While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through (...) which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (shrink)

Data heterogeneity is the obstacle for the resource sharing on Semantic Web, and ontology is regarded as a solution to this problem. However, since different ontologies are constructed and maintained independently, there also exists the heterogeneity problem between ontologies. Ontology matching is able to identify the semantic correspondences of entities in different ontologies, which is an effective method to address the ontology heterogeneity problem. Due to huge memory consumption and long runtime, the performance of the existing (...) class='Hi'>ontology matching techniques requires further improvement. In this work, an extended compact genetic algorithm-based ontology entity matching technique is proposed, which uses both the compact encoding mechanism and linkage learning approach to match the ontologies efficiently. Compact encoding mechanism does not need to store and maintain the whole population in the memory during the evolving process, and the utilization of linkage learning protects the chromosome’s building blocks, which is able to reduce the algorithm’s running time and ensure the alignment’s quality. In the experiment, ECGA-OEM is compared with the participants of ontology alignment evaluation initiative and the state-of-the-art ontology matching techniques, and the experimental results show that ECGA-OEM is both effective and efficient. (shrink)

Although from a philosophical perspective, many reflections can be brought up about the theorizing process, in this essay, we aim to reflect on the importance of the alignment between ontology and epistemology. This is particularly relevant because deeper discussions about the philosophical roots that underlay the theorizing processes remain as a lack in organizational and management studies. To support our work, we adopted the epistemic-ontological alignment model as a conceptual tool and the Resource-Based View (RBV) and some (...) of its questionings as an example to carry out a reflection exercise about its epistemic-ontological alignment. RBV is a theory that plays a prominent role in management studies, especially in the strategy field. Nevertheless, discussions regarding RBV philosophical foundations are not common in the mainstream of strategic management. After our analysis, we advise that scholars care about the philosophical roots of their theoretical proposals to promote constructive dialogue in their research communities. This can avoid empty discussions and criticisms based on incongruous worldviews. Our reflections also suggest that future research should embrace the plurality of paradigms as a source of renewal and transcendence in the production of knowledge. A multi-paradigmatic movement towards more eclecticism in Administrative Science can help produce new and underexploited combinations of knowledge in the theorizing process. (shrink)

Ontologies are computational artifacts that model consensual aspects of reality. In distributed contexts, applications often need to utilize information from several distinct ontologies. In order to integrate multiple ontologies, entities modeled in each ontology must be matched through an ontology alignment. However, imperfect alignments may introduce inconsistencies. One kind of inconsistency, which is often introduced, is the violation of the conservativity principle, that states that the alignment should not introduce new subsumption relations between entities from the (...) same source ontology. We propose a two-step quadratic-time algorithm for automatically correcting such violations, and evaluate it against datasets from the Ontology Alignment Evaluation Initiative 2019, comparing the results to a state-of-the-art approach. The proposed algorithm was significantly faster and less aggressive; that is, it performed fewer modifications over the original alignment when compared to the state-of-the-art algorithm. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of (...) these relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

A network of aligned ontologies is a distributed system, whose components are interacting and interoperating, the result of this interaction being, either the extension of local assertions, which are valid within each individual ontology, to global assertions holding between remote ontology syntactic entities through a network path, or to local assertions holding between local entities of an ontology, but induced by remote ontologies, through a cycle in the network. The mechanism for achieving this interaction is the composition (...) of relations. In this perspective, we introduce the notions of local composable relations, which relate ontology entities belonging to the same ontology, remotely induced composable relations, which relate ontology entities belonging to remote ontologies through a path of ontologies and alignments in the network, and network induced local composable relations, which relate ontology entities belonging to the same ontology, but through a path of ontologies and alignments forming a cycle starting and ending at the same ontology, to characterize the logical consequences extracted from a network of aligned ontologies, and we propose a category-based methodology for detecting semantic inconsistencies in networks of aligned ontologies, which is based on contravariant representable functors and on the definition of two composition operators suitable for propagating local knowledge through the network. (shrink)

Ontological pluralism is the view that there are different ways of being. Historically, ways of being are aligned with the ontological categories. This paper is about to investigate why there is such a connection, and how it should be understood. Ontological pluralism suffers from an objection, according to which ontological pluralism collapses into ontological monism, i.e., there is only one way to be. Admitting to ontological categories can save ontological pluralism from this objection if ways of being ground ontological categories. (...) -/- . (shrink)

