Basic of Ontology

This is opening of Chapter 5, Gene Ontology, of my thesis Empirical Study of Gene Ontology based Microarray Clustering. You can check abstract from here.

5.1 Basic of Ontology

“Ontology” has been a philosophy jargon since Aristotle times, and it means the nature of existence. Computer scientists adopted this word to express a formally structured vocabulary in a discipline. In this vocabulary, items and relations between two items are well defined to present the knowledge in this discipline.

Ontologies offer a mechanism by which knowledge can be represented in a form capable of machine processing[Lord 2003]. Ontologies can be provided in Rational Database format or XML format.

Now ontology becomes the core of Semantic Web, because the geographically distributed Web forms information islands in the Internet, and the use of ontology can interpret meanings of information in different islands, reduce the confusion, and integrate data automatically. The decentralized infrastructure makes the communication and collaboration over Internet easy. Every one can focus on her own part of the project independently and integration of their work will be streamlined since every part of the collaboration follows the same ontology and plays her own role. Every one can also build new ontologies, and cooperate with the third part without the permission of her collaborators. The collaboration will be stronger and stronger as more and more collaborators join in and share their knowledge. This decentralized infrastructure breaks down the barrier between languages, geographical distance, automates the integration of knowledge, and leads to the evolution of knowledge.