Abstract
The General Formal Ontology (GFO) is a top-level ontology that is being developed at the University of Leipzig since 1999. Besides introducing some of the basic principles of the ontology, we expound axiomatic fragments of its formalization and present ontological models of several use cases. GFO is a top-level ontology that integrates objects and processes into a unified framework, in a way that differs significantly from other ontologies. Another unique selling feature of GFO is its meta-ontological architecture, which includes set theory into ontology and which accounts for its specific role in common representation approaches. The second level of that architecture starts from the distinction of categories and individuals, which forms the backbone of the world’s structure. Furthermore, GFO comprises several kinds of categories, among them universals and concepts, and it considers several ontological regions and levels.
In the context of this special issue paper, we study five pre-determined use cases from the perspective of GFO. The results of these analyses yield insights into how the ontology treats several important notions. Very abridged, this covers material objects and their composition; roles and social entities; properties with their relations to objects and processes, and their changing; changes of processes, including a functional perspective; and, eventually, the nature and changing of concepts as well as terminology. A final part summarizes application projects that use GFO in various contexts.
Introduction
Research in ontology has become widespread in the field of information systems during the last two decades, in distinct areas of science, business, and industry. Nowadays the importance of ontologies is well recognized and it increases further in diverse fields and contexts, cf., for example, the contributions to the workshop series Formal Ontology Meets Industry (Borgo and Lesmo, 2008; Sanfilippo et al., 2018). The term ontology has two meanings: on the one hand, it stands for a research area; on the other hand, it denotes a system of organized knowledge. A system of knowledge may exhibit various degrees of formality; in the strongest form, it is an axiomatic, formally represented theory, which is denoted by the term axiomatized ontology.
We use the term formal ontology – influenced by Nino Cocchiarella (1991) – to name a science that is concerned with the systematic development of axiomatic theories describing forms, modes, and views of being of the world at different levels of abstraction and granularity. Formal ontology combines the methods of mathematical logic with principles of philosophy and methods of artificial intelligence (Herre, 2015a). We use the term ontology to name a system of organized knowledge. Ontologies may be represented at different levels of abstraction. It is a matter of debate how these levels of abstraction are to be defined. Often one distinguishes top-level, domain core or upper domain ontologies, and domain ontologies. Top-level ontologies aim at their applicability in every area of the world, in contrast to the various upper domain and domain ontologies, which are associated with more narrow fields of interest.
Historically, formal ontology as understood for this paper has developed from three main sources: artificial intelligence (knowledge-based systems, cognitive science, cognitive linguistics), formal logic (principles of formalization, axiomatic method), and philosophy (ontology and epistemology). During the 1960s a new paradigm of artificial intelligence was coined: the conception of knowledge-based systems/knowledge systems. It had turned out that the idea of a general problem solver was not realizable. Instead, the role of knowledge in problem solving was discovered, expressed in the slogan: “In the knowledge lies the power”. The first applicable knowledge systems were called expert systems, which capture the knowledge of experts of a certain domain, to be used for problem solving. Albeit, later work in the field of knowledge representation – being fundamental for developing knowledge systems – led to the insight that this field is insufficiently grounded. There is the need for a deeper understanding of the entities in the world, such as time, space, individual, object, process, property, etc. The methods of formal ontology can be used to close this gap.1
The field of (symbolic) AI is the main driving force for the timelessness and relevance of ontologies and of formal ontology (cf. the Semantic Web, OWL, semantic methods, data mining, etc.).
The research on formal ontology at the University of Leipzig started in 1999, in order to achieve a better foundation for knowledge representation in the field of medicine. First results were summarized in 2001 under the name General Ontological Language (GOL; Degen et al., 2001). A part of GOL has been further developed subsequently and independently, leading to the Basic Formal Ontology (BFO; Grenon and Smith, 2003). The original GOL was transformed into the General Formal Ontology (GFO; Herre et al., 2006, 2007; Herre, 2010). This transformation from GOL to GFO includes the following novelties:
The development of the conception of integrative realism (Herre, 2015b,2010). There is a different understanding of realism in BFO (Smith, 2008) and in GFO, as expounded by Heinrich Herre (2010, Section 14.2.5). The introduction of a meta-level ontology (of various types) (Herre and Loebe, 2005; Loebe, 2015, Section 2.3) with notions of abstract core ontology and of abstract top ontology. The latter derives from the particular role of set theory in formal representation and in ontology. The abstract core ontology can be flexibly adapted to the needs in applications (for example, by including categories of higher order). The inclusion of various kinds of categories (two kinds of universals, symbolic structures, and concepts). This approach was partly inspired by the work of the philosopher Jorge J.E. Gracia (1999). These differences are relevant in the study of categories and, in particular, of concepts as in cognitive science and cognitive psychology.2 For example, Platonic universals may be understood as an original form of the prototype representation of concepts.
The inclusion of levels, regions and strata of reality, influenced by the philosophers Nicolai Hartmann (1964) and Roberto Poli (2001), and supporting a natural modularization of top-level ontologies and introducing a new understanding of the notion of top-level ontologies.
The inclusion of the integration axiom, which integrates objects and processes into a unifying framework (Herre, 2015b, Section 2.7; Baumann et al., 2014, Section 6.4; Herre, 2010, Section 14.6), see axiom A18 in Section 3.2 below. This is a hallmark of GFO, because it bridges between 3D and 4D views and ontologies, with far-reaching consequences.
The development of a new foundational ontology of properties and attributives that is intended to contribute to a semantic foundation of data science.
The establishment of the onto-axiomatic method that can be understood as a further development of the axiomatic method in logic and the methodology of science (Hilbert, 1918; Tarski, 1965).
The particular role of set theory as a modeling framework for analyzing ontologies (as formalized theories) and for proving the consistency of axiomatic systems.
Ontologies can be explored in terms of their expressiveness with respect to applications. One can distinguish various ways of applying them. For example, an ontology can be applied to (other) theories. That means, the ontology is utilized to study and develop the foundation for another theory, to reconstruct other theories, or to develop new theories. Another kind of application is given where an ontology is used in industrial practice.
In the present article, the General Formal Ontology is explored with respect to its expressiveness in modeling certain case descriptions (‘cases’ for short). Section 2 outlines basic principles and the structure of GFO. Subsequently, Section 3 presents a selection of its axioms, formalized in first order logic (FOL). In the course of this we select and emphasize primarily axioms that play a significant role in the modeling of the cases. The ontological analysis and formalization of those cases is subject to Section 4. The final Section 5 first surveys various uses of GFO in practical – mainly industrial – applications and then discusses its impact and related community efforts. The article concludes with brief remarks and indications of two relevant future research topics.
The General Formal Ontology (GFO; Onto-Med, 2021a; Herre, 2010; Herre et al., 2006, 2007) is a foundational ontology, which is being developed by the research group Ontologies in Medicine (2021b) at the University of Leipzig since 1999.
General overview
Let us initially characterize the ontology in terms of a few important and/or special features:
GFO includes objects (3D entities) as well as processes (4D entities), both of which are integrated into one coherent framework. It presents a multi-categorial approach by admitting universals, concepts, and symbol structures and their interrelations. It includes levels of reality and ontological regions. GFO exhibits a three-layered meta-ontological architecture consisting of an abstract top level, an abstract core level, and a basic level. It is designed to support interoperability by principles of ontological mapping and reduction. Finally, the ontology is projected for applications, firstly in medical, biomedical and biological areas, but – among many others – also in the fields of economics and sociology.
