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 to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and (...) developmental stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute (...) class='Hi'>Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

ABSTRACT: In its strongest unqualified form, the principle of wholistic reference is that in any given discourse, each proposition refers to the whole universe of that discourse, regardless of how limited the referents of its non-logical or content terms. According to this principle every proposition of number theory, even an equation such as "5 + 7 = 12", refers not only to the individual numbers that it happens to mention but to the whole universe of numbers. This principle, its (...) history, and its relevance to some of Oswaldo Chateaubriand's work are discussed in my 2004 paper "The Principle of Wholistic Reference" in Essays on Chateaubriand's "Logical Forms". In Chateaubriand's réplica (reply), which is printed with my paper, he raised several important additional issues including the three I focus on in this tréplica (reply to his reply): truth-values, universes of discourse, and formal ontology. This paper is self-contained: it is not necessary to have read the above-mentioned works. The principle of wholistic reference (PWR) was first put forth by George Boole in 1847 when he espoused a monistic fixed-universe viewpoint similar to the one Frege and Russell espoused throughout their careers. Later, Boole elaborated PWR in 1854 from the pluralistic multiple-universes perspective. (shrink)

Eli Hirsch argues that certain ontological disputes involve a conflict between “equivalent” languages, and that the principle of charity compels each disputant to interpret the other as speaking truly in their own language. For Hirsch, a language’s semantics maps sentences (in context) onto sets of possible worlds but assigns no role to reference. I argue that this method leads to an overly uncharitable portrayal of the disputes at issue – whereby ontologists who speak “equivalent” languages can only argue about (...) syntax. Lack of charity stems from the fact that this portrayal likely fails to uphold the self-conception of the disputants – and particularly what I will call “the weak self-conception”. As a result, Hirsch’s deflationism falls victim of the same principle of charity that informs it. (shrink)

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

Abstract: We propose a dichotomy between object-entities and meaning-entities. The former are entities such as molecules, cells, organisms, organizations, numbers, shapes, and so forth. The latter are entities such as concepts, propositions, and theories belonging to the realm of logic. Frege distinguished analogously between a ‘realm of reference’ and a ‘realm of sense’, which he presented in some passages as mutually exclusive. This however contradicts his assumption elsewhere that every entity is a referent (even Fregean senses can be referred (...) to by means of suitably constructed expressions). We apply the meaning/object dichotomy to mathematical and fictional entities, and develop a view of mathematical and other abstract objects as the results of certain types of demarcation – as for example the North Sea is the result of demarcations built into naval charts. Such demarcations reflect demarcatory acts, which presuppose complex cognitive and social structures enabling the creation of maps, of theories (of mathematics, of natural science), and of novels. (shrink)

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

The present article arises from the reflection on the failure of external educational models applied in emerging contexts without considering contextual factors of each town. According to Carnoy (1974) there is a strong tradition between underdeveloped countries of coping the cultural forms and successful models from first world societies, without having prepared beforehand the objective and subjective conditions that would determine its success or failure. The aim of this paper is to analyze the philosophical basis of success behind the Finnish (...) educational system, with the purpose of identify in it, references to overcome problems of educational reality in emerging societies. In this way contribute to the discussion about the failure on adapting external educational models to emerging contexts. It is an exploratory, descriptive and comparative review, and the character of it is bibliographic and qualitative; in addition, it will make use of logical-scientific methods (deductive-inductive) with their respective procedures, supported by phenomenological and hermeneutical philosophical methods. The results of the copy and implementation of changes in education based on successful models from other latitudes, without considering the philosophical and epistemological substratum that sustains it, or preparing the ground for its adaptation, has resulted in poor educational systems that do not respond to the concrete needs of the educational reality of emerging societies, and limit and frustrate the autonomous and original creation of contextualized and relevant educational models too. (shrink)

