Applied Ontology, Misc

The Provenance Ontology (PROV-O) is a World Wide Web Consortium (W3C) recommended ontology used to structure data about provenance across a wide variety of domains. Basic Formal Ontology (BFO) is a top-level ontology ISO/IEC standard used to structure a wide variety of ontologies, such as the OBO Foundry ontologies and the Common Core Ontologies (CCO). To enhance interoperability between these two ontologies, their extensions, and data organized by them, a mapping methodology and set of alignments are presented according to specific (...) criteria which prioritize semantic and logical principles. The ontology alignments are evaluated by checking their logical consistency with canonical examples of PROV-O instances and querying terms that do not satisfy the alignment criteria as formalized in SPARQL. A variety of semantic web technologies are used in support of FAIR (Findable, Accessible, Interoperable, Reusable) principles. (shrink)

Mid-level ontologies are used to integrate data across disparate domains using vocabularies more specific than top-level ontologies and more general than domain-level ontologies. There are no clear, defensible criteria for determining whether a given ontology should count as mid-level, because we lack a rigorous characterization of what the middle level of generality is supposed to contain. Attempts to provide such a characterization have failed, we believe, because they have focused on the goal of specifying what is characteristic of those single (...) ontologies that have been advanced as mid-level ontologies. Unfortunately, single ontologies of this sort are generally a mixture of top- and mid-level, and sometimes even of domainlevel terms. To gain clarity, we aim to specify conditions for membership in what we call the middle architecture, which consists solely of mid-level ontologies. (shrink)

In our daily lives, as in science and in all other domains, we encounter huge numbers of dispositions (tendencies, potentials, powers) which are realized in processes such as sneezing, sweating, shedding, melting. Among this plethora of what we can think of as ‘mere dispositions’ is a subset of dispositions in whose realizations we have an interest – a car responding well when driven on ice, a rabbit’s lungs responding well when it is chased by a wolf, and so on. We (...) call the latter ‘capabilities’ and we attempt to provide an ontological account of what capabilities are that is of sufficient generality to serve a variety of purposes, for example by providing a useful extension to ontology-based research in areas where capabilities data are being collected in siloed fashion. (shrink)

The term “credential” encompasses educational certificates, degrees, certifications, and government-issued licenses. An occupational credential is a verification of an individual’s qualification or competence issued by a third party with relevant authority. Job seekers often leverage such credentials as evidence that desired qualifications are satisfied by their holders. Many U.S. education and workforce development organizations have recognized the importance of credentials for employment and the challenges of understanding the value of credentials. In this study, we identified and ontologically defined credential and (...) credential-related terms at the textual and semantic levels based on the Occupation Ontology (OccO), a BFO-based ontology. Different credential types and their authorization logic are modeled. We additionally defined a high-level hierarchy of credential related terms and relations among many terms, which were initiated in concert with the Alabama Talent Triad (ATT) program, which aims to connect learners, earners, employers and education/training providers through credentials and skills. To our knowledge, our research provides for the first time systematic ontological modeling of the important domain of credentials and related contents, supporting enhanced credential data and knowledge integration in the future. (shrink)

Background Within the Open Biological and Biomedical Ontology (OBO) Foundry, many ontologies represent the execution of a plan specification as a process in which a realizable entity that concretizes the plan specification, a “realizable concretization” (RC), is realized. This representation, which we call the “RC-account”, provides a straightforward way to relate a plan specification to the entity that bears the realizable concretization and the process that realizes the realizable concretization. However, the adequacy of the RC-account has not been evaluated in (...) the scientific literature. In this manuscript, we provide this evaluation and, thereby, give ontology developers sound reasons to use or not use the RC-account pattern. -/- Results Analysis of the RC-account reveals that it is not adequate for representing failed plans. If the realizable concretization is flawed in some way, it is unclear what (if any) relation holds between the realizable entity and the plan specification. If the execution (i.e., realization) of the realizable concretization fails to carry out the actions given in the plan specification, it is unclear under the RC-account how to directly relate the failed execution to the entity carrying out the instructions given in the plan specification. These issues are exacerbated in the presence of changing plans. -/- Conclusions We propose two solutions for representing failed plans. The first uses the Common Core Ontologies ‘prescribed by’ relation to connect a plan specification to the entity or process that utilizes the plan specification as a guide. The second, more complex, solution incorporates the process of creating a plan (in the sense of an intention to execute a plan specification) into the representation of executing plan specifications. We hypothesize that the first solution (i.e., use of ‘prescribed by’) is adequate for most situations. However, more research is needed to test this hypothesis as well as explore the other solutions presented in this manuscript. (shrink)

