The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. (...) L&C’s LinKBase® is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

The distinction between reference ontologies and application ontologies crept rather unobtrusively into the recent literature on knowledge engineering. A lot of the discourse surrounding this distinction – notably, the one framing the workshop generating this collection of papers – suggests the two types of ontologies are in some sort of opposition to one another. Thus, Borge et al. [3] characterize reference ontologies (more recently, foundational ontologies) as rich, axiomatic theories whose focus is to clarify the intended meanings of terms (...) used in specific domains. Application ontologies, by contrast, provide a minimal terminological structure to fit the needs of a specific community. Reflecting their minimal nature, Masolo et al. [7] refer to such ontologies as “lightweight” ontologies. An application ontology can be lightweight in a second respect as well, namely, that it may not necessarily take the form of fully-fledged axiomatic theory. Rather, it might only be a taxonomy of the relevant domain, a division of the domain into a salient collection of classes, perhaps ordered by the subclass relation. Importantly, though, for an application ontology to “fit the needs of a specific community” needn’t require representational accuracy. In the “worst” case (from a reference ontology perspective), to fit the needs of a community is just to represent uncritically what people in that community think about the ontology’s domain. (shrink)

Contains the following contributions: -/- Ingvar Johansson: Ontologies and Concepts. Two Proposals -/- Christopher Menzel: Reference Ontologies - Application Ontologies: Either/Or or Both/And? -/- Luc Schneider: Foundational Ontologies and the Realist Bias -/- Guenther Goerz, Kerstin Buecher, Bernd Ludwig, Frank-Peter Schweinberger, and Iman Thabet: Combining a Lexical Taxonomy with Domain Ontology in the Erlangen Dialogue System -/- Vim Vandenberghe, Burkhard Schafer, John Kingston: Ontology Modelling in the Legal Domain - Realism Without Revisionism -/- A Proposed Methodology for (...) the Development of Application-Based Formal Ontologies Eric Little . (shrink)

We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We conclude (...) with a description of how the body fluids ontology initiative may provide support to basic and translational science. (shrink)

Suppose we are asked to draw up a list of things we take to exist. Certain items seem unproblematic choices, while others (such as God) are likely to spark controversy. The book sets the grand theological theme aside and asks a less dramatic question: should mathematical objects (numbers, sets, functions, etc.) be on this list? In philosophical jargon this is the ‘ontological’ question for mathematics; it asks whether we ought to include mathematicalia in our ontology. The goal of this (...) work is to answer this question in the affirmative, by drawing on considerations on the the applicability of mathematics to natural science. (shrink)

In a number of recent publications Thomasson has defended a deflationary approach to ontological disputes, according to which ontological disputes are relatively easy to settle, by either conceptual analysis, or conceptual analysis in conjunction with empirical investigation. Thomasson’s “easy” approach to ontology is intended to derail many prominent ontological disputes. In this paper I present an objection to Thomasson’s approach to ontology. Thomasson’s approach to existence assertions means that she is committed to the view that application conditions (...) associated with any term “K” with non-trivial application conditions must refer to the existence of things other than Ks. Given other components of her meta-ontological scheme, this leads to either an infinite regress or circularity of application conditions, both of which seem objectionable. Accordingly, some part of Thomasson’s meta-ontological scheme should be modified or abandoned. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the (...) class='Hi'>application of the ontology within the ACGT project thus far. (shrink)

This article introduces a novel theoretical framework for addressing epistemic injustice—a phenomenon where certain groups or individuals are systematically excluded from knowledge creation and dissemination processes—by employing ontological relativity and conceptual analysis. “Ontological relativity” refers to a philosophical perspective that posits our understanding of reality as being shaped by our toolbox of concepts, categories, language, and social practices; “conceptual analysis” is a method of inquiry that involves the rigorous examination and deconstruction of a particular concept or set of concepts in (...) order to uncover their constituent elements, relationships, and underlying assumptions. To exemplify the effectiveness of the ontology‐based approach, two paradigmatic applications are explored: (a) educational practices and (b) clinical practice and access to health care. Through the presentation of these applications and the step‐by‐step illustration of the applied methodology, the aim of the article is to showcase the efficacy of ontology in tackling epistemic injustices, suggesting innovative paths for future research in this domain. (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)