According to the propositional view of belief, a belief situation involves a believer’s standing in the relation of belief to a proposition. It is argued that the propositional view has unacceptable implications concerning the identity conditions of belief situations involving beliefs with indexical contents, especially where such beliefs are held over a period of time during which background circumstances change. After a critical discussion of Perry’s alternative to the propositional view, a version of the adverbial theory of belief, which accounts (...) satisfactorily for the identity conditions of belief situations, is advanced. This theory, which avoids the standard objections to adverbialism, is defended against the charge that it cannot provide an account of the semantics of sentences attributing the same belief to two or more believers. In the course of this defense it is argued that the standard propositional account of such sentences is insensitive to everyday language. (shrink)

Analytic philosophers apply the term ‘object’ both to concreta and to abstracta of certain kinds. The theory of objects which this implies is shown to rest on a dichotomy between object-entities on the one hand and meaning-entities on the other, and it is suggested that the most adequate account of the latter is provided by Husserl’s theory of noemata. A two-story ontology of objects and meanings (concepts, classes) is defended, and Löwenheim’s work on class-representatives is cited as an indication (...) of how the need for higher types may be obviated, even in mathematical contexts. The paper concludes with a sketch of the taxonomy of the object realm which results from the above. (shrink)

In order to re-contextualize the otherwise ontologically privileged meaning of metaphysical debates into a more insubstantial form, metaphysical deflationism runs the risk of having to adopt potentially unwanted anti-realist tendencies. This tension between deflationism and anti-realism can be expressed as follows: in order to claim truthfully that something exists, how can deflationism avoid the anti-realist feature of construing such claims singularly in an analytical fashion? One may choose to adopt a Yablovian fallibilism about existential claims, but other approaches can be (...) appealed to as well. Amie Thomasson's Easy Ontology is one such approach, whereby the interaction of empirical as well as analytic features within the construction of its ontological theory affords a role for analytical rules without forsaking a link with empirical reality. The development of these analytical and empirical features has resulted in significant critiques regarding, one, potential reference failure of easy-ontological claims, and two, a circularity in how easy ontology explains the relation between its analytical rules and existential claims. This essay offers a response by showcasing how an easy ontological deflationism can reject these criticisms without succumbing to, one, the anti-realism of pure analyticism, and two, a further critique of wholesale referential indeterminacy in its referring terms. (shrink)

Enterprise Risk Management involves the process of identification, evaluation, treatment, and communication regarding risks throughout the enterprise. To support the tasks associated with this process, several frameworks and modeling languages have been proposed, such as the Risk and Security Overlay (RSO) of ArchiMate. An ontological investigation of this artifact would reveal its adequacy, capabilities, and limitations w.r.t. the domain of risk and security. Based on that, a language redesign can be proposed as a refinement. Such analysis and redesign have been (...) executed for the risk elements of the RSO grounded in the Common Ontology of Value and Risk. The next step along this line of research is to address the following research problems: What would be the outcome of an ontological analysis of security-related elements of the RSO? That is, can we identify other semantic deficiencies in the RSO through an ontological analysis? Once such an analysis is provided, can we redesign the security elements of the RSO accordingly, in order to produce an improved artifact? Here, with the aid of the Reference Ontology for Security Engineering (ROSE) and the ontological theory of prevention behind it, we address the remaining gap by proceeding with an ontological analysis of the security-related constructs of the RSO. The outcome of this assessment is an ontology-based redesign of the ArchiMate language regarding security modeling. In a nutshell, we report the following contributions: (1) an ontological analysis of the RSO that identifies six limitations concerning security modeling; (2) because of the key role of the notion of prevention in security modeling, the introduction of the ontological theory of prevention in ArchiMate; (3) a well-founded redesign of security elements of ArchiMate; and (4) ontology-based security modeling patterns that are logical consequences of our proposal of redesign due to its underlying ontology of security. As a form of evaluation, we show that our proposal can describe risk treatment options, according to ISO 31000. Finally, besides presenting multiple examples, we proceed with a real-world illustrative application taken from the cybersecurity domain. (shrink)

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two (...) terminological traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

