The somewhat old-fashioned concept of philosophical categories is revived and put to work in automated ontology building. We describe a project harvesting knowledge from Wikipedia’s category network in which the principled ontological structure of Cyc was leveraged to furnish an extra layer of accuracy-checking over and above more usual corrections which draw on automated measures of semantic relatedness.

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that (...) is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

Contemporary theories of consciousness are based on widely different concepts of its nature, most or all of which probably embody aspects of the truth about it. Starting with a concept of consciousness indicated by the phrase “the feeling of what happens” (the title of a book by Antonio Damásio), we attempt to build a framework capable of supporting and resolving divergent views. We picture consciousness in terms of Reality experiencing itself from the perspective of cognitive agents. Each conscious experience is (...) regarded as composed of momentary feeling events that are combined by recognition and evaluation into extended conscious episodes that bind cognitive contents with a wide range of apparent durations (0.1 secs to 2 or more secs, for us humans, depending on circumstances and context). Three necessary conditions for the existence of consciousness are identified: a) a ground of Reality, envisaged as an universal field of potentiality encompassing all possible manifestations, whether material or 'mental'; b) a transitional zone, leading to; c) a manifest world with its fundamental divisions into material, 'informational' and quale-endowed aspects. We explore ideas about the nature of these necessary conditions, how they may relate to one another and whether our suggestions have empirical implications. (shrink)

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

This article outlines a program of ethnoontology that brings together empirical research in the ethnosciences with ontological debates in philosophy. First, we survey empirical evidence from heterogeneous cultural contexts and disciplines. Second, we propose a model of cross‐cultural relations between ontologies beyond a simple divide between universalist and relativist models. Third, we argue for an integrative model of ontology building that synthesizes insights from different fields such as biological taxonomy, cognitive science, cultural anthropology, and political ecology. We conclude (...) by arguing that a program of ethnoontology provides philosophers both with insights about traditional issues such as debates about natural kinds and with novel strategies for connecting philosophy with pressing global issues such as the conservation of local environments and the self‐determination of Indigenous communities. (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)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant (...) science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

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

The Industrial Ontologies Foundry (IOF) was formed to create a suite of interoperable ontologies. Ontologies that would serve as a foundation for data and information interoperability in all areas of manufacturing. To ensure that each ontology is developed in a structured and mutually coherent manner, the IOF has committed to the tiered architecture of ontology building based on the Basic Formal Ontology (BFO) as top level. One of the critical elements of a successful tiered architecture build (...) is the domain mid-level ontologies. However, thus far there has been no mid-level manufacturing ontology that is based on BFO. The IOF has recently released the IOF Core version 1 beta to fill this gap. This paper documents the development process and gives an overview of the current content of the IOF Core. Finally, the paper describes how the IOF Core can be used as the basis for a more domain-specific Supply Chain Ontology. (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)

Fictionalism in ontology is a mixed bag. Here I focus on three main variants—which I label after the names of Pascal, Berkeley, and Hume—and consider their relative strengths and weaknesses. The first variant is just a version of the epistemic Wager, applied across the board. The second variant builds instead on the fact that ordinary language is not ontologically transparent; we speak with the vulgar, but deep down we think with the learned. Finally, on the Humean variant it’s the (...) structure of the ontological inventory, not its content, that may turn out to involve fictional elements. That is, for the Humean the fiction lies, not in the reality of common-sense ontology, but in the laws—of unity, identity, causation, etc.—in terms of which we articulate our experience of that reality. In the end, this is the kind of fictionalism that I find most interesting, sensible, and tenable. And I argue that it is even compatible with the sort of “naive” realism we have all come to appreciate in the work of Paolo Bozzi, to whom the paper is dedicated. (shrink)

