oaklib

Contents:

  • Introduction
  • Tutorial
  • The OAK Guide
  • OAK Library Documentation
  • Command Line
  • Datamodels
  • How-To Guides
    • How to Validate an OBO ontology using Obo Metadata Ontology schema
    • How to write a plugin
    • FHIR Conversions
    • Using the OAK Expression Language
    • How to use Large Language Models (LLMs) with OAK
  • Examples
  • Glossary
  • FAQ
oaklib
  • How-To Guides
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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
      • Subproperties
    • 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
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