The discipline of ontology has enjoyed a checkered history since 1606, with a significant expansion in recent years. We focus here on those developments in the recent history of philosophy which are most relevant to the understanding of the increased acceptance of ontology, and especially of realist ontology, as a valuable method also outside the discipline of philosophy.

In this paper, building on these previous works, we propose to go deeper into the understanding of crowd behavior by proposing an approach which integrates ontologi- cal models of crowd behavior and dedicated computer vision algorithms, with the aim of recognizing some targeted complex events happening in the playground from the observation of the spectator crowd behavior. In order to do that, we first propose an ontology encoding available knowledge on spectator crowd behavior, built as a spe- cialization of (...) the DOLCE foundational ontology, which allows the representation of categories belonging both to the physical and to the social realms. We then propose a simplified and tractable version of such ontology in a new temporal extension of a description logic, which is used for temporally coupling events happening on the play- ground and spectator crowd behavior. At last, computer vision algorithms provide the input information concerning what is observed on the stands and ontological reasoning delivers the output necessary to perform complex event recognition. (shrink)

Discussions on the alleged methodological specificity of social knowledge are fueled to not the least extent by a kind of retarded position of the latter against technological advancements of natural and information science based on exact methods and formal or quantitative languages. It is more or less obvious that applicability of exact scientific methods to social disciplines is highly dependent on a chosen conception of social reality, i. e., on social ontology. In the article, the author critically approaches the (...) ontological views of Tony Lawson and proposes a computational view on social ontology that is supposed to eliminate some internal contradictions of Lawson's realist conception. (shrink)

Computers may help us to better understand (not just verify) arguments. In this article we defend this claim by showcasing the application of a new, computer-assisted interpretive method to an exemplary natural-language ar- gument with strong ties to metaphysics and religion: E. J. Lowe’s modern variant of St. Anselm’s ontological argument for the existence of God. Our new method, which we call computational hermeneutics, has been particularly conceived for use in interactive-automated proof assistants. It aims at shedding light on the (...) meanings of words and sentences by framing their inferential role in a given argument. By employing automated theorem reasoning technology within interactive proof assistants, we are able to drastically reduce (by several orders of magnitude) the time needed to test the logical validity of an argu- ment’s formalization. As a result, a new approach to logical analysis, inspired by Donald Davidson’s account of radical interpretation, has been enabled. In computational hermeneutics, the utilization of automated reasoning tools ef- fectively boosts our capacity to expose the assumptions we indirectly commit ourselves to every time we engage in rational argumentation and it fosters the explicitation and revision of our concepts and commitments. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

The relationship between abstract formal procedures and the activities of actual physical systems has proved to be surprisingly subtle and controversial, and there are a number of competing accounts of when a physical system can be properly said to implement a mathematical formalism and hence perform a computation. I defend an account wherein computational descriptions of physical systems are high-level normative interpretations motivated by our pragmatic concerns. Furthermore, the criteria of utility and success vary according to our diverse purposes (...) and pragmatic goals. Hence there is no independent or uniform fact to the matter, and I advance the ‘anti-realist’ conclusion that computational descriptions of physical systems are not founded upon deep ontological distinctions, but rather upon interest-relative human conventions. Hence physical computation is a ‘conventional’ rather than a ‘natural’ kind. (shrink)

Organisations are computing systems. The university’s sports centre is a computing system for managing sports teams and facilities. The tenure committee is a computing system for assigning tenure status. Despite an increasing number of publications in group ontology, the computational nature of organisations has not been recognised. The present paper is the first in this debate to propose a theory of organisations as groups structured for computing. I begin by describing the current situation in group ontology and by (...) spelling out the thesis in more detail. I then present the example of a sports centre to illustrate why one might intuitively think of organisations as computing systems. To substantiate the thesis, I introduce Piccinini’s restrictive analysis of physical computation. As I show, organisations meet all criteria for being computing systems. Organisations are structured groups with the function of manipulating medium-independent vehicles according to rules. Furthermore, I argue for the modal claim that this is a necessary feature of organisations. Having sketched the computational account of organisations, I compare it to other proposals in the literature. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that (...) is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

This paper presents an ontology architecture concept for the European Space Agency‘s (ESA) Space Situational Awareness (SSA) Program. It incorporates the author‘s domain ontology, The Space Situational Awareness Ontology and related ontology work. I summarize computational ontology, discuss the segments of ESA SSA, and introduce an option for a modular ontology framework reflecting the divisionsof the SSA program. Among other things, ontologies are used for data sharing and integration. By applying ontology to ESA (...) data, the ESA may better achieve its integration and innovation goals, while simultaneously improving the state of peaceful SSA. (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)

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.

