PHEE Query Skill
Search PHEE annotated pharmacovigilance events by drug name, adverse effect, or free text. Substring matching is case-insensitive across all event fields.
| Input Pattern | Match Logic |
|---|---|
drug name (e.g. phenytoin) | substring on drug, treatment, combination_drug, and text |
adverse effect (e.g. hepatotoxicity) | substring on effect, treatment_disorder, and text |
| any other text | substring on all event fields and full sentence |
API
| Function | Input | Returns |
|---|---|---|
load_phee(data_dir) | directory path | list[dict] (cached) |
search(records, entity) | single entity string | list[dict] |
search_batch(records, entities) | list of entity strings | dict[str, list[dict]] |
summarize(hits, entity) | hit list + label | compact text (sentence count, ADE/PTE counts, top drugs & effects) |
to_json(hits) | hit list | list[dict] |
Record Schema
Each record returned by search:
{ "id": "8908396_3", "text": "A 52-year-old Black woman on phenytoin therapy ...", "split": "train", "events": [ { "event_type": "Adverse_event | Potential_therapeutic_event", "trigger": ["developed"], "subject": ["A 52-year-old Black woman ..."], "subject_age": ["52-year-old"], "subject_gender": ["woman"], "subject_race": ["Black"], "subject_population": [], "subject_disorder": ["post-traumatic epilepsy"], "treatment": ["phenytoin therapy ..."], "drug": ["phenytoin"], "dosage": [], "freq": [], "route": [], "duration": [], "treatment_disorder": ["post-traumatic epilepsy"], "combination_drug": [], "effect": ["transient hemiparesis"] } ] }
Usage
See if __name__ == "__main__" block in 38_PHEE.py for runnable examples
covering: single drug search, single effect search, batch search, and JSON
output.
Data
- Source: PHEE dataset (Zenodo record 7689970), EMNLP 2022
- Files:
train.json(~2,900 sentences),dev.json(~960),test.json(~960) - Path:
DATA_DIRvariable in38_PHEE.py(resources_metadata/drug_nlp/PHEE/data/json) - Event types:
Adverse_event,Potential_therapeutic_event - Main arguments: Subject, Treatment, Effect
- Sub-arguments: Subject (age, gender, race, population, disorder); Treatment (drug, dosage, freq, route, duration, disorder, combination.drug)
