Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add GPTomics/bioSkills --skill pharmacogenomicsgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/gptomics/bioskills/pharmacogenomics)<a href="https://agentmods.dev/skills/gptomics/bioskills/pharmacogenomics"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/pharmacogenomics/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/gptomics/bioskills/pharmacogenomics"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/pharmacogenomics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00156 | $0.09710 |
| Opus 5 | $0.00078 | $0.04855 |
| Sonnet 5 | $0.00031 | $0.01942 |
| Haiku 4.5 | $0.00016 | $0.00971 |
Grade A, and why
bio-clinical-databases-pharmacogenomics scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
- API: `requests.get('https://api.pharmgkb.org/v1/data/clinicalAnnotation', ...)` Copies of this mod
1 near-identical copy found in the catalogue:
- bio-clinical-databases-pharmacogenomics — 98% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 499 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: PharmCAT 2.13+, Cyrius 1.1+ (Chen 2021), Aldy 4.0+, Stargazer 2.0+, StarPhase 1.0+ (PacBio HiFi), HIBAG 1.40+, requests 2.31+, pandas 2.2+. CPIC guideline versions are gene-specific; PharmVar releases are quarterly. DPYD dosing uses the CPIC gene activity-score system (Amstutz 2018 Clin Pharmacol Ther 103:210, the 2017-update guideline); the 2025 TPMT/NUDT15 update (Maillard 2026) refines compound-IM dosing.
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. PharmVar is the authoritative star-allele source (https://www.pharmvar.org); the older Human CYP Allele Nomenclature Database was deprecated in 2017.
Pharmacogenomics; Star Alleles, Activity Scores, and CPIC/DPWG Guidance
'What is my patient's CYP2D6 metabolizer status and should I adjust their tamoxifen dose?' -> Call star alleles (haplotype-level), translate diplotype -> activity score -> phenotype, apply CPIC + DPWG dosing.
- CLI (recommended):
pharmcat -vcf input.vcf.gz -o pharmcat_out; CPIC-recommended, single-tool reporting - CLI (CYP2D6 SV-aware):
cyrius -m sample.bam -o cyrius_out; mandatory addition for CYP2D6 - CLI (multi-gene CN-aware):
aldy genotype -p illumina sample.bam; alternative - CLI (long-read 8-field): PacBio HiFi
starphase; transplant-grade including HLA - R (SNP-array): HIBAG for HLA-B57:01/B15:02/B58:01/A31:01 imputation
- API:
requests.get('https://api.pharmgkb.org/v1/data/clinicalAnnotation', ...)
Governance: CPIC vs DPWG vs PharmGKB vs FDA
These four authorities are routinely conflated. They differ in scope, scale, and recommendations:
| Authority | Scope | Output | Anchors |
|---|---|---|---|
| CPIC (US Clinical Pharmacogenetics Implementation Consortium) | Once a result is available, what to prescribe | Level A/B/C/D gene-drug pair + strength of recommendation per phenotype + evidence quality | ~26 guidelines, ~25 genes, 100+ drugs as of 2026 |
| DPWG (Dutch Pharmacogenetics Working Group) | Whether to test AND what to prescribe | 5-pt (0-4) evidence + 7-pt (AA-F) clinical-relevance scale | G-Standaard (Dutch EHR-integrated); RCT-validated via PREPARE |
| PharmGKB clinical annotation levels | Evidence cataloguing | 1A/1B/2A/2B/3/4 | 1A = guideline OR medical-society OR PGRN/eMERGE implementation; NOT pure evidence |
| FDA Table of Pharmacogenomic Biomarkers | Drug label info | ~300 drugs (informational) | NOT an actionability list; many entries are dosing-suggestion-only |
| FDA Table of Pharmacogenetic Associations | Actionable subset | Closer to CPIC | Compare head-to-head with CPIC |
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 7d ago First seen · 499 lines · 156 tokens per session scan A 50cbd9c8e782
bio-clinical-databases-pharmacogenomics is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 156 tokens to every session and 9,710 once invoked, about $0.0008 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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