gabrielmoreira 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.jsonbuilt from BRAT.txt+.annfiles - Annotations: Original spans + MedDRA + SNOMED CT normalisations
- Stats: ~1,250 documents, ~7,600 entity annotations
- Path:
DATA_PATHvariable in34_CADEC.py - Citation: Karimi et al., 2015. J Biomed Inform 55:73–81