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
How to use Large Language Models (LLMs) with OAK
Jupyter Notebooks
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
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 Mappings
Selecting alternative models
Installing LLM plugins
Mixtral via Ollama and LiteLLM
Mixtral via groq and LiteLLM