Drug-Drug Interaction Extraction from Biomedical Texts

# DDI Extraction from Biomedical Texts
# Based on Segura-Bedmar et al., SemEval 2013
# Paper: https://aclanthology.org/S13-2056/
# Dataset: https://github.com/isegura/DDICorpus
#
# This task requires annotators to identify drug entities in biomedical text
# and classify the type of interaction between drug pairs. Drug entities
# are categorized as Drug (generic), Brand (trade name), Group (drug class),
# or Drug_n (active substances not approved for human use). Interaction
# types include Mechanism, Effect, Advice, Int, and No Interaction.
#
# Entity Types:
# - Drug: Generic drug names (e.g., warfarin, methotrexate)
# - Brand: Trade/brand names (e.g., Zocor, Prilosec)
# - Group: Drug classes or families (e.g., NSAIDs, ACE inhibitors)
# - Drug_n: Active substances not approved for human use
#
# Interaction Types:
# - Mechanism: The interaction is described at a pharmacokinetic level
# - Effect: The interaction produces a pharmacodynamic effect
# - Advice: A recommendation or warning about the drug combination
# - Int: An interaction is stated without further detail
# - No Interaction: No interaction exists between the drug pair

annotation_task_name: "DDI Extraction from Biomedical Texts"
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: drug_entity_spans
    description: "Highlight all drug entities in the text and classify their type."
    labels:
      - "Drug"
      - "Brand"
      - "Group"
      - "Drug_n"
    tooltips:
      "Drug": "Generic drug name (e.g., warfarin, cyclosporine, methotrexate)"
      "Brand": "Trade or brand name of a drug (e.g., Zocor, Prilosec)"
      "Group": "Drug class or family name (e.g., NSAIDs, ACE inhibitors, statins)"
      "Drug_n": "Active substance not approved for human use or experimental compound"

  - annotation_type: radio
    name: interaction_type
    description: "What type of drug-drug interaction is described in this text?"
    labels:
      - "Mechanism"
      - "Effect"
      - "Advice"
      - "Int"
      - "No Interaction"
    keyboard_shortcuts:
      "Mechanism": "1"
      "Effect": "2"
      "Advice": "3"
      "Int": "4"
      "No Interaction": "5"
    tooltips:
      "Mechanism": "The interaction is described at the pharmacokinetic level (e.g., inhibits metabolism, reduces clearance)"
      "Effect": "The interaction produces a specific pharmacodynamic effect (e.g., increased bleeding risk)"
      "Advice": "A recommendation or warning about the drug combination (e.g., avoid concomitant use)"
      "Int": "An interaction is mentioned without specifying mechanism or effect"
      "No Interaction": "The text describes drugs but no interaction between them"

annotation_instructions: |
  You will be shown biomedical text that may describe drug-drug interactions.

  **Step 1: Entity Annotation**
  Highlight all drug mentions in the text and classify each as:
  - **Drug**: Generic drug names (e.g., warfarin, cyclosporine)
  - **Brand**: Trade names (e.g., Zocor, Prilosec)
  - **Group**: Drug classes (e.g., NSAIDs, ACE inhibitors)
  - **Drug_n**: Substances not approved for human use

  **Step 2: Interaction Classification**
  Classify the type of interaction described:
  - **Mechanism**: Pharmacokinetic interaction (metabolism, clearance, etc.)
  - **Effect**: Pharmacodynamic effect of the interaction
  - **Advice**: Recommendation or warning about the combination
  - **Int**: Interaction stated without specific details
  - **No Interaction**: No interaction between the mentioned drugs

html_layout: |
  <div style="padding: 15px; max-width: 800px; margin: auto;">
    <div style="background: #f0fdf4; border: 1px solid #86efac; border-radius: 8px; padding: 16px; margin-bottom: 16px;">
      <strong style="color: #166534;">Biomedical 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