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated (...) to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality (...) through both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

Universals appear to be as central in today's computational-based ontology as they were in medieval ontological investigations. As the author of a recent work on the history of universals (Pinzani, 2018), I was asked for a commentary on Augusto’s article “Bridging Mainstream and Formal Ontology” (Augusto, 2021), which aims at showing that medieval ontological investigations can be relevant for contemporary ontology engineering. In this commentary, I begin by saying something about my way of reading 12th-century logical literature (...) and then offer some modest considerations on the general theme addressed in Augusto's article. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use (...) of the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new (...) kinds of situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

Ontologies are being used by information scientists in order to facilitate the sharing of meaningful information. However, computational ontologies are problematic in that they often decontextualize information. The semantic content of information is dependent upon the context in which it exists and the experience through which it emerges. For true semantic interoperability to occur among diverse information systems, within or across domains, information must remain contextualized. In order to bring more context to computational ontologies, we introduce culture as an essential (...) concept for information science. Culture helps to focus our attention on and make meaning of relevant extrapersonal structures and their qualities and dimensions that comprise the context and background of the world. In our approach, culture is integral to the study of semantics and, consequently, the study of ontologies and information technologies. The meaning we make of entities and phenomena in the world is always shaped by our cultural experience. If we understand culture as the emergent interplay of intrapersonal cognitive structures and extrapersonal structures of the world, then the notion of cognitive and cultural schemas becomes essential to understanding ontology and the ways in which we might achieve authentic semantic interoperability among diverse information systems. We explore the nature of ontologies and reconceptualize them as cultural schemas. Our proposal is an alternative to the historical path from philosophical ontology to computational ontologies as one that adheres primarily to the notion of ontology as a categorization and classification system. The obvious implication for ontology as categorization is that there is a single objective world that exists and that it can be described as entirely separate from the person observing it. We draw upon Heidegger’s examination of ontology to ground ontology in a phenomenological perspective, enabling it to remain flexible and adaptable and to accommodate context. (shrink)

One famous scene in The Wolf of Wall Street (2013) is the dialogue between the young Jordan Belfort (Leonardo DiCaprio) and the expert trader Mark Hanna (Matthew McConaughey). Hanna is complaining that the stock market is unpredictable; it’s “fugazi … it’s fairy dust. It doesn’t exist. It’s never landed. It is not matter. It’s not on the element chart. It’s not real”. But the fact that something is unpredictable and non-physical does not imply that it does not exist. On the (...) other hand, its unpredictability, non-physicality, and the fact that the stock market trend is largely determined by investors’ beliefs, do make its nature difficult to grasp. -/- This special issue of Rivista di Estetica aims to explore the financial sector from an ontological point of view. While the ontology of money has been extensively studied, few scholars have focused on the stock market and, more generally, on those entities belonging to the investment landscape. Matters are made more complicated by the fact that the financial sector is characterized by an ever-increasing use of digital technology, including software elements that trade in the market themselves. We believe that a careful study of this phenomenon may help us better to understand the role of artificial agents in the social world. (shrink)

Ontology is currently perceived as the solution of first resort for all problems related to biomedical terminology, and the use of description logics is seen as a minimal requirement on adequate ontology-based systems. Contrary to common conceptions, however, description logics alone are not able to prevent incorrect representations; this is because they do not come with a theory indicating what is computed by using them, just as classical arithmetic does not tell us anything about the entities that are (...) added or subtracted. In this paper we shall show that ontology is indeed an essential part of any solution to the problems of medical terminology – but only if it is understood in the right sort of way. Ontological engineering, we shall argue, should in every case go hand in hand with a sound ontological theory. (shrink)

Ontology engineering is a hard and error-prone task, in which small changes may lead to errors, or even produce an inconsistent ontology. As ontologies grow in size, the need for automated methods for repairing inconsistencies while preserving as much of the original knowledge as possible increases. Most previous approaches to this task are based on removing a few axioms from the ontology to regain consistency. We propose a new method based on weakening these axioms to make them (...) less restrictive, employing the use of refinement operators. We introduce the theoretical framework for weakening DL ontologies, propose algorithms to repair ontologies based on the framework, and provide an analysis of the computational complexity. Through an empirical analysis made over real-life ontologies, we show that our approach preserves significantly more of the original knowledge of the ontology than removing axioms. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We (...) advance a proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines (...) and attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