Legal codes, such as the Uniform Commercial Code (UCC) examined in this article, are good points of entry for AI and ontology work because of their more straightforward adaptability to relationship linking and rules-based encoding. However, approaches relying on encoding solely on formal code structure are incomplete, missing the rich experience of practitioner expertise that identifies key relationships and decision criteria often supplied by experienced practitioners and process experts from various disciplines (e.g., sociology, political economics, logistics, operations research). This (...) research focuses on the UCC because it transcends the limitations of a formal code, functioning essentially as a composite. AI work can benefit from real-world codes like the UCC, which are essentially formal codes enlightened from a more realistic experience-base from centuries of development in international commercial transactions settings. This paper then describes our initial work in converting an expert system on the U.S. law governing the sale of goods from Article II of the Uniform Commercial Code (UCC), into a knowledge-based system using the Web Ontology Language OWL. (shrink)

The volume offers an overview of current research in ontology, distinguishing basic conceptual issues, domain applications, general frameworks, and mathematical ...

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its (...) clinical presentation including signs and symptoms. (shrink)

Speaking with understanding and force, Tillich offers a basic analysis of love, power, justice, and all concepts fundamental in the mutual relations of people, of social groups, and of humankind to God. His concern is to penetrate to the essential, or ontological foundation of the meaning of each of these words.

I wish to advance a certain program for doing metaphysics, a program in which cognitive science would play an important role.1 This proposed ingredient is absent from most contemporary metaphysics. There are one or two local parts of metaphysics where a role for cognitive science is commonly accepted, but I advocate a wider range of application. I begin by laying out the general program and its rationale, with selected illustrations. Then I explore in some detail a single application: (...) the ontology of events. I do not push hard for any particular ontological conclusion, about either events or any other topic. The focus is methodology, not a particular output of the methodology. Here is a recently published characterization of the metaphysical enterprise, one that probably captures orthodox practice pretty well and to which I take no exception. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, (...) Challenge 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (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)

The application of ontology has thus far [in 1998] been confined almost exclusively to the field of knowledge representation. Ontology has been applied, for example, in the design of medical databases and in the construction of geographical information systems. One area which is naturally suited to ontological analysis is that of the law and of social institutions in general. -/- Legal systems are composed of legal entities, such as laws, contracts, obligations, and rights. Their application yields (...) new categories of entities such as: corporations, trademarks, marriages, and parcels of real estate. The categorization of these entities by different legal systems has not, by-and-large, been conducted in ways which exploit the tools of modern ontology. Consequently, contradictions and inconsistencies often arise in the law when, for instance, one type of entity is forced into two mutually exclusive categories (e.g., when software is considered both patentable and copyrightable). Papers are invited which consider these and related issues from a philosophical point of view. (shrink)

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

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is (...) linked to multiple clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

A scientific theory is successful, according to Stanford (2000), because it is suficiently observationally similar to its corresponding true theory. The Ptolemaic theory, for example, is successful because it is sufficiently similar to the Copernican theory at the observational level. The suggestion meets the scientific realists' request to explain the success of science without committing to the (approximate) truth of successful scientific theories. I argue that Stanford's proposal has a conceptual flaw. A conceptually sound explanation, I claim, respects the ontological (...) order between properties. A dependent property is to be explained in terms of its underlying property, not the other way around. The applicability of this point goes well beyond the realm of the debate between scientific realists and antirealists. Any philosophers should keep the point in mind when they attempt to give an explanation of a property in their field whatever it may be. (shrink)

