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 (default 100; results are sorted by p-value, most significant first).

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). A free-tex…

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). A free-text disease_trait is resolved to an EFO/MONDO term first, and that resolution is disclosed in the response: ‘query_trait’ (what you asked for), ‘resolved_efo_id’, ‘resolved_efo_label’ (the term’s label in GWAS Catalog) and ‘trait_resolution_source’, plus a ‘trait_resolution_note’ whenever the resolved label is not an exact match for your query. Check those before trusting the results: e.g. ‘cardiorespiratory fitness’ resolves to EFO_0009184 ‘heart rate response to exercise’, which is a different phenotype from VO2max (EFO_0004887 ‘maximal oxygen uptake measurement’). Pass efo_id explicitly to bypass the resolver.

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:

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

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

  • gene_symbol (string) (optional) Gene name or symbol (e.g., ‘BRCA1’, ‘TP53’, ‘GBA’)

  • gene (string) (optional) Alias for gene_symbol

  • mapped_gene (string) (optional) Alias for gene_symbol

Example Usage:

query = {
    "name": "gwas_get_snps_for_gene",
    "arguments": {
    }
}
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. Accepts either ‘study_id’ or ‘accession_id’ (…

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. Accepts either ‘study_id’ or ‘accession_id’ (the same GCST identifier field name used by GWASAssociationsForStudy and returned on every association record) so IDs can be chained directly between gwas_* tools without renaming.

Parameters:

  • study_id (string) (optional) GWAS study identifier (GCST accession, e.g. ‘GCST000392’)

  • accession_id (string) (optional) Alias for study_id – the same GCST accession identifier, accepted so results from other gwas_* tools (which use the field name ‘accession_id’) can be passed straight in.

Example Usage:

query = {
    "name": "gwas_get_study_by_id",
    "arguments": {
    }
}
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. Results are sorted by p-value ascending (most significant first) by default, so the first page holds the strongest loci; override with the ‘sort’ and ‘direction’ parameters. This is the best tool for finding all GWAS variants for a disease when you do NOT already have a specific variant ID. A free-text disease_trait is resolved to an EFO/MONDO term first, and that resolution is disclosed: ‘query_trait’, ‘resolved_efo_id’, ‘resolved_efo_label’ and ‘trait_resolution_source’ are returned, plus a ‘trait_resolution_note’ whenever the resolved label is not an exact match for your query - check them before trusting the results, and pass efo_id explicitly to bypass the resolver.

Parameters:

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

  • trait (string) (optional) Alias for disease_trait. Disease or trait name (e.g., ‘type 2 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

  • limit (integer) (optional) Alias for size. Number of results to return per page

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

  • sort (string) (optional) Sort field (e.g., ‘p_value’, ‘or_value’). Defaults to ‘p_value’ so the most significant associations appear first.

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

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. Response envelope keys beyond ‘data’: ‘metadata.pagination’ (upstream page block - its totalElements/totalPages always describe the UNFILTERED result set); when a p_value threshold is given, ‘metadata.p_value_filter’, ‘metadata.p_value_filter_scope’ and ‘metadata.p_value_filter_note’ state that the threshold was applied CLIENT-SIDE (GWAS Catalog REST v2 has no server-side p-value filter), ‘metadata.pagination_totals_are_prefilter’ is true, ‘metadata.filtered_total’ / ‘filtered_total_is_exact’ / ‘filtered_total_at_least’ / ‘filtered_total_note’ give the post-filter denominator, and ‘metadata.sort_override’ records that the page was fetched p_value-ascending so the threshold could match anything. When a disease_trait is resolved to an ontology term, ‘query_trait’, ‘resolved_efo_id’, ‘resolved_efo_label’ and ‘trait_resolution_source’ are returned, plus a ‘trait_resolution_note’ whenever the resolved label is not an exact match for the trait you asked for. An empty ‘data’ comes with a ‘note’ that names the real cause: a client-side filter that removed every row is reported as such, and only a genuinely empty unfiltered result set suggests trying a trait synonym or a gene-based tool.

Parameters:

  • disease_trait (string) (optional) Disease or trait name for text-based search (e.g., ‘diabetes’, ‘coronary artery disease’, ‘breast cancer’). NOTE: GWAS associations are indexed by trait/disease, not by gene or drug name — passing a gene symbol or drug name here will fail. Use efo_id for precise filtering.

  • query (string) (optional) Alias for disease_trait. Disease or trait name (e.g., ‘type 2 diabetes’). NOTE: gene symbols and drug names are not valid GWAS trait queries.

  • 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

  • p_value (number) (optional) Maximum p-value threshold for filtering (e.g., 5e-8 for genome-wide significance). IMPORTANT: the GWAS Catalog REST API v2 has NO server-side p-value filter (its OpenAPI document lists only pubmed_id, rs_id, full_pvalue_set, accession_id, efo_trait, efo_id, show_child_trait, mapped_gene, extended_geneset, sort, direction, page and size on GET /v2/associations), so this threshold is applied CLIENT-SIDE to the page of associations fetched. To make it meaningful the page is fetched p_value-ascending (most-significant-first) whenever sort is ‘p_value’ (the default), and the surviving rows are then re-ordered into the direction you asked for. metadata.p_value_filter_scope, metadata.filtered_total and metadata.p_value_filter_note report exactly what was filtered.

  • p_value_threshold (number) (optional) Alias for p_value: maximum p-value threshold (also applied client-side; see p_value).

  • sort (string) (optional) Sort field (e.g., ‘p_value’, ‘or_value’). Defaults to ‘p_value’. When a p_value threshold is supplied and sort is ‘p_value’, the upstream page is always fetched ascending so the threshold sees the significant end; metadata.sort_override records this and the returned rows are ordered per your ‘direction’.

  • direction (string) (optional) Sort direction (‘asc’ or ‘desc’). Defaults to ‘asc’. Combined with a p_value threshold this orders the RETURNED rows; see metadata.sort_override.

  • 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)