LinkML-OWL Pizza Tutorial

In this tutorial we will walk through an example of how to generate a complete ontology from linkml data files by transforming into OWL using the linkml-owl command.

Our example draws heavily from the Manchester Pizza Tutorial. You can use the linkml tutorial without having looked at the original Pizza tutorial. However, we assume some basic knowledge of OWL, and the Mancheser Pizza tutorial is a great place to start!

Pre-requisites

Note the original Manchester tutorial tells you how to create an ontology using Protege. You don't need Protege at all for the linkml tutorial, as we will be generating OWL from YAML files which you edit.

We strongly recommend a text editor or IDE that is YAML-aware.

You may still find it useful to have Protege at hand, as Protege provides a very user-friendly way to look at the contents of the OWL files we will make along the way

Some parts of the tutorial require the use of robot to perform reasoning over the ontology. These parts can be skipped but we strongly recommend that robot is a part of your ultimate ontology release pipeline.

You don't need any programming knowledge to do this tutorial, but initial setup does require installation of a python module and running a script on the command line, so basic unix concepts are helpful.

Main LinkML tutorial

You may also find it useful to do the linkml tutorial first, or at least to have some grasp of core linkml concepts, since linkml-owl is simply an optional layer on top of linkml. However, if you are already familiar with basic data modeling concepts then you may be able to wing it by diving straight into the linkml-owl tutorial.

Installation

See the main LinkML guide for details on installation. For this tutorial you will not need to do any Python programming but you will need the linkml-owl command, which is part of the Python distribution:

pip install linkml-owl