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (...) (i.e., they belong to the domain of epistemology). We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies. (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 goal of the Department of Defense Net-Centric Data Strategy is to improve data sharing throughout the DoD. Data sharing is a critical element of interoperability in the emerging system-of-systems. Achieving interoperability requires the elimination of two types of data heterogeneity: differences of syntax and differences of semantics. This paper builds a path toward semantic uniformity through application of a disciplined approach to ontology. An ontology is a consensus framework representing the types of entities within a given domain (...) and the relations between them. The construction of an ontology begins when a Community of Interest (COI) identifies its authoritative data sources (ADS), which are usually manifest in relevant doctrinal publications, glossaries, data dictionaries, and logical data models. The identified terms are then defined in relation to a common logical framework that has been designed to ensure interoperability with other ontologies created on the basis of the same strategy. As will be described, the Command and Control (C2) Ontology will include representations of a substantial number of entities within the Command and Control (C2) domain. If domain ontologies (e.g. Strike and Counterinsurgency) semantically align with the C2 Ontology, then a substantial barrier to systems interoperability is thereby crossed. (shrink)

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques (...) such as ontology-based multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (shrink)

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)

This paper describes the construction method of a legal application ontology. This method is based on the merging of micro-ontologies built from European community directives. The terminae construction method from texts enhanced by an alignment process with a core legal ontology is used for building micro-ontologies. A merging process allows constructing the legal ontology.

The Ontology Summit 2012 explored the current and potential uses of ontology, its methods and paradigms, in big systems and big data: How ontology can be used to design, develop, and operate such systems. The systems addressed were not just software systems, although software systems are typically core and necessary components, but more complex systems that include multiple kinds and levels of human and community interaction with physical-software systems, systems of systems, and the socio-technical environments for those (...) systems which can include cultural, legal, and economic components. The focus themes used for this exploration were Big Systems Engineering, Big Data Challenge, Large Scale Domain Applications, and cross-cutting aspects Ontology Quality, and Federation and Integration of Systems. The Ontology Summit 2012 consisted of over three months of intensive virtual collaborative elaboration of these issues in presentations, panels, and group email. The culmination of these activities was a face-to-face Symposium at the US National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA, 12–13 April 2012. The primary product of this Ontology Summit is the communiqué reported here. But there are other products, some continuing as collaborative, more specifically focused analysis and modeling efforts aligned with various open standards activities. Behind all of these particular products, of course, is the real overriding purpose of the Ontology Summit 2012, which was: the joint collaboration of three distinct communities, the ontology, systems engineering and big systems stakeholder communities, who came together to address common problems, create common understanding and propose common solutions. (shrink)

Philosophers and scientists have long speculated about the nature of color. Atomists such as Democritus thought color to be "conventional," not real; Galileo and other key figures of the Scientific Revolution thought that it was an erroneous projection of our own sensations onto external objects. More recently, philosophers have enriched the debate about color by aligning the most advanced color science with the most sophisticated methods of analytical philosophy. In this volume, leading scientists and philosophers examine new problems with new (...) analytic tools, considering such topics as the psychophysical measurement of color and its implications, the nature of color experience in both normal color-perceivers and the color blind, and questions that arise from what we now know about the neural processing of color information, color consciousness, and color language. Taken together, these papers point toward a complete restructuring of current orthodoxy concerning color experience and how it relates to objective reality. Kuehni, Jameson, Mausfeld, and Niederee discuss how the traditional framework of a three-dimensional color space and basic color terms is far too simple to capture the complexities of color experience. Clark and MacLeod discuss the difficulties of a materialist account of color experience. Churchland, Cohen, Matthen, and Westphal offer competing accounts of color ontology. Finally, Broackes and Byrne and Hilbert discuss the phenomenology of color blindness. Contributors: Justin Broackes, Alex Byrne, Paul M. Churchland, Austen Clark, Jonathan Cohen, David R. Hilbert, Kimberly A. Jameson, Rolf Kuehni, Don I.A. MacLeod, Mohan Matthen, Rainer Mausfeld, Richard Niederée, Jonathan Westphal The hardcover edition does not include a dust jacket. (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)

