n2c2 2022: Social Determinants of Health Extraction

# n2c2 2022 Track 2: Social Determinants of Health Extraction
# Based on Lybarger et al., JAMIA 2023
# Paper: https://academic.oup.com/jamia/article/30/8/1367/7043152
# Dataset: https://portal.dbmi.hms.harvard.edu/projects/n2c2-2022-track2/
#
# Task: Extract SDOH entities and attributes from clinical notes
# Annotators identify mentions of social determinants and classify
# their status attributes.
#
# SDOH Entity Types:
# - Employment: job status, occupation, work-related information
# - LivingStatus: housing, living arrangements, homelessness
# - Alcohol: alcohol use, drinking behaviors
# - Drug: illicit drug use, substance abuse
# - Tobacco: smoking, tobacco/nicotine use
#
# Status Attributes: Current, Past, None, Unknown

annotation_task_name: "n2c2 SDOH Extraction from Clinical Notes"
task_dir: "."

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

output_annotation_dir: "annotation_output/"
output_annotation_format: "json"

annotation_schemes:
  # Step 1: Identify SDOH entity mentions
  - annotation_type: span
    name: sdoh_entity
    description: "Highlight mentions of social determinants of health in the clinical text"
    labels:
      - "Employment"
      - "LivingStatus"
      - "Alcohol"
      - "Drug"
      - "Tobacco"
    label_colors:
      "Employment": "#22c55e"
      "LivingStatus": "#3b82f6"
      "Alcohol": "#ef4444"
      "Drug": "#f97316"
      "Tobacco": "#eab308"
    tooltips:
      "Employment": "Mentions of job status, occupation, work, unemployment, retirement, or disability"
      "LivingStatus": "Mentions of housing situation, living arrangements, homelessness, or shelter"
      "Alcohol": "Mentions of alcohol consumption, drinking, or alcohol-related behaviors"
      "Drug": "Mentions of illicit drug use, substance abuse, or recreational drug use"
      "Tobacco": "Mentions of smoking, tobacco use, vaping, chewing tobacco, or nicotine"
    allow_overlapping: false

  # Step 2: Status of the identified SDOH entity
  - annotation_type: radio
    name: entity_status
    description: "What is the current status of the identified SDOH factor?"
    labels:
      - "Current"
      - "Past"
      - "None"
      - "Unknown"
    keyboard_shortcuts:
      "Current": "c"
      "Past": "p"
      "None": "n"
      "Unknown": "u"
    tooltips:
      "Current": "The patient currently has this SDOH status (e.g., currently smokes, currently employed)"
      "Past": "The patient had this status in the past (e.g., former smoker, previously homeless)"
      "None": "The patient explicitly does not have this status (e.g., denies alcohol, never smoked)"
      "Unknown": "The status cannot be determined from the available text"

html_layout: |
  <div style="margin-bottom: 10px; padding: 8px; background: #f8f9fa; border-radius: 6px;">
    <strong>Note Type:</strong> {{note_type}}
  </div>
  <div style="padding: 10px; border: 1px solid #ddd; border-radius: 6px; line-height: 1.8; font-family: monospace; white-space: pre-wrap;">
    {{text}}
  </div>

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