GFO is a component of a larger, community-driven evolutionary system of foundational ontologies, which leaves room for modifications, revisions, and adaptions that are influenced by the historical state of our knowledge and by applications in nature and society. We hold that the evolution of foundational ontologies is based on two primary stages of revision, (i) the integration stage and (ii) the expansion and reorganization stage. In the integration stage existing foundational ontologies are compared, interrelations between them are studied and ontological mappings between them are established. The expansion and reorganization step consists in the inclusion of new insights from science, society, and nature, and in the creation of new corresponding categories that cannot be reconstructed within the given systems. We call this type of knowledge dynamics the community-driven creative evolution of ontologies, which differs from the more rigid coordinated evolution of ontologies (Smith et al., 2007). Our conception of creative evolution is partly influenced by ideas of Paul Feyerabend (1976; 1979).
Ontologies specified in a formal language are knowledge systems, which are historically related to the field of knowledge-based systems and expert systems (from which one of the early works originates that have become frequently cited for their characterization of the notion of ontology itself, authored by Thomas Gruber (1993)). Hence, ontologies present the current stage of development of knowledge systems. They have a deeper foundation of the basic notions to be used and they are equipped with a higher degree of expressiveness. From the outset GFO has been developed with the aim of contributing to a new foundation of knowledge-based systems and knowledge representation. During our work on GFO it turned out that basic principles of GFO, notably the idea of ontological reduction (Herre and Heller, 2006, Section 5), can be used for theory reconstruction and theory formation. These principles were further developed into the onto-axiomatic method (Baumann et al., 2014, Section 2), which is in parallel a refinement of the axiomatic method in mathematical logic (Hilbert, 1918; Tarski, 1965).
Organization of GFO and GFO 2.0
We use the term entity to subsume anything that has a mode of existence. GFO distinguishes four modes of being, which are associated with the following ontological regions of the world: the region of material entities, the mental-psychological ontological region, the social region (involving socio-systemic entities), and the region of ideal entities, where the latter includes mathematical entities, idealizations, and ideas.
Furthermore, GFO has a meta-ontological architecture, introduced in 2005, which is constituted by three levels (Herre and Loebe, 2005). (1) The basic level (or object level) comprises categories related to and relevant for reality (and thus most of the categories of GFO). (2) The meta-level, called abstract core level, contains meta-categories over the basic level, for example the meta-category of all categories. (3) Finally, there is the abstract top level as a meta-meta-level, related to formalizing the levels below.
Each of these levels is constituted by one or more corresponding ontologies, which are called Abstract Top Ontology (ATO), Abstract Core Ontology (ACO), and Foundational Basic Ontology (FBO), respectively. The ATO considered for GFO is represented by set theory, with merely set and item as its only two meta-meta-categories. Abstract core ontologies are clearly arranged cores of categories and relations that are to be used as a meta-level for the categories associated to the basic level. First examples are discussed by Herre and Loebe (2005, Section 3), while a module on categories and relations has been taken further by Loebe (2015, Section 2.4 and 6.1; 2018).
Since 2020, the next release of GFO, called GFO 2.0, is under development (Burek et al., 2020,2021; Loebe et al., 2021). This new version incorporates results obtained after the release of version 1.0 and is geared to making GFO as a whole easily available for practitioners. That second release, in contrast to the previous one as well as to other top-level ontologies, should not be understood as a single, monolithic ontology. Instead, it will adopt a (much more) modular architecture. These basic modules form themselves foundational ontologies, which exhibit a rich structure and which are distinguished by well-defined principles. A meta-ontology organizes these modules and associated levels by interrelating them and by specifying the relations required in this regard. Thereby GFO 2.0 becomes a coherent framework of parts/modules that are readily applicable to specific engineering problems and that are easily replaceable as they are based on standardized interfaces. That will allow for utilizing GFO (much more) flexibly and selectively, to the extent required in a given application.
Classification of individuals of the basic level of GFO
The basic level of GFO primarily represents the interface to the reality of individuals. Hence, it provides a classification of individuals, where we first distinguish abstract from concrete individuals. Abstract individuals are independent of space and time, for example the number π, whereas concrete individuals have an immediate relation to time or to time and space.
But let us first survey briefly GFO’s placement concerning well-known ontological distinctions:
Continuants and occurrents are both available, with process as the most important sub category of occurrents. As a specialty, GFO actually comprises a trichotomy of processes, continuants and presentials. The latter can roughly be seen as snapshots of continuants at time points. The trichotomy comes with an integration law, presented in Section 3.2. GFO distinguishes independent and dependent entities. Indeed, there are several relations of existential dependence. As a major trichotomy originating from dependence, GFO has attributives, which depend on complex individuals (independent), whereas the latter are constituents of situations (with an even higher degree of independence); cf. Section 2.3.3. There are distinct notions of process and event, with a particular understanding. Processes form a central category of time-extended, immutable entities in GFO, whereas any event is relative to a process. Other top-level ontologies exhibit equally labeled notions, but with differing readings, e.g. DOLCE (Masolo et al., 2003) and YAMATO (Mizoguchi, 2010; Galton and Mizoguchi, 2009). GFO deals with qualities/properties such that an entity has a quality, which in turn has a quality value. Qualities are attributives and, typically, a quality inheres in its bearer. Quality values are associated with value structures. Section 4.3.1 reveals more details on this matter. Elaborate theories on functions (Burek, 2007; Burek et al., 2009,2021) and roles (Loebe, 2007) have been developed in the context of GFO, because both notions are of high importance and value for ontological analysis and modeling. The treatments of the two modeling cases in Section 4.4 and in Section 4.2, respectively, allow for an impression on those theories.
Figure 1 displays the GFO taxonomy, thinned out to categories of major degree of importance, in order to ease comprehensibility and readability. The key notions and distinctions surveyed just above can be identified in this figure, except for events and quality values. Note that this taxonomy is a polyhierarchy, where multiple inheritance is allowed and considered; cf. e.g. role and its three sub categories.

Taxonomic overview of selected categories of GFO. Color-filled boxes indicate classification dimensions; line colors disambiguate paths. Boldface highlights categories of major relevance for this paper.
The most general distinction of Fig. 1 is that between category and individual. GFO provides a basic classification (ontology) of categories, whereas the notion of category covers all abstract entities that can be instantiated by or are predicated of other entities. The GFO ontology of categories is inspired by work of Jorge J.E. Gracia (1999) and continues his research in a fundamental way.3
Jorge J.E. Gracia was a philosopher at the University at Buffalo, who died in 2021. Since 2000 the Onto-Med group at the University of Leipzig maintained valuable scientific contact with him.
In the remainder of this section, we focus on the classification of the individuals of the ontological region of the material entities and introduce them in greater detail; they have a relation to both space and time. The explication of these relations assumes an ontology of space and time. Space and time are considered as categories, the instances of which are stipulated to be concrete individuals.
The material ontological region admits various levels of abstraction, related to granularity and corresponding conceptual layers. For instance, the granularity level of atoms and electrons needs a certain conceptual layer, including the relevant categories and relations needed to establish an adequate ontology. Hence we may distinguish ontologies of quantum mechanics, of elementary particles, of Newtonian mechanics, an ontology for relativistic physics, and others. Another granularity level refers to macroscopic objects. In the present paper, we restrict ourselves mainly to the material region and additionally to that macroscopic level. We refer to the theory of Paul Needham (2017) as a basic reference, as there is an overlap between his ontology and GFO’s material ontological region at the macroscopic level. Note further that we consider all these ontologies as foundational ontologies.
