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-myvariant-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-myvariant-queries)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-clinical-databases-myvariant-queries"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clinical-databases-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/pku-yuangroup/openai4s/bio-clinical-databases-myvariant-queries"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-clinical-databases-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 | $0.04982 |
| Opus 5 | $0.00043 | $0.02491 |
| Sonnet 5 | $0.00017 | $0.00996 |
| Haiku 4.5 | $0.00009 | $0.00498 |
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 8d 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.
This is a copy
95% identical to bio-clinical-databases-myvariant-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 — 326 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.
- 8d ago First seen · 326 lines · 86 tokens per session scan A cf5bd631ed9c
bio-clinical-databases-myvariant-queries is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed today), licensed MIT. It adds 86 tokens to every session and 4,982 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. It is 95% identical to bio-clinical-databases-myvariant-queries, differing in 12 lines, and is treated as a copy.
Other skills, from other repositories
benchling-integration
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
Database Access Skills Index
Skills for querying and downloading data from genomic, transcriptomic, 3D-genome, and cancer-genomics databases. Covers programmatic access to public repositories, gene annotation, sequence retrieval, processed functional-genomics tracks, Hi-C / Micro-C contact matrices, TCGA-style cohorts, and large-scale single-cell…
chroma
Open-source embedding database for AI applications. Store embeddings and metadata, perform vector and full-text search, filter by metadata. Simple 4-function API. Scales from notebooks to production clusters. Use for semantic search, RAG applications, or document retrieval. Best for local development and open-source…
lamindb
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological…
mimic-patient-analysis
Comprehensive patient analysis using the MIMIC-IV clinical database. Use this skill whenever asked to analyze, summarize, or investigate a patient's medical history, hospital admissions, diagnoses, medications, procedures, or clinical course from a MIMIC-IV SQLite database. Triggers on prompts like "Analyze patient…
alphafold_database
AlphaFold DB structures and confidence analytics via VenusFactory tools. Use when the user needs predicted structures by UniProt ID, pLDDT/PAE analysis, or PDB/mmCIF download. Do NOT use for experimental PDB (rcsbdatabase), local ESMFold without UniProt (predictstructureesmfold / proteinstructurepipeline), or sequence…