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 myvariant-queriesgit 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/myvariant-queries)<a href="https://agentmods.dev/skills/gptomics/bioskills/myvariant-queries"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/myvariant-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/gptomics/bioskills/myvariant-queries"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/myvariant-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 | $0.00086 | $0.04906 |
| Opus 5 | $0.00043 | $0.02453 |
| Sonnet 5 | $0.00017 | $0.00981 |
| Haiku 4.5 | $0.00009 | $0.00491 |
Grade A, and why
bio-clinical-databases-myvariant-queries scanned grade A with 0 findings 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.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
Copies of this mod
1 near-identical copy found in the catalogue:
- bio-clinical-databases-myvariant-queries — 95% identical, 12 lines differ
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: myvariant 1.0.0+, requests 2.31+, pandas 2.2+. myvariant.info aggregates >=21 sources; the operative version of each source is queryable via the _meta field and the /v1/metadata endpoint.
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. dbNSFP version drift is the dominant staleness vector: AlphaMissense was added to dbNSFP v4.4 (~2024); querying dbnsfp.alphamissense.score returns whatever version of dbNSFP is currently loaded; check _meta.src.dbnsfp.version.
MyVariant.info Queries; Aggregated Annotation
'Annotate my variants with ClinVar + gnomAD + CADD + AlphaMissense in one batch' -> Query the BioThings myvariant.info aggregator with field selection and version tracking, then parse nested responses.
- Python:
myvariant.MyVariantInfo().getvariant(hgvs_or_rsid, fields=['clinvar', 'gnomad_exome', 'dbnsfp']) - Python (batch):
mv.getvariants(ids_list, fields=...); up to 1000 IDs per request - Python (search):
mv.query('clinvar.gene.symbol:BRCA1 AND clinvar.clinical_significance:Pathogenic') - REST:
GET https://myvariant.info/v1/variant/{hgvs_or_id}?fields=... - Bulk:
POST https://myvariant.info/v1/variantwith comma-separated IDs
BioThings Architecture (Lelong 2022 Bioinformatics)
myvariant.info is one of three flagship BioThings APIs (with MyGene.info and MyChem.info). All three share the BioThings SDK, which auto-deploys an Elasticsearch index from heterogeneous source files via per-source dataloaders. The 2022 paper formalized the SDK; the architecture itself is older (Xin 2016 Genome Biol).
- Elasticsearch-backed: queries use Lucene operators (AND, OR, NOT, range like
dbnsfp.cadd.phred:>20) - Dotted-field-name syntax for nested JSON
- The
_idfield is canonical HGVS-g per record (e.g.,chr7:g.117199644G>A)
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 · 318 lines · 86 tokens per session scan A a75eac92578d
bio-clinical-databases-myvariant-queries is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 86 tokens to every session and 4,906 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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