I analyze Deleuze’s concept of temporality in terms of its ontology and axiological (political and aesthetic) aspects. For Deleuze, the concept of temporality is non-monolithic, in the senses that it is modified throughout his works — the monographs, lectures, and those works that were co-authored with Félix Guattari — and that it is developed through reference to a dizzying array of concepts, thinkers, artistic works, and social phenomena. -/- I observe that Deleuze’s concept of temporality involves a complex (...) ontology of difference, which I elaborate through reference to Deleuze’s analyses of Ancient Greek and Stoic conceptualizations of time. From Plato through to Chrysippus, temporality gradually comes to be identified as a form that comprehends the variation of particulars. Deleuze modifies the ancients’ concept of time to suggest that time obtains as a form of ceaseless ontological variation. Through reference to Deleuze’s reading of Gilbert Simondon, I further suggest that Deleuze tends to conceive of temporality as an ontogenetic force which participates in the complex process of individuation. -/- A standout feature of this dissertation involves an analysis of how Deleuze’s concept of temporality is modified in his works on cinema. In Cinema 1: The Movement-Image and Cinema 2: The Time-Image, temporality comes to be characterized as something other than the measure of the movement of existents. In his detailed analyses of Bergson — in Cinema 1: The Movement-Image, Cinema 2: The Time-Image, and Bergsonism — Deleuze suggests that time involves an actualization of aspects of a virtual past as contemporaneous with the lived present. While not an outright denial of the relation of temporal succession, Deleuze’s claim implies a diminishment of this relation’s significance in an adequate elaboration of the nature of temporality. -/- Further, I observe —through reference to Deleuze’s readings of Marx, Kierkegaard, and Spinoza — that (the explicitly temporal) change of societal forms of economic organization is non-reducible to that suggested by linear evolution. The claim is that putatively discrete modes of economic organization do not enjoy temporal displacement with respect to one another. This suggests that linear evolutionary models of societal development are inadequate. This further implies that temporality is non-reducible to the relation of temporal succession. In concrete terms, societal change is characterized as immanent temporal variation. -/- Taken together, these analyses yield the conclusion that Deleuze tends to conceive of the nature of temporality as involving the ongoing realization of multiple — non-identical, sometimes contrary — aspects of a stochastic process of creation that is expressed in ontogenetic circumstances, social evolution, literary works, and filmic works. (shrink)

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

The 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)

Enterprise Risk Management and security have become a fundamental part of Enterprise Architecture, so several frameworks and modeling languages have been designed to support the activities associated with these areas. Archi- Mate’s Risk and Security Overlay is one of such proposals, endorsed by The Open Group. We investigate the capabilities of the proposed security-related con- structs in ArchiMate with regard to the necessities of enterprise security modeling. Our analysis relies on a well-founded reference ontology of security to uncover (...) ambiguity, missing modeling elements, and other deficiencies of the security mod- eling capabilities in ArchiMate. Based on this ontologically-founded analysis, we propose a redesign of security aspects of ArchiMate to overcome its original limitations. (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)

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

Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task remains of ensuring that the right sorts of information reach the right sorts of people. In what follows we defend the thesis that efforts to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations, and that the communication of healthcare information and knowledge needs to rest (...) on a sound ontology of social interaction. We illustrate this thesis in relation to the HL7 RIM, which is one centrally important tool for communication in the healthcare domain. (shrink)

In this paper, I argue that sentences that contain ‘omission’ tokens that appear to function as singular terms are meaningful while maintaining the view that omissions are nothing at all or mere absences. I take omissions to be fictional entities and claim that the way in which sentences about fictional characters are true parallels the way in which sentences about omissions are true. I develop a pragmatic account of fictional reference and argue that my fictionalist account of omissions implies (...) a plausible account of the metaphysics of omissions. (shrink)

The Joint Battle Management Language (JBML) is an XML-based language designed to allow Command and Control (C2) systems to interface easily with Modeling and Simulation (M&S) systems. While some of the XML-tags defined in this language correspond to types of entities that exist in reality, others are mere syntactic artifacts used to structure the messages themselves. Because these two kinds of tags are not formally distinguishable, JBML messages in effect confuse data with what the data represent. In this paper we (...) show how a realism-based ontology combined with a rule language can be used to make these distinctions explicit. The approach allows storage of the contents of JBML messages in a Referent Tracking System in a format that mimics the structure of reality thereby providing an aid to message validation. (shrink)

