tooluniverse-pharmacogenomics

COMPUTE, DON'T DESCRIBE

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

Pharmacogenomics (PGx) Research Skill

Systematic PGx analysis: resolve gene-drug pairs, retrieve CPIC dosing guidelines, annotate alleles and variants with PharmGKB, check FDA PGx biomarker labeling, and generate evidence-graded clinical recommendations.

When to Use

• "What CPIC guidelines exist for CYP2D6?"
• "Get dosing recommendations for codeine based on CYP2D6 poor metabolizer status"
• "Which drugs have FDA pharmacogenomic biomarkers for CYP2C19?"
• "Find PharmGKB clinical annotations for rs1799853"
• "Is this patient's CYP2D6 genotype relevant to tamoxifen dosing?"
• "What is the functional status of CYP2D6*4?"
• "List all CPIC level A gene-drug pairs for CYP2D6"

Workflow Overview

Input (gene/drug/variant/phenotype)
  |
  v
Phase 0: Disambiguation (resolve gene symbols, drug names, rsIDs)
  |
  v
Phase 1: Gene-Drug Pair Identification (CPIC pairs + evidence levels)
  |
  v
Phase 2: Guideline & Dosing Retrieval (CPIC recommendations + PharmGKB)
  |
  v
Phase 3: Allele & Variant Annotation (star alleles, function, activity scores)
  |
  v
Phase 4: FDA Biomarker Labeling (regulatory PGx status)
  |
  v
Phase 5: Cross-Database Enrichment (EpiGraphDB, DGIdb, OpenTargets PGx)
  |
  v
Phase 6: Report (evidence-graded clinical summary)

---

Phase 0: Disambiguation

Resolve user input to canonical identifiers before querying PGx databases.

PharmGKB_search_genes: query (string REQUIRED, e.g., "CYP2D6"). Returns {status, data: [{id, symbol, name}]}.

• Use to get PharmGKB gene accession ID (e.g., "PA128" for CYP2D6).

PharmGKB_search_drugs: query (string REQUIRED, e.g., "codeine"). Returns {status, data: [{id, name, types}]}.

• Use to get PharmGKB chemical ID (e.g., "PA449088" for codeine).