Where humans can manipulate and integrate the information they receive in subtle and ever-changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, mathematics, medicine (...) and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

We aim to provide the ontological grounds for an adequate account of persistence. We defend a perspectivalist, or moderate pluralist, position, according to which some aspects of reality can be accounted for in ontological terms only via partial and mutually complementary ontologies, each one of which captures some relevant aspect of reality. Our thesis here is that this is precisely the sort of ontological account that is needed for the understanding of persistence, specifically an account involving two independent ontologies, one (...) for continuants, and one for occurrents. (shrink)

The book’s core argument is that an artificial intelligence that could equal or exceed human intelligence—sometimes called artificial general intelligence (AGI)—is for mathematical reasons impossible. It offers two specific reasons for this claim: Human intelligence is a capability of a complex dynamic system—the human brain and central nervous system. Systems of this sort cannot be modelled mathematically in a way that allows them to operate inside a computer. In supporting their claim, the authors, Jobst Landgrebe and Barry Smith, marshal evidence (...) from mathematics, physics, computer science, philosophy, linguistics, and biology, setting up their book around three central questions: What are the essential marks of human intelligence? What is it that researchers try to do when they attempt to achieve "artificial intelligence" (AI)? And why, after more than 50 years, are our most common interactions with AI, for example with our bank’s computers, still so unsatisfactory? Landgrebe and Smith show how a widespread fear about AI’s potential to bring about radical changes in the nature of human beings and in the human social order is founded on an error. There is still, as they demonstrate in a final chapter, a great deal that AI can achieve which will benefit humanity. But these benefits will be achieved without the aid of systems that are more powerful than humans, which are as impossible as AI systems that are intrinsically "evil" or able to "will" a takeover of human society. (shrink)

Despre analogia existentă între aspectele epistemologice şi metodologice ale activităţii serviciilor de informaţii şi unele discipline ştiinţifice, pledând pentru o abordare mai ştiinţifică a procesului de culegere şi analiză de informaţii din cadrul ciclului de informaţii. Afirm că în prezent aspectele teoretice, ontologice şi epistemologice, în activitatea multor servicii de informaţii, sunt subestimate, determinând înţelegere incompletă a fenomenelor actuale şi creând confuzie în colaborarea inter-instituţională. După o scurtă Introducere, care include o istorie a evoluţiei conceptului de serviciu de informaţii după (...) al doilea război mondial, în Activitatea de informaţii definesc obiectivele şi organizarea serviciilor de informaţii, modelul de bază al acestor organizaţii (ciclul informaţional), şi aspectele relevante ale culegerii de informaţii şi analizei de informaţii. În secţiunea Ontologia evidenţiez aspectele ontologice şi entităţile care ameninţă şi sunt ameninţate. Secţiunea Epistemologie include aspecte specifice activităţii de informaţii, cu analiza principalului model (Singer) folosit în mod tradiţional, şi expun o posibilă abordare epistemologică prin prisma conceptului de cunoaştere tacită dezvoltat de omul de ştiinţă Michael Polanyi. În secţiunea Metodologii prezint diverse teorii metodologice cu accent pe tehnicile analitice structurale, şi câteva analogii, cu ştiinţa, arheologia, afacerile şi medicina. Lucrarea se încheie cu Concluziile privind posibilitatea unei abordări mai ştiinţifice a metodelor de culegere şi analiză a informaţiilor din cadrul serviciilor de informaţii. -/- Cuvinte cheie: servicii de informaţii, agenţii de informaţii, informaţii, intelligence -/- CUPRINS -/- Abstract 1. Introducere 1.1. Istorie 2. Activitatea de informaţii 2.1. Organizaţii 2.2. Ciclul informaţional 2.3. Colectarea informaţiilor 2.4. Analiza informaţiilor 2.5. Contrainformatii 2.6. Comunităţi epistemice 3. Ontologia 4. Epistemologia 4.1. Cunoaşterea tacită (Polanyi) 5. Metodologii 6. Analogii cu alte discipline 6.1. Stiinta 6.2. Arheologia 6.3. Afaceri 6.4. Medicina 7. Concluzii Bibliografie -/- ISBN: 978-606-033-160-5 , DOI: 10.58679/TW56764. (shrink)

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.

