Standpoint logic is a recently proposed formalism in the context of knowledge integration, which advocates a multi-perspective approach permitting reasoning with a selection of diverse and possibly conflicting standpoints rather than forcing their unification. In this paper, we introduce nested sequent calculi for propositional standpoint logics---proof systems that manipulate trees whose nodes are multisets of formulae---and show how to automate standpoint reasoning by means of non-deterministic proof-search algorithms. To obtain worst-case complexity-optimal proof-search, we introduce a novel technique in the context (...) of nested sequents, referred to as "coloring," which consists of taking a formula as input, guessing a certain coloring of its subformulae, and then running proof-search in a nested sequent calculus on the colored input. Our technique lets us decide the validity of standpoint formulae in CoNP since proof-search only produces a partial proof relative to each permitted coloring of the input. We show how all partial proofs can be fused together to construct a complete proof when the input is valid, and how certain partial proofs can be transformed into a counter-model when the input is invalid. These "certificates" (i.e. proofs and counter-models) serve as explanations of the (in)validity of the input. (shrink)

The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical (...) principles that is designed to comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality. (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)

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a (...) way that will support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications. (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.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary (...) for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

Access to legal information and, in particular, to legal literature is examined for the creation of a search and retrieval system for Italian legal literature. The design and implementation of services such as integrated access to a wide range of resources are described, with a particular focus on the importance of exploiting metadata assigned to disparate legal material. The integration of structured repositories and Web documents is the main purpose of the system: it is constructed on the basis of a (...) federation system with service provider functions, aiming at creating a centralized index of legal resources. The index is based on a uniform metadata view created for structured data by means of the OAI approach and for Web documents by a machine learning approach, which, in this paper, has been assessed as regards document classification. Semantic searching is a major requirement for legal literature users and a solution based on the exploitation of Dublin Core metadata, as well as the use of legal ontologies and related terms prepared for accessing indexed articles have been implemented. (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)

Great progress to digitize the world’s available Biodiversity and Biogeography data have been made recently, but managing data from many different providers and research domains still remains a challenge. A review of the current landscape of metadata standards and ontologies in Biodiversity sciences suggests that existing standards, such as the Darwin Core terminology, are inadequate for describing Biodiversity data in a semantically meaningful and computationally useful way. As a contribution to fill this gap, we present an (...) class='Hi'>ontology-based system, called BiGe-Onto, designed to manage data together from Biodiversity and Biogeography. As data sources, we use two internationally recognized repositories: the Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS). BiGe-Onto system is composed of (i) BiGe-Onto Architecture (ii) a conceptual model called BiGe-Onto specified in OntoUML, (iii) an operational version of BiGe-Onto encoded in OWL 2, and (iv) an integrated dataset for its exploitation through a SPARQL endpoint. We will show use cases that allow researchers to answer questions that manage information from both domains. (shrink)

For years, attempts at ensuring the social sustainability of digital solutions have focused on ensuring that they are perceived as helpful and easy to use. A smooth and seamless work experience has been the goal to strive for. Based on document analysis and interviews with 15 stakeholders, we trace the setting up of a data infrastructure in Danish General Practice that had achieved just this goal – only to end in a scandal and subsequent loss of public support. (...) The ease of data access made it possible for data to be extracted, exchanged and used by new actors and for new purposes – without those producing the data fully realizing the expansion of the infrastructure. We suggest that the case has wider relevance for a still more data-intensive healthcare sector and a growing data economy: when those who produce the data are not made aware of new uses of data, it makes it more difficult to resolve potential conflicts along the way. In the Danish case, conflicting views on legitimate data use led to the collapse of the infrastructure. Therefore, while seamlessness may be a solution to the old problem of a poor fit between user and technology, this celebrated virtue may also involve new problems relating to social instability. As digital solutions tend to be integrated still more seamlessly in still more of our activities, we need to develop political mechanisms to define and protect the rights and obligations of both data suppliers and users in order to ensure the long-term sustainability of digital infrastructures. (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)

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)

Disaster response requires the cooperation of multiple emergency responder organizations (EROs). However, after‐action reports relating to large‐scale disasters identity communication difficulties among EROs as a major hindrance to collaboration. On the one hand, the use of two‐radio communication, based on multiple orthogonal frequencies and uneven coverage, has been shown to degrade inter‐organization communication. On the other hand, because they reflect different areas of expertise, EROs use differing terminologies, which are difficult to reconcile. These issues lead to ambiguities, misunderstandings, and (...) inefficient exchange of data and information among those involved, which can impede the response process and slow decision making. We, therefore, hypothesize that promoting semantic interoperability across ERO information systems might improve information exchange among stakeholders and thereby allow a more coherent response to the disaster. We propose an ontology‐based messaging service on the basis of the Emergency Data Exchange Language (EDXL) standards. The parties involved will continue to use the terminologies to which they are accustomed, but the system will resolve inconsistencies and thereby enhance mutual understanding among EROs by ensuring semantic translation of the exchanged information. The evaluation of the semantic translation demonstrated the effectiveness and accuracy of the proposed service. (shrink)

