BioNLP 2011 - Gene Regulation Event Extraction

# BioNLP 2011 - Gene Regulation Event Extraction
# Based on Kim et al., ACL Workshop 2011
# Paper: https://aclanthology.org/W11-1801/
# Dataset: https://2011.bionlp-st.org/
#
# This task involves two annotation layers:
# 1. Entity annotation: Mark spans of Gene, Protein, and other biological entities
# 2. Event annotation: Identify regulatory events (expression, transcription, etc.)
#
# Event types include:
# - Gene_expression: Production of a gene product
# - Transcription: DNA to mRNA conversion
# - Protein_catabolism: Protein degradation
# - Localization: Movement of a protein to a cellular location
# - Binding: Physical interaction between proteins
# - Positive_regulation: Upregulation of a process
# - Negative_regulation: Downregulation of a process
# - Regulation: General regulatory relationship

annotation_task_name: "BioNLP 2011: Gene Regulation Event 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: entity_types
    description: "Highlight and label biological entities in the text"
    labels:
      - "Gene"
      - "Protein"
      - "Cell_type"
      - "Cell_line"
      - "DNA_domain"
      - "RNA"
    tooltips:
      "Gene": "A gene name or symbol (e.g., p53, BRCA1)"
      "Protein": "A protein name or product (e.g., NF-kB, interleukin-2)"
      "Cell_type": "A type of cell (e.g., T cell, macrophage)"
      "Cell_line": "A specific cell line (e.g., Jurkat, HeLa)"
      "DNA_domain": "A DNA region or domain (e.g., promoter, enhancer)"
      "RNA": "An RNA molecule (e.g., mRNA, miRNA)"

  - annotation_type: event_annotation
    name: regulation_events
    description: "Identify gene regulation events and their types in the text"

annotation_instructions: |
  Annotate biomedical text for gene regulation events:
  1. First, use the span tool to mark all biological entities (genes, proteins, cell types, etc.).
  2. Then, use the event annotation tool to identify regulatory events.
  3. Common event types: gene expression, transcription, binding, positive/negative regulation.
  4. Each event should have a trigger word and one or more entity arguments.

html_layout: |
  <div style="padding: 15px; max-width: 800px; margin: auto;">
    <div style="background: #f0fdf4; border: 1px solid #bbf7d0; border-radius: 8px; padding: 16px; margin-bottom: 16px;">
      <strong style="color: #166534;">Biomedical Text:</strong>
      <p style="font-size: 16px; line-height: 1.8; margin: 8px 0 0 0;">{{text}}</p>
    </div>
    <div style="background: #fefce8; border: 1px solid #fde68a; border-radius: 8px; padding: 12px;">
      <p style="font-size: 13px; color: #713f12; margin: 0;"><strong>Instructions:</strong> First mark entity spans (Gene, Protein, etc.), then annotate regulation events.</p>
    </div>
  </div>

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