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 (...) between such three facets of roles and the GFO-based three kinds of roles (relational, processual, and social) is closely examined. These three facets are also comparatively studied from linguistic (e.g. ‘have a role’ versus ‘play a role’) and methodological (realism versus conceptualism regarding ontology design) perspectives. Furthermore, the family resemblance view of roles as “epistemic trackers” is proposed: the general notion of role is merely (partially) unified by its three facets and helps to keep track of some entity with respect to its role-related aspects. Finally, defining characteristics of roles in conceptual modeling are considered in terms of the three-facet theory. This work provides the grist for future practical development of an ontological module for generic role representation. (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds of (...) situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

According to ontological perspectivism, there can be, in principle, multiple and alternative perspectives on the world that can be sliced, systematized, and conceptualized in different ways. Surely, such an ontological position has many categorial implications, which may vary depending on different disciplinary contexts. This paper explores parts of these implications in the realm of geography. In particular, it aims at discussing the ontological categories that one might use to describe the geographical world in an overarching perspective – that is, the (...) perspective that puts toether all the partial views coming from the different branches of the geographical investigation. We will see that if the overarching perspective is expected to include all the views on the geographical world, then such a perspective should be all-embracing in terms of contents and categories. This means that the overarching perspective might also comprehend inconsistencies that derive from how the various partial perspectives conceptualize differently the geographical world. (shrink)

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

The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand four-dimensionalism.

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)

Mental health research faces a suite of unresolved challenges that have contributed to a stagnation of research efforts and treatment innovation. One such challenge is how to reliably and validly account for the subjective side of patient symptomatology, that is, the patient’s inner experiences or patient phenomenology. Providing a structured, standardised semantics for patient phenomenology would enable future research in novel directions. In this contribution, we aim at initiating a standardized approach to patient phenomenology by sketching a tentative formalisation within (...) the framework of an applied ontology, in the broader context of existing open-source Open Biomedical Ontologies resources such as the Mental Functioning Ontology. We further discuss a number of prevailing challenges and observations bearing on this task. (shrink)

The initial stage for the discussion is the distinction between bona fide and fiat objects drawn by Barry Smith and collaborators in the context of formal ontology. This paper aims at both producing a rationale for introducing a hitherto unrecognized kind of object—here called ‘Interactive Fiat Objects’ (IFOs)—into the ontology of objects, and casting light on the relationship between embodied cognition and interactive ontology with the aid of the concepts of affordance and ad hoc category. I conclude that IFOs are (...) similar to fiat objects, affordances and ad hoc categories in a number of ways, yet they differ from these in important respects. Interaction is key to understanding the existence and peculiarities of IFOs. By adopting an embodied perspective on cognition, we can enrich our ontological typologies and highlight relevant features of our physical and symbolic environment that are otherwise overlooked. This should improve our understanding of object ontology and persuade us to include IFOs in our metaphysical inventories. (shrink)

Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to maximize reasoning (...) efficiency even at the price of simplifications on the side of representation, philosophical ontologists argue that representational adequacy can bring benefits for the stability and resistance to error of an ontological framework and also for its extendibility in the future. In bioinformatics, however, a third sense of ‘ontology’ has established itself, above all as a result of the successes of the Gene Ontology (hereafter: GO), which is a tool for the representation and processing of information about gene products and their biological functions [Gene Ontology Consortium 2000]. We show how Basic Formal Ontology (BFO) has established itself as an overarching ontology drawing on all three of the strands distinguished above, and describe applications of BFO especially in the treatment of biological granularity. (shrink)

John Searle’s The Construction of Social Reality and Hernando de Soto’s The Mystery of Capital shifted the focus of current thought on capital and economic development to the cultural and conceptual ideas that underpin market economies and that are taken for granted in developed nations. This collection of essays assembles 21 philosophers, economists, and political scientists to help readers understand these exciting new theories.

