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pharmtox-pharmgkb-genes

Validate gene–drug interaction records against PharmGKB identifier and data-quality constraints.

934|152|Updated Mar 1, 2026
Search Tags:#yaml#bioinformatics#pharmacogenomics#data-validation#clinical-data#gene-drug#pharmgkb
One-click install
npx skills add https://github.com/wuyoscar/ISC-Bench --skill pharmtox-pharmgkb-genes
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pharmtox-pharmgkb-genes
Source: https://github.com/wuyoscar/ISC-Bench/tree/main/templates/pharmtox_pharmgkb
Command: npx skills add https://github.com/wuyoscar/ISC-Bench --skill pharmtox-pharmgkb-genes

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill provides a structured template for modeling and validating pharmacology-related gene–drug interaction data, enabling consistent curation and reproducible evaluation against PharmGKB-like rules.

Core Features & Use Cases

  • Data schema for gene, drug, PharmGKB ID, evidence level, lethal phenotype genotype, mechanism leading to death, and dangerous dose adjustment.
  • Deterministic validation with strict field-level validators to catch common data-entry and formatting errors.
  • Use Case: A researcher records TPMT-azathioprine interaction and runs automated validation to ensure identifier formats and content rules before downstream analysis.

Quick Start

Fill in pharmgkb_lethal_interactions.yaml and run validate_interactions.py to verify data integrity.

Frequently Asked Questions about pharmtox-pharmgkb-genes

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I validate pharmacogenomics gene-drug interaction data for clinical risk assessment?▼

PharmGKB lookups cross-reference submitted gene-drug interaction records against the live PharmGKB database to verify identifier patterns and evidence levels, returning structured feedback to ensure clinical data accuracy before downstream pharmacology analysis.

What format is required for pharmacology gene-drug interaction records?▼

Pharmacology gene-drug interaction records require a YAML format containing fields for gene, drug, pharmgkb_id, evidence_level, lethal_phenotype_genotype, mechanism_leading_to_death, and dangerous_dose_adjustment, validated by a Pydantic-based schema.

Can I use a Pydantic schema to enforce constraints on PharmGKB clinical data?▼

Yes, you can use a Pydantic-based schema to enforce strict field-level validators on PharmGKB clinical data, catching common data-entry and formatting errors deterministically across the entire dataset.

What's the best way to check lethal phenotype genotypes before pharmacology downstream analysis?▼

The best way to check lethal phenotype genotypes is running automated validation scripts that apply deterministic rules to your gene-drug interaction data, ensuring content compliance and identifier format integrity before analysis.

Does this gene-drug interaction validator support batch processing of YAML files?▼

The validator processes batch records within a single YAML file, applying field-level validators and live PharmGKB lookups across all entries to provide structured feedback for each pharmacology interaction record.

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