How-To Guides

Warning

many of these guides are in-progress

Contents:

• How to Validate an OBO ontology using Obo Metadata Ontology schema
  • Steps
    • Step 1: Obtain the sqlite version of the ontology
    • Step 2: Install oaklib
    • Step 3: Validate an individual ontology
    • Step 3 (alternative): Validate multiple ontologies
  • Caveats
  • Using your own schema
  • How this works
  • Analysis
• How to write a plugin
  • What is a plugin?
  • An example plugin
  • Creating a plugin
    • Discuss on the issue tracker
    • Create a new project
    • Implement one or more interfaces
    • Implement a selector
    • Write tests
  • Release to PyPI
• FHIR Conversions
  • CLI
  • Config file
• Using the OAK Expression Language
  • Basics
    • IDs (CURIEs)
    • Lists of IDs
    • Label Queries
  • Search Queries
    • Exact Match
    • Starts With
    • Contains
    • Regular Expressions
  • Graph Queries
    • Ancestors
    • Descendants
    • MRCAs
  • Boolean Combinations
    • AND
    • OR
    • NOT
  • Nesting
  • Using files and redirects
    • IDFILE
    • STDIN
  • Other Operators
    • IN
    • FILTER
    • QUERY
    • NR
    • MRCA
    • RAND
    • SAMPLE
    • Others
• How to use Large Language Models (LLMs) with OAK
  • LLM frameworks that use OAK
    • OntoGPT
    • CurateGPT
    • Talisman
  • Using OAK in conjunction with existing LLM tools
  • OAK LLM Adapter
    • Annotation
    • Suggesting Definitions
    • Validating Definitions
    • Validating Mappings
  • Selecting alternative models
    • Installing LLM plugins
    • Mixtral via Ollama and LiteLLM
    • Mixtral via groq and LiteLLM