In “Ontologies Relevant to behaviour change interventions: A Method for their Development” Wright, et al. outline a step by step process for building ontologies of behaviour modification – what the authors call the Refined Ontology Developmental Method (RODM) – and demonstrate its use in the development of the Behaviour Change Intervention Ontology (BCIO). RODM is based on the principles of good ontology building used by the Open Biomedical Ontology (OBO) Foundry in addition to those (...) outlined in (Arp, Smith, and Spear 2015). BCIO uses as its top-level ontology Basic Formal Ontology (BFO). The methods outlined in Wright, et al. are a valuable contribution to the field, especially the use of formal mechanisms for literature annotation and expert stakeholder review, and the BCIO will certainly play an important role in the extension of OBO Foundry ontologies into the behavioural domain. (shrink)

The goal of the Department of Defense Net-Centric Data Strategy is to improve data sharing throughout the DoD. Data sharing is a critical element of interoperability in the emerging system-of-systems. Achieving interoperability requires the elimination of two types of data heterogeneity: differences of syntax and differences of semantics. This paper builds a path toward semantic uniformity through application of a disciplined approach to ontology. An ontology is a consensus framework representing the types of entities within a given domain (...) and the relations between them. The construction of an ontology begins when a Community of Interest (COI) identifies its authoritative data sources (ADS), which are usually manifest in relevant doctrinal publications, glossaries, data dictionaries, and logical data models. The identified terms are then defined in relation to a common logical framework that has been designed to ensure interoperability with other ontologies created on the basis of the same strategy. As will be described, the Command and Control (C2) Ontology will include representations of a substantial number of entities within the Command and Control (C2) domain. If domain ontologies (e.g. Strike and Counterinsurgency) semantically align with the C2 Ontology, then a substantial barrier to systems interoperability is thereby crossed. (shrink)

The notion of Mathematics as Ontology (as defined by Badiou in his work) is brought into question from a working mathematician's perspective. Notions of independence in set theory and model theory are contrasted with the original equation Mathematics=Ontology. The author builds an extension of mathematical ontology from set theory to a foliated, étale, setting.

In this article, we analyse the ontological import of adding classes to set theories. We assume that this increment is well represented by going from ZF system to NBG. We thus consider the standard techniques of reducing one system to the other. Novak proved that from a model of ZF we can build a model of NBG (and vice versa), while Shoenfield have shown that from a proof in NBG of a set-sentence we can generate a proof in ZF of (...) the same formula. We argue that the first makes use of a too strong metatheory. Although meaningful, this symmetrical reduction does not equate the ontological content of the theories. The strong metatheory levels the two theories. Moreover, we will modernize Shoenfields proof, emphasizing its relation to Herbrands theorem and that it can only be seen as a partial type of reduction. In contrast with symmetrical reductions, we believe that asymmetrical relations are powerful tools for comparing ontological content. In virtue of this, we prove that there is no interpretation of NBG in ZF, while NBG trivially interprets ZF. This challenges the standard view that the two systems have the same ontological content. (shrink)

We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pain that is elevated relative to (...) peripheral trauma, pain that is caused neuropathically (thus with no necessary peripheral stimulus), and pain reports arising through deception either of self or of others. We describe how our approach can answer some of the objections raised against the IASP definition, and sketch how it can be used to support more sophisticated discrimination of different types of pain resulting in improved data analysis that can help in advancing pain research. (shrink)

The paper offers an interpretation of a disputed portion of Plato’s Theaetetus that is often called the Secret Doctrine. It is presented as a process ontology that takes two types of processes, swift and slow motions, as fundamental building blocks for ordinary material objects. Slow motions are powers which, when realized, generate swift motions, which, in turn, are subjectively bundled to compose sensible objects and perceivers. Although the reading of the Secret Doctrine offered here—a new version of the (...) “Causal Theory interpretation”—is not without problems, these problems are acknowledged in Plato’s text, confirming that this interpretation is correct. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six (...) questions related to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

In this paper we begin categorizing a plurality of possible worlds on the basis of permitting or not permitting ontologically different things to be causally connected. We build the work on the dual principle that all universes are causally closed either because no universe causes anything outside itself or because no universe has anything in it that is caused by another universe.

