This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

The relations between ontology and information are many and fundamental, and they help us to understand the present gulf between (formal) ontology and (philosophical) Ontology: We can speak of respectively ontology-driven information and information-driven ontology as the focus on being informed vs. informed being. The question of whether these two (can) coincide is relevant to both fields, and in this article I elaborate on what needs to be addressed first of (...) all to provide us with an answer: The form. This core ontological concept rooting in Aristotelian metaphysics was central to philosophical ontology, in particular in Latin Scholasticism, when it was clearly put into relation with information as that which defines an entity. In this context, Dietrich of Freiberg synthesized this long debate in a way that matters not only to the philosophical effort of producing information-driven ontologies but also to the engineering constructs of ontology-driven information systems. (shrink)

With the current changes driven by the expansion of the World Wide Web, this book uses a different approach from other books on the market: it applies ontologies to electronically available information to improve the quality of knowledge management in large and distributed organizations. Ontologies are formal theories supporting knowledge sharing and reuse. They can be used to explicitly represent semantics of semi-structured information. These enable sophisticated automatic support for acquiring, maintaining and accessing information. Methodology and (...) tools are developed for intelligent access to large volumes of semi-structured and textual information sources in intra- and extra-, and internet-based environments to employ the full power of ontologies in supporting knowledge management from the information client perspective and the information provider. The aim of the book is to support efficient and effective knowledge management and focuses on weakly-structured online information sources. It is aimed primarily at researchers in the area of knowledge management and information retrieval and will also be a useful reference for students in computer science at the postgraduate level and for business managers who are aiming to increase the corporations' information infrastructure. The Semantic Web is a very important initiative affecting the future of the WWW that is currently generating huge interest. The book covers several highly significant contributions to the semantic web research effort, including a new language for defining ontologies, several novel software tools and a coherent methodology for the application of the tools for business advantage. It also provides 3 case studies which give examples of the real benefits to be derived from the adoption of semantic-web based ontologies in "real world" situations. As such, the book is an excellent mixture of theory, tools and applications in an important area of WWW research. * Provides guidelines for introducing knowledge management concepts and tools into enterprises, to help knowledge providers present their knowledge efficiently and effectively. * Introduces an intelligent search tool that supports users in accessing information and a tool environment for maintenance, conversion and acquisition of information sources. * Discusses three large case studies which will help to develop the technology according to the actual needs of large and or virtual organisations and will provide a testbed for evaluating tools and methods. The book is aimed at people with at least a good understanding of existing WWW technology and some level of technical understanding of the underpinning technologies (XML/RDF). It will be of interest to graduate students, academic and industrial researchers in the field, and the many industrial personnel who are tracking WWW technology developments in order to understand the business implications. It could also be used to support undergraduate courses in the area but is not itself an introductory text. (shrink)

Abstract In light of the complexity of unfolding disasters, the diversity of rapidly evolving events, the enormous amount of generated information, and the huge pool of casualties, emergency responders (ERs) may be overwhelmed and in consequence poor decisions may be made. In fact, the possibility of transporting the wounded victims to one of several hospitals and the dynamic changes in healthcare resource availability make the decision process more complex. To tackle this problem, we propose a multicriteria decision support service, (...) based on the Analytic Hierarchy Process (AHP) method, that aims to avoid overcrowding and outpacing the capacity of a hospital to effectively provide the best care to victims by finding out the most appropriate hospital that meets the victims’ needs. The proposed approach searches for the most appropriate healthcare institution that can effectively deal with the victims’ needs by considering the availability of the needed resources in the hospital, the victim’s wait time to receive the healthcare, and the transfer time that represents the hospital proximity to the disaster site. The evaluation and validation results showed that the assignment of hospitals was done successfully considering the needs of each victim and without overwhelming any single hospital. (shrink)

IS research is to some extent driven by practitioner concerns. Both practitioners and.Information Systems research has been dominated by the Cartesian worldview of duality. This has had the effect of narrowing the range of research questions addressed and focusing mainstream research on the application of scientific research methods. Heidegger’s ontology gives us an alternative view of the reality of human life. His analysis of tools in use is of particular interest for IS research. His concept of equipment (...) can be directly applied to Information and Communications Technology by both practitioners and researchers. The paper outlines some of the implications of this step for IS researchers. (shrink)