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 (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

This text is a presentation of the notion of ontological imagination. It constitutes an attempt to merge two traditions: critical sociology and science and technology studies - STS. By contrasting these two intellectual traditions, I attempt to bring together: a humanist ethical-political sensitivity and a posthumanist ontological insight. My starting point is the premise that contemporary world needs new social ontology and new critical theory based on it in order to overcome the unconsciously adapted, “slice-based” modernist vision of social (...) ontology. I am convinced that we need new ontological frameworks of the social combined with a research disposition which I refer to as ontological imagination. (shrink)

The term ‘intelligence’ as used in this paper refers to items of knowledge collected for the sake of assessing and maintaining national security. The intelligence community (IC) of the United States (US) is a community of organizations that collaborate in collecting and processing intelligence for the US. The IC relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a maximally comprehensive understanding of world actors (...) and their behaviors can be developed and updated. Herein we describe an approach to utilizing outcomes-based learning (OBL) to support these efforts that is based on an ontology of the cognitive processes performed by intelligence analysts. Of particular importance to the Cognitive Process Ontology is the class Representation that is Warranted. Such a representation is descriptive in nature and deserving of trust in its veridicality. The latter is because a Representation that is Warranted is always produced by a process that was vetted (or successfully designed) to reliably produce veridical representations. As such, Representations that are Warranted are what in other contexts we might refer to as ‘items of knowledge’. (shrink)

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

In Risk Management, security issues arise from complex relations among objects and agents, their capabilities and vulnerabilities, the events they are involved in, and the value and risk they ensue to the stakeholders at hand. Further, there are patterns involving these relations that crosscut many domains, ranging from information security to public safety. Understanding and forming a shared conceptualization and vocabulary about these notions and their relations is fundamental for modeling the corresponding scenarios, so that proper security countermeasures can be (...) devised. Ontologies are instruments developed to address these conceptual clarification and terminological systematization issues. Over the years, several ontologies have been proposed in Risk Management and Security Engineering. However, as shown in recent literature, they fall short in many respects, including generality and expressivity - the latter impacting on their interoperability with related models. We propose a Reference Ontology for Security Engineering (ROSE) from a Risk Treatment perspective. Our proposal leverages on two existing Reference Ontologies: the Common Ontology of Value and Risk and a Reference Ontology of Prevention, both of which are grounded on the Unified Foundational Ontology (UFO). ROSE is employed for modeling and analysing some cases, in particular providing clarification to the semantically overloaded notion of Security Mechanism. (shrink)

As available intelligence data and information expand in both quantity and variety, new techniques must be deployed for search and analytics. One technique involves the semantic enhancement of data through the creation of what are called ‘ontologies’ or ‘controlled vocabularies.’ When multiple different bodies of heterogeneous data are tagged by means of terms from common ontologies, then these data become linked together in ways which allow more effective retrieval and integration. We describe a simple case study to show how these (...) benefits are being achieved, and we describe our strategy for developing a suite of ontologies to serve the needs of the war-fighter in the ever more complex battlespace environments of the future. (shrink)

A common view is that natural language treats numbers as abstract objects, with expressions like the number of planets, eight, as well as the number eight acting as referential terms referring to numbers. In this paper I will argue that this view about reference to numbers in natural language is fundamentally mistaken. A more thorough look at natural language reveals a very different view of the ontological status of natural numbers. On this view, numbers are not primarily treated abstract (...) objects, but rather 'aspects' of pluralities of ordinary objects, namely number tropes, a view that in fact appears to have been the Aristotelian view of numbers. Natural language moreover provides support for another view of the ontological status of numbers, on which natural numbers do not act as entities, but rather have the status of plural properties, the meaning of numerals when acting like adjectives. This view matches contemporary approaches in the philosophy of mathematics of what Dummett called the Adjectival Strategy, the view on which number terms in arithmetical sentences are not terms referring to numbers, but rather make contributions to generalizations about ordinary (and possible) objects. It is only with complex expressions somewhat at the periphery of language such as the number eight that reference to pure numbers is permitted. (shrink)

