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Getting Started

Introduction

This is an introduction to the Tawny-OWL library. It assumes that you have a working Clojure environment; if not please see a getting started with clojure documentation. It also assumes that you have a knowledge of OWL and ontologies in general; if not please see the description of what OWL is.

Tawny-OWL is a library which supports the production of ontologies using the Ontology Web Language. It is designed to have a simple syntax, modelled after the OWL Manchester Syntax. At it's simplest, it provides the ability to write ontologies with a clearly defined syntax. Individual classes or properties can be added and removed at will, or changed straight-forwardly, as with a GUI framework. However, as it provides a readable text syntax, it is more convenient to integrate with, for example, version control systems; ontologies can be searched, and modified with a simple search and replace, or more complex regexps and so on.

However, this does not uncover the main power of Tawny; although it looks like Manchester syntax, underneath there is a full programming language. It is possible to extend and build on the core library in arbitrary ways. Many classes can be created according to a pattern in a single statement; it is possible to add specialised support for your given domain, provide new syntax for your purposes. It is also possible to use Tawny as an API to manipulate existing OWL, although it was not designed for this purpose and has some limitations.

In this document, we will explore the basic usage of the library, using examples from the tawny-pizza -- the traditional Pizza Ontology. A working version of this ontology ported to Tawny is available.

For a more complete exemplar, using most of the expressivity of OWL, we have rewritten the family ontology from the OWL Primer. Finally, for a "real" ontology in development, please see the karyotype ontology.

Creating a new project

The most straight-forward to create a new project is to use leiningen. So

lein new pizza

will create a new project in the directory pizza. This will contain a number of files, including a project.clj file, a src directory and a test directory. You need to add Tawny-OWL as a dependency to the project file as described in getting-started-with-clojure.

Creating a new ontology

Clojure has a namespacing mechanism which is used to prevent name clashes. Although, it's not necessarily true, a clojure namespace generally maps to a single file. Rather like Java, namespaces can also contain packages, which map to directories. So, for example, the tawny-pizza ontology is defined in a single namespace called pizza.pizza. This maps to a file in src/pizza/pizza.clj. In this file, we find the namespace declaration:

(ns pizza.pizza
  (:use [tawny.owl])
  (:require [tawny
             [polyglot]
             [reasoner :as r]
             [pattern :as p]]))

As well as describing the namespace of the file (pizza.pizza), it also contains a (:use [tawny.owl]) form; this imports all of the functions in the tawny.owl namespace, allowing them to be used without qualification; we also require three other namespaces from Tawny-OWL, which must be qualified in use, and define short-cuts for these.

In normal usage, Tawny-OWL uses a single ontology for in a single namespace. Before being used an ontology must be declared:

(defontology pizzaontology
  :iri "http://www.ncl.ac.uk/pizza"
  :prefix "piz:"
  :comment "An example ontology modelled on the Pizza tutorial ontology from Manchester University,
written using the tawny-owl library"
  :versioninfo "Unreleased Version")

This declares a new ontology, with the given IRI and prefix (which has no formal semantics but will be used when the ontology is serialised).

Creating a new class

Creating new classes happens in a similar manner to an ontology. The following forms created three classes. In this case, we add a set of annotation properties as well.

(defclass Pizza
  :label "Pizza")


(defclass PizzaTopping)

;; currently we have to use the annotation function with label to pass a
;; language in.
(defclass PizzaBase
  ;; the pizza ontology contains some Portuguese labels. The :label keyword
  ;; used above is a shortcut for English
  :annotation (label "BaseDaPizza" "pt"))

Declaring a class in this manner adds it to the current ontology, as well as making it available for use in later definitions. The defclass form is the usual way to declare classes because it can use the frame-like syntax to add arbitrary restrictions to the class, including superclasses, disjoints, and equivalent classes. However, where no restrictions need to be added, or where restrictions will be added later, declare-classes allows defining many classes at once. For example, four classes can be defined at once:

(declare-classes ChickenTopping
               HamTopping
               HotSpicedBeefTopping
               PeperoniSausageTopping)

Creating properties

Properties can be created in a similar manner to classes, using the defoproperty form. This also has a frame like syntax; a relatively complex example, demonstrates several of these frames:

(defoproperty hasBase
  :super hasIngredient
  :characteristic :functional
  :range PizzaBase
  :domain Pizza
  )

This requires that the various objects, such as hasIngredient, Pizza and PizzaBase already have been created; functional is defined by Tawny-OWL itself.

Annotation properties can be created similarly with defannotationproperty.

Datatype properties can be created similarly with defdproperty.

Disjoints, Inverse and subclasses

The full use of restrictions is covered later, however Tawny-OWL provides some easy to use macros which enable adding common restrictions; for example, the as-inverse macro makes object properties defined within it as inverses. For example, hasIngredient and isIngredientOf are declared as inverse here:

(as-inverse
 (defoproperty hasIngredient
   :characteristic :transitive)
 (defoproperty isIngredientOf
   :characteristic :transitive
   ))

Likewise, it is possible to add a shared superclass and disjoint statements to every class. For example, the following combines the declare-classes and as-disjoint-subclass macro.

(defclass CheeseTopping)

(as-disjoint-subclasses
 CheeseTopping

 (declare-classes
  GoatsCheeseTopping
  GorgonzolaTopping
  MozzarellaTopping
  ParmesanTopping))

There is also a as-subclasses macro which takes a number of parameters. For example, consider this definition (not from the pizza ontology) which defines the primary colours.

(defclass PrimaryColour)

(as-subclasses
    PrimaryColour
    :disjoint :cover
    (declare-classes Red Green Blue)
)

In this case, each of Red, Green and Blue are declared as being disjoint from each other, and further as "covering" PrimaryColour. This would generate the following ontology, represented in Manchester syntax:

Class: PrimaryColour
    EquivalentTo:
        Red or Green or Blue

Class: Red
    SubClassOf: PrimaryColour

Class: Green
    SubClassOf: PrimaryColour

Class: Blue
    SubClassOf: PrimaryColour

DisjointClasses:
    Red, Green, Blue

Tawny-OWL can be considerably more succinct than Manchester OWL.

Adding and Removing entities interactively.

As Tawny-OWL is based on Clojure, it is possible to use Tawny-OWL interactively, through a REPL (Read-Eval-Print-Loop). In this environment, it is possible to add and, also, to remove entities interactively. This can be useful for trying out ideas. The defclass and other macros shown so far work perfectly well in this environment. It is also possible to remove statements that have been added. For example, consider the following statement:

(defclass A)
(defclass B)
(remove-entity B)

After the last form, the ontology will only contain the class A.

Saving Ontologies

Saving an ontology is simple, using the save-ontology form. This takes a filename and potentially a format.

(save-ontology "ontology.omn" :omn)
(save-ontology "ontology.owl" :owl)

The file location is relative to the working directory of the current REPL; in practice, this means in the same directory as the project.clj file, rather than the directory of the file that contains the save-ontology form.

Visualising

Protege provides an excellent environment for visualisation and navigating through an ontology. It interacts quite nicely with Tawny-OWL, as a viewer rather like using a Web Browser while developing a web site, or a PDF viewer while writing LaTeX.

The best way to achieve this is with Tawny-OWL, is to add a save-ontology form to the end of each namespace containing an ontology, or alternatively add a main method that saves all ontologies in a project. For this use, the :owl or :rdf form work best. Protege can open files and view them; it also copes quite well with having files changes underneath it, and offers to revert to the saved version.

A similar effect can be achieved with Emacs and omn-mode which provides syntax highlighting for Manchester syntax. In this case, auto-revert-mode works to handle updating.

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