The category Time comprises (a.o.) instances called chronoids, which may be understood as closely similar to real-valued intervals with endpoints. The category Space, called phenomenal space, exhibits space regions as instances of primary importance. While every space region has an extension, there is an idealization of a greatest space region, containing any space region as part. Phenomenal space as such does not carry any metric. If we equip that idealized greatest space region with metrics, we can get various metric spaces, including Euclidian Space. We defend the position that the categories of phenomenal space and time should not be conflated into a homogeneous four-dimensional space-time continuum. The phenomena exhibited by space and time are different and there arises the problem of how these categories can be integrated into a uniform system. We believe that the integration law of GFO, see axiom A18 in Section 3.2, yields also a step forward to the solution of this integration problem.
To cover all relevant aspects of space-time that are fundamental in physics, a further space-time theory will be needed, as a four-dimensional space-time. The notion of space and time as occurring in physics differs from the phenomenal space and time in GFO. Yet there is a transformation from the theory GFO-Space (Baumann et al., 2016) into the mathematical space of physics, by extending GFO-Space to a pseudo-metric space from which, in turn, a metric space can be constructed. GFO 2.0 (the next version of GFO) will contain a further space-time module that is related to physics along these lines.4
Phenomenal space and time play a major role on the level of macroscopic entities, with inspirations from Needham (2017).
Concrete individuals can be distinguished with respect to the type of relation that they have to time and space. According to the type of this relation, spatiotemporal individuals are classified into continuants (also called endurants), presentials and processes. Continuants persist through time and are wholly present at every time point of their lifetime.5
Persistence of a continuant means that it is the same throughout its lifetime; but usually the properties of a continuant change from one time point to another. GFO provides a solution to this paradoxical situation (Baumann et al., 2014, esp. Section 6.4).
Here we assume Newton’s classical mechanics, which postulates the mass of a body as constant.
There is a complementary duality between processes and presentials: processes can never be wholly present at time points, whereas presentials possess this property. GFO provides a basic classification of processes that is related to the changes that occur in the process. A process – as a whole – cannot change, though it can possess changes, classifications of which have been examined earlier (Herre et al., 2007, Section 8.3; Herre, 2010, Section 14.4.4). Processes form a subclass of processual complexes, which are the most general kind of concrete individuals that have a temporal extension. The temporal extension of a processual complex is a mereological sum of a non-empty set of chronoids. Cohesive processes form an important subclass of all processes: a process is cohesive if any two process boundaries are causally connected, if their temporal boundaries coincide (Michalek, 2009, esp. Section 5.2). Some examples of processes include: the locomotion of a material object; sitting in front of a computer, viewed as a state extended in time; the development of a cancer; a hundred-meter-run.
There are many concrete entities that depend on processes in various ways.7
The term ‘dependent processual entity’ could cover all those entities; Essentially, it corresponds to the notion of occurrent.
Material situations are parts of the material world (at the macroscopic level) that can be consistently comprehended as a whole. We distinguish three kinds of situations: object situations, presentic situations, and situoids. Object situations consist of material objects and relations between them. A presentic situation is a snapshot of an object situation, and a situoid (or processual situation) is a part of the spatiotemporal world that arises from an object situation if all objects are replaced by the corresponding processes. An example of a situoid is a football match, happening in time, and including all necessary participating entities, among them the players, the football, the goals and other entities, but also the localization and the corresponding environment. Finally, the notion of comprehended as a whole is used here in an informal manner. We consider this notion as primitive, which is not defined by other notions, but needs to be described in terms of axioms.
Complex individuals are composed of elementary ones or components. There are various relations of composition. One type of composition uses dependency relations that glue entities together, another uses the part-of relation and the construction of mereological sums.

Elementary individuals that are related to other individuals by some kind of dependency relation are called attributives. They include, among others, qualities, relators, roles, functions, dispositions, and structural features. Material objects are wholes consisting of bundles of attributives;8
We are aware of the problems related to bundle-theory. We agree essentially with the criticism by Gustav Bergmann (1967).
Categories, the instances of which are attributives, are called properties. According to the different types of attributives (relational roles, qualities, structural features, individual functions, dispositions, etc.) we distinguish corresponding types of properties, such as quality properties, role properties, etc. More recently, an additional perspective on attributives – illustrated in Fig. 2 – has been developed as a foundation for an integrated data semantics (Herre, 2016), since attributives (and their corresponding properties) present the semantic side of data.9
An ontology of attributives contributes to an ontology of data because most data should be understood as the result of measurements of attributives. Heinrich Herre (2019) explicates this further by distinguishing the semantics of data (attributives and properties), the acquisition of data (by measurements of attributives or by interviews), and the representation of data.
With respect to their bearers we distinguish between object attributives and processual attributives. Regarding object attributives, first we consider here only genuine/intrinsic attributives, i.e., attributives without further direct connections to other objects than their bearer (in contrast to extrinsic attributives). Moreover, among object attributives we differentiate presentic and non-presentic ones. A presentic object attributive is determined fully and as a whole by the object it inheres in and a time during which it exists. For example, an individual color of red inhering in some object can be wholly accessed at time points. In accordance with GFO’s integration law (see Section 3.2), a presentic object attributive thus gives rise to a continuant, on the one hand, which itself exhibits, at each time point of its lifetime, a wholly present attributive at that time (a presential). Non-presentic object attributives inhere likewise in objects, but they require something in addition to just their bearer and a time point. For example, the age of an object at a certain point in time is not only determined by that object and that very time point, but it requires something else; say, the initial point in time of the object’s existence. Besides, note that the composition of an object with some of its qualities yields more complex entities, called object facts.
Processual attributives have processes and process boundaries as bearers and they are classified into presentic and global attributives. Presentic processual attributives are associated with process boundaries; they must be wholly accessible at time points. The isolated presentic data of process boundaries do not need any reference to a process; they can be completely reduced to object qualities. These are typical qualities of objects that participate in the process. An example of a non-isolated presentic attributive of a process is the velocity of a moving body at a time point (even if it is zero, e.g. as an initial velocity). The velocity cannot be determined and specified without a temporally extended process.
The global attributives of processes present the richest class of attributives of processes. A systematic classification of these attributives is in its initial stage. Their main feature is that it is not meaningful to specify or refer to them at a process boundary. One type of global attributives is abstracted from time series in the form of diagrams (such as curve diagrams). Examples are electro-cardiograms and long-term blood pressure measurements. Additionally, we emphasize that intrinsic global attributives of processes are themselves processes, called attributive processes. A clear separation between an attributive process and a corresponding bearer-process needs further investigation and clarification. A water wave, for example, can be considered as an attributive process that occurs on the basic process of local movements of water particles. This basic process is the bearer of the wave. Finally for processual attributives, many other global attributives of a process are not derived from time series. Examples are the duration of a process and its occupied space. Physics provides many examples of this kind, for example the average velocity of a moving body. Further investigation of the global attributives of processes should take the distinction between intrinsic and extrinsic attributives into account.
There are further kinds of attributives, including relators, roles, functions, and dispositions, which are more abstract than phenomenal attributives; they cannot be directly perceived or measured. GFO adopts the general understanding of a role presented by Frank Loebe (2007), where a role individual is defined as a relational entity that links any entity, called the role player (or filler), with some context, in which the entity plays that role. The notion of role is essential for a broad spectrum of modeling areas, one of which supported by GFO is functional modeling. Its objective is to depict a domain in teleological/functional terms, as contrasted with other aspects, such as structural or behavioral ones. The notion of function is built upon that of role: we introduce a function as a category that captures a role played by some entity in the context of a goal achievement (GA), where the GA provides a teleological specification of transitioning to something that is intended to be achieved.
