User Guide

These pages give a high-level overview of ComptoxAI, computational toxicology, and graph machine learning. For documentation of specific modules, classes, methods, and functions, please refer to the API documentation.

Video tutorials describing ComptoxAI’s major features can be found on the Video Tutorials page.

• 1. Computational Toxicology
  • 1.1. Methods used in computational toxicology
  • 1.2. Adverse Outcome Pathways
  • 1.3. Major research initiatives in computational toxicology
• 2. Database Queries
  • 2.1. Introduction
  • 2.2. Graph database representation of an entity
  • 2.3. Finding nodes using Cypher
  • 2.4. Finding nodes using Python
  • 2.5. Finding relationships using Cypher
  • 2.6. Finding relationships using Python
• 3. Graph Databases
  • 3.1. Building and installing the database locally
  • 3.2. Connecting to our instance of the database
  • 3.3. API Documentation
• 4. Graphs
  • 4.1. Behavior of Neo4j
• 5. Entity Types in ComptoxAI
  • 5.1. Entity Types
• 6. Source Databases
  • 6.1. Introduction
  • 6.2. References
• 7. Data Schema
  • 7.1. Graph data formats
• 8. Adverse Outcome Pathways
  • 8.1. What is an adverse outcome pathway?
  • 8.2. Main components of an AOP
  • 8.3. How are adverse outcome pathways used in ComptoxAI?
  • 8.4. References
• 9. Useful Cypher queries
  • 9.1. Entity search
  • 9.2. Relationship search
  • 9.3. Shortest paths
  • 9.4. Network expansion
  • 9.5. Graph data science algorithms
  • 9.6. Schema-related queries