Protege5 OWL 指南：使用Protégé 5.5和插件构建实践教程

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本资源是一份名为《Protege5构建OWL本体指南：实践与插件应用》的教程，由Michael De Bellis撰写，适用于Protege 5.5版本。它是对早期版本（如由Matthew Horridge开发的Protégé 4教程的修订版）的升级，旨在提供在使用这个流行的本体建模工具创建和管理知识图谱时的实用指导。这份教程涵盖了如何使用Protégé 5.5的最新特性以及相关的插件，以便于开发者们更好地理解和设计语义网（OWL）模型。章节可能包括但不限于以下内容： 1. **入门指南**：介绍Protege 5.5的基本界面和工作流程，让初学者快速熟悉工具的使用。 2. **OWL基础知识**：讲解OWL语言的核心概念，如类、属性、对象类、数据类型和约束，以及如何在实际项目中应用这些概念。 3. **插件使用**：介绍可用的插件如何增强功能，如推理引擎、可视化工具和数据导入/导出模块，以提高建模效率。 4. **案例研究**：通过实例展示如何使用Protege 5.5创建伦理学本体（The Ethics Ontology）或COVID-19数据收集分析本体（CODO）等具体领域的知识图谱。 5. **教程升级与改进**：强调从Protégé 4到5.5的主要变化，包括新功能和改进的地方，帮助用户适应技术发展。 6. **作者背景与贡献**：Michael De Bellis不仅是作者，还参与了多个相关项目的合作，展示了其在领域内的专业知识和经验。 7. **资源维护与更新**：提及该教程是预印本，并在2021年4月进行了第3.0版的发布，表明作者对持续学习和发展开放的态度。 8. **下载与支持**：链接至ResearchGate，读者可以在这里讨论、查看统计和作者简介，同时获取进一步的技术支持和更新。这本教程对于希望掌握Protege 5.5和OWL建模技术的专业人士来说，是一份实用且详尽的参考资料，能够帮助他们在知识表示和知识管理系统的设计中更加得心应手。

Exercise 4: Create classes: Pizza, PizzaTopping, and PizzaBase

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1. Navigate to the Entities tab

with the Class hierarchy view selected. Make sure owl:Thing is selected.

2. Press the Add Subclass icon shown in figure 4.4. This button creates a new subclass of the selected

class. In this case we want to create a subclass of owl:Thing.

3. This should bring up a dialog titled Create a new class with a field for the name of the new class. Type

in Pizza and then select OK.

4. Repeat the previous steps to add the classes PizzaTopping and PizzaBase ensuring that

owl:Thing is selected before using the add subclass icon so that all your classes are subclasses of

owl:Thing. Your user interface should now look like figure 4.5. Don’t worry that some of the classes

are highlighted in red. That is because the reasoner hasn’t run yet. We will address this shortly.

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Figure 4.5 The Classes Sub-Tab in the Entities Tab

The Entities tab is a big tab that has tabs like Classes, Object properties, Data properties, etc. as sub-tabs. Each of

these sub-tabs is also a major tab (a tab accessible from the Window>Tabs option) that can be created on its own.

Since I took screen snapshots at various times I wasn’t always completely consistent. Sometimes I used Classes as a

sub-tab of the Entities tab and sometimes as a major tab on its own. Also, at different points in time I had other

tabs open depending on what other work I was doing. Thus, your UI won’t look identical to the figures. There may

be additional tabs in the figure that aren’t in your UI or vice versa.

4.2 Using a Reasoner

You may notice that one or more of your classes is highlighted in red as in Figure 4.5. This is because we

haven’t run the reasoner yet so Protégé has not been able to verify that our new classes have no

inconsistencies. When just creating classes and subclasses in a new ontology there is little chance of an

inconsistency. However, it is a good idea to run the reasoner often. When there is an inconsistency the

sooner it is discovered the easier it is to fix. One common mistake that new users make is to do a lot of

development and then run the reasoner only to find that there are multiple inconsistencies which can make

debugging significantly more difficult. So let’s get into the good habit of running the reasoner often.

