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
• Architecture
  • Ontology Interfaces
  • Implementations
  • Other Interfaces
  • Partial and Complete Implementation
  • Datamodels used
• Interfaces
  • Basic Ontology Interface
  • Search Interface
  • Subsetting
  • Validator Interface
  • Relation Graph
  • Mapping Provider
  • OboGraph Interface
  • Text Annotator Interface
  • Summary Statistics
  • Patcher Interface
  • Semantic Similarity Interface
  • Semantic Similarity Interface
• Implementations
  • Pronto / OBO Files Implementation
  • SQL Database Implementation
  • Ontology Lookup Service (OLS) Endpoint
  • Simple OBO Implementation
  • OBO Graph Implementation
  • Bioportal Endpoint
  • Sparql Endpoint
  • Ubergraph Endpoint
  • Ontobee Endpoint
  • Ontology Lookup Service (OLS) Endpoint
  • Gilda Endpoint
  • Aggregator Implementation
• Command Line
  • General Guidelines
  • Common Patterns
  • Commands
• Ontology Implementation Selectors
  • Syntax
  • Examples
  • Schemes
  • Functions
• Datamodels
  • Ontology Metadata Ontology Schema
  • search datamodel
  • Obographs Datamodel
  • SSSOM
  • FunOwl
  • KGCL
  • Semantic Similarity
  • Summary Statistics Datamodel
  • Taxon Constraints Reporting Datamodel
  • Validation Results Datamodel
  • Lexical Index
  • Mapping Rules Datamodel
  • Text Annotator Datamodel
  • Cross-Ontology Diff
  • OAK Association Data Model
• Converters
  • Command Line Usage
  • Converting from Obo Graphs
• Utilities
  • oaklib.utilities.obograph_utils
  • oaklib.utilities.graph.relationship_walker
  • oaklib.utilities.graph.networkx_bridge
  • oaklib.utilities.lexical.lexical_indexer
  • oaklib.utilities.subsets.slimmer_utils
  • oaklib.utilities.apikey_manager
  • oaklib.utilities.table_filler
• How-To Guides
  • How to Validate an OBO ontology using Obo Metadata Ontology schema
  • How to write a plugin
• Notebooks
• Ontology Concepts
  • Ontology
  • Ontology Element
  • Imports and Ontologies within Ontologies
  • URIs and CURIEs and identifiers
  • Prefix Maps
  • Relationships / Edges
  • Mappings
  • Ontology Format
  • Statements and Axioms
  • Subsets
  • Labels/Names
• Glossary
• Frequently Asked Questions
  • How do I…
  • What is…
  • Using OAK with…
  • Command Line
  • Troubleshooting

Indices and tables

• Index

• Module Index

• Search