La communication interdisciplinaire rencontre divers problématiques : l’hétérogénéités des informations (sémantique, standardisation des formats), les confusions linguistiques (intentions dans les énoncés, polysémie des mots) ou encore épistémologiques (expertises divergentes, terminologies inadéquates). Nous proposons pour favoriser l’intercommunication entre différents domaines de spécialité, l’emploi des ontologies informatiques : des artefacts informatiques permettant une représentation des concepts au sein d’un domaine de spécialité. Autour de la notion « d’interopérabilité sémantique », la capacité pour une machine et des acteurs de communiquer ensemble, nous (...) viserons à montrer en quoi les ontologies peuvent permettre à des acteurs de différentes disciplines de clarifier les notions propres à leurs domaines en fonction d’une analyse de leurs usages des mots. Nous tâchons ici de mettre en avant la capacité des ontologies de traiter le langage selon différents niveaux du sens d’un mot (du plus concret et appliqué, au plus abstrait et conceptuel), afin de mettre en perspective ce en quoi cette analyse basée sur les textes d’un corpus, permet de rendre compte de, si ce n’est un état du réalisme d’une discipline, du moins, servir d’outils pour aider les acteurs à normaliser leurs pratiques. En ce sens, les ontologies informatiques peuvent être considérées et utilisées comme autant de bases terminologiques servant comme outils de références pour faciliter la communication interdisciplinaire. (shrink)

Community has been both celebrated and demonized as a fortress that shelters and defends its members from being exposed to difference. Instead of abandoning community as an antiquated model of relationships that is ill suited for our globalized world, this book turns to the writings of Giorgio Agamben, Roberto Esposito, and Jean-Luc Nancy in search for ways to rethink community in an open and inclusive manner. Greg Bird argues that a central piece of this task is found in how each (...) philosopher rearticulates community not as something that is proper to those who belong and improper to those who are excluded or where inclusion is based on one’s share in common property. We must return to the forgotten dimension of sharing, not as a sharing of things that we can contain and own, but as a process that divides us up and shares us out in community with one another. This book traces this problem through a wide array of fields ranging from biopolitics, communitarianism, existentialism, phenomenology, political economy, radical philosophy, and social theory. (shrink)

In this article I consider the relevance of Tomasello’s work on social cognition to the theory of communicative action. I argue that some revisions are needed to cope with Tomasello’s results, but they do not affect the core of the theory. Moreover, they arguably reinforce both its explanatory power and the plausibility of its normative claims. I proceed in three steps. First, I compare and contrast Tomasello’s views on the ontogeny of human social cognition with the main tenets of Habermas’ (...) theory of communicative action. Second, I suggest how to reframe the role of language in the theory of communicative rationality in order to integrate the two theories. Third, I show how this affects social ontology, supporting the view that the construction of social reality is normatively constrained by the bounds of reason. (shrink)

Russian abstract: В данном сборнике статей раскрывается формирование структурно-онтологического представления о таком явлении, как городское пространство. Наряду с соответствующей концептуализацией, также представлено и объяснено определение городского сообщества. Обоснована логика классификации городских сообществ. А также проанализированы факторы, обуславливающие их устойчивость. -/- English abstract: This collection of articles reveals the formation of a structural-ontological concept of such a phenomenon as urban space. Along with relevant conceptualization, the definition of an urban community is also presented and explained. The logic of classification of urban (...) communities is substantiated. And also analyzed the factors that determine their stability. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, (...) diagnosis, prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (...) (CIDO). As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

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

The aim of this research is to find a model of communication philosophy as a form of relevance to the discourse of ontology, epistemology and axiology. This research uses a qualitative method using a library study approach that uses books or literature as the main source. The library references in the form of books which are primary sources in this research are first, a book entitled On the Philosophy of Communication 1st Edition by Garry Rafford, second, a (...) book entitled Aristotle's Physics Book VIII. The results of this research are a communication philosophy model divided into three sub-models, namely a communication ontology model which is concise about what the formal and material objects of communication science are, a communication epistemology model which discusses how humans acquire knowledge in communication studies and a communication axiology model which focuses on questions regarding what and how the values ​​contained in the messages exchanged in the communication process between the communicator and the communicant. (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)

Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in support of scientific advance. This very success, however, has led to a (...) proliferation of ontologies of varying scope and quality. We define one strategy for achieving quality assurance of ontologies—a plan of action already adopted by a large community of collaborating ontologists—which consists in subjecting ontologies to a process of peer review analogous to that which is applied to scientific journal articles. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

While many bibliometric techniques have been employed to represent the structure of academic research communities over the years, much of this work has been conducted on scientific fields as opposed to those in the humanities. Here we use graphing techniques to present two networks that allow us to explore the structure of a subset of the philosophy community by mapping the citations between philosophical texts on the topic of ontology (the study of what exists). We find a citation gap (...) between philosophers studying material and abstract objects, and between analytic and continental ontologists, but other predictions were not confirmed by this method. We conclude by considering several additional methods for further exploring both the structure of philosophy and other disciplines in the humanities. (shrink)

The paper outlines a new interpretation of informational privacy and of its moral value. The main theses defended are: (a) informational privacy is a function of the ontological friction in the infosphere, that is, of the forces that oppose the information flow within the space of information; (b) digital ICTs (information and communication technologies) affect the ontological friction by changing the nature of the infosphere (re-ontologization); (c) digital ICTs can therefore both decrease and protect informational privacy but, most importantly, (...) they can also alter its nature and hence our understanding and appreciation of it; (d) a change in our ontological perspective, brought about by digital ICTs, suggests considering each person as being constituted by his or her information and hence regarding a breach of one’s informational privacy as a form of aggression towards one’s personal identity. (shrink)

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

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and (...) to describe a number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

This article examines the ontology and politics of Peter Sloterdijk's Spheres trilogy, focusing in particular upon the notion of microspherical enclosure explicated in the first volume of this series. Noting Sloterdijk's unusual alignment of his philosophy with media theory, three main contentions are put forward. Firstly, that Sloterdijk's reconfiguration of Heidegger's fundamental ontology represents a largely unacknowledged renunciation of the primacy of Being-towards-death in the authentic existence of Dasein, foregrounding instead an originary co-belonging between mother and child. Secondly, (...) that Sloterdijk borrows from media theory a concern regarding the facticity of all communication, grounding philosophical discourse in the determinate locality of its origin, but does so while exalting a pre-natal communicative immediacy that would seem to disparage the everydayness of Dasein. Finally, that Sloterdijk's oft-justified scepticism regarding globalization often retreats into an anti-cosmopolitanism that, in its nostalgia for the comfort, security and immediacy of the matrixial co-belonging, evinces a covert but potentially noxious politics of exclusion. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use (...) of the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (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)

Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of discussion. The comparison of diverse nomenclatural practices introduces a suite of epistemic and ontological difficulties and considerations. Different nomenclatures may depend on whether the communities using them rely on formalized naming conventions; cultural or spiritual valuations; or worldviews. Because of this, some argue that the different naming practices may not (...) be comparable if the ontological commitments employed differ. Comparisons between different nomenclatures cannot assume that either the naming practices or the object to which these names are intended to apply identifies some universally agreed upon object of interest. Investigating this suite of philosophical problems, I explore the role grey nomenclatures play in classification. ‘Grey nomenclatures’ are defined as those that employ names that are either intentionally or accidentally non-Linnaean. The classification of the lichen thallus (a symbiont) has been classified outside the Linnaean system by botanists relying on the International Code of Nomenclature for algae, fungi, and plants (ICN). But, I argue, the use of grey names is not isolated and does not occur exclusively within institutionalized naming practices. I suggest, ‘grey names’ also aptly describe nomenclatures employed by indigenous communities such as the Samí of Northern Finmark, the Sherpa of Nepal, and the Okanagan First Nations. I pay particular attention to how naming practices are employed in these communities; what ontological commitments they hold; for what purposes are these names used; and what anchors the community’s nomenclatural practices. Exploring the history of lichen naming and early ethnolichenological research, I then investigate the stakes that must be considered for any attempt to preserve, retain, integrate, or compare the knowledge contained in both academically formalized grey names and indigenous nomenclatures in a way that preserves their source-specific informational content. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