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)

Recent years have seen rapid progress in the development of ontologies as semantic models intended to capture and represent aspects of the real world. There is, however, great variation in the quality of ontologies. If ontologies are to become progressively better in the future, more rigorously developed, and more appropriately compared, then a systematic discipline of ontology evaluation must be created to ensure quality of content and methodology. Systematic methods for ontology evaluation will take into account representation of (...) individual ontologies, performance (in terms of accuracy, domain coverage and the efficiency and quality of automated reasoning using the ontologies) on tasks for which the ontology is designed and used, degree of alignment with other ontologies and their compatibility with automated reasoning. A sound and systematic approach to ontology evaluation is required to transform ontology engineering into a true scientific and engineering discipline. This chapter discusses issues and problems in ontology evaluation, describes some current strategies, and suggests some approaches that might be useful in the future. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

The development of manufacturing technologies for new materials involves the generation of a large and continually evolving volume of information. The analysis, integration and management of such large volumes of data, typically stored in multiple independently developed databases, creates significant challenges for practitioners. There is a critical need especially for open-sharing of data pertaining to engineering design which together with effective decision support tools can enable innovation. We believe that ontology applied to engineering (OE) represents a viable strategy for (...) the alignment, reconciliation and integration of diverse and disparate data. The scope of OE includes: consistent capture of knowledge pertaining to the types of entities involved; facilitation of cooperation among diverse group of experts; more effective ongoing curation, and update of manufacturing data; collaborative design and knowledge reuse. As an illustrative case study we propose an ontology focused on the representation of composite materials focusing in particular on the class of Functionally Graded Materials (FGM) in particular. The scope of the ontology is to provide information about the components of such materials, the manufacturing processes involved in creation, and diversity of application ranging from additive manufacturing to restorative dentistry. The ontology is developed using Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical (...) data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

This paper provides an exposition and critical assessment of a fundamental disagreement between Løgstrup’s and Levinas’s otherwise closely aligned ethical phenomenologies. The disagreement concerns the putative compatibility of ethics and ontology, where in stark contrast to Levinas’s ethics, which proceeds from a critique of the ‘primacy of ontology’ in Western thought, Løgstrup brands his own ethical project as ‘ontological ethics’. First, I provide an interpretation of Løgstrup’s ontological ethics, clarifying in particular the influence of hermeneutic and existential analysis (...) on Løgstrup’s methodology. Second, I bring Løgstrup’s ontological ethics into critical dialogue with Levinas’s thought. Here, I home in on two Levinas-style worries that appear to have traction against Løgstrup’s ontological ethics. However, ultimately, I argue that both can be defused. (shrink)

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of (...) domain ontologies in anatomy, physiology and pathology. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (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)

An approach in achieving semantic interoperability among heterogeneous systems is to offer infrastructure to assist with linking and integration using a foundational ontology. Due to the creation of multiple foundational ontologies, this also means linking and integrating those ones. In order to achieve this, we have selected the widely used foundational ontologies DOLCE, BFO, and GFO, and their related modules, on which to perform ontology mediation (alignment, mapping, and merging). The foundational ontologies were aligned by identifying correspondences (...) between ontology entities using seven tools, documentation, and our manual alignments, and comparing their effectiveness. Thereafter, based on the alignments, we created correspondences in the ontology files resulting in entity mappings and merged ontologies. However, during the mapping process, it was found that differences in foundational ontologies, such as their hierarchical structure, conflicting axioms due to complement and disjointness, and incompatible domain and range restriction, cause logical inconsistencies in foundational ontology alignments, thereby greatly reducing the number of mappings. We analyse and present these logical inconsistencies with possible solutions to some of them. (shrink)

Ontologies are today being applied in almost every field to support the alignment and retrieval of data of distributed provenance. Here we focus on new ontological work on dance and on related cultural phenomena belonging to what UNESCO calls the “intangible heritage.” Currently data and information about dance, including video data, are stored in an uncontrolled variety of ad hoc ways. This serves not only to prevent retrieval, comparison and analysis of the data, but may also impinge on our (...) ability to preserve the data that already exists. Here we explore recent technological developments that are designed to counteract such problems by allowing information to be retrieved across disciplinary, cultural, linguistic and technological boundaries. Software applications such as the ones envisaged here will enable speedier recovery of data and facilitate its analysis in ways that will assist both archiving of and research on dance. (shrink)

