Ontology Access Kit (OAK) Documentation

Contents:

• Introduction
  • Basic Python Example
  • Basic Command Line Example
• Tutorial
  • Part 1: Getting Started
  • Part 2: Basic Python
  • Part 3: Triplestore Backends
  • Part 4: OboGraphs
  • Part 5: Graph Visualization
  • Part 6: Working With OWL
  • Part 7: SQLite files
  • Part 8: Applying Changes to Ontologies
• The OAK Guide
  • OAK Basics
  • Identifying entities: CURIEs and URIs
  • Primary Labels
  • Aliases and Synonyms
  • Mappings and Cross-References
  • Obsoletion
  • Relationships and Graphs
  • Associations and Curated Annotations
  • Enrichment and Over-Representation Analysis
  • Computing Similarity between Entities
  • Learning More
• OAK Library Documentation
  • Architecture
  • Interfaces
  • Implementations
  • Ontology Adapter Selectors
  • Converters
  • Utilities
• Command Line
  • General Guidelines
  • Common Patterns
  • Cache Control
  • Commands
• Datamodels
  • Ontology Metadata Ontology Schema
  • search datamodel
  • Obographs Datamodel
  • SSSOM
  • FunOwl
  • KGCL
  • Semantic Similarity
  • Summary Statistics Datamodel
  • Taxon Constraints Reporting Datamodel
  • Validation Results Data Model
  • Lexical Index
  • Mapping Rules Datamodel
  • Text Annotator Datamodel
  • Cross-Ontology Diff
  • OAK Association Data Model
• How-To Guides
  • How to Validate an OBO ontology using Obo Metadata Ontology schema
  • How to write a plugin
  • FHIR Conversions
  • Using the OAK Expression Language
  • How to use Large Language Models (LLMs) with OAK
• Examples
  • Commands
  • Ontologies
  • Adapter Examples
  • Interfaces Examples
  • Ad Hoc Examples
• Glossary
• FAQ
  • FAQ: General
  • FAQ: Ontologies
  • FAQ: Architecture and Design
  • FAQ: Contributing
  • FAQ: Troubleshooting

Indices and tables

• Index

• Module Index

• Search