Analysis of Clinical Text: Disorder Identification and Normalization

# Clinical Text Analysis - Disorder Identification
# Based on Elhadad et al., SemEval 2015
# Paper: https://aclanthology.org/S15-2070/
# Dataset: https://www.i2b2.org/NLP/DataSets/
#
# This task requires annotators to identify disorder mentions and their
# attributes in de-identified clinical discharge summaries and progress
# notes. Annotators mark disorder spans, body locations, severity
# indicators, disease course markers, and negation cues, then classify
# the assertion status of each disorder.
#
# Span Types:
# - Disorder Mention: A disease, condition, or clinical finding
# - Body Location: An anatomical site associated with a disorder
# - Severity: An indicator of disorder severity (e.g., severe, mild, moderate)
# - Course: A marker of disease progression (e.g., progressive, worsening, stable)
# - Negation Indicator: A cue that negates a disorder (e.g., denies, no, negative for)
#
# Assertion Types:
# - Present: The disorder is currently present in the patient
# - Absent: The disorder has been ruled out or is not present
# - Possible: The disorder is suspected but not confirmed
# - Conditional: The disorder occurs under certain conditions
# - Hypothetical: The disorder is discussed as a future possibility
# - Associated with Someone Else: The disorder is attributed to someone other than the patient

annotation_task_name: "Clinical Text Analysis - Disorder Identification"
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: clinical_entity_spans
    description: "Highlight disorder mentions and their associated attributes in the clinical text."
    labels:
      - "Disorder Mention"
      - "Body Location"
      - "Severity"
      - "Course"
      - "Negation Indicator"
    tooltips:
      "Disorder Mention": "A disease, condition, symptom, or clinical finding (e.g., congestive heart failure, pneumonia, diabetes mellitus)"
      "Body Location": "An anatomical site or body part associated with a disorder (e.g., right knee, lower extremity, chest)"
      "Severity": "An indicator of how severe the disorder is (e.g., severe, mild, moderate, significant)"
      "Course": "A marker describing disease progression or trajectory (e.g., progressive, worsening, stable, acute)"
      "Negation Indicator": "A word or phrase that negates the presence of a disorder (e.g., denies, no, negative for, ruled out)"

  - annotation_type: radio
    name: assertion_status
    description: "What is the assertion status of the primary disorder mentioned in this text?"
    labels:
      - "Present"
      - "Absent"
      - "Possible"
      - "Conditional"
      - "Hypothetical"
      - "Associated with Someone Else"
    keyboard_shortcuts:
      "Present": "1"
      "Absent": "2"
      "Possible": "3"
      "Conditional": "4"
      "Hypothetical": "5"
      "Associated with Someone Else": "6"
    tooltips:
      "Present": "The disorder is currently present and confirmed in the patient"
      "Absent": "The disorder has been ruled out or is explicitly stated as not present"
      "Possible": "The disorder is suspected or being considered but not yet confirmed"
      "Conditional": "The disorder is present only under specific conditions or circumstances"
      "Hypothetical": "The disorder is discussed as a future possibility or preventive concern"
      "Associated with Someone Else": "The disorder is mentioned in reference to someone other than the patient (e.g., family history)"

annotation_instructions: |
  You will be shown de-identified clinical text from discharge summaries
  or progress notes.

  **Step 1: Entity Annotation**
  Highlight and classify the following spans in the text:
  - **Disorder Mention**: Any disease, condition, symptom, or finding
    (e.g., "congestive heart failure", "pneumonia", "edema")
  - **Body Location**: Anatomical sites associated with disorders
    (e.g., "right knee", "lower lobe", "bilateral lower extremity")
  - **Severity**: Severity indicators (e.g., "severe", "mild", "moderate")
  - **Course**: Disease progression markers (e.g., "progressive", "worsening", "acute")
  - **Negation Indicator**: Words negating a disorder (e.g., "denies", "no", "negative for")

  **Step 2: Assertion Classification**
  Classify the assertion status of the primary disorder:
  - **Present**: Disorder is confirmed in the patient
  - **Absent**: Disorder is ruled out or explicitly absent
  - **Possible**: Disorder is suspected but unconfirmed
  - **Conditional**: Disorder present only under certain conditions
  - **Hypothetical**: Discussed as a future possibility
  - **Associated with Someone Else**: Attributed to another person

html_layout: |
  <div style="padding: 15px; max-width: 800px; margin: auto;">
    <div style="background: #fef2f2; border: 1px solid #fca5a5; border-radius: 8px; padding: 12px; margin-bottom: 16px;">
      <strong style="color: #991b1b;">Note Type:</strong>
      <span style="font-size: 15px; margin-left: 8px; text-transform: capitalize;">{{note_type}}</span>
    </div>
    <div style="background: #f0f9ff; border: 1px solid #bae6fd; border-radius: 8px; padding: 16px; margin-bottom: 16px;">
      <strong style="color: #0369a1;">Clinical Text:</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