In a number of papers, Kit Fine introduced a theory of embodiment which distinguishes between rigid and variable embodiments, and has been successfully applied to clarify the ontological nature of entities whose parts may or may not vary in time. In particular, he has applied this theory to describe a process such as the erosion of a cliff, which would be a variable embodiment whose manifestations are the different states of erosion of the cliff. We find this theory very powerful, (...) and especially appropriate to capture the intuition that the same process may go on at different times. However, its formal principles have been subject to some criticisms, mainly concerning the mereological structure of a variable embodiment. Moreover, since the notion of variable embodiment is very general, simply saying that processes are variable embodiments is not enough to understand their ontological nature. To address these concerns, in this paper we proceed in two phases: first, we propose a revised version of Fine’s original theory adapted to the case of processes, which adopts a classical mereology instead of Fine’s hylomorphic mereology, and a temporalized constitution relation in place of Fine’s function of variable embodiment; second, we go deeper into the ontological nature of processes by revisiting the notions of homogeneity, intentionality, and telicity discussed in the literature, and propose an account based on ontological principles and not on semantic properties of predicates. This allows us to organize processes into a novel taxonomy based exclusively on their unity and individuation principles. (shrink)

The Common Core Ontologies(CCO) are designed as a mid-level ontology suite that extends the Basic Formal Ontology. In 2017,CUBRC, Inc. made CCO openly available. CCO has since been increasingly adopted by a broad group of users and applications and is proposed as the first standard mid-level ontology. Despite these successes, documentation of the contents and design patterns of the CCO has been comparatively minimal. This paper is a step toward providing enhanced documentation for the mid-level ontology suite through a discussion (...) of the contents of the eleven ontologies that collectively comprise the Common Core Ontology suite. (shrink)

This paper introduces a set of terms that are intended to act as an interface between cyber ontologies (like a file system ontology or a data fusion ontology) and top- and mid-level ontologies, specifically Basic Formal Ontology and the Common Core Ontologies. These terms center on what makes cyberinformation management unique: numerous acts of copying items of information, the aggregates of copies that result from those acts, and the faithful members of those aggregates that represent all other members.

The paper is a partly provocative essay edited as a humanitarian study in philosophy of science and social philosophy, reflecting on the practical, “anti-metaphysical” turn taken place since the 20th century and continuing until now. The article advocates that it is about time it to be overcome because it is the main obstacle for the further development of exact and natural sciences including mathematics therefore restoring the unity of philosophy and sciences in the dawn of modern science when the great (...) scientists were philosophers as a necessary condition for their revolutionary achievements, and the physicists were simultaneously mathematicians not less than philosophers and even theologians as Descartes, Newton, Leibnitz were just as their predecessors, Copernicus or Galileo Galilei. The revolution in science accomplished by them needed philosophy since any scientific revolution, then necessarily growing into social, needs philosophy; and if ones wish to prevent social revolutions originating from fundamental scientific discoveries, in turn relying on the close link of sciences and philosophy, they are to cut the link at issue, and just that happened in the 20th centuries therefore implicitly heralding a “brave new world” of eternal normal science without revolutions whether scientific or social. Fukuyama’s “end of history” requires an “end of scientific history” as it is an obligatory premise, and separating sciences from philosophy is sufficient for that, though proclaimed quite otherwise: as overcoming metaphysics preventing sciences and substituting them by quasi-sciences. Particularly, that “anti-metaphysical turn” has established for science to obey society absolutely and thoroughly, obviously a condition contradicting the scientific and social revolutions in Modernity featured by the domination of science over society by the mediation of philosophy able to translate all epochal scientific discoveries as social corollaries. A special attention is paid to quantum mechanics, being the frontier of physics in the 20th century, where that anti-metaphysical turn is discernibly concentrated and may be notated by the famous slogan “Shut up and calculate!” regardless of its authorship. Just the revolutionary discoveries in physics, for example those of “dark mass” and “dark energy” or entanglement force now its rejection therefore restoring the unity of philosophy, mathematics and physics, made ever possible the establishment of modern science by its emancipation from religion, and thus and ind final analysis, from society. (shrink)

