Pharmgkb Tools

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

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

Available Tools

PharmGKB_get_clinical_annotations (Type: PharmGKBTool)

Get clinical annotations showing gene-drug-phenotype relationships. Returns variant-level clinica…

PharmGKB_get_clinical_annotations tool specification

Tool Information:

  • Name: PharmGKB_get_clinical_annotations

  • Type: PharmGKBTool

  • Description: Get clinical annotations showing gene-drug-phenotype relationships. Returns variant-level clinical significance data. Always provide a specific ‘annotation_id’ — filtering by gene_id is unreliable and may return empty results.

Parameters:

  • annotation_id (string) (optional) PharmGKB clinical annotation ID (e.g., ‘1447954390’). Required for reliable results.

  • gene_id (string) (optional) PharmGKB Gene Accession ID (e.g., ‘PA128’). NOTE: Filtering by gene_id is unreliable and may return empty results silently. Use annotation_id instead.

Example Usage:

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

PharmGKB_get_dosing_guidelines (Type: PharmGKBTool)

Get pharmacogenetic dosing guidelines (CPIC/DPWG) from PharmGKB by guideline_id. IMPORTANT: use t…

PharmGKB_get_dosing_guidelines tool specification

Tool Information:

  • Name: PharmGKB_get_dosing_guidelines

  • Type: PharmGKBTool

  • Description: Get pharmacogenetic dosing guidelines (CPIC/DPWG) from PharmGKB by guideline_id. IMPORTANT: use the ‘clinpgxid’ field from CPIC_list_guidelines (e.g., ‘PA166251454’), NOT the ‘pharmgkbid’ field — old-format pharmgkbid values (e.g., ‘PA166104996’) return HTTP 404. The test example PA166251465 is for the warfarin guideline.

Parameters:

  • guideline_id (string) (required) PharmGKB ClinPGx guideline ID from CPIC_list_guidelines ‘clinpgxid’ field (e.g., ‘PA166251465’ for warfarin, ‘PA166251454’ for opioids/codeine, ‘PA166251458’ for tamoxifen). Use clinpgxid, NOT pharmgkbid.

  • gene (string) (optional) Gene symbol (e.g., ‘CYP2D6’). NOTE: Filtering by gene symbol is unreliable and may return a generic prompt instead of actual guidelines. Use guideline_id instead.

Example Usage:

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

PharmGKB_get_drug_details (Type: PharmGKBTool)

Get detailed information for a drug using its PharmGKB Chemical ID. Returns structural info, cros…

PharmGKB_get_drug_details tool specification

Tool Information:

  • Name: PharmGKB_get_drug_details

  • Type: PharmGKBTool

  • Description: Get detailed information for a drug using its PharmGKB Chemical ID. Returns structural info, cross-references, and related genes.

Parameters:

  • drug_id (string) (required) PharmGKB Chemical ID (e.g., ‘PA452637’).

Example Usage:

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

PharmGKB_get_gene_details (Type: PharmGKBTool)

Get detailed information for a gene using its PharmGKB Accession ID. Returns chromosomal location…

PharmGKB_get_gene_details tool specification

Tool Information:

  • Name: PharmGKB_get_gene_details

  • Type: PharmGKBTool

  • Description: Get detailed information for a gene using its PharmGKB Accession ID. Returns chromosomal location, cross-references, and other metadata.

Parameters:

  • gene_id (string) (required) PharmGKB Gene Accession ID (e.g., ‘PA128’).

Example Usage:

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

PharmGKB_search_drugs (Type: PharmGKBTool)

Search for drugs in PharmGKB by name or PharmGKB ID. Returns drug name, ID, and basic metadata.

PharmGKB_search_drugs tool specification

Tool Information:

  • Name: PharmGKB_search_drugs

  • Type: PharmGKBTool

  • Description: Search for drugs in PharmGKB by name or PharmGKB ID. Returns drug name, ID, and basic metadata.

Parameters:

  • query (string) (required) Drug name or PharmGKB Chemical ID (e.g., ‘warfarin’, ‘PA452637’).

Example Usage:

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

PharmGKB_search_genes (Type: PharmGKBTool)

Search for genes in PharmGKB by name, symbol, or ID. Returns PharmGKB Gene ID and basic gene meta…

PharmGKB_search_genes tool specification

Tool Information:

  • Name: PharmGKB_search_genes

  • Type: PharmGKBTool

  • Description: Search for genes in PharmGKB by name, symbol, or ID. Returns PharmGKB Gene ID and basic gene metadata.

Parameters:

  • query (string) (required) Gene name, symbol, or PharmGKB Accession ID (e.g., ‘CYP2D6’, ‘PA128’).

Example Usage:

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

PharmGKB_search_variants (Type: PharmGKBTool)

Search for genetic variants in PharmGKB by rsID or name. Returns variant IDs and associated gene …

PharmGKB_search_variants tool specification

Tool Information:

  • Name: PharmGKB_search_variants

  • Type: PharmGKBTool

  • Description: Search for genetic variants in PharmGKB by rsID or name. Returns variant IDs and associated gene info.

Parameters:

  • query (string) (required) Variant name or rsID (e.g., ‘rs1799853’).

Example Usage:

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