. Use when you know the canonical trait string.

  • size (integer) (optional) Number of results to return per page

  • page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_search_associations (Type: GWASAssociationSearch)

Search the GWAS Catalog for genome-wide association study results by keyword. Accepts free-text d…

gwas_search_associations tool specification

Tool Information:

  • Name: gwas_search_associations

  • Type: GWASAssociationSearch

  • Description: Search the GWAS Catalog for genome-wide association study results by keyword. Accepts free-text disease/trait names (e.g., ‘melanoma’, ‘diabetes’, ‘breast cancer’), SNP rs IDs, EFO ontology IDs, or study accession IDs. This is the primary tool for discovering GWAS associations when you do NOT already have a specific association ID. Returns SNPs, p-values, odds ratios, mapped genes, and study metadata with pagination support.

Parameters:

  • disease_trait (string) (optional) Disease or trait name for text-based search (e.g., ‘diabetes’, ‘coronary artery disease’, ‘breast cancer’). WARNING: free-text search is broad and may return many unrelated associations. Prefer efo_id for precise filtering.

  • efo_uri (string) (optional) Full EFO ontology URI (e.g., ‘http://www.ebi.ac.uk/efo/EFO_0001645’)

  • efo_id (string) (optional) EFO/OBA term ID (e.g., ‘EFO_0001645’, ‘OBA_2050062’). Recommended for reliable trait filtering.

  • efo_trait (string) (optional) Exact EFO trait label (e.g., ‘serum alanine aminotransferase amount’). Use when you know the canonical trait string.

  • rs_id (string) (optional) dbSNP rs identifier

  • accession_id (string) (optional) Study accession identifier

  • sort (string) (optional) Sort field (e.g., ‘p_value’, ‘or_value’)

  • direction (string) (optional) Sort direction (‘asc’ or ‘desc’)

  • size (integer) (optional) Number of results to return

  • page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_search_snps (Type: GWASSNPSearch)

Search the GWAS Catalog for single nucleotide polymorphisms (SNPs) by rs ID (e.g., ‘rs7903146’) o…

gwas_search_snps tool specification

Tool Information:

  • Name: gwas_search_snps

  • Type: GWASSNPSearch

  • Description: Search the GWAS Catalog for single nucleotide polymorphisms (SNPs) by rs ID (e.g., ‘rs7903146’) or mapped gene name (e.g., ‘TCF7L2’). Returns SNP details including chromosomal location, mapped genes, and functional class. Use this to look up specific variants or find all GWAS-catalogued SNPs for a gene.

Parameters:

  • rs_id (string) (optional) dbSNP rs identifier

  • mapped_gene (string) (optional) Gene name or symbol

  • size (integer) (optional) Number of results to return

  • page (integer) (optional) Page number for pagination

Example Usage:

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

gwas_search_studies (Type: GWASStudySearch)

Search for GWAS studies by various criteria including disease trait, cohort, GxE interactions, an…

gwas_search_studies tool specification

Tool Information:

  • Name: gwas_search_studies

  • Type: GWASStudySearch

  • Description: Search for GWAS studies by various criteria including disease trait, cohort, GxE interactions, and summary statistics availability.

Parameters:

  • disease_trait (string) (optional) Disease or trait name for text-based search (e.g., ‘diabetes’, ‘breast cancer’)

  • efo_uri (string) (optional) Full EFO ontology URI (e.g., ‘http://www.ebi.ac.uk/efo/EFO_0001645’)

  • efo_id (string) (optional) EFO/OBA term ID (e.g., ‘EFO_0001645’, ‘OBA_2050062’). Recommended for reliable trait filtering.

  • efo_trait (string) (optional) Exact EFO trait label. Use when you know the canonical trait string.

  • cohort (string) (optional) Cohort name (e.g., ‘UKB’ for UK Biobank)

  • gxe (boolean) (optional) Filter for Gene-by-Environment interaction studies

  • full_pvalue_set (boolean) (optional) Filter for studies with full summary statistics

  • size (integer) (optional) Number of results to return

  • page (integer) (optional) Page number for pagination

Example Usage:

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