We propose a new account of vagueness and approximation in terms of the theory of granular partitions. We distinguish different kinds of crisp and non-crisp granular partitions and we describe the relations between them, concentrating especially on spatial examples. We describe the practice whereby subjects use regular grid-like reference partitions as a means for tempering the vagueness of their judgments, and we demonstrate how the theory of reference partitions can yield a natural account of this practice, which is referred to (...) in the literature as ‘approximation’. (shrink)

Abstract: We propose a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this semantic view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being its extension. We provide a new formulation of these ideas in terms of a theory of granular partitions. We show that this (...) theory provides a general framework within which we can understand the relation between vague terms and concepts and the corresponding crisp portions of reality. We also sketch how it might be possible to formulate within this framework a theory of vagueness which dispenses with the notion of truth-value gaps and other artifacts of more familiar approaches. Central to our approach is the idea that judgments about reality involve in every case (1) a separation of reality into foreground and background of attention and (2) the feature of granularity. On this basis we attempt to show that even vague judgments made in naturally occurring contexts are not marked by truth-value indeterminacy. We distinguish, in addition to crisp granular partitions, also vague partitions, and reference partitions, and we explain the role of the latter in the context of judgments that involve vagueness. We conclude by showing how reference partitions provide an effective means by which judging subjects are able to temper the vagueness of their judgments by means of approximations. (shrink)

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. (...) It is further distinguished from other maps in that it represents not some specific portion of spatial reality (say: Leeds in 1996), but rather the generalized or idealized spatial reality associated with a generalized or idealized human being at some generalized or idealized instant of time. It will be our concern in what follows to outline the approach to ontology that is represented by the FMA and to argue that it can serve as the basis for a new type of anatomical information science. We also draw some implications for our understanding of spatial reasoning and spatial ontologies in general. (shrink)

An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from the (...) context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

To address the problems of both structured coordination of linked and modularised ontologies and to query a large dynamic ontology system, we propose a basic granularity framework and a set of functions to query such a granulated system. The granularity framework enforces a constrained and structured modularization. This facilitates automation of both dividing a large body of represented information as well as relinking the pieces. The functions enable basic cross-granular querying in a transparent and scalable way, as they rely on (...) the unambiguous management layer provided by the granularity framework, and are reusable for ontologies represented and stored in different formats. (shrink)

Formalisms such as description logics (DL) are sometimes expected to help terminologies ensure compliance with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) complies with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED CT classes with respect to these principles. Our major results are: 31% of (...) the classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with multiple inheritance. (shrink)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in the (...) WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (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)

The human body is a system made of systems. The body is divided into bodily systems proper, such as the endocrine and circulatory systems, which are subdivided into many sub-systems at a variety of levels, whereby all systems and subsystems engage in massive causal interaction with each other and with their surrounding environments. Here we offer an explicit definition of bodily system and provide a framework for understanding their causal interactions. Medical sciences provide at best informal accounts of basic notions (...) such as system, process, and function, and while such informality is acceptable in documentation created for human beings, it falls short of what is needed for computer representations. In our analysis we will accordingly provide the framework for a formal definition of bodily system and of associated notions. (shrink)

In this research work I take into account the relation of indistinguishability. This relation seems to be prima facie reflexive, symmetric and transitive; in short, an equivalence relation. However, there are some cases where the relation under consideration fails to be transitive. In this thesis I will discuss two of those cases: vagueness of gradabale adjectives and count nouns, and identity criteria involving perceptual phenomena. My research attempts to answer the following question: how is it possible to communicate and to (...) make meaningful judgments using vague terms and non-transitive identity criteria? This thesis presents an analysis of vagueness and identity criteria that shows that speakers always consider the elements which vague expressions refer to or whose names compose identity statements within a context and from a certain level of precision. I also attempt to provide a formal treatment of vague adjectives and count nouns on the one hand, and of identity criteria on the other. I employ two key concepts in both the treatments: context dependence and granularity. (shrink)

