Tutorial

Note

The tutorial is currently being extended. Additions welcome!

Contents:

• Part 1: Getting Started
  • Installation
    • Install from PyPI
    • Run the OAK command
  • Basics
    • Query the OBO Library
    • Search
    • Working with local files
  • Introduction to graphs and trees
    • Fetching ancestors
    • Predicate Abbreviations
    • Ancestor Statistics
    • Oak Trees
  • Advanced Search
    • Using search terms as parameters
  • Chaining Commands
  • Visualization
  • Using other backends
    • Using Ubergraph
    • Using Ontobee
    • Using BioPortal and OntoPortal
    • Using OLS
  • Next steps
• Part 2: Basic Python
  • Install Poetry
  • Create a new project
  • Basic Concepts
  • Code the first example
  • Extending the example
• Part 3: Triplestore Backends
  • Triplestore Concepts
  • Ubergraph
    • Connecting
    • Basic Operations
    • Relationships
• Part 4: OboGraphs
  • OboGraphs
  • OboGraph Interface
  • Commands
  • Code examples
• Part 5: Graph Visualization
  • Install Graphviz
  • Install OBOGraphViz
  • Command Line Usage
  • How this works
  • Programmatic usage
• Part 6: Working With OWL
  • OWL Datamodel
  • OwlInterface
  • ROBOT Plugin
• Part 7: SQLite files
  • Download a SQLite file
    • Example
    • Fetching ready-made SQLite files
  • Building your own SQLite files
    • With docker
    • Without docker
  • Validating an ontology
  • Other RDBMSs
  • Python ORM
• Part 8: Applying Changes to Ontologies
  • About KGCL
  • Command Line
    • Example: Sqlite3
    • Example: OBO Files