synthetic-sciences/openscience is an AI workbench that carries out scientific research by reading papers, forming hypotheses, writing and running code, conducting experiments, analyzing results, and preparing reports. Researchers use it for work in machine learning, biology, physics, and chemistry with remote or local models. Catalogue add-ons extend its scientific workflows through skills and instructions.
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 synthetic-sciences/openscience --skill clinvar-databasegit clone --depth 1 https://github.com/synthetic-sciences/openscienceWrote 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/synthetic-sciences/openscience/clinvar-database)<a href="https://agentmods.dev/skills/synthetic-sciences/openscience/clinvar-database"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/clinvar-database/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/synthetic-sciences/openscience/clinvar-database"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/clinvar-database.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00045 | $0.03226 |
| Opus 5.5 | $0.00018 | $0.01290 |
| Sonnet 5.5 | $0.00009 | $0.00645 |
| Haiku 4.5 | $0.00005 | $0.00323 |
Grade A, and why
clinvar-database 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 1mo 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.
**Quick example using curl:** Copies of this mod
8 near-identical copies found in the catalogue:
- clinvar-database — 100% identical, 7 lines differ
- clinvar-database — 100% identical, 7 lines differ
- clinvar-database — 100% identical, 13 lines differ
- alterlab-clinvar — 88% identical, 137 lines differ
- clinvar-database — 88% identical, 10 lines differ
- clinvar-database — 88% identical, 10 lines differ
- clinvar-database — 88% identical, 10 lines differ
- clinvar-database — 88% identical, 10 lines differ
How it starts
The opening of the file, as written. The whole thing — 368 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ClinVar Database
Overview
ClinVar is NCBI's freely accessible archive of reports on relationships between human genetic variants and phenotypes, with supporting evidence. The database aggregates information about genomic variation and its relationship to human health, providing standardized variant classifications used in clinical genetics and research.
When to Use This Skill
This skill should be used when:
- Searching for variants by gene, condition, or clinical significance
- Interpreting clinical significance classifications (pathogenic, benign, VUS)
- Accessing ClinVar data programmatically via E-utilities API
- Downloading and processing bulk data from FTP
- Understanding review status and star ratings
- Resolving conflicting variant interpretations
- Annotating variant call sets with clinical significance
Core Capabilities
1. Search and Query ClinVar
Web Interface Queries
Search ClinVar using the web interface at https://www.ncbi.nlm.nih.gov/clinvar/
Common search patterns:
- By gene:
BRCA1[gene] - By clinical significance:
pathogenic[CLNSIG] - By condition:
breast cancer[disorder] - By variant:
NM_000059.3:c.1310_1313del[variant name] - By chromosome:
13[chr] - Combined:
BRCA1[gene] AND pathogenic[CLNSIG]
Programmatic Access via E-utilities
Access ClinVar programmatically using NCBI's E-utilities API. Refer to references/api_reference.md for comprehensive API documentation including:
- esearch - Search for variants matching criteria
- esummary - Retrieve variant summaries
- efetch - Download full XML records
- elink - Find related records in other NCBI databases
Quick example using curl:
# Search for pathogenic BRCA1 variants
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=BRCA1[gene]+AND+pathogenic[CLNSIG]&retmode=json"
Best practices:
- Test queries on the web interface before automating
- Use API keys to increase rate limits from 3 to 10 requests/second
- Implement exponential backoff for rate limit errors
- Set
Entrez.emailwhen using Biopython
What ships with it
3 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.
- 1mo ago Changed · +6 lines 1d487fb8dfdc
- 1mo ago First seen · 362 lines · 45 tokens per session scan A eee35b0a2435
clinvar-database is a skill published in the GitHub repository synthetic-sciences/openscience (4,251 stars, last pushed today), licensed Apache-2.0. It adds 45 tokens to every session and 3,226 once invoked, about $0.0002 per session on Opus 5.5. 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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