This package is a documentation-first Agent Skill for medical/scientific manuscript writing. Unlike zero-network skills, it intentionally uses network access for literature work: WebSearch/WebFetch and literature APIs (PubMed, OpenAlex, Europe PMC, Semantic Scholar) during Phase −1 novelty checks, Phase 1 literature search, and Phase 5 citation verification. No credentials are required for any of these.
The utility scripts under scripts/ are optional. They read local files, write
local Markdown/plot outputs, and make no network calls. Analysis and PDF
utilities use the Python packages listed in requirements.txt.
This skill is built for clinicians working with real patient data. The data
rules below mirror templates/data-management.md and the AI-for-Science model
(references/ai-for-science-model.md):
- Raw clinical data stays local. Always. Generated project directories keep
original data under
data/raw/, which is treated as read-only and is gitignored — it must never be committed or pushed anywhere. - Never commit PHI. Only de-identified, processed data belongs in
data/processed/. De-identification happens before anything leaves the raw folder. - Never paste identifiable patient information into any AI chat, including the agent running this skill. Work from de-identified extracts.
- AI never originates data. The skill must never fabricate a data point, participant, or result (📊 DATA sovereignty). Any output that appears to contain invented data is a bug — report it.
| Capability | Used | Notes |
|---|---|---|
| Network access | Yes | Literature APIs and web search only; no telemetry |
| Filesystem write | Yes | Manuscript project directories and script outputs |
| External tools | Optional | Python packages from requirements.txt; pandoc for docx/pdf compile |
| Credentials | No | No API keys required |
| Background execution | No |
- Do not add hidden scripts or install-time automation.
- Do not add new network destinations without documenting them here.
- Do not embed real patient data — even "harmless" fragments — in examples, tests, or case studies. All repo examples are illustrative and PHI-free.
- Do not weaken the 💡 IDEA / 📊 DATA human-sovereignty gates in SKILL.md.
Open a GitHub issue for suspected vulnerabilities, unsafe instructions, or hidden behavior. Do not include patient data or other confidential material in public reports.