Adverse Drug Event Extraction (CADEC)

# Adverse Drug Event Extraction (CADEC-style)
# Based on Karimi et al., J Biomed Inform 2015
# Paper: https://pubmed.ncbi.nlm.nih.gov/25817970/
# Dataset: https://data.csiro.au/collection/csiro:10948
#
# Entity Types:
# - Drug: medication names (brand or generic)
# - ADR (Adverse Drug Reaction): side effects caused by the drug
# - Disease: conditions for which the patient takes medication
# - Symptom: symptoms of a disease leading to medication use
# - Finding: clinical concepts with unclear categorization
#
# Note: CADEC uses colloquial language from patient forums (askapatient.com)
# Annotations are mapped to SNOMED-CT and MedDRA vocabularies

port: 8000
server_name: localhost
task_name: "Adverse Drug Event Extraction"

data_files:
  - sample-data.json
id_key: id
text_key: text

output_file: annotations.json

annotation_schemes:
  # Primary entity annotation
  - annotation_type: span
    name: entities
    description: "Highlight and classify medical entities in the text"
    labels:
      - Drug
      - ADR
      - Disease
      - Symptom
      - Finding
    label_colors:
      Drug: "#3b82f6"
      ADR: "#ef4444"
      Disease: "#8b5cf6"
      Symptom: "#f59e0b"
      Finding: "#6b7280"
    tooltips:
      Drug: "Medication name - brand name (e.g., Lipitor) or generic name (e.g., atorvastatin)"
      ADR: "Adverse Drug Reaction - side effect or negative reaction caused by the drug (e.g., 'terrible muscle pain', 'made me dizzy')"
      Disease: "Medical condition for which the patient takes the medication (e.g., 'high cholesterol', 'arthritis')"
      Symptom: "Symptom of the underlying disease, not caused by the drug (e.g., 'joint pain' that led to taking the drug)"
      Finding: "Other clinical concepts that don't clearly fit above categories"
    allow_overlapping: false

  # Severity of ADR (for ADR spans)
  - annotation_type: radio
    name: adr_severity
    description: "If an ADR is present, how severe does the patient describe it?"
    labels:
      - Mild
      - Moderate
      - Severe
      - Life-threatening
      - Not specified
      - N/A (no ADR)
    keyboard_shortcuts:
      Mild: "1"
      Moderate: "2"
      Severe: "3"
      "Life-threatening": "4"
      "Not specified": "5"
      "N/A (no ADR)": "0"
    tooltips:
      Mild: "Minor inconvenience, patient continued medication"
      Moderate: "Significant discomfort, may have affected daily activities"
      Severe: "Serious reaction, patient stopped medication or sought medical help"
      "Life-threatening": "Emergency situation, hospitalization, or risk of death"
      "Not specified": "Severity not clearly indicated in text"
      "N/A (no ADR)": "No adverse drug reaction in this text"

  # Temporal relation to drug
  - annotation_type: radio
    name: temporal_relation
    description: "When did the ADR occur relative to taking the drug?"
    labels:
      - "Immediate (within hours)"
      - "Short-term (days to weeks)"
      - "Long-term (months)"
      - "After stopping drug"
      - "Not specified"
      - "N/A"
    tooltips:
      "Immediate (within hours)": "Reaction occurred shortly after taking the medication"
      "Short-term (days to weeks)": "Reaction developed within days or weeks of starting"
      "Long-term (months)": "Reaction appeared after prolonged use"
      "After stopping drug": "Reaction occurred after discontinuing the medication"
      "Not specified": "Timing not clearly indicated"
      "N/A": "Not applicable (no ADR present)"

  # Drug-ADR relationship certainty
  - annotation_type: radio
    name: causality_certainty
    description: "How certain is the patient that the drug caused the reaction?"
    labels:
      - "Definite"
      - "Probable"
      - "Possible"
      - "Uncertain"
      - "N/A"
    keyboard_shortcuts:
      "Definite": "d"
      "Probable": "p"
      "Possible": "o"
      "Uncertain": "u"
      "N/A": "n"
    tooltips:
      "Definite": "Patient explicitly states drug caused the reaction (e.g., 'this drug gave me...')"
      "Probable": "Strong implication of causation (e.g., 'started having X after taking Y')"
      "Possible": "Temporal association but causation unclear"
      "Uncertain": "Patient unsure if drug is responsible"
      "N/A": "Not applicable (no ADR present)"

allow_all_users: true
instances_per_annotator: 100
annotation_per_instance: 2
allow_skip: true
skip_reason_required: false