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 PKU-YuanGroup/OpenAI4S --skill bio-clinical-databases-clinvar-lookupgit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote 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/pku-yuangroup/openai4s/bio-clinical-databases-clinvar-lookup)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-clinical-databases-clinvar-lookup"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clinical-databases-clinvar-lookup/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/pku-yuangroup/openai4s/bio-clinical-databases-clinvar-lookup"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clinical-databases-clinvar-lookup.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 | $0.00079 | $0.05815 |
| Opus 5 | $0.00039 | $0.02908 |
| Sonnet 5 | $0.00016 | $0.01163 |
| Haiku 4.5 | $0.00008 | $0.00581 |
Grade A, and why
bio-clinical-databases-clinvar-lookup 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 9d 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.
- Python (REST): `requests.get()` against the E-utilities `clinvar` database This is a copy
100% identical to bio-clinical-databases-clinvar-lookup — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 318 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: requests 2.31+, cyvcf2 0.30+, pandas 2.2+, bcftools 1.19+, Entrez Direct 21.0+, lxml 5.0+ (for v2 XML schema).
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. ClinVar XML schema v2 (rolled out in 2024) replaces <ClinVarSet> with <VariationArchive> as the top-level anchor; XSLT or parsers targeting the legacy element silently emit zero records.
ClinVar Lookup and Clinical-Significance Triangulation
'Look up the clinical significance of this variant' -> Retrieve ClinVar VCV-level aggregate, SCV-level submissions, ClinGen Variant Curation Expert Panel (VCEP) overrides, and conflict-resolution status.
- Python (REST):
requests.get()against the E-utilitiesclinvardatabase - Python (local VCF):
cyvcf2.VCF('clinvar.vcf.gz')for batch queries against the weekly snapshot - CLI:
bcftools annotate -a clinvar.vcf.gz -c INFO/CLNSIG,INFO/CLNREVSTAT,INFO/CLNDN - Cross-database: ClinGen Allele Registry CA ID via
https://reg.clinicalgenome.org/
The Identifier Hierarchy (VCV / SCV / RCV): Get This Wrong and Everything Downstream Breaks
| Level | Format | What it aggregates | When to use | Fails when |
|---|---|---|---|---|
| SCV | SCVxxxxxxxxx.N |
One submitter, one variant, one condition (atomic submission unit) | Auditing who said what; conflict triangulation | Aggregated reporting (use VCV); cross-condition analysis |
| RCV | RCVxxxxxxxxx.N |
All SCVs for a single (variant, condition) pair | Condition-stratified analysis; legacy aggregation | Variant-level reporting across all conditions (use VCV) |
| VCV | VCVxxxxxxxxx.N |
All RCVs for one variant across all conditions | Canonical anchor since 2017; default API entrypoint | Condition-specific clinical action (use RCV); CLNSIG collapses multi-condition |
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.
- 9d ago First seen · 318 lines · 79 tokens per session scan A 9318cf2b0a3c
bio-clinical-databases-clinvar-lookup is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 79 tokens to every session and 5,815 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). It is 100% identical to bio-clinical-databases-clinvar-lookup, differing in 12 lines, and is treated as a copy.
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