The COVID-19 pandemic has made relevant questions regarding the limits and the justifications of sovereign power as nation states utilize high degrees of power over populations in their strategies of countering the virus. In our article, we analyze a particularly important facet of the strategy of sovereignty in managing the affects caused by a pandemic, which we term the ontology of war. We analyze the way in which war plays a significant role in the political ontology of our (...) societies, through its aiming to produce a unified political subject and an external enemy. Taking our theoretical cue from Butler’s thinking on frames of recognizability we extend her theory through augmenting it with affect theory to argue for how the frame of recognizability produced by the ontology of war fails to guide our understanding of the pandemic as a political problem, a failure that we analyze through looking at the affective register. We argue that the main affect that the nation state tries to manage, in relation to the pandemic, through the ontology of war is anxiety. We show that the nation state tries to alleviate anxiety by framing it through the ontology war, this leads to the appearance of a potentially racist and nationalist affective climate where the “enemy” is no longer felt to be the virus, but members of other nations as well as minorities. We argue that the pandemic reveals both the political ontology of war central to the foundation of our political communities, and how this ontology is used by the nation state to manage feelings of anxiety and insecurity. Ultimately, as we will discuss at the end of this article, this leads to failure. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT community, (...) and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more efficient interoperation with other ontologies and information resources. Results: SNOMED CT and the OBO Foundry differ considerably in their general approach.Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions: Future efforts in ontology development have to address the need for harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a prerequisite. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality (...) through both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

In addition to protecting agents’ autonomy, consent plays a crucial social role: it enables agents to secure partners in valuable interactions that would be prohibitively morally risk otherwise. To do this, consent must be observable: agents must be able to track the facts about whether they have received a consent-based permission. I argue that this morally justifies a consent-practice on which communicating that one consents is sufficient for consent, but also generates robust constraints on what sorts of behaviors can be (...) taken as consent- communicating. (shrink)

