Cpic Tools

Configuration File: cpic_tools.json Tool Type: Local Tools Count: 9

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

Available Tools

CPIC_get_alleles (Type: BaseRESTTool)

Get pharmacogenomics alleles and their functional status for a gene from CPIC. Returns allele nam…

CPIC_get_alleles tool specification

Tool Information:

  • Name: CPIC_get_alleles

  • Type: BaseRESTTool

  • Description: Get pharmacogenomics alleles and their functional status for a gene from CPIC. Returns allele names, functional status (normal, decreased, no function, increased, uncertain, unknown), and activity values. Critical for translating genotype to phenotype (e.g., CYP2D6 *4 = no function, CYP2D6 *1 = normal function).

Parameters:

  • genesymbol (string) (required) Gene symbol (e.g., ‘CYP2D6’, ‘CYP2C19’, ‘TPMT’, ‘DPYD’)

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of alleles to return (default 50)

Example Usage:

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

CPIC_get_drug_info (Type: BaseRESTTool)

Get pharmacogenomics information for a drug from the CPIC database. Returns drug identifiers incl…

CPIC_get_drug_info tool specification

Tool Information:

  • Name: CPIC_get_drug_info

  • Type: BaseRESTTool

  • Description: Get pharmacogenomics information for a drug from the CPIC database. Returns drug identifiers including PharmGKB ID, RxNorm, DrugBank, and ATC codes. Use to find pharmacogenomics guidelines for a specific drug. Example drugs: warfarin, codeine, clopidogrel, simvastatin, tamoxifen, fluorouracil, mercaptopurine.

Parameters:

  • name (string) (required) Drug name in lowercase (e.g., ‘warfarin’, ‘codeine’, ‘clopidogrel’, ‘simvastatin’)

Example Usage:

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

CPIC_get_gene_drug_pairs (Type: BaseRESTTool)

Get all gene-drug pairs for a pharmacogene from CPIC. Shows which drugs are affected by variants …

CPIC_get_gene_drug_pairs tool specification

Tool Information:

  • Name: CPIC_get_gene_drug_pairs

  • Type: BaseRESTTool

  • Description: Get all gene-drug pairs for a pharmacogene from CPIC. Shows which drugs are affected by variants in a specific gene, with CPIC evidence level and PharmGKB clinical annotation level. Evidence levels: A (strongest) to D (weakest). Useful for understanding the clinical significance of a pharmacogene.

Parameters:

  • genesymbol (string) (required) Gene symbol (e.g., ‘CYP2D6’, ‘CYP2C19’, ‘SLCO1B1’, ‘TPMT’, ‘DPYD’, ‘VKORC1’)

Example Usage:

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

CPIC_get_gene_info (Type: BaseRESTTool)

Get pharmacogenomics information for a gene from the Clinical Pharmacogenomics Implementation Con…

CPIC_get_gene_info tool specification

Tool Information:

  • Name: CPIC_get_gene_info

  • Type: BaseRESTTool

  • Description: Get pharmacogenomics information for a gene from the Clinical Pharmacogenomics Implementation Consortium (CPIC) database. Returns gene coordinates, sequence IDs, and cross-references to PharmGKB, HGNC, NCBI, and Ensembl. Use this to find which genes are pharmacogenomically relevant. Example genes: CYP2D6, CYP2C19, CYP2C9, SLCO1B1, TPMT, DPYD, UGT1A1, VKORC1, G6PD.

Parameters:

  • symbol (string) (required) Gene symbol (e.g., ‘CYP2D6’, ‘CYP2C19’, ‘SLCO1B1’, ‘TPMT’, ‘DPYD’)

Example Usage:

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

CPIC_get_recommendations (Type: BaseRESTTool)

Get drug dosing recommendations from a specific CPIC pharmacogenomic guideline. Returns clinicall…

CPIC_get_recommendations tool specification

Tool Information:

  • Name: CPIC_get_recommendations

  • Type: BaseRESTTool

  • Description: Get drug dosing recommendations from a specific CPIC pharmacogenomic guideline. Returns clinically actionable recommendations that link genotype/phenotype to drug prescribing actions. Each recommendation includes the classification strength (Strong, Moderate, Optional, No recommendation), the drug recommendation text, allele status context, and clinical implications. Use CPIC_list_guidelines first to obtain valid guideline IDs. Key guideline IDs: 100421 (HLA-B/abacavir), 100414 (CYP2D6/codeine), 100412 (CYP2C9,VKORC1/warfarin), 100416 (CYP2D6/amitriptyline).