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and (...) use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

On March 14-15, 2006, at the US National Institute of Standards and Technology (NIST) in Gaithersburg, MD there took place the first Upper Ontology Summit (UOS). This was a convening of custodians of several prominent upper ontologies, key technology participants, and interested other parties, with the purpose of finding a means to relate the different ontologies to each other. The result is reflected in a joint communiqué, directed to the larger ontology community and the general public, and expressing (...) a joint intent to build bridges among the existing upper ontologies in ways designed to increase and rationalize their utilization and to enhance their semantic interoperability. (shrink)

We examine how insights made in socio-anthropological and evolutionary schools of thought necessitate us to reevaluate the classic philosophical distinction between epistemology and ontology. We adopt an applied evolutionary epistemological stance and demonstrate that both epistemology and ontology evolve. Epistemology is broadened to include all knowledge and information that all life forms evolve, and ontology encompasses all biologically informed realities that life builds. Through processes such as symbiosis and niche construction, organisms acquire and extend information and knowledge (...) into their offspring, onto unrelated organisms, and onto their niches. Life builds biorealities that change over time. Consequently, knowledge and reality are mutable and truth is spatiotemporally bounded. We conclude that the classic distinction between epistemology and ontology has become superfluous and instead, we argue that the evolving knowledge that comes in the form of organisms and their extended niches equals ontological realities. (shrink)

Social ontology is concerned with the nature of the social world, constituents, or building blocks of social entities in general. Some theories claim that social entities are built from people's psychological states, others are built up of actions, others from practice, and other theories deny that even a distinction can be made between social and non-social. There are different philosophical views on how the ontological significance of narrative can contribute to our understanding of the social world and the (...) way in which social reality is modeled. Some researchers consider that narrative is an instrumental cognitive skill or linguistic tool, while others regard it as an ontological category related to how people exist in the world, or understand human life as a narrative. DOI: 10.13140/RG.2.2.14051.09763. (shrink)

The main purpose of the paper is to outline the formal-logical, general theory of language treated as a particular ontological being. The theory itself is called the ontology of language, because it is motivated by the fact that the language plays a special role: it reflects ontology and ontology reflects the world. Language expressions are considered to have a dual ontological status. They are understood as either concretes, that is tokens – material, physical objects, or types – (...) classes of tokens, which are abstract objects. Such a duality is taken into account in the presented logical theory of syntax, semantics and pragmatics. We point to the possibility of building it on two different levels; one which stems from concretes, language tokens of expressions, whereas the other one – from their classes, types conceived as abstract, ideal beings. The aim of this work is not only to outline this theory as taking into account the functional approach to language, with respect to the dual ontological nature of its expressions, but also to show that the logic based on it is ontologically neutral in the sense that it abstracts from accepting some existential assumptions, related with the ontological nature of these linguistic expressions and their extra-linguistic ontological counterparts (objects). (shrink)

Foundational relations play an important role in the ontological foundations of conceptual modeling. Their investigation has been theoretically addressed in philosophical/ontological theories, and empirically offered in foundational ontologies (FOs). FOs are comprehensive theories that model the world as top-level entities and relations. Empirically, for modelers aiming to use foundational relations without an urge for entity types, FOs seem to be complex to comprehend, comply with, and integrate in practice. And since the practice of these relations is critical for conceptual modeling (...) tasks, we present an approach that builds a well-founded entity-type free relations theory within a first-order-logic formalization, besides large complex FOs. The theory contributes to a minimal set of foundational ontological relations (FORT) by importing extant theories (mereotopology and location) and (re-)formalizing other relations (dependence, membership, constitution, and entity-location), while no FO has compromised this set. (shrink)

This paper gives significance to the concept of continuity in addressing the contemporary mind-body problem. Building upon philosophical definitions and insights from empirical brain science, the paper argues for "ontology of continuity" as a way to bridge between the mental and physical. To overcome the challenge of Kim’s causal overdetermination, the paper introduces a dual-neural process model, where subjective experiences and neural activities co-depend and influence each other in a quasi-parallel manner. This model seeks to reconcile idealism and (...) physicalism, proposing that continuity serves as a fundamental ontological construct connecting the mental and physical realms. (shrink)