The ontology of language is concerned with the relations between uses of language, both overt and covert, and other entities, whether in the world or in the mind of the thinking subject. We attempt a first survey of the sorts of relations which might come into question for such an ontology, including: relations between referring uses of expressions and their objects, relations between the use of a (true) sentence and that in the world which makes it true, relations (...) between mental acts on the one hand and underlying mental states (attitudes, beliefs), on the other, relations between my acts and states, associated uses of language and overt actions on my part and on the part of those other subjects with whom I communicate. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the (...) Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The paper (...) provides a detailed overview of ontology services and concludes with a discussion of some implications of the product-service system approach for the understanding of the nature of applied ontology. Ontology developer communities are compared in this respect with developers of scientific theories and of standards (such as W3C). For each of these we can ask: what kinds of products do they develop and what kinds of services do they provide for the users of these products? (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical (...) data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Could a person ever transcend what it is like to be in the world as a human being? Could we ever know what it is like to be other creatures? Questions about the overcoming of a human perspective are not uncommon in the history of philosophy. In the last century, those very interrogatives were notably raised by American philosopher Thomas Nagel in the context of philosophy of mind. In his 1974 essay What is it Like to Be a Bat?, Nagel (...) offered reflections on human subjectivity and its constraints. Nagel’s insights were elaborated before the social diffusion of computers and could not anticipate the cultural impact of technological artefacts capable of materializing interactive simulated worlds as well as disclosing virtual alternatives to the “self.” In this sense, this article proposes an understanding of computers as epistemological and ontological instruments. The embracing of a phenomenological standpoint entails that philosophical issues are engaged and understood from a fundamentally practical perspective. In terms of philosophical praxis, or “applied philosophy,” I explored the relationship between human phenomenologies and digital mediation through the design and the development of experimental video games. For instance, I have conceptualized the first-person action-adventure video game Haerfest (Technically Finished 2009) as a digital re-formulation of the questions posed in Nagel’s famous essay. Experiencing a bat’s perceptual equipment in Haerfest practically corroborates Nagel’s conclusions: there is no way for humans to map, reproduce, or even experience the consciousness of an actual bat. Although unverifiable in its correspondence to that of bats, Haerfest still grants access to experiences and perceptions that, albeit still inescapably within the boundaries of human kinds of phenomenologies, were inaccessible to humans prior to the advent of computers. Phenomenological alterations and virtual experiences disclosed by interactive digital media cannot take place without a shift in human kinds of ontologies, a shift which this study recognizes as the fundamental ground for the development of a new humanism (I deem it necessary to specify that I am not utilizing the term “humanism” in its common connotation, that is to say the one that emerged from the encounter between the Roman civilization and the late Hellenistic culture. According to this conventional acceptation, humanism indicates the realization of the human essence through “scholarship and training in good conduct” (Heidegger 1998, p. 244). However, Heidegger observed that this understanding of humanism does not truly cater to the original essence of human beings, but rather “is determined with regard to an already established interpretation of nature, history, world, and […] beings as a whole.” (Heidegger 1998, p. 245) The German thinker found this way of embracing humanism reductive: a by-product of Western metaphysics. As Heidegger himself specified in his 1949 essay Letter on Humanism, his opposition to the traditional acceptation of the term humanism does not advocate for the “inhuman” or a return to the “barbaric” but stems instead from the belief that the humanism can only be properly understood and restored in culture as more original way of meditating and caring for humanity and understanding its relationship with Being.). Additionally, this study explicitly proposes and exemplifies the use of interactive digital technology as a medium for testing, developing and disseminating philosophical notions, problems and hypotheses in ways which are alternative to the traditional textual one. Presented as virtual experiences, philosophical concepts can be accessed without the filter of subjective imagination. In a persistent, interactive, simulated environment, I claim that the crafting and the mediation of thought takes a novel, projective (In Martin Heidegger’s 1927 Being and Time, the term “projectivity” indicates the way a Being opens to the world in terms of its possibilities of being (Heidegger 1962, pp. 184–185, BT 145). Inspired by Heidegger’s and Vilem Flusser’s work in the field of philosophy of technology as well as Helmuth Plessner’s anthropological position presented in his 1928 book Die Stufen des Organischen und der Mensch. Einleitung in die philosophische Anthropologie, this study understands the concept of projectivity as the innate openness of human beings to construct themselves and their world by means of technical artefacts. In this sense, this study proposes a fundamental understanding of technology as the materialization of mankind’s tendency to overcome its physical, perceptual and communicative limitations.) dimension which I propose to call “augmented ontology.”. (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)

Two main claims are defended in this paper: first, that typical disputes in the literature about the ontology of physical objects are merely verbal; second, that the proper way to resolve these disputes is by appealing to common sense or ordinary language. A verbal dispute is characterized not in terms of private idiolects, but in terms of different linguistic communities representing different positions. If we imagine a community that makes Chisholm's mereological essentialist assertions, and another community that makes Lewis's (...) four-dimensionalist assertions, the members of each community speak the truth in their respective languages. This follows from an application of the principle of interpretive charity to the two communities. (shrink)

The current industrial revolution is said to be driven by the digitization that exploits connected information across all aspects of manufacturing. Standards have been recognized as an important enabler. Ontology-based information standard may provide benefits not offered by current information standards. Although there have been ontologies developed in the industrial manufacturing domain, they have been fragmented and inconsistent, and little has received a standard status. With successes in developing coherent ontologies in the biological, biomedical, and financial domains, an effort (...) called Industrial Ontologies Foundry (IOF) has been formed to pursue the same goal for the industrial manufacturing domain. However, developing a coherent ontology covering the entire industrial manufacturing domain has been known to be a mountainous challenge because of the multidisciplinary nature of manufacturing. To manage the scope and expectations, the IOF community kicked-off its effort with a proof-of-concept (POC) project. This paper describes the developments within the project. It also provides a brief update on the IOF organizational set up. (shrink)