Concluding this part, let us emphasize again that the ontology of attributives provides a foundation for the semantics of data (Herre, 2019,2016). Moreover, we mention that interfacing between attributives and knowledge occurs through the transformation from facts to propositions,10
This transformation from a fact (being a part of reality) to a proposition is the (mysterious) pivot of the mind’s ability to transcend the sense-data to achieve a meta-level view on the world. This is an extraordinary ability of the human mind.
The formal representation of the ontology is specified in the framework of type-free first order logic (FOL). The formal representation is built upon the principles of the axiomatic method (Hilbert, 1918), extended and refined to the onto-axiomatic method (Baumann et al., 2014, Section 2). According to the axiomatic method certain predicates and relations must be introduced as primitives; that means that they are not explicitly defined by other notions, but they are specified by axioms.
A formal representation in FOL is determined by a signature Σ and by axioms
We use the convention of model theory and logic and summarize the basic notions. For every signature
In the sequel, we follow the structure of Section 2.3.3, selecting only few axioms as examples for each sub section; furthermore, we restrict ourselves to the basic level of GFO. The first-order formulas are to be read as universally quantified w.r.t. all variables, typically denoted by single lower-case letters (say, x, y, z). Only some signature elements are specified explicitly before their use. The intended reading of the remaining ones can be derived from natural language paraphrases provided for the axioms. In addition, the Appendix comprises a listing of all GFO symbols used herein, including hints on renamings compared to other publications.
Space and time
A full axiomatization of time for GFO is presented by Baumann et al. (2014), who have also developed a more detailed theory on space (Baumann et al., 2016). The terminology of the time module involves centrally chronoids (basically, connected time intervals;
The subsequent examples of axioms belong to those that connect the basic level with the
If we want to say that “Space” is a category we must introduce a constant “
In this section we present some selected axioms on concrete entities, particularly, on continuants, presentials, and processes. The understanding of these kinds of entities in GFO is important as they are most relevant for the integration of objects and processes (Herre, 2015b). These notions are primitive. They can be accessed by informal descriptions and are characterized axiomatically.
A continuant persists through its lifetime and is wholly present at every time point of its lifetime. The lifetime of a continuant is an extended interval with an initial point and an endpoint. Examples are this cup, this car, this tree, this dog, and the person Socrates.
A process evolves through time and has a temporal extension which is a time interval with endpoints. If a process is restricted to a time point of its temporal extension, then the resulting entity is called a process boundary. The main distinction between a process and a material object (material continuant) is that a process can never be wholly present at a time point.
Individuals are divided into entities of time and space as well as concrete and abstract individuals.
Continuants, presentials and processes are a (non-exhaustive) subdivision of concrete entities.
For every time point during the lifetime of a continuant, there is a presential that the continuant exhibits at this time point.
A continuant exhibits a presential iff the continuant exhibits that presential at a time point.
Material structures are presentials and occupy a uniquely determined connected space region.12
Since a material object can move in space, we stipulate that only material structures, being presentials, occupy a uniquely determined space region.
If an entity is the temporal extension of another entity, the former is a chronoid, the latter a process.
The final axiom of this section is the integration law for objects and processes in GFO.
For every material object there exists a uniquely determined process, the temporal extension of which equals the lifetime of the material object, and at every time point of that lifetime of the object the presential exhibited by the object is likewise the process boundary of that associated process (at the very same time point).13
We emphasize that processes, derived from material objects, form only a small subclass of the class of all processes. GFO (Herre et al., 2007, Section 8) comprises a first classification of processes in general.
For this continuant(-associated) process in A18 we introduce a relation
The integration axiom needs further explication, because it is a unique selling feature of GFO which has many implications. Frequently, top-level ontologies are classified into 3D und 4D ontologies. Via A18 GFO integrates both approaches into a uniform system. Any top-level ontology should admit as basic categories processes and objects, where (material) objects are to be understood as continuants. Commonly, a material continuant has a lifetime, persists through that lifetime, and is (taken to be) wholly present at any time point of its lifetime. Any top-level ontology must clarify how processes and (material) objects are related. There are various approaches to tackle this problem. In 4D ontologies, there are only processes, while material objects are considered as particular processes. This applies to the ontology of ISO 15926 (ISO TC 184 SC 4, 2003; Teijgeler, 2021), co-developed by Matthew West (Stell and West, 2004, Section 2.3), and it is even more elaborated in the ontology of Johanna Seibt (2003). In 3D ontologies (and particularly in BFO) instead, processes are, so to say, properties/qualities of continuants, hence a process/occurrent/event inheres in a continuant. Baumann et al. (2014, Section 4.4 and 6.4) discuss that the notion of continuant leads to certain difficulties if they are assumed to be entities that are independent of the mind.
In GFO, the integration problem (of processes and material objects) is solved by the integration law. How can the persistence of a material object (continuant) be understood? Every material object M is identical during its lifetime. At any time point t of its lifetime, M exhibits a presential, denoted by
Here we use the representation of concepts by prototypes (Rosch, 1983), emphasizing that the interpretation of persistence by individual prototypes is an approach established in connection with GFO. Heinrich Herre (2015b) formulates the hypothesis that the identity over time of continuants is finally grounded on the phenomenon of personal identity of the (an individual) mind.
We remark that there are processes that cannot be derived from material objects by the integration law. An example is given by processes related to the local changes of the field forces of a physical field, for example, the electromagnetic field. Yet another application of the integration law is a new interpretation of the particle-wave duality in quantum mechanics. Here, a particle P is understood to be a material object with a lifetime. A wave, associated with this particle P, is a global attributive of the continuant process that is associated with P via the integration law. We conjecture that the wave associated with a particle P depends on a basic process, which is exactly the process defined by the integration law.
Material objects are individuals that are constituted by more elementary individuals. Objects consist of matter, have a certain structure in terms of their parts and properties, and they are governed by identity criteria and criteria of wholeness.
Dependence and attributives
There are various relations of dependence between entities, among which Section 2.3.3 briefly addresses existential dependence in a general sense as well as inherence. For example, an attributive cannot exist independently of a bearer and we may say that the bearer has higher degree of existential independence than the attributive. The notion of existential dependence is used throughout this paper in an informal manner. The basic schema of complexity is summarized as follows, cf. also the lower part of Fig. 1 (Section 2.3) and the categories highlighted in green: attributives/properties are constituents of material objects and material processes, resp., while those latter are included in material situations and situoids/situational processes.
We introduce some axioms w.r.t. the dependence relations
Properties (
Besides the mere inherence of a quality, GFO relies on values to characterize a quality bearer (with some analogy to DOLCE (Masolo et al., 2003) in that respect). Insofar, the phrase “an individual color of red inheres in this apple” in Section 2.3.3 can be more precisely extended to “an individual color of the value red inheres in this apple”. In order to understand value attributions, we need to consider both the individual and the categorial level. The individual quality of the apple instantiates the property color, which is associated with a property value ‘red’. The latter is not only a category of quality values (themselves individuals), but typically also part of a measurement system or, more technically, a value structure. As categories, properties and their values can be considered independently of individuals. Properties correspond to determinables in the philosophical literature, e.g., described by Ingvar Johansson (1989), whereas property values equate determinates. Note that both notions need not be taken to be absolute, but both can depend on the assumed granularity. Finally, we use another dependence relation, namely
On this basis, we selectively illustrate some connections in axiomatic form.
Continuants, presentials and processes are subject to the inherence of qualities.
