A computational ontology consists of a number of different components, such as Classes, Individuals and Relations which are described in this article.
An Ontology consists of a number of different components. The names of these components differ between ontologies depending on the ontology language used, philosophical persuasion or background of the authors. Despite this, their core components are largely shared between different ontologies. These components can be separated into two kinds: those that describe the Entities of the domain — here called concepts, individuals and relationships; and those which either enable the use of the ontology or describe the ontology itself — described in the last section of this article.
Concepts, also called Classes, Types or Universals are a core component of most ontologies. A Concept represents a group of different Individuals, that share common characteristics, which may be more or less specific.
For example, (most) humans share certain characteristics, such as related DNA, a set of specific body parts, the ability to speak a complex language. Likewise, all mammals share these characteristics, except for the ability to speak.
Most ontology languages allow the author to define Concepts on the basis of these characteristics; additionally, some languages, such as OWL also allow definition of Concepts extensionally by their membership. For example, the Concept “members of the beatles” could be defined as the set of “John, Paul, George and Ringo”.
One Concept may be a subconcept (also known as subclass, or kind of) another Concept; this means that if the Concept C' is a subconcept of C, then any individual of type C' will also be an individual of type C. It is possible within an ontology to explicitly state that C' is a subconcept of C; in some languages, including OWL it is also possible to infer this.
Concepts may also share relationships with each other; these describe the way individuals of one Concept relate to the individuals of another.
Individuals also known as instances or particulars are the base unit of an ontology; they are the things that the ontology describes or potentially could describe. Individuals may model concrete objects such people, machines or proteins; they may also model more abstract objects such as this article, a person’s job or a function.
Individuals are a formal part of an ontology and are one way of describing the entities of interest. Perhaps more common within bioinformatics is the development of ontologies consisting only of Concepts which are then used to annotate data records directly.
Relations in an ontology describe the way in which individuals relate to each other. Relations can normally be expressed directly between individuals (this article has author Phillip Lord) or between Concepts (an article has author a person); in the latter case, this describes a relationship between all individuals of the Concepts.
Although it is dependant on the ontology language, it is often possible to express different categories of relationships between Concepts. Consider, for example, “person has father person”. This is an existentially quantified relationship; it is the case that every person has a father, and that this individual is also a person. This can be contrasted from “person is father of person”; this is a universal quantified relationship. It is true that every individual which is father of a person is, themselves, a person; however, it would be wrong to assert that every person is the father of another.
As well as the formal ontological aspects already described, most ontology languages have many other features. These are often critical to the use of the ontology.
Documentation or formal definitions are normally provided for each concept, relation and individual. These provide plain or formal English definitions for the other components of an ontology. They are useful for ontology authors as they can be used to ensure that the intention of the entity (given in the documentation) is accurately reflected in the ontology; they are also useful for users of the ontology to understand these intentions.
Many ontologies also have editor notes or procedural documentation which describe the current state of the entity within the editorial process; for example, whether the term has been deprecated (should no longer be used), under review (likely to change) or released (likely to remain stable).
Ontology metadata provides documentation for the ontology as a whole, describing, for example, the purpose and scope of the ontology, the release date or version number, and the authorship of the ontology.
Depending on the ontology language being used, an ontology may define imports; other ontologies from which entities have been used and which are required to have a full understanding of the domain, as well as using the ontology computationally.
Although this article describe the basic components which are found in most ontologies, there are many other components which are specific to individual technologies or ontology languages such as OBO Format or OWL.
This paper is an open access work distributed under the terms of the Creative Commons Attribution License 2.5, which permits unrestricted use, distribution, and reproduction in any medium, provided that the original author and source are attributed.
The paper and its publication environment form part of the work of the Ontogenesis Network, supported by EPSRC grant EP/E021352/1.