In this paper we provide an ontological analysis of so-called “artifactual functions” by deploying a realizable-centered approach to artifacts which we have recently developed within the framework of the upper ontology Basic Formal Ontology (BFO). We argue that, insofar as material artifacts are concerned, the term “artifactual function” can refer to at least two kinds of realizable entities: novel intentional dispositions and usefactual realized entities. They inhere, respectively, in what we previously called “canonical artifacts” and “usefacts”. We show how this (...) approach can help to clarify functions in BFO, whose current elucidation includes reference to the term “artifact”. In our framework, having an artifactual function implies being an artifact, but not vice versa; in other words, there are artifacts that lack an artifactual function. (shrink)

Artifacts remain nebulous entities, notwithstanding their relevance to various domains such as engineering, art and archeology. In this paper we investigate the interconnection between artifacts and realizable entities, as illustrated by dispositions, functions, and roles within the framework of the upper ontology Basic Formal Ontology (BFO). More concretely, we propose the notions of canonical artifact (something that is intentionally produced for some purpose) and usefact (something that is intended to be used for some non-original purpose) which can correspond to various (...) usages of the term “artifact”. We also characterize them in terms of intentional realizable entities and novel realizable entities: material canonical artifacts and material usefacts can be analyzed in terms of novel intentional realizable entities and a special kind of non-novel intentional realizable entities, respectively. (shrink)

In this article, we advocate the use of “epistemic” ontologies, i.e., systems of categories representing our knowledge of the world, rather than the world directly. We first expose a metaphysical framework based on a dual mental and physical realism, which underpins the development of these epistemic ontologies. To this end, we refer to the theories of intentionality and representation established within the school of Franz Brentano at the turn of the 20th century and choose to rehabilitate the notion of a (...) ‘representation object’, as theorized by Kasimir Twardowski. We therefore propose that the categories of epistemic ontologies correspond to ‘general representation objects’. Secondly, we apply these proposals to the treatment of technical artefacts, material qualities of objects and events (notably as a continuation of our previous work on events). This leads us to sketch out a foundational epistemic ontology. (shrink)

Only a catastrophe could save us. Being-towards-death in the era of the ecological crisis The aim of this essay is to develop a theoretical background to approach the problem of climate change, starting from the question of death as theorized by Heidegger in his masterpiece Being and Time. In order to do that, I start from the concept of the Anthropocene in relation with the problem of human and natural history and introducing the Heideggerian concept of history as epiphenomenon of (...) temporal structure of the Dasein. On this basis, the being-toward-death, the as exposed in the abovementioned work, will help to provide a hermeneutic criterion to approach an ethic of the catastrophe. (shrink)

