Clinical TempEval - Temporal Information Extraction from Clinical Notes

# Clinical TempEval - Temporal Information Extraction from Clinical Notes
# Based on Bethard et al., SemEval 2016
# Paper: https://aclanthology.org/S16-1165/
# Dataset: http://alt.qcri.org/semeval2016/task12/
#
# This task asks annotators to identify time expressions and event
# mentions in clinical text, and classify the temporal relation between
# events and times.
#
# Span Labels:
# - Time Expression: Date, time, duration, or frequency expression
# - Event Mention: Clinical event (procedure, condition, medication, etc.)
#
# Temporal Relation Labels:
# - Before: The event occurred before the time reference
# - After: The event occurred after the time reference
# - Overlap: The event overlaps with the time reference
# - Before-Overlap: The event began before and overlaps the time reference
# - Contains: The time reference contains the event

annotation_task_name: "Clinical TempEval - Temporal Extraction"
task_dir: "."

data_files:
  - sample-data.json

item_properties:
  id_key: "id"
  text_key: "text"

output_annotation_dir: "annotation_output/"
output_annotation_format: "json"

port: 8000
server_name: localhost

annotation_schemes:
  - annotation_type: span
    name: temporal_entities
    description: "Highlight time expressions and clinical event mentions in the text."
    labels:
      - "Time Expression"
      - "Event Mention"

  - annotation_type: radio
    name: temporal_relation
    description: "What is the temporal relation between the primary event and time reference?"
    labels:
      - "Before"
      - "After"
      - "Overlap"
      - "Before-Overlap"
      - "Contains"
    keyboard_shortcuts:
      "Before": "1"
      "After": "2"
      "Overlap": "3"
      "Before-Overlap": "4"
      "Contains": "5"
    tooltips:
      "Before": "The event occurred before the time reference"
      "After": "The event occurred after the time reference"
      "Overlap": "The event and the time reference overlap temporally"
      "Before-Overlap": "The event began before the time reference and continues into it"
      "Contains": "The time period contains the event entirely"

annotation_instructions: |
  You will be shown a clinical note excerpt. Your task is to:
  1. Highlight all time expressions (dates, times, durations) and event mentions
     (procedures, conditions, medications, symptoms).
  2. Classify the temporal relation between the primary event and time reference.

html_layout: |
  <div style="padding: 15px; max-width: 800px; margin: auto;">
    <div style="background: #f0f9ff; border: 1px solid #bae6fd; border-radius: 8px; padding: 16px; margin-bottom: 16px;">
      <strong style="color: #0369a1;">Clinical Note:</strong>
      <p style="font-size: 16px; line-height: 1.7; margin: 8px 0 0 0;">{{text}}</p>
    </div>
  </div>

allow_all_users: true
instances_per_annotator: 50
annotation_per_instance: 2
allow_skip: true
skip_reason_required: false