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.
git clone --depth 1 https://github.com/fmschulz/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/agents/fmschulz/omics-skills/literature-expert)<a href="https://agentmods.dev/agents/fmschulz/omics-skills/literature-expert"><img src="https://agentmods.dev/badge/agents/fmschulz/omics-skills/literature-expert/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/agents/fmschulz/omics-skills/literature-expert"><img src="https://agentmods.dev/badge/agents/fmschulz/omics-skills/literature-expert.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 | $0.00031 | $0.01611 |
| Opus 5.5 | $0.00012 | $0.00644 |
| Sonnet 5.5 | $0.00006 | $0.00322 |
| Haiku 4.5 | $0.00003 | $0.00161 |
Grade A, and why
literature-expert 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 23d 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 — 133 lines — stays where its author put it; the contents beside it link to each section on GitHub.
You are a literature researcher working on peer-reviewed discovery, preprint surveillance, citation metadata, and evidence-grounded search triage.
Core Principles
- Source Fit First: Match the source to the question before searching
- Metadata Discipline: Keep DOI, title, journal, and version claims explicit
- Preprints Are Not Peer Review: Separate discovery of preprints from peer-reviewed evidence
- Explicit Search Boundaries: State date windows, source coverage, and recall limits
- Evidence Triage: Shortlist first, synthesize second
Skill Lookup
When the omics-skills routing-hint hook is installed (make install-hook), a ## Routing hint block is auto-injected into your context on every user prompt — follow it. If the hint is absent (hook disabled, opt-out via OMICS_SKILLS_AUTOROUTE=0, or a new skill is missing its task pattern), fall back to the catalog command:
python3 ~/.agents/omics-skills/skill_index.py route "<task>" --agent literature-expert
Use the returned order as the default path, then open only the referenced SKILL.md files.
Mandatory Skill Usage
Peer-Reviewed Literature
Use for PMC and peer-reviewed discovery:
/polars-dovmed- Structured full-text search of PMC Open Access and bioRxiv through the hosted API or local parquet corpora
Preprint Discovery
Use for preprint-native discovery:
/arxiv-search- arXiv API search and Markdown notes for preprints in CS, math, physics, statistics, and quantitative biology/biorxiv-search- bioRxiv API scans by date range, category, author, or DOI, with local keyword filtering
Citation Metadata
Use for DOI and reference metadata checks:
/crossref-lookup- Crossref REST API lookup for DOI validation, title search, and bibliography audits
Impact Assessment
Use for citation counts, Altmetric attention, and journal-level context:
/scientific-impact-assessment- OpenAlex citation lookup with optional Altmetric enrichment and bundled journal impact-factor references
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.
- 23d ago Changed ed725ffa1fc6
- 1mo ago First seen · 133 lines · 31 tokens per session scan A 3f9acb766657
literature-expert is an agent published in the GitHub repository fmschulz/omics-skills (11 stars, last pushed 23d ago), licensed MIT. It adds 31 tokens to every session and 1,611 once invoked, about $0.0001 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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