In this paper, building on these previous works, we propose to go deeper into the understanding of crowd behavior by proposing an approach which integrates ontologi- cal models of crowd behavior and dedicated computer vision algorithms, with the aim of recognizing some targeted complex events happening in the playground from the observation of the spectator crowd behavior. In order to do that, we first propose an ontology encoding available knowledge on spectator crowd behavior, built as a spe- cialization (...) of the DOLCE foundational ontology, which allows the representation of categories belonging both to the physical and to the social realms. We then propose a simplified and tractable version of such ontology in a new temporal extension of a description logic, which is used for temporally coupling events happening on the play- ground and spectator crowd behavior. At last, computer vision algorithms provide the input information concerning what is observed on the stands and ontological reasoning delivers the output necessary to perform complex event recognition. (shrink)

This article reconsiders Husserl’s concept of Leib in light of Merleau‐Ponty’s interpretation of the human body as an ontologically significant phenomenon. I first analyze Husserl’s account of the body as a “two‐fold unity” and demonstrate the problematic nature of its four implications, namely, the ambiguous ontological status of the body as subject‐object, the view of “my body” as “my object,” the preconstitutive character of the unity of the body, and the restriction of the constitution of the body to touch alone. (...) Building on this analysis, I explain how Merleau‐Ponty resolves the difficulties raised by Husserl’s account by reversing it. According to Merleau‐Ponty, “flesh” is not a two‐fold reality comprising subjective and objective aspects, but an ontological dimension from which these aspects can be abstracted through specific cognitive operations. Consequently, all subjective and objective aspects, even beyond the boundaries of one’s body, must be understood as founded in the indivisible unity of flesh. I argue that a thorough phenomenological description of the human body requires abandoning Husserl’s concept of Leib because it contributes to perpetuating subject‐object dualism. In contrast, Merleau‐Ponty’s notion of flesh reveals the circularity between subject and object and its general ontological significance. (shrink)

In the thesis I offer an analysis of the metaphysical underpinnings of the extended cognition thesis via an examination of standard views of metaphysical building (or, dependence) relations. -/- In summary form, the extended cognition thesis is a view put forth in naturalistic philosophy of mind stating that the physical basis of cognitive processes and cognitive processing may, in the right circumstances, be distributed across neural, bodily, and environmental vehicles. As such, the extended cognition thesis breaks substantially with the (...) still widely held view in cognitive science and philosophy of mind, namely that cognitive processes and cognitive processing take place within the skin-and-skull of individual organisms. The standard view of metaphysical building relations can be expressed as the conjunction of two theses. First, that a metaphysical building relation – such as composition, constitution, realization, supervenience or emergence – is a relation of ontological dependence, because if a metaphysical building relation holds between X (or the Xs) and Y, then it is in virtue of X (or the Xs) that Y exists. Second, metaphysical building relations are synchronic (durationless) relations of ontological dependence. In the thesis, I propose an alternative diachronic framework by which to extend the standard synchronic accounts of metaphysical dependence relations, and by which to reformulate the metaphysical foundation of the extended cognition thesis. The project fills an important gap between analytical metaphysics (in particular, the metaphysics of dependence relations) and naturalistic philosophy of mind (especially the extended cognition thesis). To my knowledge there has been no attempt to establish a robust diachronic account of metaphysical building (or, dependence) relations such as, e.g., composition and constitution. However, this is precisely what I argue is required to properly advance and ground the metaphysics of extended cognition. Ultimately, my aim of reformulating the metaphysics of extended cognition consists in taking several steps toward a third-wave of extended cognition. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General (...) Medical Science (OGMS) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

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 firm is a real entity and not an imaginary, fictitious or linguistic entity. This implies that the firm as a whole exhibits a sufficient degree of unity or cohesiveness and is durable and persistent through time. The firm is essentially composed of a particular combination of constituents that are bound together by something that acts as an ontological glue, and is therefore non-reducible to other more basic entities, i.e., to its parts or its members. From our perspective, the firm (...) is not simply an aggregate or a collection. It is a real integrated entity and a dynamic causal system. Institutional and organizational aspects enter the picture. These assertions stand in sharp contrast with mainstream theories of the firm whose proponents are more preoccupied with questions of contractual provisions, vertical integration or opportunism than the general and more fundamental questions related to what firms really are. (shrink)