We propose as a UCGIS research priority the topic of “Ontological Foundations for Geographic Information.” Under this umbrella we unify several interrelated research subfields, each of which deals with different perspectives on geospatial ontologies and their roles in geographic information science. While each of these subfields could be addressed separately, we believe it is important to address ontological research in a unitary, systematic fashion, embracing conceptual issues concerning what would be required to establish an exhaustive ontology of (...) the geospatial domain, issues relating to the choice of appropriate methods for formalizing ontologies, and considerations regarding the design of ontology-driven information systems. This integrated approach is necessary, because there is a strong dependency between the methods used to specify an ontology, and the conceptual richness, robustness and tractability of the ontology itself. Likewise, information system implementations are needed as testbeds of the usefulness of every aspect of an exhaustive ontology of the geospatial domain. None of the current UCGIS research priorities provides such an integrative perspective, and therefore the topic of “Ontological Foundations for Geographic Information Science” is unique. (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 interrogates the fundamental logic of data-driven decision-making as it has taken hold in education and argues for a critical analysis of data-driven education via an attitude of historical ontology. Though influenced by Foucault’s understanding of this concept, I center Colin Koopman’s recent analysis of the ‘informational person’ to point attention to the ways in which the very formatting of data may be understood as historically contingent and, thus, more contestable. After examining the background of DDDM (...) and relevant critiques of it, I suggest that investigating the socio-historical formations of data itself are important for indicating its potential dangers within education. Such a critical analysis identifies the doubled politics of data formatting, with its ability to tether subjectivity to data, while potentially baking modes of power into a variety of technological data apparatuses. To conclude, I consider Koopman’s work in terms of how it may extend critical studies of educational datafication. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic (...) expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by (...) philosophers, the term ‘ontology’ has gained currency in the field of computer and information science, and in information-driven research in bioinformatics and related areas. We examine these new developments in applied ontology, and show what lessons they might have for both philosophers and information scientists. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. (...) In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (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)

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by (...) philosophers, the term ‘ontology’ has gained currency in the field of computer and information science, and in information-driven research in bioinformatics and related areas. We examine these new developments in applied ontology, and show what lessons they might have for both philosophers and information scientists. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking (...) account of certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter may nonetheless support (...) the Foundry’s goal of consistent and non-redundant annotation if appropriate mappings of data annotated with their aid can be achieved. To construct such mappings in reliable fashion, however, it is necessary to analyze terminological resources from an ontologically realistic perspective in such a way as to identify the exact import of the ‘concepts’ and associated terms which they contain. We propose a framework for such analysis that is designed to maximize the degree to which legacy terminologies and the data coded with their aid can be successfully used for information-driven clinical and translational research. (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)

The current industrial revolution is said to be driven by the digitization that exploits connected information across all aspects of manufacturing. Standards have been recognized as an important enabler. Ontology-based information standard may provide benefits not offered by current information standards. Although there have been ontologies developed in the industrial manufacturing domain, they have been fragmented and inconsistent, and little has received a standard status. With successes in developing coherent ontologies in the biological, biomedical, and (...) financial domains, an effort called Industrial Ontologies Foundry (IOF) has been formed to pursue the same goal for the industrial manufacturing domain. However, developing a coherent ontology covering the entire industrial manufacturing domain has been known to be a mountainous challenge because of the multidisciplinary nature of manufacturing. To manage the scope and expectations, the IOF community kicked-off its effort with a proof-of-concept (POC) project. This paper describes the developments within the project. It also provides a brief update on the IOF organizational set up. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let (...) alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and (...) pharmacology needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

