The OAK Guide

This guide provides an explanation of basic concepts in OAK, how to use both the Python library, and the command line.

For a quick introduction, see the Tutorial

Contents:

• OAK Basics
  • What is an ontology and why would I want to access one?
  • Ontology languages, standards, and formats
  • Core OAK concepts
• Identifying entities: CURIEs and URIs
  • Prefix maps
  • Querying prefixmaps
  • Non-default prefixmaps
  • Structure of identifiers
• Primary Labels
  • Looking up labels
  • Custom label annotation properties
  • Multilingual ontologies
  • Other edge cases
  • Further reading
• Aliases and Synonyms
  • Use Cases
    • Search
    • Text mining and NLP
    • Different aliases for different communities
    • Different Languages
  • Different approaches to representing synonym metadata
  • Representation of synonyms in OAK
    • Simple Core Model
    • Obo Graph Data Model
• Mappings and Cross-References
  • SSSOM
  • Mappings in OAK
  • Further reading
• Obsoletion
  • Looking up obsoleted entities
  • Conventions and standards
    • obsolete entities should not be in the signature of any logical axiom
    • obsolete entities should be accompanied by metadata that provides additional context for humans and machines
  • Merged entities