Social media plays an important role in forming, maintaining, and reproducing norms and practices (Flanagan et. al 2008). Content shared on social media has the power to reaffirm certain norms and practices merely by being shared (Caldeira et al., 2018; Burns, 2015; Krijnen & Van Bauwel, 2015). When it comes to questions of identity and questions surrounding representation of certain identity groups in the media, social media content is often taken to play a significant role in the constitution of certain (...) identities (Haimson, 2018, 2021; Frissen et al., 2015; Eickers & Rath, 2021). This chapter specifically explores the role social media plays in trans peoples’ transitioning processes. Transitioning, as understood here, can be social – e.g., performing gender differently via clothing or behavior, using a different name or pronouns – and legal – e.g., changing one’s gender category on formal identification documents, official name changes, and medical – e.g., undergoing hormone replacement therapy or other gender-affirming medical care like gender-reassignment surgeries. Transitioning can encompass all or any combination of these aspects (Bettcher, 2009, 2017). The chapter homes in on the impact that the representation of trans people on social media has on the transitioning processes. Here, questions around bodies and their representation through and with technologies and increasing digitization emerge. One might ask, for example, whether representation on social media platforms facilitates someone’s discovery of their gender identity and/or supports their coming to terms with it. This kind of representation may also provide people before or in transitioning processes with different ways to conceive of their future self. There are numerous social media accounts of trans people documenting their transitioning processes (Horak, 2014; Gauthier & Chaudoir, 2004). Displaying one’s own gender transition online may not only be important to some trans people because they feel like it makes a difference for the community, it may also become a vital part of the transitioning process itself, influencing and shaping the way the transition is taking place (Rawson, 2014; McInroy & Craig, 2015). Indeed, the representation of trans people on social media matters to trans communities and trans individuals because, by seeing images and perceiving narratives of trans people, one might, first, conceive of the possibility of one’s existence as a trans person, including the possibility of embodying another gender, and, second, think of the possibility of representing oneself (as a trans person) too (Cavalcante, 2016; Cannon et al., 2017). Accordingly, this chapter argues that social media can be viewed as a form of corporeal technology that is involved in transitioning processes. Social media can help the individual to reconceive their identity by means of representing themselves to themselves and others online. (shrink)

Disagreement about the nature of ‘addiction’, such as whether it is a brain disease, arises in part because the label is applied to a wide range of phenomena. This creates conceptual and definitional confusions and misunderstandings, often leading to researchers talking past one another. Ontologies have been successfully implemented in other fields to help solve these problems by creating unifying frameworks that can accommodate divergence while clarifying the basis for it. We argue that ontologies can help transform the way we (...) think and communicate about addiction as well, providing a basis for a shared understanding of the domain and a shared means for communicating and achieving that understanding. -/- We introduce the use of ontologies in science and medicine and show how they can unify differing perspectives on addiction. We also show how ontologies provide a practical tool for organizing our collective knowledge in this field, even, and especially, when that knowledge is garnered through distinct disciplinary approaches adopting disparate methodologies or perspectives (e.g., neurobiological, psychological, sociological, etc.). In the end, we believe that ontologies can help to avoid letting questions like “Is addiction a brain disease?” divide the field, hamper communication, or otherwise disrupt the ability to make meaningful progress. (shrink)

Barry Smith recently discussed the diagraphs of book eight of Jacob Lorhard’s Ogdoas scholastica under the heading “birth of ontology” (Smith, 2022; this issue). Here, I highlight the commonalities between the original usage of diagraphs in the tradition of Ramus for didactic purposes and the the usage of their present-day successors–modern ontologies–for computational purposes. The modern ideas of ontology and of the universal computer were born just two generations apart in the breakthrough century of instrumental reason.

Ontologies and standards are strongly interrelated and can often be seen as two sides of the same coin. Indeed, standards reflect consensus on the semantics of terms, though different standards might employ different ways to explain the same or very similar concepts semantically. Given the crucial role played by both aspects in OntoCommons, we have interviewed Barry Smith, SUNY Distinguished Professor of Philosophy at the University at Buffalo and one of the External Advisory Board (EAB) members of the OntoCommons project, (...) to better understand what are the challenges and priorities to focus on in this context. (shrink)

The paper compares Comenius’ usage of the terms unum, verum and bonum in his metaphysical writings both with the expression of the image of the Trinity in De civitate dei by Aurelius Augustinus and with the concept of existence as three basic movements in the philosophical work of Jan Patočka. The purpose of the text is to show, despite the differences in historical periods, language and life experience, the possible similarity or connection of the vision that Augustine, Comenius and Patočka (...) mediate in their works. (shrink)

This is the first book in the series Rebooting Science 1 based on E-theory, a novel line of theory that aims at "rebooting" science, giving it a new start. If you dive into it be prepared with an open mind and patience. In this introduction you are let in on a struggle to defend what science seems incapable of defending, our mortal but immaterial soul, our very subject. In Rebooting Science 1.0 Johan Gamper publishes the first part of the theoretical (...) structure that lies behind his seminal paper from 2017, On a Loophole in Causal Closure, where he proved that our mind can be viewed as separate from our brain without violating the basic rules of science. The unrevised manuscript e-theory from the mid-nineties is commented to explain its impact on the most fundamental levels of science. Its original understanding of objects and dimensions opens up for new perspectives on ourselves and the world around us. (shrink)

In his “Bridging mainstream and formal ontology”, Augusto (2021) gives an excellent analysis of Dietrich von Freiberg’s idea of using causality as a partitioning principle for upper ontologies. For this Dietrich’s notion of extrinsic principles is crucial. The question whether causation can and indeed should be used as a partitioning principle for ontologies is discussed using mathematics and physics as examples.