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

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 constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry (...) ontology that provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime (...) in which all clinically salient particulars – from the concrete disorder on the side of the patient and the body parts in which it occurs to the concrete treatments given – should be uniquely identified. This will allow us to achieve interoperability among different systems of records at the level where it really matters: in regard to what is happening in the real world. It will also allow us to keep track of particular disorders and of the effects of particular treatments in a precise and unambiguous way. We discuss the ontological and epistemological aspects of our claim and describe a scenario for implementation within EHR systems. (shrink)

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ is often used by philosophers as a synonym for ‘metaphysics’ (literally: ‘what comes after the Physics’), a term which was used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. The term ‘ontology’ (or ontologia) was itself coined in 1613, independently, by two (...) philosophers, Rudolf Göckel (Goclenius), in his Lexicon philosophicum and Jacob Lorhard (Lorhardus), in his Theatrum philosophicum. The first occurrence in English recorded by the OED appears in Bailey’s dictionary of 1721, which defines ontology as ‘an Account of being in the Abstract’. (shrink)

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 realism-based ontologies (capturing what is generic) combined with referent tracking (capturing what is specific) can play a key role in building the robust and useful corporate memories of the future. (shrink)

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

As physicalisms of various kinds have faced difficulties in recent years, the time has come to explore possible alternatives, one of which is yinyang ontology. A yinyang theorist is expected to provide a plausible account of causation to replace the traditional notion of causation. The present paper is critical of the Humean tradition, which understands the relata of causal relations in terms of passive materiality so that humans use referential terms to describe causal relations constructively. But an alternative notion (...) of reference is available according to which causal relata are active processors of the information with which they interact. On this latter view, humans use referential language to describe the structure in which the relata interrelate themselves so that the structure can be understood hermeneutically. Reference on this view is naturalized. In this article I advance two arguments for this thesis, one concerning the informationality of states and the other related to the essentiality of properties. (shrink)

In this paper, I develop a criticism to a method for metaontology, namely, the idea that a discourse’s or theory’s ontological commitments can be read off its sentences’ truth- conditions. Firstly, I will put forward this idea’s basis and, secondly, I will present the way Quine subscribed to it. However, I distinguish between two readings of Quine’s famous ontological criterion, and I center the focus on the one currently dubbed “ontological minimalism”, a kind of modern Ockhamism applied to the mentioned (...) metaontological view. I show that this view has a certain application via Quinean thesis of reference inscrutability but that it is not possible to press that application any further and, in particular, not for the ambitious metaontological task some authors try to employ. The conclusion may sound promising: having shown the impossibility of a semantic ontological criterion, intentionalist or subjectivist ones should be explored. (shrink)

The paradigm of referent tracking is based on a realist presupposition which rejects so-called negative entities (congenital absent nipple, and the like) as spurious. How, then, can a referent tracking-based Electronic Health Record deal with what are standardly called ‘negative findings’? To answer this question we carried out an analysis of some 748 sentences drawn from patient charts and containing some form of negation. Our analysis shows that to deal with these sentences we need to introduce a new ontological relationship (...) between a particular and a universal, which holds when no instance of the universal has a specific qualified ontological relation with the particular. This relation is found to be able to accommodate nearly all occurrences of negative findings in the examined sample, in ways which involve no reference to negative entities. (shrink)

Management of information is facilitated by unambiguously tracking portions of reality over time. To track the portions of reality, a referent tracking system is used. The referent tracking system is able to communicate with other tracking systems and/or tradition information systems. Errors in the referent tracking system are detected and corrected to maintain actual representations of the portions of reality.