The addiction literature is fraught with conceptual confusions, stalled debates, and an unfortunate lack of clear and careful attempts to delineate the phenomenon of addiction in a way that might lead to consensus. My dissertation has two overarching aims, one metaphysical and one practical. -/- The first aim is to defend an account of addiction as the systematic disposition to fail to control one’s desires to engage in certain types of behaviors. I defend the inclusion of desires and impaired control (...) in the definition, and I flesh out the notion of systematicity central to my dispositionalist framework. I engage the so-called ‘disease vs. choice’ debate, criticizing its presupposition that we are dealing here with a dichotomy and arguing that the movement towards a middle ground is the right track to take. I explain how the dispositionalist account can capture this middle ground and how it serves to expand upon existing views, in particular by filling in the metaphysical details. -/- The second aim is to show how the account I defend can help to unify the extant views and disciplinary perspectives in the literature. Both the dispositionalist aspect of my framework and the methodology adopted (applied ontology and systematic metaphysics) can move the literature towards both substantive and methodological unification. This will help to clear up conceptual confusions, resolve (or sometimes dissolve) apparently intractable disputes, situate different research perspectives with respect to each other, facilitate interdisciplinary dialogue, and help to frame important questions about addiction. Finally, I offer the beginnings of an ontology of addiction, which will provide a terminologically well-structured guide to the addiction literature in a way that will facilitate more effective and efficient communication and data management across disciplines. (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)

Consider a game of blind chess between two chess masters that is recorded in some standard chess notation. The recording is a representation of the game. But what is the game itself? This question is, we believe, central to the entire domain of social ontology. We argue that the recorded game is a special sort of quasi-abstract pattern, something that is: (i) like abstract entities such as numbers or forms, in that it is both nonphysical and nonpsychological; but at the (...) same time, (ii) through its association with specific players and a specific occasion, tied to time and history. We discover other abstract patterns of this sort especially in the domains of law and commerce. This essay draws on the work in social ontology, we of Hernando de Soto and of John Searle to develop an ontology of the social world based on an analysis of the peculiar interdependence between quasi-abstract patterns and their representations in documents of different sorts. (shrink)

The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its (...) external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the interconnections (...) between them. (shrink)

The present essay is devoted to the application of ontology in support of research in the natural sciences. It defends the thesis that ontologies developed for such purposes should be understood as having as their subject matter, not concepts, but rather the universals and particulars which exist in reality and are captured in scientific laws. We outline the benefits of a view along these lines by showing how it yields rigorous formal definitions of the foundational relations used in many influential (...) ontologies, illustrating our results by reference to examples drawn from the domain of the life sciences. (shrink)

In intelligence, the ontological problem is related to the nature and characteristics of entities that threaten and are threatened. Developing a threat ontology requires a taxonomy. An ontology for threat analysis and action must be able to shape ontological distinctions between potential and viable threats. This provides a better understanding of how threats (ie intentions, capabilities, and opportunities) can exist and can be changed over time. Escalating threats from a state of potency to a state of viability could be avoided (...) by using appropriate threat mitigation techniques. DOI: 10.13140/RG.2.2.25163.54569 . (shrink)

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)

Multiple different understandings and uses exist of what granularity is and how to implement it, where the former influences success of the latter with regards to storing granular data and using granularity for reasoning over the data or information. We propose a taxonomy of types of granularity and discuss for each leaf type how the entities or instances relate within its granular level. Such unambiguous distinctions can guide a conceptual modeler to better distinguish between the types of granularity and the (...) software developer to improve on implementations of granularity. (shrink)

The theory of granular partitions is designed to capture in a formal framework important aspects of the selective character of common-sense views of reality. It comprehends not merely the ways in which we can view reality by conceiving its objects as gathered together not merely into sets, but also into wholes of various kinds, partitioned into parts at various levels of granularity. We here represent granular partitions as triples consisting of a rooted tree structure as first component, a domain satisfying (...) the axioms of Extensional Mereology as second component, and a mapping (called ’projection’) of the first into the second as a third component. We define ordering relations among granular partitions the resulting structures are called partition frames. We then introduce an axiomatic theory which sentences are interpreted in partition frames. (shrink)

