What is an ontology?

From dictionary.com:

ontology
An explicit formal specification of how to represent the objects, concepts and other entities that are assumed to exist in some area of interest and the relationships that hold among them.

In other words, ontologies represent domains of knowledge by defining entities within the domain (and the terms used to refer to them) as well as how the entities are related to each other. An ontology thus provides a vocabulary for communicating knowledge about a topic, as well as a computable representation of the underlying reality.

Many ontologies, including OBO ontologies, model concepts in terms of classes (types of entities) and relations (features of an entity). Classes are related to each other via relations.

Special software (known as a reasoner) can use the network of classes and relations in an ontology to check the ontology for errors, discover the logical implications of existing structures, and suggest new concepts that might be added to the ontology.