As it emerged from philosophical analyses and cognitive research, most concepts exhibit typicality effects, and resist to the efforts of defining them in terms of necessary and sufficient conditions. This holds also in the case of many medical concepts. This is a problem for the design of computer science ontologies, since knowledge representation formalisms commonly adopted in this field (such as, in the first place, the Web Ontology Language - OWL) do not allow for the representation of concepts in (...) terms of typical traits. The need of representing concepts in terms of typical traits concerns almost every domain of real world knowledge, including medical domains. In particular, in this article we take into account the domain of mental disorders, starting from the DSM-5 descriptions of some specific disorders. We favour a hybrid approach to concept representation, in which ontology oriented formalisms are combined to a geometric representation of knowledge based on conceptual space. As a preliminary step to apply our proposal to mental disorder concepts, we started to develop an OWL ontology of the schizophrenia spectrum, which is as close as possible to the DSM-5 descriptions. (shrink)

Could a person ever transcend what it is like to be in the world as a human being? Could we ever know what it is like to be other creatures? Questions about the overcoming of a human perspective are not uncommon in the history of philosophy. In the last century, those very interrogatives were notably raised by American philosopher Thomas Nagel in the context of philosophy of mind. In his 1974 essay What is it Like to Be a Bat?, Nagel (...) offered reflections on human subjectivity and its constraints. Nagel’s insights were elaborated before the social diffusion of computers and could not anticipate the cultural impact of technological artefacts capable of materializing interactive simulated worlds as well as disclosing virtual alternatives to the “self.” In this sense, this article proposes an understanding of computers as epistemological and ontological instruments. The embracing of a phenomenological standpoint entails that philosophical issues are engaged and understood from a fundamentally practical perspective. In terms of philosophical praxis, or “applied philosophy,” I explored the relationship between human phenomenologies and digital mediation through the design and the development of experimental video games. For instance, I have conceptualized the first-person action-adventure video game Haerfest (Technically Finished 2009) as a digital re-formulation of the questions posed in Nagel’s famous essay. Experiencing a bat’s perceptual equipment in Haerfest practically corroborates Nagel’s conclusions: there is no way for humans to map, reproduce, or even experience the consciousness of an actual bat. Although unverifiable in its correspondence to that of bats, Haerfest still grants access to experiences and perceptions that, albeit still inescapably within the boundaries of human kinds of phenomenologies, were inaccessible to humans prior to the advent of computers. Phenomenological alterations and virtual experiences disclosed by interactive digital media cannot take place without a shift in human kinds of ontologies, a shift which this study recognizes as the fundamental ground for the development of a new humanism (I deem it necessary to specify that I am not utilizing the term “humanism” in its common connotation, that is to say the one that emerged from the encounter between the Roman civilization and the late Hellenistic culture. According to this conventional acceptation, humanism indicates the realization of the human essence through “scholarship and training in good conduct” (Heidegger 1998, p. 244). However, Heidegger observed that this understanding of humanism does not truly cater to the original essence of human beings, but rather “is determined with regard to an already established interpretation of nature, history, world, and […] beings as a whole.” (Heidegger 1998, p. 245) The German thinker found this way of embracing humanism reductive: a by-product of Western metaphysics. As Heidegger himself specified in his 1949 essay Letter on Humanism, his opposition to the traditional acceptation of the term humanism does not advocate for the “inhuman” or a return to the “barbaric” but stems instead from the belief that the humanism can only be properly understood and restored in culture as more original way of meditating and caring for humanity and understanding its relationship with Being.). Additionally, this study explicitly proposes and exemplifies the use of interactive digital technology as a medium for testing, developing and disseminating philosophical notions, problems and hypotheses in ways which are alternative to the traditional textual one. Presented as virtual experiences, philosophical concepts can be accessed without the filter of subjective imagination. In a persistent, interactive, simulated environment, I claim that the crafting and the mediation of thought takes a novel, projective (In Martin Heidegger’s 1927 Being and Time, the term “projectivity” indicates the way a Being opens to the world in terms of its possibilities of being (Heidegger 1962, pp. 184–185, BT 145). Inspired by Heidegger’s and Vilem Flusser’s work in the field of philosophy of technology as well as Helmuth Plessner’s anthropological position presented in his 1928 book Die Stufen des Organischen und der Mensch. Einleitung in die philosophische Anthropologie, this study understands the concept of projectivity as the innate openness of human beings to construct themselves and their world by means of technical artefacts. In this sense, this study proposes a fundamental understanding of technology as the materialization of mankind’s tendency to overcome its physical, perceptual and communicative limitations.) dimension which I propose to call “augmented ontology.”. (shrink)