An entity has a property iff an instance of that property inheres in the entity.
Stuff
The concept of stuff (denoted by
Few examples of axioms follow, focusing on the dependence relation Every material object consists of an amount of stuff.
Every amount of stuff is part of the stuff of some material aggregate.
Every amount of stuff overlaps with a material object’s stuff.
Function introduction for the (uniquely determined) stuff of material structures.
Material objects, material boundaries, material aggregates and material object-processes
Solid material objects have a natural boundary. This does not apply to all natural objects, for instance, what are the natural material boundaries of a rock or of a mountain? The earth is a material object, while certain parts of it do not satisfy all conditions for material objects. For example, a mountain lacks the existence of a natural material boundary. Another example of a natural boundary of a material object is the separation of an airplane from the surrounding air. The latter has a boundary and the airplane as a material object has its material boundary; both boundaries belong to distinct material objects, can be clearly distinguished by different properties, and they touch.
Further notions that play a role in the analyses of the subsequent Section 4 are material aggregates, object-processes and the notion of solidity. A material aggregate is a collective of material objects; hence, it is a continuant. A material object-process satisfies the condition that every process boundary is an aggregate of material structures. This kind of processes is the counterpart of material aggregate. Solidity is a presentic quality of a material object, i.e., it derives from the presential with that quality and applies at each time point (even though the test for solidity requires a process).
Solid material objects are continuants that exhibit solidity at every time point of their lifetime.
Material facts, situations, situoids and collectives
Considering relational facts, material objects can be connected by relators. Material facts, in turn, are composed of a relator and material objects playing the corresponding roles. Material facts are continuants. Material situations are composed of material facts, such that this system of material facts can be comprehended as a whole. Material situations are continuants, with a relation to collectives.15
Our understanding of the notion of a collective is partly influenced by Antony Galton’s work (Wood and Galton, 2009). A (material) collective is a hybrid entity combining a set of material objects with a category.
by the material objects included in it, by relators connecting these objects, and by cognitive principles, combining the material facts into a whole.
An ontological model of any part of reality is a description of it by a set of formalized axioms that use a selection of concepts and relations applicable to that part of reality. A foundational ontology specifies more general categories, whereas additional domain-specific axioms capture the specialized domain. The original description of a part of reality is usually expressed in a natural language or in some specialized natural language, for example, the language of physics, chemistry or technology. Informal and semi-formal descriptions can be transformed into a strict formalization within FOL. It is important to note that such formalizations are not uniquely determined.
In the following sub sections we analyze, discuss and partially formalize five cases in order to demonstrate their “appearance” against the background of GFO.
Composition/constitution
“There is a four-legged table made of wood. Some time later, a leg of the table is replaced. Even later, the table is demolished so it ceases to exist although the wood is still there after the demolition.”
Basic assumptions and relations to GFO
Every material object is composed of stuff; formally,
Semi-formal description and domain specific signature

A timeline that surveys and relates temporally the material objects, aggregates and processes involved in the composition/constitution example.
Figure 3 indicates the temporal extensions of the individuals named in the case description (and a few more) and interrelates them w.r.t. several temporal phases (chronoids
The indices of the material entities refer to the indices of the temporally associated chronoids
In order to express interrelations in connection with the replacement process
In addition,
We gather compactly a first group of axioms on the basis of the previous sub section. Roughly following its structure, the case-specific signature as well as the constants (see Fig. 3) introduced there are used in combination with symbols of GFO (remember also the Appendix).
In particular, to capture the relation between the table
Deliberately, the extensive, but not more instructive representation of the fact that
Formulas E1–E10 represent the modeling case rather “literally” so far. Primarily E10 starts to reveal additional considerations, namely on how to understand “the wood is still there after the demolition” from the case description. Indeed, the formalization should be extended by further axioms in order to capture more of the intended semantics of the symbols introduced. We constrain ourselves to a number of sample formulas that come into question in this respect, starting with more general axioms that relate the domain level to the foundational level. Then a few proposals concerning the central predicates
At the start of a replacement in an object, there is a to-be-replaced part of it.
At the start of a replacement in an object, the to-be-new part is not yet a part of it.
A demolished object has ceased to exist and its remains are not connected any more.
Many more potential axioms could be considered, while we conclude this overall case with two further points. First, regarding replacement there is the highly interesting question of whether and which requirements can be posed w.r.t. the relationship/similarity among the replaced part and its substitute. Would a similar shape/form suffice, perhaps extended with an appropriate material? (E.g., thinking of required stability in the case of a table leg.) Should one enforce that the substitute object can fulfill the same function? Those questions may easier be tackled in a more specific application context.
Secondly, this first modeling gets close to the puzzle of the ship of Theseus and its variants. Applied to the table case, how much can the table change to remain the same? Of what nature is the entity during the replacement? We see no absolute metaphysical solutions to these problems. There is no uniquely determined identity criterion, in our opinion. Instead, there are various equivalence criteria. What is important is the fact that a foundational ontology is expressive enough to distinguish these different forms of equivalence explicitly.
“Mr. Potter is the teacher of class 2C at Shapism School and resigns at the beginning of the spring break. After the spring break, Mrs. Bumblebee replaces Mr. Potter as the teacher of 2C. Also, student Mary left the class at the beginning of the break and a new student, John, joins in when the break ends.”
Basic assumptions and relations to GFO
The described situation clearly exhibits social aspects and we stipulate first that all mentioned terms (teacher, class, school and summer break) refer to, at least among others, kinds of entities in the social ontological region. The latter is one out of four major ontological regions distinguished in GFO and only briefly mentioned in Section 2.2. In parentheses, we list a few example categories for illustration here:
the material region (e.g., with ‘human body’, ‘mass’ and ‘breathing’)
the mental-psychological region (e.g., with ‘human mind’, ‘consciousness’ and ‘thinking’)
the social region (e.g., with ‘teacher’, ‘school’, ‘right’ and ‘communication’)
the ideal region (e.g., with ‘number’, ‘circularity’ and ‘calculation’)
Considering entities w.r.t. these ontological regions is inspired by the theory of levels of reality (Poli, 2001). Poli uses the term ‘stratum’ instead of ‘region’, and strata are further divided into more fine-grained levels. For instance, the material region comprises levels such as the physical, chemical and the biological level. There are tight relations among the regions, e.g., where most entities at the mental-psychological region as well as at the social region rely on entities at the material region (more technically, overforming or building-above (Poli, 2001; Hartmann, 1964)). Put differently, one may say they have a material basis. Moreover, there are categories and individuals that involve aspects associated with multiple regions. A ‘human’, for instance, typically involves (at least) a ‘human body’ as well as a ‘human mind’. ‘Person’ may be understood to add social aspects on top of ‘human’, such as bearing a (socially agreed upon) ‘name’ and ‘human rights’.
A second line of work that is highly relevant for the situation described in the case is concerned with the notion of ‘role’. The approach to roles developed for GFO originates from an early analysis in 2003 (Loebe, 2003) and was covered in more detail later (Loebe, 2007). At the gist of it, there is a fairly general understanding of a role as a kind of entities that depend on (i) a context and (ii) a player. The context typically comprises of several roles (up to singular exceptions), which complement each other, such as teacher, student and subject. The player of a role is an entity that plays/fills/has/holds the role,18
Terminologically, we follow much of the literature in using ‘playing a role’ for the relationship between an entity that adopts/holds a role and that role itself, whereas ‘playing a role’ in the sense of pretending something or acting as a temporary substitute, for instance, is not meant and is a more specific relation out of our current scope.