The book is a collection of papers and aims to unify the questions of syntax and semantics of language, which are included in logic, philosophy and ontology of language. The leading motif of the presented selection of works is the differentiation between linguistic tokens (material, concrete objects) and linguistic types (ideal, abstract objects) following two philosophical trends: nominalism (concretism) and Platonizing version of realism. The opening article under the title “The Dual Ontological Nature of Language Signs and the Problem (...) of Their Mutual Relations” provides a broad introduction into the problem area connected with this differentiation, while the logic-formal characteristics of the distinction are framed in the work entitled “On the Type-Token Relationships” (Chapter 1). The basic part of the book deals with issues relating to syntax (Chapters 2-4) and semantics of language (Chapters 5-6), as well as pertaining to syntactic-semantic pragmatic questions (Chapters 7-13). Throughout the book, language, categorial language, is characterized syntactically as generated by classical categorial grammar (Chapter 2) and formalized on two opposing levels: as language of expression-tokens (level of tokens) and language of expression-types (level of types). The author’s considerations contained in Chapters 2 and 4 lead to the important philosophical conclusion that in formal-logical syntactic studies on language the assumption that expression-types constitute the primary language layer while expression-tokens make the secondary one, can be neglected; thus, this speaks in favour of the opposing standpoint—the concretistic one—in the ontology of language syntax. In the works “Meaning and Interpretations”, Parts I and II (Chapters 5 and 6), it is underlined, however, that such semantic concepts as: meaning, denotation and interpretation are defined on the types level, yet their formal definitions require making use of notions of the tokens level. The semantic notions introduced in the above-mentioned articles are also used in the following works of the present selection, under the titles: “Three Principles of Compositionality” and “On Metaknowledge and Truth” (Chapters 7 and 8). They formalize two principles of compositionality that are well known in the literature on the subject, deriving from Frege, i.e. those of meaning and of denotation; they are related to the syntactic principle of compositionality which was introduced by the author. All the three principles are, at the same time, three conditions of homomorphism of categorial language algebra into three kinds of non-standard models of language (one syntactic and two semantic ones: intensional and extensional), which allows introducing three definitions of truthfulness into these models. The next two works in the collection, entitled: “On Language Adequacy” and “What is the Sense in Logic and Philosophy of Language” (Chapters 9 and 10) concern adequacy of categorial language syntax along with its dual semantics: intensional and extensional, and categorial compatibility of any of its syntactic categories with two corresponding semantic categories: intensional and extensional, based on the compatibility the syntactic category of each language expression with the ontological category assigned to its denotatum. The well-known problem of categorial compatibility for first-order quantifiers finds its solution in the paper “Categories of First-Order Quantifiers” (Chapter 11). In the work “Logic and Ontology of Language” (Chapter 12), being in a sense a summary of the considerations presented in the preceding chapters of the book, language is treated as an ontological being, characterized in compliance with the logical conception of language proposed by Ajdukiewicz. Application—like throughout the book—of tools of classical logic and set theory has resulted in emergence of a general formal logical theory of syntax, semantics and pragmatics of language, which takes into account duality in the understanding of linguistic expressions as tokens (concretes) and types (abstract objects). In terms that take into account a functional approach to language itself, there comes out an ontological neutrality of logic with respect to existential assumptions relating to the ontological nature of linguistic expressions and their extra-linguistic ontological counterparts. The issues connected with applying logic while explaining the manner of using linguistic tokens and linguistic types to determine notions of language communication are raised and illustrated in the last chapter of the work, bearing the title “A Logical Conceptualization of Knowledge on the Notion of Language Communication”. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize (...) and integrate data relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