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

The labor market is an area with diverse data structures and multiple applications, such as matching job seekers with the right training or job. For this reason, the multilingual classification of European Skills, Competences, Qualifications and Occupations (ESCO) is a good example of the central role of ontologies in this area. However, ESCO cannot provide all the details of local labor market needs and does not provide links to other hierarchies of competences. For example, other taxonomies of occupations and skills (...) are widely used in German-speaking countries, but they are not in a state where they are easily accessible for interoperability and reasoning. In this paper, we present a first version of a German Labor Market Ontology (GLMO) that uses ESCO as a top-level ontology for the target domain. This makes it highly interoperable and comparable to existing ontologies by providing details for the regional structures in German-speaking countries. In addition, we present a detailed evaluation of the provided data and applications, as well as an extensive discussion of future work. (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)

The objective of this research programme is to contribute to the establishment of the emerging science of Formal Ontology in Information Systems via a collaborative project involving researchers from a range of disciplines including philosophy, logic, computer science, linguistics, and the medical sciences. The re­searchers will work together on the construction of a unified formal ontology, which means: a general framework for the construction of ontological theories in specific domains. The framework will be constructed using the axiomatic-deductive method (...) of modern formal ontology. It will be tested via a series of applications relating to on-going work in Leipzig on medical taxonomies and data dictionaries in the context of clinical trials. This will lead to the production of a domain-specific ontology which is designed to serve as a basis for applications in the medical field. (shrink)

'Ontological dependence' is a term of philosophical jargon which stands for a rich family of properties and relations, often taken to be among the most fundamental ontological properties and relations. Notions of ontological dependence are usually thought of as 'carving reality at its ontological joints', and as marking certain forms of ontological 'non-self-sufficiency'. The use of notions of dependence goes back as far as Aristotle's characterization of substances, and these notions are still widely used to characterize other concepts and to (...) formulate metaphysical claims. This paper first gives an overview of the varieties of these notions, and then discusses some of their main applications. (shrink)

In the last decades ontology has been successfully developed in many directions and has fostered various approaches for depicting the contemporary ontological landscapes. An important task is to outline recent thought on the conceptual interfaces between science and philosophy. The present volume opens up a view onto the plurality of different ontological schemes. The papers collected here discuss the interfaces between ontology and empirical research that are created by the notions of a whole, a thought, a number, a (...) quality, an ability, a kind, notions of causation, dynamicity, and social objects, the application of relevant logical tools for the reconsideration of ontological paradigms, as well as the investigation of the consequences in cognitive sciences on the development of ontology. (shrink)

This book explores two questions that are integral to the question of the existence of God. The first question concerns the meaning of "existence" and the second concerns the meaning of "God". Regarding the first question, this book motivates, presents and defends the meta-ontology found in Gottlob Frege's writings and defended by Michael Dummett, Crispin Wright and Bob Hale. Frege's approach to questions of existence has mainly found use in connection with abstract objects such as numbers. This is one (...) of the first studies to systematically present Fregean meta-ontology and apply it to theology. Frege's meta-ontology is informed by his context principle. According to this, logico-syntactic notions such as "singular term" and "predicate" are pivotal to questions of what exists. These notions serve to throw light on the second question. Through thorough engagement with Old as well and New Testament texts, the book shows how Frege's logico-syntactic notions are of crucial importance when seeking to understand the meaning and use of "God". To complete the defence of Fregean meta-ontology, the book concludes by pointing to important differences between the otherwise closely associated concepts of an object found in Wittgenstein's Tractatus Logico-Philosophicus and Frege's writings. (shrink)

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those (...) who created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

As conceived by analytic philosophers ontology consists in the application of the methods of mathematical logic to the analysis of ontological discourse. As conceived by realist philosophers such as Meinong and the early Husserl, Reinach and Ingarden, it consists in the investigation of the forms of entities of various types. The suggestion is that formal methods be employed by phenomenological ontologists, and that phenomenological insights may contribute to the construction of adequate formal-ontological languages. The paper sketches an account (...) of what might be involved in this new discipline, an account which is illustrated in application to the formal-ontological problems raised by negative states of affairs. (shrink)