From the literature study, it was observed that there are significantly fewer studies that review ontology- based narrative models. This motivates the current work. A parametric approach was adopted to report the existing ontology-driven models for narrative information. The work considers the narrative and ontology components as parameters. This study hopes to encompass the relevant literature and ontology models together. The work adopts a systematic literature review methodology for an extensive literature selection. The models (...) were selected from the literature using a stratified random sampling technique. The findings illustrate an overview of the narrative models across domains. The study identifies the differences and similarities of knowledge representation in ontology-based narrative information models. This paper will explore the basic concepts and top-level concepts in the models. Besides, this study provides a study of the narrative theories in the context of ongoing research. It also identifies the state-of-the-art literature for ontology-based narrative information. Keywords: ontologies, narrative information, modelling. (shrink)

As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and (...) different national strategies have been established. The workshop summarizes the requirements for such advanced EHR systems and their underlying architecture, presents different strategies and solutions advocated by corresponding protagonists, discusses pros and cons as well as harmonization and migration strategies for those approaches. It particularly highlights a turn towards ontology-driven architectures. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to (...) breast cancer hot-spot detection with the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

The importance of relationality in ethical leadership has been the focus of recent attention in business ethics scholarship. However, this relational component has not been sufficiently theorized from different philosophical perspectives, allowing specific Western philosophical conceptions to dominate the leadership development literature. This paper offers a theoretical analysis of the relational ontology that informs various conceptualizations of selfhood from both African and Western philosophical traditions and unpacks its implications for values-driven leadership. We aim to broaden Western conceptions of (...) leadership development by drawing on twentieth century European philosophy’s insights on relationality, but more importantly, to show how African philosophical traditions precede this literature in its insistence on a relational ontology of the self. To illustrate our theoretical argument, we reflect on an executive education course called values-driven leadership into action, which ran in South Africa, Kenya, and Egypt in 2016, 2017, and 2018. We highlight an African-inspired employment of relationality through its use of the ME-WE-WORLD framework, articulating its theoretical assumptions with embodied experiential learning. (shrink)

In the era of increasingly defined ontological insecurity and uncertainty driven by the ravages of COVID-19, urban informal settlement has emerged as a source of resilience. Indeed, the effects of a pandemic transcends its epidemiological characteristics to political economy and societal resilience. If resilience is the capacity of a system to adapt successfully to significant challenges that threaten the function or development of the human society, then ontological insecurity is about the lack of such capacity. Drawing on Keith Hartian’s (...) understanding of ‘informality’ of spaces, this policy brief attempts to identify and frame a research agenda for the future. The agenda would assist future researchers and policymakers provide responses that appropriately recognize groups and actors that define the urban informal space. (shrink)

Babylon Knowledge Explorer (BKE) is an integrated suite of tools and information sources developed in GlaxoSmithKline's Analysis, Applications, and Research Technologies Department to support the prototyping and implementation of ontology-driven information systems and ontology-enhanced knowledge applications. In this paper we describe the current state of BKE development and focus on some of its distinctive or novel approaches, highlighting -/- * How BKE makes use of multiple large pre-existing ontologies in support of text and data mining. (...) * The methodology employed for importing an ontology and making it immediately accessible to BKE's tools, interfaces, and API. * A formal description of BKE's ontology-based fact model and how this is employed in implementing information retrieval and data mining capabilities. * A sample application built on BKE that illustrates an ontologyenhanced machine learning tool. (shrink)

Network analysis views complex systems as networks with well-defined structural properties that account for their complexity. These characteristics, which include scale-free behavior, small worlds and communities, are not to be found in networks such as random graphs and lattices that do not correspond to complex systems. They provide therefore a robust ground for claiming the existence of “complex networks” as a non-trivial subset of networks. The theory of complex networks has thus been successful in making systematically explicit relevant marks of (...) complexity in the form of structural properties, and this success is at the root of its current popularity. Much less systematic has been, on the other hand, the definition of the properties of the building components of complex networks. The obvious assumption is that these components must be nodes and links. Generally, however, the internal structure of nodes is not taken into account, and links are serendipitously identified by the perspective with which one looks at the network to be analyzed. For instance, if the nodes are Web pages that contain information about scientific papers, one point of view will match the relevant links with hyperlinks to similar Web pages, and another with citations of other articles. We intend to contribute here a systematic approach to the identification of the components of a complex network that is based on information theory. The approach hinges on some recent results arising from the convergence between the theory of complex networks and probabilistic techniques for content mining. At its core there is the idea that nodes in a complex network correspond to basic information units from which links are extracted via methods of machine learning. Hence the links themselves are viewed as emergent properties, similarly to the broader structural properties mentioned above. Indeed, beside rounding up the theory, this approach based on learning has clear practical benefits, in that it makes networks emerge from arbitrary information domains. We provide examples and applications in a variety of contexts, starting from an information-theoretic reconstruction of the well-known distinction between “strong links” and “weak links” and then delving into specific applications such as business process management and analysis of policy making. (shrink)