General Relativity generated various early philosophical interpretations. His adherents have highlighted the "relativization of inertia" and the concept of simultaneity, Kantians and Neo-Kantians have underlined the approach of certain synthetic "intellectual forms" (especially the principle of general covariance, and logical empirics have emphasized the philosophical methodological significance of the theory. Reichenbach approached the GR through the "relativity of geometry" thesis, trying to build a "constructive axiomatization" of relativity based on "elementary matters of fact" (Elementartatbestande) for the observable behavior of light (...) rays, rods and clocks. The mathematician Hermann Weyl attempted a reconstruction of Einstein's theory based on the epistemology of a "pure infinitesimal geometry", an extended geometry with additional terms that formally identified with the potential of the electromagnetic field. DOI: 10.13140/RG.2.2.11641.93281. (shrink)

The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best practices in modeling, some of (...) which have been advocated in the biomedical domain. We illustrate each step of our method with examples from a re-engineering case study about agricultural fertilizers based on the AGROVOC thesaurus. Our method makes clear that re-engineering thesauri requires far more than just a syntactic conversion into a formal language or other easily automatable steps. The method can not only be used for re-engineering thesauri, but does also summarize steps for building ontologies in general, and can hence be adapted for the re-engineering of other types of vocabularies or terminologies. (shrink)

I argue that current projects in ‘naturalized metaphysics’ fail to be properly naturalistic, and thereby fail in their stated aim to take one’s metaphysics from science. I argue that naturalism must involve the idea of taking science seriously, and that this can only be spelled out in terms of taking not only the theories of science seriously, but also its practice and its socio-linguistic situatedness seriously as well. This accords with naturalism because not doing so draws an artificial (non-natural) distinction (...) between the epistemic products of science as essence, and its socio-linguistic and practical features as accidents. The picture of naturalism which falls out of this is a form of pragmatism. Once this is spelled out, the question becomes, what is the appropriate attitude for the pragmatist/naturalist to have toward ontology? It is not the same as that of traditional metaphysics, since such an attitude (that metaphysical theorizing can make positive epistemic contributions) requires a priori commitments which themselves are (1) not subject to empirical review, and (2) are anthropocentric and so potentially distorted. But the pragmatist/naturalist will not go the opposite way, and say that metaphysics is meaningless either, since (true to their pragmatic commitments) ontology does things for the scientist and the layperson. It is a mistake to reject it wholesale, since the task of asserting what there is, exposing such an ontology to criticism, both empirical and logical, and revising it, has both small-scale and large-scale consequences. On the small-scale, ontologies are a guide for thinking—scientists, engineers, and lay people can and do use models of existence to navigate occurent problems in their day-to-day lives. Whether this is posing research hypotheses, developing protocols for generating new materials, or cooling off a cup of coffee, ontology plays a role. Large-scale consequences are more weighty, and more difficult to see. These large-scale consequences have to do with the aims and values which individuals and societies possess, and their interrelation with ontology. This certainly was at the forefront of the earliest ontologies—the Epicureans and Stoics built their moral philosophy on the basis of what ontology they thought was correct. This sort of practice goes on, unabated, today, though with virtually no overt acknowledgement of this important interdependency. How, for the pragmatist, do we make sense of ontological talk, if we are to eschew traditional metaphysics? Ontology—the naturalist/pragmatist declares—is a tool. Ontology helps us do things, whether it be predict behavior, understand phenomena, blame or forgive someone, and hope or despair about a life after this one (for example). Building an ontology is about building our own concepts, and this, in turn is a negotiation between our beliefs, experiences, and commitments, and the beliefs, experiences, and commitments of with whom we’re discursively engaged. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO (...) provides a framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