When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be (...) aligned with joint doctrine. It requires also that the separate information systems used by the different elements of a joint force must be interoperable, in the sense that data and information that is generated by each element must be usable (understandable, processable) by all the other elements that need them. Currently, such interoperability is impeded by multiple inconsistencies among the different data and software standards used by warfighters. We describe here the on-going project of creating a Joint Doctrine Ontology (JDO), which uses joint doctrine to provide shared computer-accessible content valid for any field of military endeavor, organization, and information system. JDO addresses the two previously mentioned requirements of unified action by providing a widely applicable benchmark for use by developers of information systems that will both guarantee alignment with joint doctrine and support interoperability. (shrink)

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate (...) representation of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

Background: In order to improve ontology quality, tool- and language-related tutorials are not sufficient. Care must be taken to provide optimized curricula for teaching the representational language in the context of a semantically rich upper level ontology. The constraints provided by rigid top and upper level models assure that the ontologies built are not only logically consistent but also adequately represent the domain of discourse and align to explicitly outlined ontological principles. Finally such a curriculum must take into (...) account the pre-existing skills and knowledge of the target audience. -/- Objective: To develop a well-structured curriculum aligned to the particular requirements of life science professionals, in order to enable them to create logically sound, domain adequate and predicable ontologies using the Web Ontology Language (OWL) in Protégè. -/- Methods: Content selection for the curriculum was based on the literature, pre-existing tutorials, and a guideline for good ontology development (i.e ontology design enhancing domain adequacy, sustainability and interoperability) that drew on the authors previous experiences with large ontology development projects. Learning objectives were formulated according to a needs assessment of the targeted learners, who were students trained in life sciences with basic knowledge and practical skills in computer science. As instructional format we choose an approach with a high amount of practical exercises. The curriculum was first implemented with 24 Students and 7 lecturers/ tutors over 5 full days. The curriculum was evaluated by gathering the participants feedback via a questionnaire. -/- Results: Curricular development produced 16 modules of approximately 2 hours each, which covered basic principles of Applied Ontology, description logic syntax and semantics, as well as best design practices outlined in ontology design patterns and variants of the BioTop upper ontology. An opinion survey based on questionnaires indicated that the participants took advantage from the teaching strategies applied, as they indicated good knowledge gain and acknowledged the relevance of the modules. The difficulty was rated slightly lower. -/- Conclusion: The development of teaching material for principled ontology design and best practices is of crucial importance in order to enhance the quality of biomedical ontologies. Here, we present a curriculum for a week long workshop, leveraging on current educational principles, focusing on interactive hands-on exercises, group interactions, and problem-oriented learning. Whereas evaluation clearly showed the success of this approach, in particular regarding student’s satisfaction, the objective measurement of traceable effects on the quality of the generated ontology, although of much higher interest, has just started. (shrink)

Since cognitive neuroscience aims at giving an integrated account of mind and brain, its ontology should include both neural and cognitive entities and specify their relations. According to what we call the standard ontological framework of cognitive neuroscience, the aim of cognitive neuroscience should be to establish one-to-one mappings between neural and cognitive entities. Where such entities do not yet closely align, this can be achieved by reforming the cognitive ontology, the neural ontology, or both. In order (...) to assess the limits and the possibilities of the SOFCN, we will examine a paradigmatic case study: the concept of Broca’s area, which indicates an alleged mapping between the left inferofrontal gyrus and the production of language. We review evidence showing that such a mapping does not hold, thus calling into question either the status of Broca’s area or the validity of the SOFCN. We then propose some strategies for addressing the issue and suggest that it may be solved within the SOFCN by adopting both of the following strategies: first, more accurately defining the relevant neural structures and second, switching the focus of neural ontology from structures to events, individuated by a where conjoint with a how. (shrink)

Frege's strict alignment between his syntactic and ontological categories is not, as is commonly assumed, some kind of a philosophical thesis. There is no thesis that proper names refer only to objects, say, or that what refers to an object is a proper name. Rather, the alignment of categories is internal to Frege's conception of what syntax and ontology are. To understand this, we need to recognise the pride of place Frege assigns within his theorising to the (...) notion of truth. For both language and the world, the Fregean categories are logical categories, categories, that is, of truth. The elaboration of this point makes clear the incoherence of supposing that they might not align. (shrink)

