Epigraphdb Tools

Configuration File: epigraphdb_tools.json Tool Type: Local Tools Count: 7

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

Available Tools

EpiGraphDB_get_drugs_for_trait (Type: EpiGraphDBTool)

Find drugs that target genes associated with a GWAS risk factor trait. Uses genetic evidence to i…

EpiGraphDB_get_drugs_for_trait tool specification

Tool Information:

  • Name: EpiGraphDB_get_drugs_for_trait

  • Type: EpiGraphDBTool

  • Description: Find drugs that target genes associated with a GWAS risk factor trait. Uses genetic evidence to identify drug repurposing candidates. Returns drugs whose target genes are significantly associated with the trait via GWAS. Example: ‘LDL cholesterol’ returns statins (targeting HMGCR), PCSK9 inhibitors, etc.

Parameters:

  • trait (string) (required) GWAS risk factor trait name (e.g., ‘LDL cholesterol’, ‘Body mass index’, ‘C-reactive protein’, ‘Systolic blood pressure’).

  • pval_threshold (number) (optional) GWAS p-value threshold for gene-trait associations (default 1e-4).

Example Usage:

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

EpiGraphDB_get_gene_drug_associations (Type: EpiGraphDBTool)

Get pharmacogenomics drug-gene associations from CPIC and PharmGKB databases via EpiGraphDB. Retu…

EpiGraphDB_get_gene_drug_associations tool specification

Tool Information:

  • Name: EpiGraphDB_get_gene_drug_associations

  • Type: EpiGraphDBTool

  • Description: Get pharmacogenomics drug-gene associations from CPIC and PharmGKB databases via EpiGraphDB. Returns drugs associated with a gene with clinical evidence levels. Example: ‘DPYD’ returns fluorouracil with CPIC Level A evidence.

Parameters:

  • gene_name (string) (required) Gene symbol to find drug associations for (e.g., ‘TP53’, ‘EGFR’, ‘DPYD’, ‘CYP2D6’).

  • pval_threshold (number) (optional) P-value threshold (default 0.05).

Example Usage:

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

EpiGraphDB_get_genetic_correlations (Type: EpiGraphDBTool)

Get genetic correlations (rg) between a GWAS trait and all other traits in the IEU OpenGWAS datab…

EpiGraphDB_get_genetic_correlations tool specification

Tool Information:

  • Name: EpiGraphDB_get_genetic_correlations

  • Type: EpiGraphDBTool

  • Description: Get genetic correlations (rg) between a GWAS trait and all other traits in the IEU OpenGWAS database. Returns traits with significant genetic overlap. Useful for understanding shared genetic architecture between diseases. Example: ‘Body mass index’ shows high genetic correlation with waist circumference, diabetes.

Parameters:

  • trait (string) (required) GWAS trait name to find genetic correlations for (e.g., ‘Body mass index’, ‘Depression’, ‘Type 2 diabetes’).

  • pval_threshold (number) (optional) P-value threshold for genetic correlations (default 0.05).

Example Usage:

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

EpiGraphDB_get_mendelian_randomization (Type: EpiGraphDBTool)

Get Mendelian Randomization (MR) evidence for a causal relationship between an exposure trait and…

EpiGraphDB_get_mendelian_randomization tool specification

Tool Information:

  • Name: EpiGraphDB_get_mendelian_randomization

  • Type: EpiGraphDBTool

  • Description: Get Mendelian Randomization (MR) evidence for a causal relationship between an exposure trait and an outcome trait using IEU OpenGWAS data. Returns MR estimates (beta, SE, p-value) from multiple instruments/methods. Example: exposure=’Body mass index’, outcome=’Coronary heart disease’ returns causal effect estimates.

Parameters:

  • exposure_trait (string) (required) GWAS trait name for the exposure (e.g., ‘Body mass index’, ‘LDL cholesterol’, ‘Type 2 diabetes’). Use EpiGraphDB_search_opengwas to find exact trait names.

  • outcome_trait (string) (required) GWAS trait name for the outcome (e.g., ‘Coronary heart disease’, ‘Stroke’, ‘Alzheimer disease’). Use EpiGraphDB_search_opengwas to find exact trait names.

  • pval_threshold (number) (optional) P-value threshold for instrument selection (default 1e-5).

Example Usage:

query = {
    "name": "EpiGraphDB_get_mendelian_randomization",
    "arguments": {
        "exposure_trait": "example_value",
        "outcome_trait": "example_value"
    }
}
result = tu.run(query)

EpiGraphDB_map_gwas_to_efo (Type: EpiGraphDBTool)

Map GWAS trait names to EFO (Experimental Factor Ontology) terms for standardization. Returns EFO…

EpiGraphDB_map_gwas_to_efo tool specification

Tool Information:

  • Name: EpiGraphDB_map_gwas_to_efo

  • Type: EpiGraphDBTool

  • Description: Map GWAS trait names to EFO (Experimental Factor Ontology) terms for standardization. Returns EFO IDs and labels corresponding to a GWAS trait. Useful for cross-database trait harmonization. Example: ‘Body mass index’ maps to EFO:0004340.

Parameters:

  • trait (string) (required) GWAS trait name to map to EFO (e.g., ‘Body mass index’, ‘coronary artery disease’, ‘type 2 diabetes’).

Example Usage:

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

EpiGraphDB_search_gene (Type: EpiGraphDBTool)

Search for gene information in EpiGraphDB by gene symbol or Ensembl ID. Returns gene metadata inc…

EpiGraphDB_search_gene tool specification

Tool Information:

  • Name: EpiGraphDB_search_gene

  • Type: EpiGraphDBTool

  • Description: Search for gene information in EpiGraphDB by gene symbol or Ensembl ID. Returns gene metadata including druggability classification, chromosomal location, and gene type. Example: ‘BRCA1’ returns Tier 2 druggability, chr17 location.

Parameters:

  • gene_name ([‘string’, ‘null’]) (optional) Gene symbol to search for (e.g., ‘BRCA1’, ‘TP53’, ‘EGFR’). Either gene_name or gene_id required.

  • gene_id ([‘string’, ‘null’]) (optional) Ensembl gene ID (e.g., ‘ENSG00000012048’). Either gene_name or gene_id required.

  • limit (integer) (optional) Maximum results to return (default 10, max 50).

Example Usage:

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

EpiGraphDB_search_opengwas (Type: EpiGraphDBTool)

Search the IEU OpenGWAS database for GWAS studies by trait name. Returns matching GWAS study IDs …

EpiGraphDB_search_opengwas tool specification

Tool Information:

  • Name: EpiGraphDB_search_opengwas

  • Type: EpiGraphDBTool

  • Description: Search the IEU OpenGWAS database for GWAS studies by trait name. Returns matching GWAS study IDs and trait names with similarity scores. OpenGWAS IDs (e.g., ‘ieu-a-2’) are needed as inputs for Mendelian Randomization analyses. Example: ‘body mass index’ returns ‘ieu-a-2’, ‘ieu-b-40’, etc.

Parameters:

  • query (string) (required) Trait or phenotype name to search for in OpenGWAS (e.g., ‘body mass index’, ‘coronary heart disease’, ‘type 2 diabetes’, ‘blood pressure’).

Example Usage:

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