The purpose of this work is to find out how different library classification systems and linguistic ontologies arrange a particular domain of interest and what are the limitations for information retrieval. We use knowledge representation techniques and languages for construction of a domain specific ontology. This ontology would help not only in problem solving, but it would demonstrate the ease with which complex queries can be handled using principles of domain ontology, thereby facilitating better information (...) retrieval. Facet-based methodology has been used for ontology formalization for quite some time. Ontology formalization involves different steps such as, Identification of the terminology, Analysis, Synthesis, Standardization and Ordering. Firstly, for purposes of conceptualization OntoUML has been used which is a well-founded and established language for Ontology driven Conceptual Modelling. Phase transformation of “the same mode” has been subsequently obtained by OWL-DL using Protégé software. The final OWL ontology contains a total of around 232 axioms. These axioms comprise 148 logical axioms, 76 declaration axioms and 43 classes. These axioms glue together classes, properties and data types as well as a constraint. Such data clustering cannot be achieved through general use of simple classification schemes. Hence it has been observed and established that domain ontology using faceted principles provide better information retrieval with enhanced precision. This ontology should be seen not only as an alternative of the existing classification system but as a Knowledge Base system which can handle complex queries well, which is the ultimate purpose of any classification system or indexing system. In this paper, we try to understand how ontology-based information retrieval systems can prove its utility as a useful tool in the field of library science with a particular focus on the education domain. (shrink)

Designing an ontology that meets the needs of end-users, e.g., a medical team, is critical to support the reasoning with data. Therefore, an ontology design should be driven by the constant and efficient validation of end-users needs. However, there is not an existing standard process in knowledge engineering that guides the ontology design with the required quality. There are several ontology design processes, which range from iterative to sequential, but they fail to ensure the practical (...) application of an ontology and to quantitatively validate end-user requirements through the evolution of an ontology. In this paper, an ontology design process is proposed, which is driven by end-user requirements, defined as Competency Questions. The process is called CQ-Driven Ontology DEsign Process and it includes activities that validate and verify the incremental design of an ontology through metrics based on defined CQs. CODEP has also been applied in the design and development of an ontology in the context of a Mexican Hospital for supporting Neurologist specialists. The specialists were involved, during the application of CODEP, in collecting quality measurements and validating the ontology increments. This application can demonstrate the feasibility of CODEP to deliver ontologies with similar requirements in other contexts. (shrink)

The Information Artifact Ontology (IAO) was created to serve as a domain‐neutral resource for the representation of types of information content entities (ICEs) such as documents, data‐bases, and digital im‐ages. We identify a series of problems with the current version of the IAO and suggest solutions designed to advance our understanding of the relations between ICEs and associated cognitive representations in the minds of human subjects. This requires embedding IAO in a larger framework of ontologies, including most (...) importantly the Mental Func‐tioning Ontology (MFO). It also requires a careful treatment of the aboutness relations between ICEs and associated cognitive representa‐tions and their targets in reality, which implies in turn a new treatment of the relation of truthmaking. (shrink)

