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 zamushwani/biomedical-ai-skills --skill clinical-nlpgit clone --depth 1 https://github.com/zamushwani/biomedical-ai-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/zamushwani/biomedical-ai-skills/clinical-nlp)<a href="https://agentmods.dev/skills/zamushwani/biomedical-ai-skills/clinical-nlp"><img src="https://agentmods.dev/badge/skills/zamushwani/biomedical-ai-skills/clinical-nlp/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/zamushwani/biomedical-ai-skills/clinical-nlp"><img src="https://agentmods.dev/badge/skills/zamushwani/biomedical-ai-skills/clinical-nlp.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 | $0.00000 | $0.05089 |
| Opus 5 | $0.00000 | $0.02544 |
| Sonnet 5 | $0.00000 | $0.01018 |
| Haiku 4.5 | $0.00000 | $0.00509 |
Grade A, and why
clinical-nlp 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 11d 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 — 448 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Clinical NLP
Information extraction from clinical free text. Covers note parsing and sectioning, biomedical named entity recognition, concept normalization to UMLS and ICD-10, assertion and negation detection, temporal relation extraction, adverse event identification, and de-identification. Written for public and credentialed research corpora, not for live patient records.
When to Use This Skill
Activate when the user requests:
- Entity extraction from clinical notes, discharge summaries, or pathology reports
- scispaCy, medspaCy, cTAKES, MedCAT, or QuickUMLS pipelines
- Concept normalization to UMLS CUIs, SNOMED CT, RxNorm, or ICD-10
- Negation, uncertainty, or family-history assertion detection
- Adverse event or medication extraction from narrative text
- Temporal relation extraction from notes
- De-identification of clinical text
- Choosing between a rule-based pipeline and a clinical transformer
Inputs
| Data Type | Format | Source |
|---|---|---|
| Clinical notes | Plain text, one note per record | MIMIC-IV-Note, n2c2 (both credentialed) |
| Annotated corpora | BRAT .ann, BioC XML, CoNLL |
n2c2, BC5CDR, NCBI-Disease, MedMentions |
| Terminology | UMLS Metathesaurus (RRF) | NLM, licence required |
| Biomedical abstracts | PubMed XML | E-utilities, unrestricted |
Before Any Code: The Access Question
Clinical text is not like expression data. The corpus decides what you can do.
PubMed abstracts open. No agreement. Use freely.
BC5CDR, NCBI-Disease open annotated corpora. Good for benchmarking NER.
MedMentions open, UMLS-linked. Good for entity linking.
MIMIC-IV-Note PhysioNet credentialed: CITI training + signed DUA.
Cannot be redistributed, posted, or pasted into a
hosted LLM API. The DUA prohibits it.
n2c2 (formerly i2b2) separate DUA through the hosting institution.
UMLS Metathesaurus free but licensed. Required by QuickUMLS, MedCAT
and the scispaCy UMLS linker. You must accept the
licence and download it yourself; no package ships it.
Two consequences that catch people:
- Sending credentialed note text to an external API is a DUA breach, not a
grey area. Run models locally on that text.
- Never commit note text, even "de-identified" text, to a repository.
De-identification is imperfect (below), and the DUA governs regardless.
Develop on the open corpora. Move to credentialed data only inside the
environment the DUA allows.
What ships with it
6 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.
- 11d ago First seen · 448 lines · 0 tokens per session scan A d000b90a426b
clinical-nlp is a skill published in the GitHub repository zamushwani/biomedical-ai-skills (1 stars, last pushed 13d ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 5,089 tokens. 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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