The term ‘social role’ hints at another aspect of the GFO account of roles: contexts are utilized for distinguishing broad role types. Three types have been considered so far. We quote their informal short-hand characterizations as provided by Loebe (2007, p. 133):
relational role – corresponds to the way in which an argument participates in some relation;
processual role – corresponds to the manner in which a single participant behaves in some process;
social role – corresponds to the involvement of a social object within some society.
Admittedly, especially the characterization of social roles simplifies matters significantly and the notion of ‘society’ may be rather vague as the context of social roles. ‘Social system’ would be another, perhaps slightly better choice. What remains hidden from that characterization is that social roles are, on the one hand, object-like entities that are equipped with their own properties and behavior. On the other hand, as roles they depend on their players, for which they are like (complex) properties. This dependence lets social roles appear also akin to attributives in GFO. The second dependence that social roles exhibit is that on a context. It will be more instructive, however, to view the concrete problem case at hand. Relational and processual roles are less relevant in that analysis and can be covered only briefly.
Let us start with the phrase “Mr. Potter is the teacher of class 2C at Shapism School […]”. We argue that ‘teacher’ is suggestive of a social role, but language use is not as simple as that. Mr. Potter should/can be viewed as an instance of the role category teacher. Instead, there is an individual social role
Besides depending on its player,
Regarding the replacements of Mr. Potter by Mrs. Bumblebee as well as of student Mary with student John (after a gap), we advocate the view that Mrs. Bumblebee plays her own social role
Formalization
We can only partially formalize the given situation, where we start with two background axioms of GFO, followed by three exemplary specialization axioms, connecting domain with top-level categories.
A role implies a player and a context, of/in which it is a role.19
We restrict to roles which are played by an entity. We are aware of vacant roles which are not yet (or even never) played by an entity. The present theory of roles needs an extension to cover this case. We thank one of the reviewers for pointing to this phenomenon.
Several predicates for domain-specific constellations should first be introduced explicitly as signature elements:
Next the major part of the analysis in Section 4.2.2 must be established by further axioms. As the case description itself does not specify more explicitly, this can become a boundless enterprise. We illustrate matters by some specific axioms that relate to the analysis given, well aware that this is far from complete in any sense. The first two axioms formulate domain-specific conditions.
There is only one class teacher per class and term.
The class teacher of a class must be a teacher at the school of that class.
Another important kind of axiom links the “short-hand” predicates to a more detailed formal description. For instance, the ternary teacher predicate is intended to be bound to teacher as a social role, signified by
Any teacher at any school during any term plays a teacher role in the context of that school that encompasses the school term.
The class teacher of a class must be a teacher at the school of that class.
The teacher role is equipped with the right to mark students.
Finally, being a class teacher (
Having a class teacher at a school during some term implies that there is a corresponding relator with exactly three roles, played by class teacher, school and term.
“A flower is red in the summer. As time passes, the color changes. In autumn, the flower is brown.”
“A man is walking when suddenly he starts walking faster and then breaks into a run.”
A flower of changing color
In order to analyze the color statements in sub case (a), we need to consider both the individual and the categorial level. Colors of objects lead to qualities and thus to the realm of attributives (individuals), properties (categories of attributives), and property values in GFO, introduced in some detail in Section 2.3.3. We analyze color as a property and red as a property value, typically being part of a measurement system. When we turn to a particular flower, “the same” entities exist at the level of individuals. That means, the flower is an individual in which qualities can inhere (a.o., the color of that flower). A quality, in turn, has an individual value assigned, such as the particular red that is the value of the color of the flower and an instance of the property value red.
Accordingly, the change of the color of a flower is in fact a switch from one value of an individual quality to another quality value. In real life ontology engineering, however, the dynamics of modeled entities rarely involves a change of only a single property as in our case. Instead, usually the modeled entities undergo changes of multiple properties and the change can have diverse forms of temporal distribution – they can change simultaneously, with overlap, follow one other, etc. For example, a growing cell can both move and change its shape and size in parallel. The basic principles of modeling change explained just above can be applied to such diverse and complex scenarios, as well, but they can be beneficially augmented with modeling patterns that support a given scenario best. The performance of several patterns for modeling the change of qualities based on GFO is discussed by Burek et al. (2019a).
The next question in the case of the flower, call it F, is what sort of change it is. Clearly, it is not an instantaneous one, but a continuous change instead, during a part of the lifetime of F. If, in accordance with the integration law (A18, Section 3.2), we consider the flower F as a process
Let us capture some aspects more formally, limiting ourselves to the fact that the color of F is red in summer and brown in autumn and only referring to F as continuant (which exhibits presentials). F is a material object with a certain lifetime. We consider a sub interval/chronoid
This can be formalized as follows, using F,
Summer and autumn are in the same year
The flower is red in summer.
The flower is brown in autumn.
Importantly, we stipulate that changes are only possible with respect to the values of one property. For example, there is no property that subsumes the properties weight and color. Hence, these properties have distinct values and it is not plausible that a color value changes into one of the property color. One may still see a gap in this argumentation, however: Why is that plausibility not given? This gap can be closed by looking at the processes behind the material objects. First of all, according to the integration law (cf. Section 3.2), there is a process
If we consider an object as a bundle of attributives then we assume that the change of their values is triggered by causality, and that the causality is in the process. The change of the values of a property P does not cause the change of the values of an arbitrary other property Q. We doubt, for example, that the change of the spatial location of a material object causes the change of its color. On the other hand, there must be – of course – certain causal patterns, connecting the value changes of its properties. The change of the temperature of an iron body, for example, causes a change of its size.
We claim that causality is a phenomenon defined for processes (that occurs in connection with processes), but not (directly) for continuants. A presentic attributive of a continuant can be considered without any process, and we reject the possibility that a causal relation between two coinciding presentials, exhibited by the continuant, can be established by the continuant alone. Causality is in the process, but not (in itself) in the set of the exhibited presentials of a continuant (Michalek, 2009).
The second sub-case of property change is (b) “A man is walking when suddenly he starts walking faster and then breaks into a run.” It will be necessary to consider the man M, categorized as a material object in GFO, in connection with the process
We see two options of interpreting the motions of “walking” and “running”. In GFO they can be seen (1) as global attributives of processes or (2) as processes themselves. Under both options the process
The remaining problem for capturing the case is a specification of the concepts
We note that these considerations refer mainly to the second option above, of viewing walking and running as processes. While we cannot elaborate an in-depth characterization, we explore this option a bit further, first considering those three temporal parts of
The expression
The process associated with the man M is composed of three consecutive parts
The first two parts are instances of
The three parts have associated temporal extensions
The velocity of the first and third part is constant.
The velocity during the second part is increasing.
However, the description according to physical parameters like velocity and acceleration is surely not enough to describe the whole process in detail. Such a description could likewise be attributed to, say, a driven car (constant velocity, acceleration to a maximum speed, etc.). The specific motions of walking and running can be further analyzed. A key difference between walking and running is that a walking man does not lose the contact to the ground. Running, in contrast, involves touching the ground and jumping in between, i.e., a runner is without ground contact for short time intervals. These intervals could be measured and then serve as a parameter for the description of the running. Of course, there is more to say about walking and running, for instance, there are certain coordinated movements of the man’s arms and legs. There is, for example, a parallel forward movement of the left leg and the right arm, or of the right leg and the left arm. There are consecutive sub-processes of the walking process that satisfy a well-defined regularity. For instance, the sub processes (left-arm, right-leg) and (right-arm, left-leg) occur alternately. Running allows for similar observations.