The emerging field of synthetic biology aims to engineer novel biological entities. The envisioned future bio-based economy builds largely on “cell factories”: organisms that have been metabolically engineered to sustainably produce substances for human ends. In this paper, we argue that synthetic biology’s goal of creating efficient production vessels for industrial applications implies a set of ontological assumptions according to which living organisms are machines. Traditionally, a machine is understood as a technological, isolated and controllable production unit consisting of parts. (...) But modified organisms, or hybrids, require us to think beyond the machine paradigm and its associated dichotomies between artificial and natural, organisms and artefacts. We ask: How may we conceptualise hybrids beyond limiting ontological categories? Our main claim is that the hybrids created by synthetic biology should be considered not as machines but as metabolic systems. We shall show how the philosophical account of metabolism can inform an ontology of hybrids that moves beyond what we call the “machine ontology”, considering that metabolism enables thinking beyond the dominant dichotomies and allows us to understand and design lifeforms in a bio-based economy. Thus, the aim of this paper is twofold: first, to develop the philosophical ontology of hybrids, and second, to move synthetic biology beyond the problematically limiting view of hybrids. (shrink)

Ontologies formally represent reality in a way that limits ambiguity and facilitates automated reasoning and data fusion, but is often daunting to the non-technical user. Thus, many researchers have endeavored to hide the formal syntax and semantics of ontologies behind the constructs of Controlled Natural Languages (CNLs), which retain the formal properties of ontologies while simultaneously presenting that information in a comprehensible natural language format. In this paper, we build upon previous work in this field by evaluating prospects of implementing (...) International Technology Alliance Controlled English (ITACE) as a middleware for ontology editing. We also discuss at length a prototype of a natural language conversational interface application designed to facilitate ontology editing via the formulation of CNL constructs. (shrink)

Types are fundamental for conceptual modeling and knowledge representation, being an essential construct in all major modeling languages in these fields. Despite that, from an ontological and cognitive point of view, there has been a lack of theoretical support for precisely defining a consensual view on types. As a consequence, there has been a lack of precise methodological support for users when choosing the best way to model general terms representing types that appear in a domain, and for building (...) sound taxonomic structures involving them. For over a decade now, a community of researchers has contributed to the development of the Unified Foundational Ontology (UFO) - aimed at providing foundations for all major conceptual modeling constructs. At the core of this enterprise, there has been a theory of types specially designed to address these issues. This theory is ontologically well- founded, psychologically informed, and formally characterized. These results have led to the development of a Conceptual Modelling language dubbed OntoUML, reflecting the ontological micro-theories comprising UFO. Over the years, UFO and OntoUML have been successfully employed on conceptual model design in a variety of domains including academic, industrial, and governmental settings. These experiences exposed improvement opportunities for both the OntoUML language and its underlying theory, UFO. In this paper, we revise the theory of types in UFO in response to empirical evidence. The new version of this theory shows that many of OntoUML’s meta-types (e.g. kind, role, phase, mixin) should be considered not as restricted to substantial types but instead should be applied to model endurant types in general, including relator types, quality types, and mode types. We also contribute with a formal characterization of this fragment of the theory, which is then used to advance a new metamodel for OntoUML (termed OntoUML 2). To demonstrate that the benefits of this approach are extended beyond OntoUML, the proposed formal theory is then employed to support the definition of UFO-based lightweight Semantic Web ontologies with ontological constraint checking in OWL. Additionally, we report on empirical evidence from the literature, mainly from cognitive psychology but also from linguistics, supporting some of the key claims made by this theory. Finally, we propose a computational support for this updated metamodel. (shrink)

Advances in emotion and affective science have yet to translate routinely into psychiatric research and practice. This is unfortunate since emotion and affect are fundamental components of many psychiatric conditions. Rectifying this lack of interdisciplinary integration could thus be a potential avenue for improving psychiatric diagnosis and treatment. In this contribution, we propose and discuss an ontological framework for explicitly capturing the complex interrelations between affective entities and psychiatric disorders, in order to facilitate mapping and integration between affective science and (...) psychiatric diagnostics. We build on and enhance the categorisation of emotion, affect and mood within the previously developed Emotion Ontology, and that of psychiatric disorders in the Mental Disease Ontology. This effort further draws on developments in formal ontology regarding the distinction between normal and abnormal in order to formalize the interconnections. This operational semantic framework is relevant for applications including clarifying psychiatric diagnostic categories, clinical information systems, and the integration and translation of research results across disciplines. (shrink)