This book provides a detailed discussion of the theoretical and practical implications of the change driven by ICTs. Such a change is often much more profound than an emphasis on information technology and society can capture, for not only does it bring about ethical and policy vacuums that call for a new understanding of ethics, politics and law, but it also "re-ontologizes reality", as propounded by Luciano Floridi's philosophy and ethics of information. The informational turn is transforming (...) our understanding of reality by challenging the conventional ways we have of thinking about our world and our identities in terms of stable and enduring structures and beliefs. The information age we inhabit brings to completion our self-understanding as informational systems that produce, process, and exchange information with other informational systems, in an environment that is itself made up of information. The present volume provides us with a better understanding of the normative nature and role of information, helping us to grasp the sense and extent to which informational resources serve as "constraining affordances" guiding our behaviours. It does so by delineating the background against which we build our beliefs about reality, make decisions, and behave, through our interactions with a multi-agent system that is increasingly dependent on ICTs. The book will be of interest to a vast audience, ranging from information technologists, ethicists, policy makers, social and legal scholars, and all those willing to embrace the following three tenets: we construct our world and ourselves informationally; by constructing our world and ourselves we thereby become aware of our limits; it is precisely these limits that make us become human beings. (shrink)

The growing diffusion of perspectivism within the debate on information system ontologies [ISOs] does not correspond to a thorough analysis of what perspectivism specifically consists of. This paper aims to fill this void. First, I show what supporting perspectivism in information system ontologies [PISO] means in terms of (minimal) claims and implications; then I argue that the definitions of ISO implicitly assume PISO’s (minimal) claims or, in other words, that ISOs presuppose and maintain PISO. Section 2 presents the (...) main definitions of ISO. Section 3 specifies what claims are common to all perspectivists in ISO. Sects. 4–7 analyze the implications of those claims. Section 8 explores the chance of multiple perspectivisms within ISOs’ domain. Finally, Sects. 9–10 assume that, if PISO’s (minimal) claims and (their) implications can be inferred from ISO’s definitions, then ISOs are perspectivist, or PISO’s minimal claims are assumptions underlying ISOs. (shrink)

In the domain of information systems ontologies, the notion of completeness refers to ontological contents by demanding that they be exhaustive with respect to the domain that the ontology aims to represent. The purpose of this paper is to analyze such a notion, by distinguishing different varieties of completeness and by questioning its consistency with the open-world assumption, which formally assumes the incompleteness of conceptualizations on information systems ontologies.

We study experimentally a coordination game with N heterogeneous individuals under different information treatments. We explore the effects of information on the emergence of Pareto-efficient outcomes, by means of a gradual decrease of the information content provided to the players in successive experiments. We observe that successful coordination is possible with private information alone, although not on a Pareto-optimal equilibrium. Reinforcement-based learning models reproduce the qualitative trends of the experimental results.

Insofar as disagreement may in principle regard most of (maybe all) facets of information system ontologies’ [ISOs] debate, it may also produce a plurality of views – sometimes inconsistent with each other – on ISOs’ development and design. This paper analyzes a view that makes the recognition of – and provides a theoretical foundation for – such a plurality of views a trademark: perspectivism (on ISOs). The aim is to show what exactly endorsing perspectivism consists of, and how perspectivism (...) differs from different, competing views. Section 2 introduces the main claims of perspectivism, and remarks that perspectivism mainly deals with ISOs’ development and design. As for ISOs’ development, Sect. 3 considers domain’s partition and systematization, by distinguishing perspectivism from realism and relativism. Section 3 also shows that perspectivism implies some sort of variantism on ISOs’ representational primitives, about which perspectivism may not differ from its rivals. As for the ISOs’ design, Sect. 4 points out that despite perspectivism grants the possibility to use any procedural approach, principle, and ontological language, it is not committed to uphold that all those approaches, principles, and languages are legitimate. Finally, Sect. 5 focuses on both perspectivism’s weaknesses and (theoretical) contribution to ISOs’ debate. (shrink)

As one may have noticed, the title of this paper is somewhat provocative. We found Roman Krzanowski’s (2020a,b,c; 2022) proposed approach to the problem of information very intriguing. Our aim here is to highlight some advantages when it comes to answering some fundamental questions in the philosophy of physics and metaphysics, as well as the philosophy of information and computer science. This issue is of great importance, so we propose that the introduction of some subtle distinctions between ontological (...) and epistemological information can be regarded as being analogous to G.F.R. Ellis’s analyses of the passage of time in his concept of the Crystallizing Block Universe (Ellis and Goswami, 2012). This analogy could be useful when further studying the relations between different types of information. We also suggest some subjects for further study, ones where Krzanowski’s proposal could serve as a very solid foundation for examining traditional metaphysical issues by combining classical philosophical doctrines with the new approach. (shrink)