This sketches basic ideas and indicates a few directions towards a more detailed treatment – all limited to the material ontological region so far. The next case involves additional aspects.
“A man is walking to the station, but before he gets there, he turns around and goes home.”
Analysis focusing on the material region
First and from a physical point of view, one may distinguish various movements that occur. The first is a process, starting at a certain time point and being a movement towards the station. The station is not reached, though, instead there is another process that starts beforehand. That process can be divided into a processual segment of turning around, followed by a process of walking that is directed home. This is a description of process segments of the case at the physical level/the material ontological region.
Keeping the illustration of a corresponding, fairly straightforward formalization brief, we consider two processes that involve a material object – a man M. The first, say
Processes
Process
However, the whole process cannot merely be described based on physical laws alone. In particular, there is no physical causality between the first and the second process segment. This means that the whole process is conducted by an actor that is more than a material object.
Analysis involving teleological aspects
For GFO, we introduced a layered architecture that permits to separate (1) non-functional descriptions specifying what is present in a domain, which structure it has and how it behaves from (2) a functional layer that represents which goals and rationale are behind (Burek, 2007; Burek et al., 2016). Section 4.4.1 elaborates a purely non-functional description, abstracting away from the teleological character of the above processes. In order to grasp their teleological character, we need to ask the question of why
In GFO the teleological character is depicted by a category of Goal Achievement (GA) understood as a purposeful transition, i.e., a transition to a situation that is (considered to be) a goal. That is founded on the notions of Goal, Situation and Transition. A goal is a teleological situation, i.e., a situation (considered to be) of utility.22
Following Burek et al. (2016), we index predicates with argument category indicators, with I for individual and C for category. The index is part of the symbol, hence
A situation is understood as a state of affairs that is composed of facts and can be comprehended as a whole, which can vary in its complexity depending, e.g., on the number of objects involved. In our case we speak about situations
The formalization of situations with their constituent parts, i.e., facts and their decomposition into relators that mediate between/connect entities in terms of relational roles is technically more tedious than conceptually instructive. It is therefore omitted here, but examples detailing relation/relator analysis are given by Loebe (2015, Section 4.4.3.2, 2018, Section 2.3).
The notion of utility is considered as primitive (and is denoted by
We remark further that a goal as such is modeled first on the categorial level, before an individual situation can be identified as its instance. A goal can therefore also be captured adequately if it is not achieved. This applies in the use case: e.g., there is no situation (instance) in which M is at the station. We list five exemplary axioms formalizing transitions and GAs at the categorial and individual levels.
A transition (individual) transitions causally from one situation to another.
A goal achievement (individual) is a causal transition to a goal.
A goal achievement (cat.) is a transition (cat.) the instances of which lead to a shared goal (cat.).
Overall, a goal achievement category accounts for a teleological specification of transitioning to what is intended to be achieved, hence, to a goal. It describes the context in which an item has (and possibly realizes) a function. Typically, GAs are realized by processes, and therefore certain process categories can be understood as goal achievement categories.
Returning to the use case, we have seen two levels of description – a non-teleological one of two processes
What is still missing is an insight on the intentions behind, i.e., why those processes happened. This demands another layer of description and is represented in GFO by means of a family of has-function relations. These capture the intuitions that entities may have some functions for some agents due to certain reasons, e.g. because they have been designed, used, or desired to do something (Patryk Burek (2007, esp. ch. 6) developed a detailed classification). Notably, in GFO a function can be assigned not only to objects, but also to processes. That way we may say that the process
As a final remark, functional/teleological modeling frequently requires a more advanced toolset for handling more detailed descriptions of goal achievements. These can involve (1) objects contributing to the goal achievement, which can be classified as doers, contributors, operands or instruments, depending on their role in the GA. Further aspects are (2) the mode of realization and (3) side effects as well as the modeling of interdependencies between goal achievements and between functions, such as functional decompositions (Burek et al., 2016,2009,2017).
“A marriage is a contract that is regulated by civil and social constraints. These constraints can change but the meaning of marriage continues over time.”
This final use case is clearly a challenge and we tackle it more indirectly than the previous ones. For a first observation, the term “meaning” has been used to mean a great number of different things (Speaks, 2021). Hence, this task in particular may have various solutions. We shall consider how to approach that spectrum to an extent possible in this section.
A term is a symbolic structure, in the form of something abstract or as a token. The meaning of a term is different from the term and we say that a term may denote (or designate) a meaning. In understanding a term, that meaning is presented in the mind. On that basis we consider it as a part of a concept.
Any concept has an extension and an intension (or, put differently, content). The extension of a concept C is defined as the set of its instances:
This is a simplified version of the intension of a concept. In a more complete definition (and theory) of intension these categorial parts are additionally connected by further ontological relations. Another approach presents a concept by a theory and a meaning as certain of its sub-theories. Results in cognitive science clearly suggest that concepts have an internal structure, which, moreover, often indicate tacit assumptions taken by the concept holders (Margolis and Laurence, 1999).
It is not clear how to define the change of the meaning of a term. If the meaning of a term is identified with its intension, then any change of that intension is a change of the meaning. However, if the meaning of a term is contained in the intension of the concept that the term denotes, then it seems possible that the intension of a concept changes, while the meaning of the term persists. Yet one must assume limits of concept evolution, as not all changes of an intension would be acceptable. For instance, if marriage were defined as a one-to-one relation between a man and a woman, would a change of gender-related conditions or a change of the cardinality be as easy acceptable as, say, a change in the access policy regarding health records? Certainly no, for some cultures.
One approach to handle that problem in the context of GFO refers to psychological essentialism, according to which humans act in a way suggesting that cognitive representations of concepts are not mere sets of features or of undifferentiated necessary and sufficient conditions, but instead they exhibit more complex structures. Those structures are organized around essential properties, which provide criteria for concept membership and which are responsible for other features, called peculiar, for which they provide some sort of explanation or justification (Medin and Ortony, 1989).
The findings of psychological essentialism can be applied to the modeling case in two ways. In the first approach, all characteristics of the marriage concept are grouped into two separate concepts: one constituted by all essential characteristics, the other by the peculiar ones. This approach is similar to Borgida’s and Brachman’s suggestion in the context of conceptual modeling with description logics (Baader et al., 2010) to distinguish in definitional form incidental (though necessary) concept conditions and not to include non-essential knowledge in concept definitions, but to model them directly in the ABox (Baader et al., 2010, Section 10.4.1). In our suggested approach, we would keep both in the concept space, but group them into two distinct concepts, one of essential, the other of peculiar characteristics. This explicit separation of characteristics allows for handling a “true” meaning of marriage (whatever it is in a given socio-cultural setting) separately from peculiar constraints (e.g. specific legal characteristics). By the explicit separation of essential from non-essential characteristics it further indicates the border that cannot be crossed without losing the “true” meaning of marriage. The drawback of this approach, however, is that resulting ontologies are overly complicated. A decision on separating essential from peculiar characteristics for each concept is in many cases neither easy, nor even needed. That leads to complicated and crowded resulting ontologies, violating the principle of Ockham’s razor.
An alternative approach is to handle the distinction between the essential and peculiar characteristics not at the domain level, but at the meta-level. In early works (Burek, 2004,2005) in connection with GFO, the conceptual structure is represented by a meta-ontology that accounts for representing the distinction between essential and peculiar characteristics and their interdependence. Burek (2005, Section 3.2) says (here with minor adaptations) that a necessary characteristic
Altogether, a proper, in-depth treatment of concept evolution remains to be taken much further and is on our future agenda.
