Biomedical Named Entity Recognition (JNLPBA)

# Biomedical Named Entity Recognition
# Based on standard biomedical NER annotation guidelines
# (JNLPBA, BC5CDR, NCBI Disease, i2b2, etc.)
#
# Entity Types:
# - Disease/Condition: Diseases, disorders, symptoms, findings
# - Medication/Drug: Medications, drugs, therapeutic agents
# - Procedure: Medical procedures, surgeries, treatments
# - Anatomy: Body parts, organs, tissues, cells
# - Gene/Protein: Genes, proteins, gene products
# - Chemical: Chemical compounds (non-drug)
# - Organism: Species, pathogens, organisms
#
# Annotation Guidelines:
# 1. Annotate the full noun phrase, including modifiers
#    - "severe acute respiratory syndrome" not just "syndrome"
# 2. Include abbreviations when they stand alone
#    - "COVID-19", "HIV", "NSAID"
# 3. Do NOT include articles (a, the) in the span
# 4. For nested entities, annotate the outermost mention
# 5. Annotate each mention, even if repeated
# 6. When uncertain, prefer broader entity boundaries
#
# Difficult Cases:
# - "Heart attack" → Disease (entire phrase)
# - "Blood pressure" → can be Anatomy or finding depending on context
# - "Insulin treatment" → Medication (insulin) + Procedure (treatment)

annotation_task_name: "Biomedical Named Entity Recognition"
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:
  - annotation_type: span
    name: entities
    description: "Highlight all biomedical entities in the text"
    labels:
      # Core clinical entities
      - "Disease"
      - "Symptom"
      - "Medication"
      - "Procedure"
      - "Anatomy"
      # Molecular/biological entities
      - "Gene"
      - "Protein"
      - "Chemical"
      - "Organism"
      # Clinical values
      - "Lab_Value"
      - "Dosage"
    label_colors:
      "Disease": "#ef4444"
      "Symptom": "#f97316"
      "Medication": "#3b82f6"
      "Procedure": "#8b5cf6"
      "Anatomy": "#22c55e"
      "Gene": "#06b6d4"
      "Protein": "#0891b2"
      "Chemical": "#eab308"
      "Organism": "#84cc16"
      "Lab_Value": "#a855f7"
      "Dosage": "#ec4899"
    tooltips:
      "Disease": "Diseases, disorders, conditions, syndromes (e.g., 'diabetes', 'hypertension', 'COVID-19')"
      "Symptom": "Signs, symptoms, clinical findings (e.g., 'fever', 'chest pain', 'fatigue')"
      "Medication": "Drugs, medications, therapeutic agents (e.g., 'aspirin', 'metformin', 'insulin')"
      "Procedure": "Medical procedures, surgeries, treatments (e.g., 'biopsy', 'MRI', 'chemotherapy')"
      "Anatomy": "Body parts, organs, tissues, cells (e.g., 'liver', 'left ventricle', 'neurons')"
      "Gene": "Gene names and symbols (e.g., 'BRCA1', 'TP53', 'insulin gene')"
      "Protein": "Protein names (e.g., 'hemoglobin', 'albumin', 'cytokines')"
      "Chemical": "Chemical compounds, non-drug chemicals (e.g., 'glucose', 'sodium chloride')"
      "Organism": "Species, pathogens, microorganisms (e.g., 'E. coli', 'SARS-CoV-2', 'Staphylococcus')"
      "Lab_Value": "Laboratory measurements and values (e.g., 'blood glucose 120 mg/dL', 'WBC count')"
      "Dosage": "Drug dosages and frequencies (e.g., '500mg twice daily', '10mg/kg')"
    allow_overlapping: false

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