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 hossainlab/omics-skills --skill omics-dataset-retrievalgit clone --depth 1 https://github.com/hossainlab/omics-skillsWrote 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/hossainlab/omics-skills/omics-dataset-retrieval)<a href="https://agentmods.dev/skills/hossainlab/omics-skills/omics-dataset-retrieval"><img src="https://agentmods.dev/badge/skills/hossainlab/omics-skills/omics-dataset-retrieval/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/hossainlab/omics-skills/omics-dataset-retrieval"><img src="https://agentmods.dev/badge/skills/hossainlab/omics-skills/omics-dataset-retrieval.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 | $0.00156 | $0.02250 |
| Opus 5.5 | $0.00062 | $0.00900 |
| Sonnet 5.5 | $0.00031 | $0.00450 |
| Haiku 4.5 | $0.00016 | $0.00225 |
Grade A, and why
omics-dataset-retrieval 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 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.
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.
How it starts
The opening of the file, as written. The whole thing — 170 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Omics Dataset Retrieval
Build a deduplicated, relevance-audited catalog of public omics datasets for a disease, phenotype, gene, or biological process. Query every reachable public repository, classify each hit by omics type, score its relevance, and emit a CSV catalog + Markdown summary (+ optional landscape figure).
Boundary: catalog metadata only. This skill does not download raw data files and does not perform downstream analysis.
Worked examples (Alzheimer's, BCL11A/erythroid, PDAC) are in
references/examples.md.
Inputs
| Parameter | Type | Description |
|---|---|---|
disease_or_topic |
string | Disease, phenotype, gene, or process (e.g. "sickle cell disease", "BCL11A") |
synonyms |
list[str] | Alternative names, abbreviations, gene symbols (e.g. ["SCD","SCA","HbSS"]) |
omics_types |
list[str] or "all" |
Restrict to omics types, or "all" (default) |
organism |
string | "all" (default) — human, mouse, and all others. Restrict to "human"/"mouse" only if explicitly requested |
year_min |
int | Earliest publication year (default: no limit) |
output_dir |
path | Where to write outputs (default: /mnt/results/) |
Outputs
| File | Description |
|---|---|
<disease>_omics_datasets_MASTER.csv |
Full catalog with all metadata + relevance labels |
<disease>_omics_datasets_VALIDATED.csv |
Filtered to CORE/DIRECT + ADJACENT only |
<disease>_omics_summary.md |
Counts by omics type / repository, top datasets, limitations |
<disease>_omics_landscape.png |
Optional overview: donut + repository bar + timeline |
Workflow
Step 1 — Ask clarification questions (MANDATORY before any search)
Not optional. Before querying, use AskUserQuestion to collect the items below
in a single call. Skip only questions already answered in the user's initial
message; always ask the rest. Answers materially change which repositories run,
result counts, and relevance tuning.
What ships with it
5 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 First seen · 170 lines · 156 tokens per session scan A 1b0926348774
omics-dataset-retrieval is a skill published in the GitHub repository hossainlab/omics-skills (2 stars, last pushed 3mo ago), licensed MIT. It adds 156 tokens to every session and 2,250 once invoked, about $0.0006 per session on Opus 5.5. 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 2026-08-31.
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