An important part of the Unified Medical Language System (UMLS) is its Semantic Network, consisting of 134 Semantic Types connected to each other by edges formed by one or more of 54 distinct Relation Types. This Network is however for many purposes overcomplex, and various groups have thus made attempts at simplification. Here we take this work further by simplifying the relations which involve the three Semantic Types – Diagnostic Procedure, Laboratory Procedure and Therapeutic or Preventive Procedure. We define operators (...) which can be used to generate terms instantiating types from this selected set when applied to terms designating certain other Semantic Types, including almost all the terms specifying clinical tasks. Usage of such operators thus provides a useful and economical way of specifying clinical tasks. The operators allow us to define a mapping between those types within the UMLS which do not represent clinical tasks and those which do. This mapping then provides a basis for an ontology of clinical tasks that can be used in the formulation of computer-interpretable clinical guideline models. (shrink)

Published in extended form as "Endurants and Perdurants in Directly Depicting Ontologies", -/- We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate in such processes. For this purpose we distinguish between ontologies and metaontology. Ontologies are based on very simple directly depicting languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct (...) though compatible systems of categories. In a SNAP (snapshot) ontology we have the enduring entities in a given domain as they exist to be inventoried at some given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontology are required, together with the meta-ontology which joins them together. On the level of meta-ontology we are able to impose constraints on ontologies of a sort which can support efficient processing of large amounts of data. (shrink)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate therein. For this purpose we introduce the notion a directly depicting ontology. Directly depicting ontologies are based on relatively simple languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and employ distinct though compatible systems of categories. A SNAP (snapshot) ontology comprehends enduring entities such as (...) organisms, geographic features, or qualities as they exist at some given moment of time. A SPAN ontology comprehends perduring entities such as processes and their parts and aggregates as they unfold themselves through some temporal interval. We give an axiomatic account of the theory of directly depicting ontologies and of the core parts of the metaontological fragment within which they are embedded. (shrink)

Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these are (...) two quite different tasks, whose simultaneous realization is by no means trivial. The paper is structured as follows. We begin by laying out the methodological and philosophical background of our approach. We then summarize the structure and elements of the Basic Formal Ontology on which it rests, in particular the SNAP ontology of objects and the SPAN ontology of processes. Finally, we apply the general framework to the specific domain of biomedicine. (shrink)

Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED (...) CT classes with respect to these principles. Our major results are: 31% of these classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with the phenomenon of multiple inheritance. The advantages and limitations of our approach are also discussed. (shrink)

We provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of granularity. (...) For this purpose our ontology offers a variety of distinct partitions � of substances, processes and functions � and integrates these together within a single framework via transitive networks of part-whole and dependence relations among the entities in each of these categories. The paper concludes with a comparison of this methodology with the approaches of GOTM, KEGG, DIP and BIND and provides an outline of how the methodology is currently being applied in the field of biomedical database integration. (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)

Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of are realized through the actions of individuals organized into teams. We provide various levels of (...) implementation representing different levels of conformity on the part of health care organizations. Implementations built in conformity with our framework are marked by two dimensions of flexibility that are designed to make them more likely to be accepted by health care professionals than standard guideline-based management systems. They do justice to the fact 1) that responsibilities within a health care organization are widely shared, and 2) that health care professionals may on different occasions be non-compliant with guidelines for a variety of well justified reasons. The advantage of the framework lies in its built-in flexibility, its sensitivity to clinical context, and its ability to use inference tools based on a robust ontology. One disadvantage lies in its complicated implementation. (shrink)

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 (...) this paper, we describe the theoretical foundations of this paradigm and show how it is being applied to the solution of analogous problems of ambiguous identification in the fields of digital rights management, corporate memories and decision algorithms. (shrink)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The meta-ontological level then describes the relationships between the different token ontologies. In (...) a SNAP (snapshot) ontology we have enduring entities such as substances, qualities, roles, functions as these exist to be inventoried at a given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontological theory are required, together with the metaontology which joins them together, in order to give a non-reductionistic account of both static and dynamic aspects of the geospatial world. (shrink)