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)

The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems (...) are used in what is called “clinical coding”. In this paper we describe the components of a referent tracking system in an informal way and we outline the procedures that would have to be followed by healthcare personnel in using such a system. We argue that the referent tracking paradigm can be introduced with only minor – though nevertheless ontologically important – technical changes to existing EHR infrastructures, but that it will require a radically different mindset on the part of those involved in clinical coding and terminology development from that which has prevailed hitherto. (shrink)

Many philosophers use “physicalism” and “naturalism” interchangeably. In this paper, I will distinguish ontological naturalism from physicalism. While broad versions of physicalism are compatible with naturalism, naturalism doesn't have to be committed to strong versions of physical reductionism, so it cannot be defined as equivalent to it. Instead of relying on the notion of ideal physics, naturalism can refer to the notion of ideal natural science that doesn't imply unity of science. The notion of ideal natural science, as well as (...) the notion of ideal physics, will be vindicated. I will shortly explicate the notion of ideal natural science, and define ontological naturalism based on it. (shrink)

This paper argues for a distinction between fictional characters, as parts of intentionally created abstract artifacts, and intentional objects, as nonexistent objects generated by referential acts that fail to refer. It argues that intentional objects as the nonexistent objects of imagination and other objectual attitudes are well-reflected in natural language, though in a highly restricted way, reflecting their ontological dependence on referential acts. The paper elaborates how that ontological dependence can be understood.

While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...) We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology and in the application of BFO in the Ontology of General Medical Science. We analyzed statements about what counts as a mental disease provided in the research agenda for the DSM-V, and in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future. (shrink)

dolce, the first top-level ontology to be axiomatized, has remained stable for twenty years and today is broadly used in a variety of domains. dolce is inspired by cognitive and linguistic considerations and aims to model a commonsense view of reality, like the one human beings exploit in everyday life in areas as diverse as socio-technical systems, manufacturing, financial transactions and cultural heritage. dolce clearly lists the ontological choices it is based upon, relies on philosophical principles, is richly formalized, (...) and is built according to well-established ontological methodologies, e.g. OntoClean. Because of these features, it has inspired most of the existing top-level ontologies and has been used to develop or improve standards and public domain resources. Being a foundational ontology, dolce is not directly concerned with domain knowledge. Its purpose is to provide the general categories and relations needed to give a coherent view of reality, to integrate domain knowledge, and to mediate across domains. In these 20 years dolce has shown that applied ontologies can be stable and that interoperability across reference and domain ontologies is a reality. This paper briefly introduces the ontology and shows how to use it on a few modeling cases. (shrink)

According to the accepted translation-failure interpretation, the problem of incommensurability involves the nature of the meaning-referential relation between scientific languages. The incommensurability thesis is that some competing scientific languages are mutually untranslatable due to the radical variance of meaning or/and reference of the terms they employ. I argue that this interpretation faces many difficulties and cannot give us a tenable, coherent, and integrated notion of incommensurability. It has to be rejected. ;On the basis of two case studies, I find (...) that the confrontations between many classical incommensurable languages are not confrontations between two untranslatable languages with different distribution of truth values, but rather the confrontations between incompatible fundamental presuppositions at the ontological level. We can always identify a truth-value gap between two incommensurable languages. Such a truth-value gap indicates a communication breakdown between the two language communities on the one hand, and is caused by the incompatible fundamental presuppositions underlying them on the other. ;I thereby identify the truth-value functional relationship between sentences, instead of the meaning-referential relationship between terms, as the dominant semantic relation between two incommensurable languages. According to my presuppositional interpretation of incommensurability, the real secret of incommensurability lies in the ontological setup of two competing presuppositional languages. When two presuppositional languages with incompatible factual commitments encounter with each other, the confrontation leads to a truth-value gap, and consequently a communication breakdown between them. Formally put, two scientific languages are incommensurable when core sentences of one language, which have truth values when considered within its own context, lack truth values when considered within the context of the other due to an ontological gap between them. ;The presuppositional interpretation makes many significant contributions to the discussion of the issue of incommensurability and the related metaphysical and epistemological issues: It confirms the existence of the phenomenon of incommensurability and makes it metaphysically and epistemologically significant. It establishes the tenability and integrity of the notion of incommensurability. It avoids many alleged unattractive epistemological and metaphysical consequences of the translation-failure interpretation. (shrink)

This paper gives a characterization of the ontology implicit in natural language and the entities it involves, situates natural language ontology within metaphysics, and responds to Chomskys' dismissal of externalist semantics.

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)