Parameters:

  • guideline_id (integer) (required) CPIC guideline numeric ID (e.g., 100421 for HLA-B/abacavir, 100414 for CYP2D6/codeine). Obtain IDs from CPIC_list_guidelines.

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of recommendations to return (default 50)

  • offset ([‘integer’, ‘null’]) (optional) Number of recommendations to skip for pagination (default 0)

Example Usage:

query = {
    "name": "CPIC_get_recommendations",
    "arguments": {
        "guideline_id": 10
    }
}
result = tu.run(query)

CPIC_list_drugs (Type: BaseRESTTool)

List all drugs in the CPIC database that have pharmacogenomic annotations. Returns drug names and…

CPIC_list_drugs tool specification

Tool Information:

  • Name: CPIC_list_drugs

  • Type: BaseRESTTool

  • Description: List all drugs in the CPIC database that have pharmacogenomic annotations. Returns drug names and their associated CPIC guideline IDs. Drugs without a guideline ID have annotations but no full CPIC dosing guideline yet. Use the guidelineid with CPIC_get_recommendations to retrieve dosing recommendations. Covers 100+ drugs including commonly used medications like warfarin, codeine, clopidogrel, simvastatin, tamoxifen, fluorouracil, and abacavir.

Parameters:

No parameters required.

Example Usage:

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

CPIC_list_guidelines (Type: BaseRESTTool)

List all CPIC pharmacogenomic guidelines. Returns 31 evidence-based guidelines for using pharmaco…

CPIC_list_guidelines tool specification

Tool Information:

  • Name: CPIC_list_guidelines

  • Type: BaseRESTTool

  • Description: List all CPIC pharmacogenomic guidelines. Returns 31 evidence-based guidelines for using pharmacogenomic test results to optimize drug therapy. Each guideline covers one or more gene-drug pairs with specific dosing recommendations based on genotype/phenotype. Includes guideline ID, name, URL, associated genes, and PharmGKB IDs. Use the returned guideline ID with CPIC_get_recommendations to retrieve specific dosing recommendations.

Parameters:

No parameters required.

Example Usage:

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

CPIC_list_pgx_genes (Type: BaseRESTTool)

List all pharmacogenomics genes curated by the Clinical Pharmacogenomics Implementation Consortiu…

CPIC_list_pgx_genes tool specification

Tool Information:

  • Name: CPIC_list_pgx_genes

  • Type: BaseRESTTool

  • Description: List all pharmacogenomics genes curated by the Clinical Pharmacogenomics Implementation Consortium (CPIC). Returns 130+ genes with known drug interactions including CYP enzymes, transporters, and other pharmacogenes. Includes gene coordinates, sequence IDs, and database cross-references.

Parameters:

No parameters required.

Example Usage:

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

CPIC_search_gene_drug_pairs (Type: BaseRESTTool)

Search CPIC gene-drug pairs by gene symbol and/or CPIC evidence level. Gene symbol should be the …

CPIC_search_gene_drug_pairs tool specification

Tool Information:

  • Name: CPIC_search_gene_drug_pairs

  • Type: BaseRESTTool

  • Description: Search CPIC gene-drug pairs by gene symbol and/or CPIC evidence level. Gene symbol should be the standard HGNC symbol (e.g., “CYP2D6”, “DPYD”, “TPMT”). CPIC level indicates evidence strength: A=highest evidence, B=moderate, C=limited, D=for information only. Returns gene-drug pairs with guideline IDs for further lookup.

Parameters:

  • genesymbol ([‘string’, ‘null’]) (optional) PostgREST filter for gene symbol, prefix with ‘eq.’ (e.g., ‘eq.CYP2D6’, ‘eq.DPYD’, ‘eq.TPMT’). Omit to search all genes.

  • cpiclevel ([‘string’, ‘null’]) (optional) PostgREST filter for CPIC evidence level, prefix with ‘eq.’ (e.g., ‘eq.A’, ‘eq.B’, ‘eq.B/C’, ‘eq.C’, ‘eq.D’). Omit to include all levels.

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of results to return (default 50)

Example Usage:

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