John Searle’s theory of social ontology posits that there are indispensable normative components in the linguistic apparatuses termed status functions, collective intentionality, and collective recognition, all of which, he argues, make the social world. In this paper, I argue that these building blocks of Searle’s theory are caught in a petitio of constitutive circularity. Moreover, I note how Searle fails to observe language in reciprocal relation to the institutions which not only are shaped by it but also shape (...) language’s practical applications. According to Searle, social theorists that tried to show a connection between society, culture, and language all failed to see the constitutive role of language in the making of social reality. Consequently, I believe that Searle is himself guilty of a certain kind of blind presumption, and argue that Hegel’s philosophy of culture, which Searle dismisses as implausible, offers a more cohesive account of the normative transactions between human beings and their social world. (shrink)

This Special Issue is dedicated to building a bridge between different disciplines concerned in the investigation of the qualitative dimension of experience and reality. The two main objectives of the Issue can be summarized as follows: 1) to elucidate the need for a revision of categories to account for the qualitative dimension in various disciplines (that include, for example, the cognitive sciences, neurosciences, biology, linguistics, informatics, artificial intelligence, robotics, newly emerging computer technologies) in order to develop an ontology (...) that can better account for the qualitative, dynamic and relational aspects of different domains of reality; 2) to explore the implications of the enactivist view for a relational and ecological account of the qualitative dimensions of life and cognition. (shrink)

‘Eruv’ is a Hebrew word meaning literally ‘mixture’ or ‘mingling’. An eruv is an urban region demarcated within a larger urban region by means of a boundary made up of telephone wires or similar markers. Through the creation of the eruv, the smaller region is turned symbolically (halachically = according to Jewish law) into a private domain. So long as they remain within the boundaries of the eruv, Orthodox Jews may engage in activities that would otherwise be prohibited on the (...) Sabbath, such as pushing prams or wheelchairs, or carrying walking sticks. There are eruvim in many towns and university campuses throughout the world. There are five eruvim in Chicago, five in Brooklyn, twenty three in Queens and Long Island, and at least three in Manhattan. The US Supreme Court is (like most other major US Federal Government buildings) located within the eruv of Washington DC. In many cases, not all of those living within or near the area of an actual or proposed eruv will themselves be Orthodox Jews, and this has sometimes led to protests against eruv creation. It is such protests which triggered the writing of this essay. (shrink)

Approaching mental health on a global scale with particular reference to low- and mid-income countries raises issues concerning the disregard of the local context and values and the imposition of values characteristic of the Global North. Seeking a philosophical viewpoint to surmount these problems, the present paper argues for a value-laden framework for psychiatry with the specific incorporation of value pluralism, particularly in relation to the Global South context, while also emphasizing personal values such as the choice of treatment. In (...) sketching out this framework, the paper aims to overcome the clash between universalism and relativism about psychiatric categories by focusing on how overlaps between cultures can contribute to ontology-building. A case study analyzing ethnopsychiatric research in the context of South India will illustrate the proposed view, while also pointing out avenues for further research on the causal efficacy of local shared beliefs about mental disorder. If approaches across different traditions and theoretical frames are shown to work in treating similar ailments, causal connections appear to cut across the different ontologies. Ethnopsychiatry would play a central role in such research, namely in disclosing the variables and mechanisms at work within the local approaches. (shrink)

