RadGraph-XL: Radiology Entity and Relation Extraction

# RadGraph-XL: Radiology Entity and Relation Extraction
# Based on Delbrouck 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 (each entity is Anatomy or Observation, with a certainty level):
# - Anatomy: Body parts, organs, anatomical structures
#   (e.g., lungs, heart, mediastinum, pleural space)
# - Observation: Clinical findings, conditions, abnormalities
#   (e.g., opacity, effusion, consolidation, pneumothorax)
# Certainty levels: Definitely Present, Uncertain, Definitely Absent
#   (e.g., "no pericardial effusion" is an Observation: Definitely Absent)
#
# Relation Types:
# - located_at: an Observation is located at an Anatomy
# - suggestive_of: an Observation suggests another Observation/condition
# - modify: one entity modifies another of the same type
#
# Annotation Guidelines:
# 1. Read the radiology report sentence in context
# 2. Identify all Anatomy and Observation entities
# 3. Assign each entity a certainty level (present / uncertain / absent)
# 4. For each entity pair, determine the relation type
# 5. Observation-anatomy pairs typically use located_at
# 6. Consider negation and hedging when assigning certainty

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 (Anatomy / Observation) with certainty
  - annotation_type: span
    name: clinical_entities
    description: "Highlight all Anatomy and Observation entities, marking each with a certainty level"
    labels:
      - "Observation: Definitely Present"
      - "Observation: Uncertain"
      - "Observation: Definitely Absent"
      - "Anatomy: Definitely Present"
      - "Anatomy: Uncertain"
      - "Anatomy: Definitely Absent"
    label_colors:
      "Observation: Definitely Present": "#ef4444"
      "Observation: Uncertain": "#f59e0b"
      "Observation: Definitely Absent": "#9ca3af"
      "Anatomy: Definitely Present": "#3b82f6"
      "Anatomy: Uncertain": "#38bdf8"
      "Anatomy: Definitely Absent": "#a5b4fc"
    keyboard_shortcuts:
      "Observation: Definitely Present": "1"
      "Observation: Uncertain": "2"
      "Observation: Definitely Absent": "3"
      "Anatomy: Definitely Present": "4"
      "Anatomy: Uncertain": "5"
      "Anatomy: Definitely Absent": "6"
    tooltips:
      "Observation: Definitely Present": "A finding stated to be present (e.g., opacity, effusion, consolidation, pneumothorax)"
      "Observation: Uncertain": "A finding stated with hedging or uncertainty (e.g., 'concerning for', 'possible', 'may represent')"
      "Observation: Definitely Absent": "A finding explicitly negated (e.g., 'no pericardial effusion', 'lungs are clear')"
      "Anatomy: Definitely Present": "A body part or anatomical structure referenced as present (e.g., lungs, heart, mediastinum)"
      "Anatomy: Uncertain": "An anatomical structure referenced with uncertainty"
      "Anatomy: Definitely Absent": "An anatomical structure referenced as absent (e.g., surgically removed)"
    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"
    tooltips:
      "located_at": "An Observation is located at an anatomical structure (e.g., opacity located_at right lung)"
      "suggestive_of": "An Observation suggests or indicates another Observation/condition (e.g., air-fluid level suggestive_of abscess)"
      "modify": "One entity modifies another of the same type (e.g., 'small' modify effusion; 'lower' modify lobe)"

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