The paper examines connections between ontology and finance. The ontological debates concerning the role of finance are examined between two opposing schools of thought that can be labelled, very broadly, ‘instrumentalist’ and ‘realist’. These two schools of thought have had momentous repercussions in understanding what is a good society. Each school defines Nature in particular ways which can be explored using ontology and philosophical insight. Our theoretical investigation aims to accommodate Nature in community financial deliberations. A positive role (...) for government is advocated to finance environmental infrastructure initiatives. For example, precautionary strategies to address climate change must be funded. New roles for finance and government are proposed to align human relationships with Nature. Environmental precautionary principles must be developed in conjunction with finance theory to maintain decent standards of living for all. Reliance on impersonal market forces will not be enough to save the planet given the power of some over the many in the neoliberal arena. (shrink)

Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results: (...) We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation. (shrink)

One of the fundamental and seemingly simple aims of mathematical knowledge management (MKM) is to develop and standardize formats that allow to “represent the meaning of the objects of mathematics”. The open formats OpenMath and MathML address this, but differ subtly in syntax, rigor, and structural viewpoints (notably over calculus). To avoid fragmentation and smooth out interoperability obstacles, effort is under way to align them into a joint format OpenMath/MathML 3. We illustrate the issues that come up in such an (...) alignment by looking at three main areas: bound variables and conditions, calculus (which relates to the previous) and “lifted” n-ary operators. (shrink)

The epistemic form of structural realism asserts that our knowledge of the world is restricted to its structural features. Several proponents of this view assume that the world possesses non-structural features; features which, according to their view, cannot be known. In other words, they assume that there is, or, there ought to be (on the basis of normative arguments in epistemology), always a gap between our epistemological and ontological commitments. The ontic form of structural realism denies that this is, or (...) ought to be, the case. Proponents of this view argue that the perfect alignment of epistemological and ontological commitments is a highly desirable metatheoretical feature. They argue this on the basis of the prima facie sensible principle that our ontological commitments ought never to overreach our epistemic ones. Naturally the issue of alignment transcends the debate between the epistemic and the ontic structural realists. Is it in principle impossible for there to be circumstances under which we ought to subscribe to the misalignment of epistemological and ontological commitments? What do the different answers to this question entail for ontic structural realism? (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and (...) challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

This paper describes the role of information architecture in the design of socially sustainable pervasive information spaces. The framing of information architecture as an essential part of Design Thinking extends current and historic notions of the field of information architecture. The discussion introduces the notion of the ‘contrived ontology’ which can be understood as the intentional meaning that design infuses in its artefacts, services and systems. Further, we argue that contrived ontology aligns with central themes within humanistic frameworks (...) which view reality as subjective construct. This forms the central theoretical meditation herein: we contend that while design is always an act of interpreted cultural determination, at the scale of Floridi’s infosphere, the immediacy and immersive social reality of technology will become frictionless within our human experience. As this occurs, there is a moral and ethical imperative to ensure social sustainability and to this end that the meanings and intentions that inform the mature design of our human-made world are visible and accountable. It is towards this end that information architecture can make a valuable contribution. (shrink)

Ontologies have been successfully used to assign semantics in the Semantic Web context, to support integration of data from different systems or different sources, and to enable reasoning. However, building ontologies is not a trivial task. Ontology reuse can help in this matter. The search and selection of ontologies to be reused should consider the alignment between their scope and the scope of the ontology being developed. In this paper, we discuss how goal modeling can be helpful (...) in this context and we present GO-FOR, a framework in which goals are the central elements to promote ontology reuse. GO-FOR comprises a conceptual architecture, a goal-oriented ontology development process and a supporting tool. In GO-FOR we introduce Goal-Oriented Ontology Patterns as a new type of pattern to be applied to develop ontologies in a goal-oriented approach. Results of the use of GO-FOR to build an ontology used to integrate patient examination data are also shown in this paper. (shrink)