In the early modern period, contempt emerged as a persistent theme in moral philosophy. Most of the moral philosophers of the period shared two basic commitments in their thinking about contempt. First, they argued that we understand the value of others in the morally appropriate way when we understand them from the perspective of the morally relevant community. And second, they argued that we are naturally inclined to judge others as contemptible, and that we must therefore interrupt that natural movement (...) of sense-bestowal in order to value others in the morally appropriate way. In this paper I examine in detail the arguments of Nicolas Malebranche and Immanuel Kant concerning the wrongness of contempt, emphasizing the ways in which they depend on conceptions of community and of the interruption of moral sense-bestowal. After showing how each of these arguments fails to comprehend the nature and the wrongness of contempt, I argue that we can find the resources for a more adequate account in the work of Jean-Luc Nancy, and specifically in his reflections on ontology and on the meaning of community. (shrink)

This article addresses ontological negotiations in the Global South through three case studies of community-based research in Brazil and Ghana. We argue that ontological perspectives of Indigenous and other subjugated communities require an ontological pluralism that recognizes the plurality of both representational tools and ways of being in the world. Locating these two readings of ontological pluralism in the politics of the Global South, the article highlights a wider dynamic from ontological paternalism to ontological diversity to ontological decolonization. We conclude (...) by arguing that this dynamic provides important lessons for reorienting agendas in social ontology through Southern Ontologies. (shrink)

In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies (...) at the level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories. (shrink)

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata (...) registries, thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning. (shrink)

Ontologies represent principled, formalised descriptions of agents’ conceptualisations of a domain. For a community of agents, these descriptions may differ among agents. We propose an aggregative view of the integration of ontologies based on Judgement Aggregation (JA). Agents may vote on statements of the ontologies, and we aim at constructing a collective, integrated ontology, that reflects the individual conceptualisations as much as possible. As several results in JA show, many attractive and widely used aggregation procedures are prone to return (...) inconsistent collective ontologies. We propose to solve the possible inconsistencies in the collective ontology by applying suitable weakenings of axioms that cause inconsistencies. (shrink)

Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of terms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been little (...) effort directed towards such formal representation for affective phenomena, in part because of widespread debates within the affective science community on matters of definition and categorization. To address this requirement, we are developing an Emotion Ontology (EMO). (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all (...) plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

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. This ontology has led to the development of an Ontology-Driven Conceptual Modeling language dubbed OntoUML, reflecting the ontological micro-theories comprising UFO. Over the years, UFO and OntoUML have been successfully employed in a number of academic, industrial and governmental settings to create conceptual models in a variety (...) of different domains. These experiences have pointed out to opportunities of improvement not only to the language itself but also to its underlying theory. In this paper, we take the first step in that direction by revising the theory of types in UFO in response to empirical evidence. The new version of this theory shows that many of the meta-types present in OntoUML (differentiating Kinds, Roles, Phases, Mixins, etc.) 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 a formal characterization of this fragment of the theory, which is then used to advance a metamodel for OntoUML 2.0. Finally, we propose a computational support tool implementing this updated metamodel. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) (...) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (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)

Information may be defined as the conceptual or communicable part of the content of mental acts. The content of mental acts includes sensory data as well as concepts, particular as well as general information. An information system is an external (non-mental) system designed to store such content. Information systems afford indirect transmission of content between people, some of whom may put information into the system and others who are among those who use the system. In order for communication to (...) happen, the conceptual systems of the originators and users of the information must be sufficiently similar. A formal conceptual framework that can provide the basis for exchange of information is termed an ontology. In its most fundamental form, ontology studies the most basic constituents of reality. Traditionally, ontology seeks to reflects structures that are independent of thought and cognition. The term ontology is used more broadly in artificial intelligence and software engineering, to refer to the conceptual basis for an information system. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper (...) summarises ENVO’s motivation, content, structure, adoption, and governance approach. (shrink)

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as a (...) standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (shrink)

This is a short editorial to introduce the double issue of Applied Ontology that celebrates the journal's tenth anniversary. At a time when information technology of all kinds depends on the use of explicit ontologies, our journal addresses the modeling issues that underlie the next generation of computational systems. As the editors of Applied Ontology, we are excited by how far we have come in the past decade and by the opportunities that await our research community.