ChemProt - Chemical-Protein Interaction Annotation

# ChemProt - Chemical-Protein Interaction Annotation
# Based on Krallinger et al., BioCreative VI 2017
# Paper: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vi/track-5/
# Dataset: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vi/track-5/
#
# Annotate biomedical abstracts to identify chemical and gene/protein entities,
# then classify the type of interaction between them. This supports automated
# mining of drug-target interactions from scientific literature.
#
# Entity Types:
# - Chemical: Drug names, small molecules, compounds (e.g., ibuprofen, methotrexate)
# - Gene/Protein: Gene or protein names (e.g., EGFR, p53, cyclooxygenase-2)
#
# Relation Types (between chemical and gene/protein):
# - Inhibitor: Chemical inhibits the protein/gene activity
# - Substrate: Chemical is a substrate for the protein/enzyme
# - Agonist: Chemical activates or enhances the protein receptor
# - Antagonist: Chemical blocks or reduces the protein receptor activity
# - Product: Chemical is a product of the protein/enzyme reaction
# - Activator: Chemical increases the protein/gene expression or activity
# - No Relation: Entities co-occur but have no direct interaction
#
# Guidelines:
# 1. Mark all chemical and gene/protein entities in the text
# 2. Select the primary relation type between the key entities
# 3. If multiple entity pairs exist, classify the most prominent interaction

annotation_task_name: "ChemProt: Chemical-Protein Interaction Annotation"
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: biomedical_entities
    description: "Highlight and label chemical and gene/protein entities in the text"
    labels:
      - "Chemical"
      - "Gene/Protein"
    tooltips:
      "Chemical": "Drug name, small molecule, or chemical compound (e.g., aspirin, methotrexate, glucose)"
      "Gene/Protein": "Gene name, protein name, or enzyme (e.g., EGFR, p53, COX-2, insulin receptor)"

  - annotation_type: radio
    name: relation_type
    description: "What is the primary type of interaction between the chemical and protein/gene?"
    labels:
      - "Inhibitor"
      - "Substrate"
      - "Agonist"
      - "Antagonist"
      - "Product"
      - "Activator"
      - "No Relation"
    keyboard_shortcuts:
      "Inhibitor": "1"
      "Substrate": "2"
      "Agonist": "3"
      "Antagonist": "4"
      "Product": "5"
      "Activator": "6"
      "No Relation": "7"
    tooltips:
      "Inhibitor": "The chemical inhibits or blocks the activity of the protein/gene"
      "Substrate": "The chemical serves as a substrate for the enzyme/protein"
      "Agonist": "The chemical activates or stimulates the receptor/protein"
      "Antagonist": "The chemical blocks or reduces the receptor/protein activity"
      "Product": "The chemical is produced as a result of the protein/enzyme reaction"
      "Activator": "The chemical increases the expression or activity of the protein/gene"
      "No Relation": "The chemical and protein co-occur but have no direct interaction described"

annotation_instructions: |
  Annotate biomedical abstracts for chemical-protein interactions.

  For each abstract:
  1. Read the text carefully to identify all chemicals and gene/protein entities.
  2. Use the span tool to highlight each entity and assign the correct type.
  3. Determine the primary relation type between the key chemical-protein pair.

  Tips:
  - Chemicals include drugs, small molecules, and compounds
  - Gene/Protein includes gene names, protein names, enzymes, and receptors
  - Focus on the most prominent chemical-protein pair if multiple exist
  - Select "No Relation" if entities co-occur without described interaction

html_layout: |
  <div style="padding: 15px; max-width: 800px; margin: auto;">
    <div style="background: #faf5ff; border: 1px solid #e9d5ff; border-radius: 8px; padding: 16px;">
      <strong style="color: #6b21a8;">Biomedical Abstract:</strong>
      <p style="font-size: 16px; line-height: 1.8; 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