Despite thinking that an appropriately nonanthropocentric approach to the more-than-human world requires understanding phenomena to be ontologically basic, Karen Barad engages with phenomenology only fleetingly. Here, I suggest that Barad ought to take Maurice Merleau-Ponty’s phenomenology more seriously for two reasons. First, Barad’s objections to his prospects for a suitably nonanthropocentric phenomenology rely upon a misdirected charge of representationalism. Second, Merleau-Ponty offers theoretical and methodological tools corrective to our tendencies toward metaphysical and behavioral colonialism which align with Barad’s project, yet, (...) insofar as her agential realism remains committed to a very strong metaphysical naturalism, appear unavailable to her. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

This paper revisits the scope of Catherine Malabou’s thinking as a development of the ontological turn in continental philosophy. It puts this excursion of thinking alongside an account of education in modernity as the apotheosis of biopower. It aligns biopower, as manifest in education, as form of ‘technological enframing’. In this it challenges the dominant assumption that education is somehow, ultimately, independently of its manifest form, a force for good. Foregoing the idealist addiction to education as redemption, then, it sees (...) Malabou’s contribution as significant in terms of a fundamental, ontological rethinking of education and the social politics of our time. It is argued that Malabou’s contribution offers a significant contribution to rethinking education as biopower and clearing away the dominant, redemptive myths of modern and contemporary ontotheology. This is a position never entertained in the field of philosophy of education. (shrink)

Abstractabstract:Christianity is a religion with deep utopian undercurrents that find their articulation in narratives about a utopian past, a dystopian present and a utopian future. The natural world is also part of this utopian trend, most prominently in the form of the lost Garden of Eden. While both Western and Eastern Orthodox Christianity recognize nature as part of this past utopia, their views regarding its role in the dystopian present, the future utopian condition as well as the path toward it, (...) significantly differ, leading to quite different responses to the current ecological crisis. For Western Christianity, ecological questions are a matter of ethics, while for the Eastern Orthodox they are an ontological issue. Utilizing Bloch's ideas about "educated hope" and the distinction between abstract and concrete utopias, the article discusses these different positions and their possibility to change believers' attitudes toward nature and align their behavior with that of environmentalism and ecology. (shrink)

In developing the concept of assemblages, Gilles Deleuze draws at least some inspiration from Gilbert Simondon’s concept of information. While his acknowledgement of Simondon’s influence is almost entirely positive, Deleuze explicitly distances himself from the concept of information in order to avoid its link to the field of cybernetics. However, a Deleuzian informational ontology could instead be leveraged as an alternative to cybernetics. Drawing on the Spinozan link between the work of Deleuze and Simondon, it is possible to develop (...) a hybrid informational ontology. This system can not only offer a different approach to information, data and technology than the essentialist concept of information embraced by cybernetics, but also aligns well with recent research in the biological sciences that has disrupted a long-held concept of individuals as entirely separate and autonomous. Shifting away from the Platonic Form to a Deleuzian/simondonian in-formation furthers the post-human project aimed at understanding processes of subjectivation at multiple scales, including the micro and macro. (shrink)

This paper addresses questions of universality related to ontological engineering, namely aims at substantiating (negative) answers to the following three basic questions: (i) Is there a ‘universal ontology’?, (ii) Is there a ‘universal formal ontology language’?, and (iii) Is there a universally applicable ‘mode of reasoning’ for formal ontologies? To support our answers in a principled way, we present a general framework for the design of formal ontologies resting on two main principles: firstly, we endorse Rudolf Carnap’s principle (...) of logical tolerance by giving central stage to the concept of logical heterogeneity, i.e. the use of a plurality of logical languages within one ontology design. Secondly, to structure and combine heterogeneous ontologies in a semantically well-founded way, we base our work on abstract model theory in the form of institutional semantics, as forcefully put forward by Joseph Goguen and Rod Burstall. In particular, we employ the structuring mechanisms of the heterogeneous algebraic specification language HetCasl for defining a general concept of heterogeneous, distributed, highly modular and structured ontologies, called hyperontologies. Moreover, we distinguish, on a structural and semantic level, several different kinds of combining and aligning heterogeneous ontologies, namely integration, connection, and refinement. We show how the notion of heterogeneous refinement can be used to provide both a general notion of sub-ontology as well as a notion of heterogeneous equivalence of ontologies, and finally sketch how different modes of reasoning over ontologies are related to these different structuring aspects. (shrink)