Words are indispensable linguistic tools for beings like us. However, there is not much philosophical work done about what words really are. In this paper, I develop a new ontology for words. I argue that words are abstract artifacts that are created to fulfill various kinds of purposes, and words are abstract in the sense that they are not located in space but they have a beginning and may have an end in time given that certain conditions are met. (...) What follows from this two-fold argument is that words, from an ontological point of view, are more like musical works, fictional characters or computer programs, than numbers or sets. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, (...) diagnosis, prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move (...) beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

Each annual Ontology Summit initiative makes a statement appropriate to each Summit’s theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology (...) repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed." -/- We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize (...) and integrate data relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and (...) use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata (...) registries, thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) (...) data exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

Fundamental Science is undergoing an acute conceptual-paradigmatic crisis of philosophical foundations, manifested as a crisis of understanding, crisis of interpretation and representation, “loss of certainty”, “trouble with physics”, and a methodological crisis. Fundamental Science rested in the "first-beginning", "first-structure", in "cogito ergo sum". The modern crisis is not only a crisis of the philosophical foundations of Fundamental Science, but there is a comprehensive crisis of knowledge, transforming by the beginning of the 21st century into a planetary existential crisis, which has (...) exacerbated the question of the existence of Humanity and life on Earth. Due to the unsolved problem of justification of Mathematics, paradigm problems in Computational mathematics have arisen. It's time to return ↔ Into Dialectics. The solution to the problem of the foundations of Mathematics, and therefore knowledge in general, is the solution to the problem of modeling (constructing) the ontological basis of knowledge - the ontological model of the primordial generating process. The idea and model of the primordial generating process, its ontological structure directs thinking to the need for the introduction of superconcept → ontological (cosmic, structural) memory, concept-attractor, supercategory, substantial semantic core of the scientific picture of the world of the nuclear-ecological-information age. Model of basic Ideality→ “Space-MatterMemory-Time” [S-MM-T]. (shrink)

Common sense is on the one hand a certain set of processes of natural cognition - of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...) treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (shrink)

Where humans can manipulate and integrate the information they receive in subtle and ever changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, (...) mathematics, medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force Research Laboratory (...) (Rome) with the goal of addressing problems of these sorts through cyclical collaborative plan review and maintenance. The interactions of world state, blue force status and associated plans are too complex for manual adaptive processes, and computer-aided plan review and maintenance is thus indispensable. We argue that appropriate semantic technology can 1) provide richer representation of plan-related data and semantics, 2) allow for flexible, non-disruptive, agile, scalable, and coordinated changes in plans, and 3) support more intelligent analytical querying of plan-related data. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to (...) move beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes (...) of making computers understand medical natural language. (shrink)

The paper argues that digital ontology (the ultimate nature of reality is digital, and the universe is a computational system equivalent to a Turing Machine) should be carefully distinguished from informational ontology (the ultimate nature of reality is structural), in order to abandon the former and retain only the latter as a promising line of research. Digital vs. analogue is a Boolean dichotomy typical of our computational paradigm, but digital and analogue are only “modes of presentation” of Being (...) (to paraphrase Kant), that is, ways in which reality is experienced or conceptualised by an epistemic agent at a given level of abstraction. A preferable alternative is provided by an informational approach to structural realism, according to which knowledge of the world is knowledge of its structures. The most reasonable ontological commitment turns out to be in favour of an interpretation of reality as the totality of structures dynamically interacting with each other. The paper is the first part (the pars destruens) of a two-part piece of research. The pars construens, entitled “A Defence of Informational Structural Realism”, is developed in a separate article, also published in this journal. (shrink)

Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist paradigm (...) in ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonisation is becoming ever more urgent. We describe one example of such harmonisation within the ACGT project, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research. (shrink)

In recent decades, the internet has become our predominant public space and yet the role of art in this space remains largely unthought. This paper argues that graphic art, and in particular digital graphic art, has great power to shape and transform our thinking and experience. But with that power comes an enormous political and ethical responsibility, a responsibility too often ignored by programmers and computer scientists. This paper uses the work of Denis Schmidt and Jacques Taminiaux as important resources (...) for developing a Heideggerian response to this lack. (shrink)

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among leaders in (...) the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

While situation theory and situation semantics provide an appropriate framework for a realistic model-theoretic treatment of natural language, serious thinking on their 'computational' aspects has just started. Existing proposals mainly offer a Prolog- or Lisp-like programming environment with varying degrees of divergence from the ontology of situation theory. In this paper, we introduce a computational medium (called BABY-SIT) based on situations. The primary motivation underlying BABY-SIT is to facilitate the development and testing of programs in domains ranging from linguistics (...) to artificial intelligence in a unified framework built upon situation-theoretic constructs. (shrink)

