Table of Contents

• About ComptoxAI
  • Authors
  • Citing ComptoxAI
    • Other Publications
  • Source databases
  • Contact Us
  • Contributing
  • Funding and Acknowledgements
• Installing and Building
  • What parts of ComptoxAI should I install?
    • “I just want to explore the data and/or the graph database”
    • “I need to run some Cypher queries on the graph database”
    • “I want to perform machine learning using data from ComptoxAI”
    • “I want to run a few Python analyses using some of ComptoxAI’s data”
    • “I want to create a similar data infrastructure, but for a different purpose”
  • Installing the comptox_ai Python package
  • Installing Neo4j and importing the ComptoxAI graph database
    • Install Neo4j
    • Create an empty graph database
    • Install plugins and configure the database
    • Download the ontology RDF file
    • Import the RDF data into the DBMS
    • Finish tidying up
  • Building and accessing the website
• 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
• 1. Computational Toxicology
  • 1.1. Methods used in computational toxicology
    • 1.1.1. Quantitative Structure-Activity Relationship (QSAR) modeling
    • 1.1.2. Read-across
    • 1.1.3. Trend Analysis
  • 1.2. Adverse Outcome Pathways
  • 1.3. Major research initiatives in computational toxicology
    • 1.3.1. Tox21
    • 1.3.2. AOP-Wiki / AOP-DB / SAAOP
• 7. Data Schema
  • 7.1. Graph data formats
    • 7.1.1. Graph
    • 7.1.2. Nodes
    • 7.1.3. Relationships
• 6. Source Databases
  • 6.1. Introduction
  • 6.2. References
• 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
• 5. Entity Types in ComptoxAI
  • 5.1. Entity Types
    • 5.1.1. Node types
    • 5.1.2. Relationship types
• 4. Graphs
  • 4.1. Behavior of Neo4j
    • 4.1.1. Induced Subgraphs
• 3. Graph Databases
  • 3.1. Building and installing the database locally
    • 3.1.1. Populating the ontology with individuals
    • 3.1.2. Importing the ontology into Neo4j
  • 3.2. Connecting to our instance of the database
  • 3.3. API Documentation
• User Guide
  • 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
• Video Tutorials
  • Using the Neo4j database browser
• 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
• REST Web API
  • API Routes
  • Web API Implementation
  • Contributions and Suggestions
• ComptoxAI Databases
• Graph
• Graph Algorithms
• API Reference
  • comptox_ai.db: ComptoxAI’s graph database
  • comptox_ai.graph: Graphs
    • comptox_ai.graph.Graph
    • comptox_ai.graph.io
  • comptox_ai.ml: Machine learning models
    • Graph ML
    • Non-graph ML
• Miscellaneous tools and utilities
• Machine Learning library
• Contact Us