This paper will discuss the peace building efforts of the National Democratic Front of the Philippines (NDFP) and the Government of the Philippines (GRP) and argue that these efforts follow the proceduralist conception of Habermas’ deliberative democracy. Habermas, like Kant, contends that peace has a “chronological and ontological priority over violence.”1 The paper will problematize the gap between legality and legitimacy as highlighted by Habermas and relate how such a gap triggered conflicts the same as that of the GRP (...) and the NDFP. I will then propose a communicative process of critique and intervention from civil liberty groups, especially the Church sector, as an avenue to possibly remedy the gaps and its effects. Finally, I will outline possible problems arising from this model of deliberative democracy. (shrink)

The study aims to expose vulnerabilities of the subject-object paradigm in modern philosophy. The article concentrates upon ontological limitations of the concept of a subject and changing the status of an object in subject-object relations in the context of changing characteristics of the object existence. Scientific novelty of the work lies in identifying points of ontological stability and limitations of the subject concept, which could be used in its further theoretical development. As a result of the research, the aspects necessary, (...) from the author’s viewpoint, for building a theoretical model of the modern subject, which would be based on ontological symbiosis of subjective and objective characteristics, are determined. (shrink)

Models are being used extensively for practicing and understanding scientific, engineering and mathematical subjects, but are rarely used as art analyzing tools, particularly, in learning environments. Contrarily, using art to explain mathematical ideas is not unprecedented. Strogatz (1988), for example, built a model based on Romeo and Juliet’s love story and used it to explain the idea of differential mathematics, and system dynamics. Artwork, specially written and plastic classics, is a fixed form of art. We frame them and put them (...) in a gallery, or a book (digital or physical). We don’t try to “fix” them or optimize their functioning, we analyze them to find meaning, intention, and patterns. In this article, we aim to show how, by building models combined with simple mathematical representations and analogies, it is possible to understand literary texts, from the prism of system and complexity theories, which emphasize the dynamic, non-linear, and non-reductionist aspects of the observed. We’ll demonstrate how modeling processes of three cultural assets, allow active correspondence with the original textual art, by treating them as systemic objects with interactions and dynamics. They will be analyzed while raising questions about the significance of modeling as a cognitive learning process. (shrink)

‘Eruv’ is a Hebrew word meaning literally ‘mixture’ or ‘mingling’. An eruv is an urban region demarcated within a larger urban region by means of a boundary made up of telephone wires or similar markers. Through the creation of the eruv, the smaller region is turned symbolically (halachically = according to Jewish law) into a private domain. So long as they remain within the boundaries of the eruv, Orthodox Jews may engage in activities that would otherwise be prohibited on the (...) Sabbath, such as pushing prams or wheelchairs, or carrying walking sticks. There are eruvim in many towns and university campuses throughout the world. There are five eruvim in Chicago, five in Brooklyn, twenty three in Queens and Long Island, and at least three in Manhattan. The US Supreme Court is (like most other major US Federal Government buildings) located within the eruv of Washington DC. In many cases, not all of those living within or near the area of an actual or proposed eruv will themselves be Orthodox Jews, and this has sometimes led to protests against eruv creation. It is such protests which triggered the writing of this essay. (shrink)

This article discusses some continuous limit cases of Susan Haack’s crossword puzzle metaphor for the coherent development and foundation of science. The main objective of this discussion is to build a bridge between Haack’s foundherentism and the epistemological framework of objective cognitive constructivism, including its key metaphor of objects as tokens for eigen-solutions. The historical development of chemical affinity tables is used to illustrate our arguments.

Wikipedia is a goldmine of information; not just for its many readers, but also for the growing community of researchers who recognize it as a resource of exceptional scale and utility. It represents a vast investment of manual effort and judgment: a huge, constantly evolving tapestry of concepts and relations that is being applied to a host of tasks. This article provides a comprehensive description of this work. It focuses on research that extracts and makes use of the concepts, relations, (...) facts and descriptions found in Wikipedia, and organizes the work into four broad categories: applying Wikipedia to natural language processing; using it to facilitate information retrieval and information extraction; and as a resource for ontology building. The article addresses how Wikipedia is being used as is, how it is being improved and adapted, and how it is being combined with other structures to create entirely new resources. We identify the research groups and individuals involved, and how their work has developed in the last few years. We provide a comprehensive list of the open-source software they have produced. (shrink)