Babylon Knowledge Explorer (BKE) is an integrated suite of tools and information sources developed in GlaxoSmithKline's Analysis, Applications, and Research Technologies Department to support the prototyping and implementation of ontology-driven information systems and ontology-enhanced knowledge applications. In this paper we describe the current state of BKE development and focus on some of its distinctive or novel approaches, highlighting -/- * How BKE makes use of multiple large pre-existing ontologies in support of text and data mining. * The (...) methodology employed for importing an ontology and making it immediately accessible to BKE's tools, interfaces, and API. * A formal description of BKE's ontology-based fact model and how this is employed in implementing information retrieval and data mining capabilities. * A sample application built on BKE that illustrates an ontologyenhanced machine learning tool. (shrink)

The collection and dissemination of data on human and nonhuman organisms has become a central feature of 21st-century biology and has been endorsed by funding agencies in the United States and Europe as crucial to translating biological research into therapeutic and agricultural innovation. Large molecular data sets, often referred to as “big data,” are increasingly incorporated into digital databases, many of which are freely accessible online. These data have come to be seen as resources that play (...) a key role in mediating global market exchange, thus achieving a prominent social and economic status well beyond science itself. At the same time, calls to make all such data publicly and freely available have garnered strength and visibility, most prominently in the form of the Open Data movement. I discuss these developments by considering the conditions under which data journey across the communities and institutions implicated in globalized biology and biomedicine, and what this indicates about how Internet-based communication and the use of online databases affect scientific research and its role within contemporary society. (shrink)

In this paper we study the semantic data complexity of several controlled fragments of English designed for natural language front-ends to OWL (Web Ontology Language) and description logic ontology-based systems. Controlled languages are fragments of natural languages, obtained by restricting natural language syntax, vocabulary and semantics with the goal of eliminating ambiguity. Semantic complexity arises from the formal logic modelling of meaning in natural language and fragments thereof. It can be characterized as the computational complexity of (...) the reasoning problems associated to their semantic representations. Data complexity (the complexity of answering a question over an ontology, stated in terms of the data items stored therein), in particular, provides a measure of the scalability of controlled languages to ontologies, since tractable data complexity implies scalability of data access. We present maximal tractable controlled languages and minimal intractable controlled languages. (shrink)

Late in a career of more than sixty years, Thomas Burch, an internationally known social demographer, undertook a wide-ranging methodological critique of demography. This open access volume contains a selection of resulting papers, some previously unpublished, some published but not readily accessible [from past meetings of The International Union for the Scientific Study of Population and its research committees, or from other small conferences and seminars]. Rejecting the idea that demography is simply a branch of applied statistics, his work views (...) it as an autonomous and complete scientific discipline. When viewed from the perspective of modern philosophy of science, specifically the semantic or model-based school, demography is a balanced discipline, with a rich body of techniques and data, but also with more and better theories than generally recognized. As demonstrated in this book, some demographic techniques can also be seen as theoretical models, and some substantive/behavioral models, commonly rejected as theory because of inconsistent observations, are now seen as valuable theoretical models, for example demographic transition theory. This book shows how demography can build a strong theoretical edifice on its broad and deep empirical foundation by adoption of the model-based approach to science. But the full-fruits of this approach will require demographers to make greater use of computer modeling [both macro- and micro-simulation], in the statement and manipulation of theoretical ideas, as well as for numerical computation. This book is open access under a CC BY license. (shrink)

Biomedical Ontologies integrate diverse biomedical data and enable intelligent data-mining and help translate basic research into useful clinical knowledge. We present the RNA Ontology (RNAO), an o...

