oaklib

Contents:

  • Introduction
  • Tutorial
  • The OAK Guide
    • OAK Basics
    • Identifying entities: CURIEs and URIs
    • Primary Labels
    • Aliases and Synonyms
    • Mappings and Cross-References
    • Obsoletion
  • Architecture
  • Interfaces
  • Implementations
  • Command Line
  • Ontology Implementation Selectors
  • Datamodels
  • Converters
  • Utilities
  • How-To Guides
  • Notebooks
  • Ontology Concepts
  • Glossary
  • Frequently Asked Questions
oaklib
  • The OAK Guide
  • View page source

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
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