Protégé comes with some reasoners bundled in and others available as plugins. Since we are going to

write some SWRL rules later in the tutorial, we want to use the Pellet reasoner. It has the best support for

SWRL at the time this tutorial is being written.

Exercise 5: Install and Run the Pellet Reasoner

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1. Check to see if the Pellet reasoner is installed. Click on the Reasoner menu. At the bottom of the menu

there will be a list of the installed reasoners such as Hermit and possibly Pellet. If Pellet is visible in that

menu then select it and skip to step 3.

2. If Pellet is not visible then do File>Check for plugins and select Pellet from the list of available plugins

and then select Install. This will install Pellet and you should get a message that says it will take effect the

next time you start Protégé. Do a File>Save to save your work then quit Protégé and restart it. Then go to

File>Open recent. You should see your saved Pizza tutorial in the list of recent ontologies. Select it to

load it. Now you should see Pellet under the Reasoner menu and be able to select it so do so.

3. With Pellet selected in the Reasoner menu execute the command Reasoner>Start reasoner. The

reasoner should run very quickly since the ontology is so simple. You will notice that the little text

message in the lower right corner of the Protégé window has changed to now say Reasoner active. The

next time you make a change to the ontology that text will change to say: Reasoner state out of sync with

active ontology. With small ontologies the reasoner runs very quickly, and it is a good idea to get into the

habit of running it often, as much as after every change.

4. It is possible that one or more of your classes will still be highlighted in red after you run the reasoner.

If that happens do: Window>Refresh user interface and any red highlights should go away. Whenever

your user interface seems to show something you don’t expect the first thing to do is to try this command.

There are no mandatory naming conventions for OWL entities. In chapter 7, we will discuss

names and labels in more detail. A best practice is to select one set of naming conventions and

then abide by that convention across your organization. For this tutorial we will follow the

standard where class and individual names start with a capital letter for each word and do not

contain spaces. This is known as CamelBack notation. For example: Pizza, PizzaTopping,

etc. Also, we will follow the standard that class names are always singular rather than plural.

E.g., Pizza rather than Pizzas, PizzaTopping rather than PizzaToppings.

5. One last thing we want to do is to configure the reasoner. By default, the reasoner does not perform all

possible inferences because some inferences can take a long time for large and complex ontologies. In

this tutorial we will always be dealing with small and simple ontologies so we want to see everything the

reasoner can do. Go to: Reasoner>Configure. This will bring up a dialog with several check boxes of

inferences that the reasoner can perform. If they aren’t all checked then check them all. You may receive

a warning that some inferences can take a lot of time, but you can ignore those since your ontology will

be small.

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4.3 Disjoint Classes

Having added the classes Pizza, PizzaTopping, and PizzaBase to the ontology, we now want to say

that these classes are disjoint. I.e., no individual can be an instance of more than one of those classes. In

set theory terminology the intersection of these three classes is the empty set: owl:Nothing.

Exercise 6: Make Pizza, PizzaTopping, and PizzaBase disjoint from each other

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1. Select the class Pizza in the class hierarchy.

2. Find the Disjoint With option in the Description view and select the (+) sign next to it. See the red

circle in figure 4.6.

3. This should bring up a dialog with two tabs: Class hierarchy and Expression editor. You want Class

hierarchy for now (we will use the expression editor later). This gives you an interface to select a class

that is identical to the Class hierarchy view. Use it to navigate to PizzaBase. Hold down the shift key and

select PizzaBase and PizzaTopping. Select OK.

4. Do a Reasoner>Synchronize reasoner. Then look at PizzaBase and PizzaTopping. You should see

that they each have the appropriate disjoint axioms defined to indicate that each of these classes is disjoint

with the other two.

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