In my paper I will focus my attention on some philosophical aspects of the Information Ethics displayed by Luciano Floridi. Floridi’s Information Ethics has the methodological merit of providing the interpretation of the Informational Turn with a solid philosophical basis, the roots of which deserve a careful investigation. In this perspective, I will analyse a key question, which is essential not only from a theoretical but also from a practical (moral, political and legal) point of view, i.e. whether (...) or not Floridi’s construction of information is consistent with a pluralistic conception of Being. (shrink)

In my paper I will focus my attention on some philosophical aspects of the Information Ethics displayed by Luciano Floridi. Floridi’s Information Ethics has the methodological merit of providing the interpretation of the Informational Turn with a solid philosophical basis, the roots of which deserve a careful investigation. In this perspective, I will analyse a key question, which is essential not only from a theoretical but also from a practical point of view, i.e. whether or not Floridi’s construction (...) of information is consistent with a pluralistic conception of Being. (shrink)

The current (still limited) use of the notion of informativeness in the domain of information system ontologies seems to indicate that such ontologies are informative if and only if they are understandable for their final recipients. This paper aims at discussing some theoretical issues emerging from that use which, as we will see, connects the informativeness of information system ontologies to their representational primitives, domains of knowledge, and final recipients. Firstly, we maintain that informativeness interacts not only with (...) the actual representational primitives, but also with their variability over time. Secondly, we discuss the correspondence between representational primitives and domains of knowledge of those ontologies. Finally, we explore the possibility of an epistemological discrepancy between human beings and software systems on the understanding of ontological contents. (shrink)

Despite the fact that information systems ontologies [ISOs] support the mutual understanding between human beings and software applications, human beings and software applications do not understand ISOs' contents in the same way. The same applies to ontological integration. This paper attempts to account for such discrepancies by emphasizing that while human being can have access to entities represented in ISOs, software applications cannot.

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)

The purpose of this study was to evaluate, revise, and extend the Informed Consent Ontology (ICO) for expressing clinical permissions, including reuse of residual clinical biospecimens and health data. This study followed a formative evaluation design and used a bottom-up modeling approach. Data were collected from the literature on US federal regulations and a study of clinical consent forms. Eleven federal regulations and fifteen permission-sentences from clinical consent forms were iteratively modeled to identify entities and their relationships, followed by (...) community reflection and negotiation based on a series of predetermined evaluation questions. ICO included fifty-two classes and twelve object properties necessary when modeling, demonstrating appropriateness of extending ICO for the clinical domain. Twenty-six additional classes were imported into ICO from other ontologies, and twelve new classes were recommended for development. This work addresses a critical gap in formally representing permissions clinical permissions, including reuse of residual clinical biospecimens and health data. It makes missing content available to the OBO Foundry, enabling use alongside other widely-adopted biomedical ontologies. ICO serves as a machine-interpretable and interoperable tool for responsible reuse of residual clinical biospecimens and health data at scale. (shrink)

FOIS is the flagship conference of the International Association for Ontology and its Applications, a non-profit organization which promotes interdisciplinary research and international collaboration at the intersection of philosophical ontology, linguistics, logic, cognitive science, and computer science. This book presents the papers delivered at FOIS 2023, the 13th edition of the Formal Ontology in Information Systems conference. The event was held as a sequentially-hybrid event, face-to-face in Sherbrooke, Canada, from 17 to 20 July 2023, and online (...) from 18 to 20 September 2023. In total, 62 articles from 19 different countries were submitted, out of which 25 were accepted for inclusion in the conference and for publication; corresponding to an acceptance rate of 40 percent. The contributions are separated into the book’s three sections: (1) Foundational ontological issues; (2) Methodological issues around the development, alignment, verification and use of ontologies; and (3) Domain ontologies and ontology-based applications. In these sections, ontological aspects from a wide variety of fields are covered, primarily from various engineering domains including cybersecurity, manufacturing, petroleum engineering, and robotics, but also extending to the humanities, social sciences, medicine, and dentistry. A noticeable trend among the contributions in this edition of the conference is the recognition that improving the tools to analyze, align, and improve ontologies is of paramount importance in continuing to advance the field of formal ontology. The book will be of interest to all formal and applied ontology researchers, and to those who use formal ontologies and information systems as part of their work. (shrink)

