Access ClinPGx pharmacogenomics data (successor to PharmGKB) when you need to query gene-drug interactions, CPIC guidelines, allele functions, and drug-label PGx content for precision medicine and genotype-guided dosing.
Access ClinPGx pharmacogenomics data (successor to PharmGKB) when you need to query gene-drug interactions, CPIC guidelines, allele functions, and drug-label PGx content for precision medicine and genotype-guided dosing.
ClinPGx (Clinical Pharmacogenomics Database) is a curated pharmacogenomics resource and successor to PharmGKB. It integrates content from sources such as CPIC, DPWG, PharmCAT, and regulatory drug labels to support genotype-informed prescribing, safety screening, and evidence review via a REST API.
When to Use
Use this skill when the request matches its documented task boundary.
Use it when the user can provide the required inputs and expects a structured deliverable.
Prefer this skill for repeatable, checklist-driven execution rather than open-ended brainstorming.
Key Features
Scope-focused workflow aligned to: Access ClinPGx pharmacogenomics data (successor to PharmGKB) when you need to query gene-drug interactions, CPIC guidelines, allele functions, and drug-label PGx content for precision medicine and genotype-guided dosing.
Clinical annotations may be graded from higher to lower strength, commonly:
1A, 1B, 2A, 2B, 3, 4
Use evidence filters (e.g., evidenceLevel=1A) when building clinical decision support or prioritizing literature review.
Phenotype categories (typical metabolizer labels)
For many pharmacogenes, phenotype groupings may include:
Ultrarapid Metabolizer (UM)
Normal Metabolizer (NM)
Intermediate Metabolizer (IM)
Poor Metabolizer (PM)
Notes on clinical use
Always confirm guideline version/date, evidence strength, and population context (allele frequencies vary).
Consider phenoconversion (drug-drug interactions altering enzyme activity) and non-genetic factors (age, organ function, comedications).
If you need phenoconversion and multi-drug interpretation workflows, ClinPGx also provides the PharmDOG decision-support tool on the ClinPGx website.
When Not to Use
Do not use this skill when the required source data, identifiers, files, or credentials are missing.
Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.
Required Inputs
A clearly specified task goal aligned with the documented scope.
All required files, identifiers, parameters, or environment variables before execution.
Any domain constraints, formatting requirements, and expected output destination if applicable.
Recommended Workflow
Validate the request against the skill boundary and confirm all required inputs are present.
Select the documented execution path and prefer the simplest supported command or procedure.
Produce the expected output using the documented file format, schema, or narrative structure.
Run a final validation pass for completeness, consistency, and safety before returning the result.
Deterministic Output Rules
Use the same section order for every supported request of this skill.
Keep output field names stable and do not rename documented keys across examples.
If a value is unavailable, emit an explicit placeholder instead of omitting the field.
Output Contract
Return a structured deliverable that is directly usable without reformatting.
If a file is produced, prefer a deterministic output name such as clinpgx_database_result.md unless the skill documentation defines a better convention.
Include a short validation summary describing what was checked, what assumptions were made, and any remaining limitations.
Validation and Safety Rules
Validate required inputs before execution and stop early when mandatory fields or files are missing.
Do not fabricate measurements, references, findings, or conclusions that are not supported by the provided source material.
Emit a clear warning when credentials, privacy constraints, safety boundaries, or unsupported requests affect the result.
Keep the output safe, reproducible, and within the documented scope at all times.
Failure Handling
If validation fails, explain the exact missing field, file, or parameter and show the minimum fix required.
If an external dependency or script fails, surface the command path, likely cause, and the next recovery step.
If partial output is returned, label it clearly and identify which checks could not be completed.
Completion Checklist
Confirm all required inputs were present and valid.
Confirm the supported execution path completed without unresolved errors.
Confirm the final deliverable matches the documented format exactly.
Confirm assumptions, limitations, and warnings are surfaced explicitly.
Quick Validation
Run this minimal verification path before full execution when possible:
python scripts/query_clinpgx.py --help
Expected output format:
Result file: clinpgx_database_result.md
Validation summary: PASS/FAIL with brief notes
Assumptions: explicit list if any
Scope Reminder
Core purpose: Access ClinPGx pharmacogenomics data (successor to PharmGKB) when you need to query gene-drug interactions, CPIC guidelines, allele functions, and drug-label PGx content for precision medicine and genotype-guided dosing.
