Automatic classification
========================

## EXERCISE: Basic classification

Go to the [basic-classification](https://github.com/geneontology/protege-tutorial/tree/master/basic-classification) folder and follow the instructions in the README.txt

## EXERCISE: Classification using Unions (Optional)

Optional additional exercise if time permits:

Go to [taxon-union](taxon-union) folder

This introduces classification using “or” and “not”

### Futher reading

[owl primer - advanced class relationships](https://www.w3.org/TR/owl2-primer/#Advanced_Class_Relationships])


## Introduction to property axioms

### Property heirarchy:

![image](https://user-images.githubusercontent.com/112839/29339527-58e8a4c6-81cf-11e7-8ed2-1f2a19ff6dfb.png)

Navigate to 'occurs in' (object property tab) in Protege to see this.

## Excercise: 

  * make a git branch of the go-ontology repo
  * open go-edit.obo in Protege
  * GO has the class 'regulation of cvt pathway'
  
  ![image](https://user-images.githubusercontent.com/112839/29340084-26dc5b3c-81d2-11e7-99ab-7303ae0380ce.png)

  * Create a new class, using the same pattern, for 'negative regulation of cvt pathway' (Hint - you can use duplicate to do this, editing the newly created class).
  * Run the reasoner.  Do you understand the inferred classifications? (Use the explanation plugin to check).
  

### Property chains:

![image](https://user-images.githubusercontent.com/112839/29339591-bfdac506-81cf-11e7-8ef0-d657d4175bbb.png)

Navigate to 'occurs in' (object property tab) in Protege to see this.

### EXERCISE: transport & property chains


Go to the [transport property chain exercise](https://github.com/geneontology/protege-tutorial/tree/master/transport_property_chain_excercise) folder and follow the instructions in the README