Cadec

Skill BioTender-max/awesome-bio-agent-skills/skills/drugclaw/cadec

Query the CADEC (CSIRO Adverse Drug Event Corpus). Use whenever the user asks about adverse drug event mentions in consumer health text, entity annotations from patient forum posts, MedDRA/SNOMED-CT normalised ADR spans, or wants to look up drugs, symptoms, or coded entities in the CADEC corpus.From its SKILL.md

Install

npx -y skills add BioTender-max/awesome-bio-agent-skills --skill cadec

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

One thing to look at

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SKILL.md

1.8 KB, 440 tokens by cl100k_base, as published. Nobody here has run it

CADEC Query Skill

Search CADEC annotated patient forum posts by any entity. Auto-detects type:

Input Pattern	Detected As	Match Logic
`10019211` (8 digits)	MedDRA code	exact on normalizations.code
`22253000` (6-18 digits)	SNOMED CT code	exact on normalizations.code
anything else	free text	substring on entity text, type, or doc_id

API

Function	Input	Returns
`load_cadec(path)`	JSON path	list[dict] (cached)
`search(entity)`	single entity string	list[dict]
`search_batch(entities)`	list of entity strings	dict[str, list[dict]]
`summarize(hits, entity)`	hits + label	compact text
`to_json(hits)`	list[dict]	same list (JSON-ready)

Entity Types in Corpus

Type	Description
ADR	Adverse Drug Reaction
Drug	Medication mention
Disease	Pre-existing condition
Symptom	Patient-reported symptom
Finding	Clinical finding

Usage

See if __name__ == "__main__" block in 34_CADEC.py for runnable examples: drug name search, ADR text search, MedDRA code lookup, batch search, JSON output.

Data

Source: CADEC v2, CSIRO (AskaPatient.com forum posts)
Local file: cadec_combined.json built from BRAT .txt + .ann files
Annotations: Original spans + MedDRA + SNOMED CT normalisations
Stats: ~1,250 documents, ~7,600 entity annotations
Path: DATA_PATH variable in 34_CADEC.py
Citation: Karimi et al., 2015. J Biomed Inform 55:73–81

What ships with it: 5 files

12.9 KB alongside SKILL.md, 4 of them executable

cadec_skill.pyruns4.4 KB
example.pyruns6.1 KB
__init__.pyruns126 B
README.md1.5 KB
retrieve.pyruns776 B