In philosophy, the term formal ontology is used to refer to an ontology defined by axioms in a formal language with the goal to provide an unbiased (domain- and application-independent) view on reality, which can help the modeler of domain- or application-specific ontologies to avoid possibly erroneous ontological assumptions encountered in modeling large-scale ontologies.

By maintaining an independent view on reality, a formal (upper level) ontology gains the following properties:

Theories on how to conceptualize reality date back as far as Plato and Aristotle. The term 'formal ontology' itself was coined by Edmund Husserl in the second edition of his Logical Investigations (1900–01), where it refers to an ontological counterpart of formal logic. Formal ontology for Husserl embraces an axiomatized mereology and a theory of dependence relations, for example between the qualities of an object and the object itself. 'Formal' signifies not the use of a formal-logical language, but rather: non-material, or in other words domain-independent (of universal application). Husserl's ideas on formal ontology were developed especially by his Polish student Roman Ingarden in his Controversy over the Existence of the World. The relations between the Husserlian tradition of formal ontology and the Polish tradition of mereology are set forth in Parts and Moments. Studies in Logic and Formal Ontology, edited by Barry Smith.

The differences in terminology used between separate formal upper-level ontologies can be quite substantial, but most formal upper-level ontologies apply one foremost dichotomy: that between endurants and perdurants.

Also known as continuants, or in some cases as "substance", endurants are those entities that can be observed-perceived as a complete concept, at no matter which given snapshot of time. Were we to freeze time we would still be able to perceive/conceive the entire endurant.

Examples include material objects (such as an apple or a human), and abstract "fiat" objects (such as an organization, or the border of a country).

Also known as occurrents, accidents or happenings, perdurants are those entities for which only a part exists if we look at them at any given snapshot in time. When we freeze time we can only see a part of the perdurant. Perdurants are often what we know as processes, for example: "running". If we freeze time then we only see a part of the running, without any previous knowledge one might not even be able to determine the actual process as being a process of running. Other examples include an activation, a kiss, or a procedure.

In a broad sense, qualities can also be known as properties or tropes.