The paper outlines a new interpretation of informational privacy and of its moral value. The main theses defended are: (a) informational privacy is a function of the ontological friction in the infosphere, that is, of the forces that oppose the information flow within the space of information; (b) digital ICTs (information and communication technologies) affect the ontological friction by changing the nature of the infosphere (re-ontologization); (c) digital ICTs can therefore both decrease and protect informational privacy but, (...) most importantly, they can also alter its nature and hence our understanding and appreciation of it; (d) a change in our ontological perspective, brought about by digital ICTs, suggests considering each person as being constituted by his or her information and hence regarding a breach of one’s informational privacy as a form of aggression towards one’s personal identity. (shrink)

Information modeling (also known as conceptual modeling or semantic data modeling) may be characterized as the formulation of a model in which information aspects of objective and subjective reality are presented (the application), independent of datasets and processes by which they may be realized (the system).A methodology for information modeling should incorporate a number of concepts which have appeared in the literature, but should also be formulated in terms of constructs which are understandable to and expressible by (...) the system user as well as the system developer. This is particularly desirable in connection with certain intimate relationships, such as being the same as or being a part of. (shrink)

Mobile health tools are often said to empower users by providing them with the information they need to exercise control over their health. We aim to bring clarity to this claim, and in doing so explore the relationship between empowerment and autonomy. We have identified three distinct models embedded in the empowerment rhetoric: empowerment as information, empowerment as control, and empowerment as values. Each distinct model of empowerment gives rise to an associated problem. These problems, the Problem of (...) Interpretation, the Value Alignment Problem, and the Priority Problem, show that mobile health tools in their current form are either insufficient for empowerment or are self‐defeating. These digital health technologies encourage users to adopt an individualized conception of autonomy, one that may weaken the doctor–patient relationship and undermine practices in shared decision making, and ultimately may not deliver on improving the health outcomes for those that need it the most. (shrink)

The number of available legal documents has presented an enormous growth in recent years, and the digital processing of such materials is prompting the necessity of systems that support the automatic relevant information extraction. This work presents a system for ontology-based information extraction from natural language texts, able to identify a set of legal events. The system is based on an innovative methodology based on domain ontology of legal events and a set of linguistic rules, integrated (...) through inference mechanism, resulting in a flexible approach and scalable approach. A case study with the use of documents from the Superior Court in Brazil is related, with satisfactory results in precision and recall. (shrink)

In a development that has still been hardly noticed by philosophers, a conception of ontology has been advanced in recent years in a series of extra-philosophical disciplines as researchers in linguistics, psychology, geography and anthropology have sought to elicit the ontological commitments (‘ontologies’, in the plural) of different cultures or disciplines. Exploiting the terminology of Quine, researchers in psychology and anthropology have sought to establish what individual human subjects, or entire human cultures, are committed to, ontologically, in their everyday (...) cognition, in much the same way in which philosophers of science have attempted to elicit the ontological commitments of the natural sciences. Thus they have engaged in inquiries designed to establish how folk ontologies (or folk biologies, folk theories of physics, folk psychologies, and so on) develop through infancy and childhood, or to establish the degree to which given elements of folk ontologies reflect universal features of the human cognitive system. In a parallel development, researchers in biomedicine developed what they called 'ontologies' as controlled vocabularies to ensure interoperability of the way in which, for example, genomic data is described in different biological disciplines. We describe in what follows some of the relations between these efforts and the more traditional concerns of philosophers. (shrink)