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-dbsnp-queriesgit 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-dbsnp-queries)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-clinical-databases-dbsnp-queries"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clinical-databases-dbsnp-queries/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-dbsnp-queries"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clinical-databases-dbsnp-queries.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 | $0.05467 |
| Opus 5 | $0.00039 | $0.02733 |
| Sonnet 5 | $0.00016 | $0.01093 |
| Haiku 4.5 | $0.00008 | $0.00547 |
Grade A, and why
bio-clinical-databases-dbsnp-queries 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 (direct): `requests.get(f'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid_int}')` This is a copy
95% identical to bio-clinical-databases-dbsnp-queries — 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 — 345 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: myvariant 1.0+, requests 2.31+, biopython 1.83+, Entrez Direct 21.0+. dbSNP Build 156 (September 2022) is the current schema; Build 151 (2017) was the last with relational SQL dumps. Builds 152-155 dual-released JSON+SQL; 156+ is JSON-only.
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. The Variation Services REST API uses path-based versioning (/variation/v0/); E-utilities db=snp returns thin legacy summaries missing build-156 schema fields.
dbSNP Queries and rsID Normalization
'Look up this rsID / normalize variant representations' -> Resolve rsIDs through merge chains, compute canonical SPDI, and convert between rsID, HGVS-g, HGVS-c, and VCF allele representations.
- Python (aggregator):
myvariant.MyVariantInfo().getvariant(rsid, fields=['dbsnp', 'clinvar', 'gnomad_exome']) - Python (direct):
requests.get(f'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid_int}') - Python (E-utilities, legacy):
Bio.Entrez.esearch(db='snp', term=rsid); returns thin summary - Bulk:
ftp.ncbi.nlm.nih.gov/snp/latest_release/JSON/refsnp-chr{N}.json.bz2
rsID Is a Cluster Identifier, Not a Variant Identifier
This is the load-bearing concept. dbSNP cluster definition: ss records (submitted SNPs) are mapped to the genome and clustered into RefSNPs by position + variant type, not by allele. A single rsID can point to a locus with multiple alleles:
rs12345may resolve to {A>G, A>T, A>C} at one position; the RefSNP JSONprimary_snapshot_data.placements_with_allele[*].allelesenumerates them.- ~6-8% of dbSNP rsIDs are multi-allelic.
- PLINK and many older tools historically misuse rsIDs as if they were variant identifiers, which fails for multi-allelic sites and yields wrong genotype assignments.
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 · 345 lines · 79 tokens per session scan A ef96fdaca79a
bio-clinical-databases-dbsnp-queries 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 5,467 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 95% identical to bio-clinical-databases-dbsnp-queries, differing in 12 lines, and is treated as a copy.
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