Ontology usage
The foundational framework of GFO has been further elaborated continuously since its inception, while its application in various industrial and research projects has intensified since 2007. We summarize this development by listing some of the major novel results and application projects. For each project we indicate the GFO aspects and modules (as outlined for GFO 2.0 (Burek et al., 2020); cf. Section 2.2 above) that have been utilized.
The notion of core ontology was analyzed and then applied to the development of a core ontology for biology (Hoehndorf et al., 2008). It turned out that autopoietic systems are at the core of biology. This work uses some ideas of the category-individual module.
The method of search ontologies was introduced and employed in the projects Ontovigilance and OntoPMS (Uciteli et al., 2019b). That work uses the notions of categories and individuals, and in particular the relation between symbolic structures and denoted concepts.
The project OntoMedRisk was devoted to developing a tool for minimizing the risks in hospitals (Uciteli et al., 2017). The approach, by providing information from various sources, organizes processes in hospitals in a way that allows for avoiding adverse events. A notion of possible situation was introduced to calculate the probability of risks. In this project the module of spatio-temporal entities was used, especially the ontology of processes combined with that of situations.
BioPass and COMPASS are two projects devoted to the navigation in minimally invasive surgery, where navigation is a basic problem (Siemoleit et al., 2017). The aim of these projects was the development of a new approach for navigation that improves the reliability by using data and information from images and from the course of the surgical intervention. For this purpose the ontology of situations combined with an ontology of processes was used.
The MDR-Project was aimed at the specification and prototypical implementation of a metadata repository for clinical and epidemiological research. This project uses the ISO Standard 11179 (ISO/IEC JTC 1 SC 32, 2003–2005). In the same context Uciteli et al. (2011) present a complete ontological theory of the notion of data element.
The Leipzig Health Atlas (LHA) is aimed at the development of an integrative data semantics in systems medicine. It provides an interoperable ontology-based semantic platform to share highly annotated data, novel ontologies, usable models and working software tools. Additionally, LHA delivers an advanced, application-oriented analytic pipeline for a clinical and scientific user community providing disease-related phenotype classifications, omics-based disease sub-classifications, risk predictions and simulation models for diseases and organ functions (Uciteli et al., 2019a). In this project the attributives module plays a significant role, which is the basis for specifying complex phenotypes.
The SMITH project (Winter et al., 2008) integrates clinical care and clinical research to enable a more rapid and creative innovation cycle by improving discovery based on real world care data. The goal is to improve patient care. This is to be achieved, first, by using innovative medical informatics technologies and novel modalities of data management and data modeling to deliver recommendations for tailored risk assessment and for preventive, diagnostic and therapeutic procedures. Secondly, electronic medical records are to be utilized in an innovative way to understand connections and dependencies within the records (e.g. medication and side effects), and to deduce phenotypic profiles and induce specific clinical or organizational actions (e.g., alerts, triggers). In this project, the module of attributives plays a central role.
The Function Modeling Language (FueL; Burek et al., 2016) is a UML dialect designed for capturing functions in an ontologically founded way, which enables the systematic, graphical representation of functions and their interrelations. FueL has been successfully applied for suggesting refactoring options for the Molecular Function Ontology (Burek et al., 2017), a sub-ontology of Gene Ontology (GO) – the largest resource for cataloging gene products. FueL utilizes the attributives module and functions sub module particularly.
The Cell Tracking Ontology (CTO; Burek et al., 2019b) is a project targeted towards cell tracking and time-lapse microscopy. The increasing amount of cell tracking data demands the creation of tools in order to make extracted data searchable and interoperable between experiment and data types. CTO focuses on describing, querying and integrating data from complementary experimental techniques in the domain of single cell analysis. CTO is built upon the notions of core temporal entities and spatio-temporal individuals.
Finally, recent work is concerned with a lightweight and integrated approach of modeling processes and objects (Burek and Herre, 2020). For that purpose, the Simple Process Object Ontology has been derived from GFO. In addition to the combined modeling of objects and processes, multiple perspectives on processes can be handled.
Note that the projects in (2–7) use a newly established method of ontology-based software engineering, which we call the three-ontology method, initially presented by Robert Hoehndorf et al. (2009). This method is a unique specialty in software projects related to GFO. Another approach provided by GFO is the onto-axiomatic method (Baumann et al., 2014, Section 2), which is a refinement and extension of Hilbert’s axiomatic method (1918). The onto-axiomatic method utilizes top-level ontologies of the basic ontological regions that are integrated into GFO. It will be further developed as we continue transitioning from the former idea of a monolithic foundational ontology to defending an approach of a system of modular foundational ontologies, which are organized by a meta-level ontology.
Community impact and community building
The research on ontology around GFO was established in 1999 as a common project at the Computer Science Institute and the Institute of Medical Informatics, Statistics and Epidemiology (IMISE) of the University of Leipzig. This activity led to the foundation of the research group Ontologies in Medicine (Onto-Med), the program of which is expounded at its website (Onto-Med, 2021b). This research group conducts basic research in formal ontology, designs formal tools for constructing and managing ontologies and develops top-level ontologies as well as domain and core ontologies for medicine, bio-medicine and biology, but also for other fields. The Onto-Med group pursues an interdisciplinary approach, combining methods from logic, computer science, and philosophy.
Since its early days, a number of further working groups have been established. These include the group Ontologies in Biomedicine and Life Sciences (OBML), part of the German Informatics Society (GI) and running a workshop series on the topic of Ontologies of Data and Life Sciences (ODLS) (Hastings and Loebe, 2021). Another working group is the logic group, devoted to developing axiomatizations primarily of top-level subjects, e.g. theories of time (Baumann et al., 2014), space (Baumann et al., 2016), and categories and relations (Loebe, 2018), among other matters. Last, but not least, there is a group aiming at an ontological foundation of developmental biology (Burek et al., 2019a,b,2020), which is realized in cooperation with partners at the Max Planck Institute for Human Cognitive and Brain Sciences in Leipzig, the Technical University in Dresden, both in Germany, the Maria Curie-Skłodowska University in Lublin, Poland, and the Bio-Ontology Research Group (BORG, 2021) led by Robert Hoehndorf at King Abdullah University of Science and Technology (KAUST) in Thuwal, Saudi-Arabia.
Concluding remarks
On the one hand, Section 4 demonstrates that GFO is a framework that allows for suitable ontological analyses and modeling, formally based on representations in first order logic. On the other hand, it has become clear that the modeling of the use cases remains limited to a certain depth only. For more fine-grained modeling, additional notions would have to be introduced, in combination with a substantially more extensive analysis. For example, this is well visible in several cases in connection with the modeling of physical processes. This needs to respect physical laws, the integration of which into a top-level ontology we see as an important future task. Another highly relevant task is the development of an ontology that allows for establishing a common and uniform basis for data and knowledge (and their handling). Ontology can make important contributions in this connection – and, overall, in many other contexts. On that basis it might become a reality in the future that artificial intelligence systems achieve novel, scientifically outstanding results.
Footnotes
Acknowledgements
We are highly grateful to all reviewers of the several versions of the manuscript and we greatly thank Bärbel Hanle for technical improvements and support in final stages of preparing this article.
GFO signature elements
The following list of symbols covers formal signature elements of GFO notions, introduced throughout this article, most of them in Section 3 and several further in Section 4. Note that the wording “is a” in intended readings of unary predicates is geared towards readability, while it should be understood more precisely as “is an instance of” (in contrast to and thus not as “is a specialization of”). Abbreviations in remarks: “syn.” for “synonymous”, “equiv.” for “equivalent”.