The main goal of this paper is to outline a general formal-logical theory of language construed as a particular ontological being. The theory itself will be referred to as an ontology of language, because it is motivated by the fact that language plays a special role: it reflects ontology, and ontology reflects the world. Linguistic expressions will be regarded as having a dual ontological status: they are to be understood as either concreta – i.e. tokens, in the sense of material, (...) physical objects – or types, in the sense of classes of tokens – i.e. abstract objects. Such a duality will then be taken into account in the logical theory of syntax, semantics and pragmatics presented here. We point to the possibility of constructing the latter on two different levels, one stemming from concreta, construed as linguistic tokens of expressions, the other from their classes – namely types, conceived as abstract, ideal beings. The aim of this work is not only to outline such a theory with respect to the dual ontological nature of the expressions of language in terms that take into account a functional approach to language itself, but also to show that the logic based on it is ontologically neutral in the sense that it is abstracted from the level at which certain existential assumptions relating to the ontological nature of these linguistic expressions and their extra-linguistic ontological counterparts (objects) would have to be embraced. (shrink)

Intelligent defence support systems are confronted with the need to manage ever-increasing floods of data in a way that raises significant challenges because the data are described and presented using different terminologies and formats. How, on this basis, is it possible to reach a common understanding of the information content of these data among people and software agents? How is it possible to ensure that domain knowledge is reused in consistent fashion in a way that makes this information available for (...) integration and analysis? How can we support the identification, selection, composition, and orchestration of services based on such diverse data providing homogeneous support by a service-oriented architecture? This collection is devoted to the use of ontologies to answer questions such as these. -/- Contents -/- Bill Mandrick: Creating an extensible command and control ontology, 215-231 -/- Chris Partridge; Mike Lambert; Mike Loneragan; Andrew Mitchell; Pawel Garbacz: A novel ontological approach to semantic interoperability between legacy air defence command and control systems, 232-262 -/- Michael Gerz; Olivier Meyer: Defining C2 semantics by a platform-independent JC3IEDM, 263-285 -/- Kevin Gupton; Curtis Blais; Kevin Heffner: Management of C2 data standards with modular OWL ontologies, 286-307. (shrink)

Wikipedia is a goldmine of information; not just for its many readers, but also for the growing community of researchers who recognize it as a resource of exceptional scale and utility. It represents a vast investment of manual effort and judgment: a huge, constantly evolving tapestry of concepts and relations that is being applied to a host of tasks. This article provides a comprehensive description of this work. It focuses on research that extracts and makes use of the concepts, relations, (...) facts and descriptions found in Wikipedia, and organizes the work into four broad categories: applying Wikipedia to natural language processing; using it to facilitate information retrieval and information extraction; and as a resource for ontology building. The article addresses how Wikipedia is being used as is, how it is being improved and adapted, and how it is being combined with other structures to create entirely new resources. We identify the research groups and individuals involved, and how their work has developed in the last few years. We provide a comprehensive list of the open-source software they have produced. (shrink)

In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer science has (...) always meant the theory of processes and of computation. We measure the complexity of computer programs in terms of how long it takes machines to execute them, not in terms of how long it takes people to understand and to represent the data on which those programs might operate. We typically describe computer code in terms of algorithms that operate on formal parameters, often without pausing to discuss where the data that might satisfy those parameters come from. This journal was founded on the premise that workers in computer science, informatics, and information science are overdue in paying as much attention to contents as they do to algorithms. (shrink)

What makes "digital pets" pets? This article posits four necessary and jointly sufficient conditions for an individual to be a pet, concluding that digital pets fail to meet these sufficient criteria and thus are not pets.