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The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) |
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Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed (...) |
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Referent tracking (RT) is a new paradigm, based on unique identification, for representing and keeping track of particulars. It was first introduced to support the entry and retrieval of data in electronic health records (EHRs). Its purpose is to avoid the ambiguity that arises when statements in an EHR refer to disorders or other entities on the side of the patient exclusively by means of compound descriptions utilizing general terms such as ‘pimple on nose’ or ‘small left breast tumor’. In (...) |
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In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a and part_of can support new types of auto-mated reasoning about biomedical phenomena. We here extend this approach to the transformation_of characteristic of pathologies. |
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Biomedical terminologies are focused on what is general, Electronic Health Records (EHRs) on what is particular, and it is commonly assumed that the step from the one to the other is unproblematic. We argue that this is not so, and that, if the EHR of the future is to fulfill its promise, then the foundations of both EHR architectures and biomedical terminologies need to be reconceived. We accordingly describe a new framework for the treatment of both generals and particulars in (...) |
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For corporate memory and enterprise ontology systems to be maximally useful, they must be freed from certain barriers placed around them by traditional knowledge management paradigms. This means, above all, that they must mirror more faithfully those portions of reality which are salient to the workings of the enterprise, including the changes that occur with the passage of time. The purpose of this chapter is to demonstrate how theories based on philosophical realism can contribute to this objective. We discuss how (...) |
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The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organisms reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular is often controversial. We here propose a rule-based (...) |
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Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) |
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The Foundational Model of Anatomy (FMA) is a map of the human body. Like maps of other sorts – including the map-like representations we find in familiar anatomical atlases – it is a representation of a certain portion of spatial reality as it exists at a certain (idealized) instant of time. But unlike other maps, the FMA comes in the form of a sophisticated ontology of its objectdomain, comprising some 1.5 million statements of anatomical relations among some 70,000 anatomical kinds. (...) |
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Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object. |
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The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) |
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In the domain of ontology design as well as in Knowledge Representation, modeling universals is a challenging problem.Most approaches that have addressed this problem rely on Description Logics (DLs) but many difficulties remain, due to under-constrained representation which reduces the inferences that can be drawn and further causes problems in expressiveness. In mathematical logic and program checking, type theories have proved to be appealing but, so far they have not been applied in the formalization of ontologies. To bridge this gap, (...) |
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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 (...) |
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We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) |
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The discipline of ontology has enjoyed a checkered history since 1606, with a significant expansion in recent years. We focus here on those developments in the recent history of philosophy which are most relevant to the understanding of the increased acceptance of ontology, and especially of realist ontology, as a valuable method also outside the discipline of philosophy. |
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Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) |
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Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński. |
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Roles remain nebulous entities, notwithstanding their extensive interdisciplinary research. This paper argues through a meta-ontological conceptual tool of grounding that there are three key facets of roles: a role position, a role specification, and a role potential. A foundational perspective on roles can be specified by “role choices” as to which facet of roles is primary. Role choices are illustrated with theories of roles that are built in compliance with four well-known upper ontologies: GFO, DOLCE, BFO, and UFO. The relationship (...) |
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The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data on (...) |
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Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) |
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We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within a single framework. We (...) |
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The goal of this paper is two-fold: first, to emphasize causality in disease ontology and knowledge representation, presenting a general and cursory discussion of causality and causal chains; and second, to clarify and develop the River Flow Model of Diseases (RFM). The RFM is an ontological account of disease, representing the causal structure of pathology. It applies general knowledge of causality using the concept of causal chains. The river analogy of disease is explained, formal descriptions are offered, and the RFM (...) |
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Cognitive neuroscience aims to map mental processes onto brain function, which begs the question of what “mental processes” exist and how they relate to the tasks that are used to manipulate and measure them. This topic has been addressed informally in prior work, but we propose that cumulative progress in cognitive neuroscience requires a more systematic approach to representing the mental entities that are being mapped to brain function and the tasks used to manipulate and measure mental processes. We describe (...) |
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This paper presents an enhanced ontology formalization, combining previous work in Conceptual Structure Theory and Order-Sorted Logic. Most existing ontology formalisms place greater importance on concept types, but in this paper we focus on relation types, which are in essence predicates on concept types. We formalize the notion of ‘predicate of predicates’ as meta-relation type and introduce the new hierarchy of meta-relation types as part of the ontology definition. The new notion of closure of a relation or meta-relation type is (...) |
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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 (...) |
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In a series of papers over a period of several years Barry Smith andWerner Ceusters have offered a number of cogent criticisms of historical approaches to creating, maintaining, and applying biomedical terminologies and ontologies. And they have urged the adoption of what they refer to as a “realism-based” approach. Indeed, at times they insist that the realism-based approach not only offers clear advantages and a well-founded methodological basis for ontology development and evaluation, but that such a realist perspective is in (...) |
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Knowledge-making practices in biology are being strongly affected by the availability of data on an unprecedented scale, the insistence on systemic approaches and growing reliance on bioinformatics and digital infrastructures. What role does theory play within data-intensive science, and what does that tell us about scientific theories in general? To answer these questions, I focus on Open Biomedical Ontologies, digital classification tools that have become crucial to sharing results across research contexts in the biological and biomedical sciences, and argue that (...) |
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Bio-ontologies are digital frameworks for handling biological and biomedical data. They consist of theoretical entities and relations with explicitly defined logical structures and precise definitions, whose purpose is to provide a shared language for representing information to be distributed and integrated across diverse scientific contexts. It is tempting to view bio-ontologies as clear and formal expressions of a scientific community’s ontological commitments about their domain of inquiry, and to view their integration as tantamount to the metaphysical unification of science that (...) |
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Many types of part-whole relations have been proposed in the literature to aid the conceptual modeller to choose the most appropriate type, but many of those relations lack a formal specification to give clear and unambiguous semantics to them. To remedy this, a formal taxonomy of types of mereological and meronymic part-whole relations is presented that distinguishes between transitive and intransitive relations and the kind of entity types that are related. The demand to use it effectively brings afore new requirements (...) |
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We defend the fundamental ontological-pragmatic principle that where there are continua in reality science is often forced to make partly fiat terminological delimitations. In particular, this principle applies when it comes to describing biological organisms, their parts, properties, and relations. Human-made fiat delimitations are indispensable at the level of both individuals and the natural kinds which they instantiate. The kinds of pragmatically based ‘fiatness’ that we describe can create incompatibilities and lack of interoperability even between properly designed ontologies, if not (...) |
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Statements about the behavior of biochemical entities (e.g., about the interaction between two proteins) abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that have to be taken into account in the practice of biomedical ontology engineering: Such statements can not only be understood as event reporting statements, but also as ascriptions of (...) |
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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 (...) |
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Reuse of elements from existing ontologies in the construction of new ontologies is a foundational principle in ontological design. It offers the benefits, among others, of consistency and interoperability between such knowledge structures as well as sharing resources. Reuse is widely found within important collections of established ontologies, such as BioPortal and the OBO Foundry. However, reuse comes with its own potential problems involving ontological commitment, granularity, and ambiguity. Guidelines are proposed to aid ontology developers and curators in their prospective (...) |
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We describe an ontology of philosophy that is designed to aid navigation through philosophical literature, including literature in the form of encyclopedia articles and textbooks and in both printed and digital forms. The ontology is designed also to serve integration and structuring of data pertaining to the philosophical literature, and in the long term also to support reasoning about the provenance and contents of such literature, by providing a representation of the philosophical domain that is oriented around what philosophical literature (...) |
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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 (...) |
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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 (...) |
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The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) |
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