La communication interdisciplinaire rencontre divers problématiques : l’hétérogénéités des informations (sémantique, standardisation des formats), les confusions linguistiques (intentions dans les énoncés, polysémie des mots) ou encore épistémologiques (expertises divergentes, terminologies inadéquates). Nous proposons pour favoriser l’intercommunication entre différents domaines de spécialité, l’emploi des ontologies informatiques : des artefacts informatiques permettant une représentation des concepts au sein d’un domaine de spécialité. Autour de la notion « d’interopérabilité sémantique », la capacité pour une machine et des acteurs de communiquer ensemble, nous viserons (...) à montrer en quoi les ontologies peuvent permettre à des acteurs de différentes disciplines de clarifier les notions propres à leurs domaines en fonction d’une analyse de leurs usages des mots. Nous tâchons ici de mettre en avant la capacité des ontologies de traiter le langage selon différents niveaux du sens d’un mot (du plus concret et appliqué, au plus abstrait et conceptuel), afin de mettre en perspective ce en quoi cette analyse basée sur les textes d’un corpus, permet de rendre compte de, si ce n’est un état du réalisme d’une discipline, du moins, servir d’outils pour aider les acteurs à normaliser leurs pratiques. En ce sens, les ontologies informatiques peuvent être considérées et utilisées comme autant de bases terminologiques servant comme outils de références pour faciliter la communication interdisciplinaire. (shrink)

The problem of merging several ontologies has important applications in the Semantic Web, medical ontology engineering and other domains where information from several distinct sources needs to be integrated in a coherent manner.We propose to view ontology merging as a problem of social choice, i.e. as a problem of aggregating the input of a set of individuals into an adequate collective decision. That is, we propose to view ontology merging as ontology aggregation. As a first step (...) in this direction, we formulate several desirable properties for ontology aggregators, we identify the incompatibility of some of these properties, and we define and analyse several simple aggregation procedures. Our approach is closely related to work in judgment aggregation, but with the crucial difference that we adopt an open world assumption, by distinguishing between facts not included in an agent’s ontology and facts explicitly negated in an agent’s ontology. (shrink)

The descriptions and theoretical laws scientists write down when they model a system are often false of any real system. And yet we commonly talk as if there were objects that satisfy the scientists’ assumptions and as if we may learn about their properties. Many attempt to make sense of this by taking the scientists’ descriptions and theoretical laws to define abstract or fictional entities. In this paper, I propose an alternative account of theoretical modelling that draws upon Kendall Walton’s (...) ‘make-believe’ theory of representation in art. I argue that this account allows us to understand theoretical modelling without positing any object of which scientists’ modelling assumptions are true. (shrink)

This work aims to make tense logic a more robust tool for ontologists, philosophers, knowledge engineers and programmers by outlining a fusion of tense logic and ontology of time. In order to make tense logic better understandable, the central formal primitives of standard tense logic are derived as theorems from an informal and intuitive ontology of time. In order to make formulation of temporal propositions easier, temporal operators that were introduced by Georg Henrik von Wright are developed, and (...) mapped to the ontology of time. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist (...) framework for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

When reusing existing ontologies for publishing a dataset in RDF (or developing a new ontology), preference may be given to those providing extensive subcategorization for important classes (denoted as focus classes). The subcategories may consist not only of named classes but also of compound class expressions. We define the notion of focused categorization power of a given ontology, with respect to a focus class and a concept expression language, as the (estimated) weighted count of the categories that can (...) be built from the ontology’s signature, conform to the language, and are subsumed by the focus class. For the sake of tractable initial experiments we then formulate a restricted concept expression language based on existential restrictions, and heuristically map it to syntactic patterns over ontology axioms (so-called FCE patterns). The characteristics of the chosen concept expression language and associated FCE patterns are investigated using three different empirical sources derived from ontology collections: first, the concept expression pattern frequency in class definitions; second, the occurrence of FCE patterns in the Tbox of ontologies; and last, for class expressions generated from the Tbox of ontologies (through the FCE patterns); their ‘meaningfulness’ was assessed by different groups of users, yielding a ‘quality ordering’ of the concept expression patterns. The complementary analyses are then compared and summarized. To allow for further experimentation, a web-based prototype was also implemented, which covers the whole process of ontology reuse from keyword-based ontology search through the FCP computation to the selection of ontologies and their enrichment with new concepts built from compound expressions. (shrink)