FAQ

Welcome to the OAK FAQ?

Contents:

• FAQ: General
  • What is OAK?
  • Are there any tutorials for OAK?
  • Are there runnable examples of how to use OAK?
  • I am familiar with both Python and Ontologies. Where should I start?
  • I find ontologies confusing. Is there a general guide to help me?
  • Why is it called OAK?
  • How do I install OAK?
  • Can I use OAK if I don’t know Python?
  • Can I contribute to OAK?
  • Is OAK just for bio-ontologies?
  • Can OAK access ontologies in ontology portals such as MatPortal or BioPortal?
  • Can OAK access ontologies in triplestores such as OntoBee or Ubergraph?
  • Can OAK access local files?
  • Can OAK access OBO Format files?
  • Does OAK support all of OWL?
  • Does OAK support reasoning?
  • Can I use OAK to do graph queries over ontologies?
  • Can I use OAK to do lexical search?
  • Can I use OAK as a text annotator?
• FAQ: Ontologies
  • What is an ontology?
  • Do we need ontologies now we have ChatGPT?
  • What is OWL?
  • What is OBO Format?
  • What is OBO
  • What’s a synonym and how do I access them?
• FAQ: Architecture and Design
  • What is an interface?
  • What is a Data Model?
  • What is an iterator and why does OAK use them so much?
• FAQ: Contributing
  • How can I contribute?
  • How do I stay involved?
• FAQ: Troubleshooting
  • Why do I get a “Error: No such option: -i” message
  • How do I get a BioPortal API key?
  • My OBO Format file won’t parse
  • My OWL file takes too long to load
  • My cached SQLite ontology is out of date
  • I don’t understand the interface/method I want to use