RadGraph-XL: Radiology Entity and Relation Extraction

# RadGraph-XL: Radiology Entity and Relation Extraction
# Based on Khanna et al., Findings ACL 2024
# Paper: https://aclanthology.org/2024.findings-acl.765/
# Dataset: https://physionet.org/content/radgraph-xl/
#
# RadGraph-XL provides expert annotations of radiology reports with clinical
# entities and relations. This enables automated extraction of structured
# information from free-text radiology reports.
#
# Entity Types:
# - Anatomy: Body parts, organs, anatomical structures
#   (e.g., lungs, heart, mediastinum, pleural space)
# - Observation: Clinical findings, conditions, abnormalities
#   (e.g., opacity, effusion, consolidation, pneumothorax)
# - Medical Device: Tubes, lines, implants, equipment
#   (e.g., endotracheal tube, central line, pacemaker)
# - Procedure: Medical procedures, interventions
#   (e.g., intubation, thoracentesis, CABG)
# - Descriptor: Modifiers describing size, severity, change
#   (e.g., bilateral, small, stable, worsening, new)
#
# Relation Types:
# - located_at: Observation/device is located at an anatomy
# - suggestive_of: Observation suggests a condition
# - modify: Descriptor modifies an entity
# - part_of: Anatomy is part of another anatomy
#
# Annotation Guidelines:
# 1. Read the radiology report sentence in context
# 2. Identify all clinical entities and assign types
# 3. For each entity pair, determine the relation type
# 4. Anatomy-observation pairs typically use located_at
# 5. Descriptor-entity pairs typically use modify
# 6. Consider negation and uncertainty in observations

annotation_task_name: "RadGraph-XL: Radiology Relation 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"

annotation_schemes:
  # Step 1: Identify clinical entities
  - annotation_type: span
    name: clinical_entities
    description: "Highlight all clinical entities in the radiology report"
    labels:
      - "Anatomy"
      - "Observation"
      - "Medical Device"
      - "Procedure"
      - "Descriptor"
    label_colors:
      "Anatomy": "#3b82f6"
      "Observation": "#ef4444"
      "Medical Device": "#22c55e"
      "Procedure": "#f59e0b"
      "Descriptor": "#8b5cf6"
    keyboard_shortcuts:
      "Anatomy": "1"
      "Observation": "2"
      "Medical Device": "3"
      "Procedure": "4"
      "Descriptor": "5"
    tooltips:
      "Anatomy": "Body parts, organs, anatomical structures (e.g., lungs, heart, mediastinum, pleural space)"
      "Observation": "Clinical findings, conditions, abnormalities (e.g., opacity, effusion, consolidation, pneumothorax)"
      "Medical Device": "Tubes, lines, implants, equipment (e.g., endotracheal tube, central line, pacemaker)"
      "Procedure": "Medical procedures or interventions (e.g., intubation, thoracentesis, sternotomy)"
      "Descriptor": "Modifiers describing size, severity, or change (e.g., bilateral, small, stable, worsening)"
    allow_overlapping: false

  # Step 2: Link entities with clinical relation types
  - annotation_type: span_link
    name: clinical_relations
    description: "Draw relations between clinical entities"
    labels:
      - "located_at"
      - "suggestive_of"
      - "modify"
      - "part_of"
    tooltips:
      "located_at": "Observation or device is located at an anatomical structure (e.g., opacity located_at right lung)"
      "suggestive_of": "Observation suggests or indicates a clinical condition (e.g., air-fluid level suggestive_of abscess)"
      "modify": "Descriptor modifies another entity (e.g., bilateral modify effusion; small modify opacity)"
      "part_of": "Anatomical structure is part of another structure (e.g., right lobe part_of liver)"

html_layout: |
  <div style="margin-bottom: 10px; padding: 8px; background: #f0f4f8; border-radius: 4px;">
    <strong>Report Section:</strong> {{report_section}}
  </div>
  <div style="font-size: 16px; line-height: 1.6; font-family: 'Courier New', monospace;">
    {{text}}
  </div>

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