The demand for integrating and sharing heterogeneous data online has attracted the interest of cultural institutions in making information access and retrieval more effective via Semantic Web technologies. The present study proposes a digital repository for 3D scans of modernist sculptures in public spaces in the city of Rio de Janeiro, Brazil, with a view to ensuring access, use, reuse and preservation of this information. This is a qualitative exploratory experimental study based on the scientific literature and specific (...) empirical material. It presents the analysis results of vocabularies for physical artifact documents and their digital counterparts on the Semantic Web and a discussion on how these align with the nature of the metadata determined here, as well as a metadata modeling prototype implemented on the Tainacan platform and aimed at cataloging digital 3D replicas. We claim that the proposed model for documenting cultural heritage assets on Tainacan is easy to implement, in that it uses accessible technology with a wide internet user base, highly expressive in its descriptions of 3D and multimedia content and based on well-established metadata and ontology standards recommended by regulatory bodies and communities such as the World Wide Web Consortium and International Organization for Standardization. Keywords: networked heritage documents, digital repositories, 3D digitization, semantic annotation. (shrink)

Key activities in biomedicine and related research rely on collections of biological samples and related files. Access to such resources in industry and in academic contexts has become strategic and represents a central issue in the general framework of rising patenting practices and in debates about the knowledge economy. It raises important issues concerning the organisation of scientific and medical work, the outline of data-sharing guidelines, and science policy's contribution to the elaboration of an adapted framework. This paper presents (...) an ethnographic study of three French human biobanks. Building on field work (participant observation and in-depth interviews), the study focuses on data access in the concrete practices in biobanks. The paper develops a perspective based on an analysis of different exchange regimes. We argue that access practices are submitted to the different regimes that can coexist and be articulated within the daily activities of each biobank. We also discuss how this perspective can further our understanding of biomedical research, and how it might inform data access policy. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:History of Philosophy and the Reflective Society by Riccardo PozzoRobert R. ClewisPOZZO, Riccardo. History of Philosophy and the Reflective Society. Berlin: Walter de Gruyter, 2021. vi + 231 pp. Cloth, $94.99In a forward-looking proposal, Pozzo lays out his vision for a multidisciplinary history of philosophy "from a global perspective." This book is "a long position paper, an extended essay dedicated to twenty-first century policies of philosophical research from (...) a global perspective." The chosen format is a Denkschrift, that is, a memorandum in the sense of a document that experts lay out for their government to ponder. Perhaps, Pozzo suggests, the history of philosophy could even have an impact on economic authorities and policymakers. Indeed, the work seems driven by the laudable aim of promoting access and equality around the world. The author reveals a just concern for migrants in particular, since they bring [End Page 156] with them their intellectual traditions and philosophical texts, which can be translated and thereby foster intercultural dialogue.The book consists of an introduction (chapter 1) followed by nine chapters. It has a thirty-page references list as well as subject and name indexes. In part one, Pozzo argues for the need for new narratives in the history of philosophy (chapter 2), in order to establish its role in addressing migration (chapter 3). The second part concerns reflective society (chapter 4). It considers societal readiness (chapter 5) and cultural innovation (chapter 6). Part three explores the paradigm shift from a close reading of texts to a "distant" reading of corpora (chapter 7), a shift Pozzo endorses. It examines implications for the translation of languages (chapter 8) and the translation of studies (knowledge) and competencies (chapter 9). Chapter 10 concludes by briefly reflecting on the notions of the "fluidity" of peoples and their ideas, biodiversity (and food), and spiritual humanism based on dignity.Scholars in the history of philosophy "should be open to the idea of a pluriversum of a history of facts and places, whereby history of philosophy finds its grounding in spatial heterogeneity." Nowadays, when people migrate and transfer competencies at increasing velocity, the "history of philosophy can be usefully reinvented on the basis of its consideration of intercultural dialogue." Pozzo considers the World Digital Library to be "one of the most exciting examples of corpora that talk to each other"—an idea he uses not merely metaphorically. By "corpora" is meant not just the sum of separate books, but XML-accessible complete collections of traditions of texts, with corresponding dictionaries, thesauri, and reference works, which make it possible to analyze a number of original texts as well as transliterations into other alphabets or hanzi characters. The result would be a "data-driven" history of philosophy.Given that history of philosophy is a product of culture, it is influenced by migrating peoples, who bring philosophical ideas and religious traditions with them. Research on migration thus ought to also consider translations of texts and competencies from one to another context, be it linguistic, economic, political, or cultural. The humanities, and a reflective society more generally, might provide a partial basis for intercultural dialogue. The history of philosophy might even thereby improve the quality of life of citizens.Pozzo rightly emphasizes that we need multilingual philosophers and historians of philosophy. History of philosophy ought to also be based on robust lexical and historical considerations, and historians of philosophy should be trained in a number of the world's languages as well as face the challenge of dealing with multilingualism and with validating translations. Pozzo's proposed methodology, informed by computational techniques, relies on tools such as vocabularies, ontologies, concordances, frequencies, or the analysis of texts and corpora, which integrates quantitative and formal methods into the portfolio of the methods of history of philosophy and intellectual history. Since Pozzo has published [End Page 157] widely on Kant, it is fitting that he explores Kant on migration as well as the editorial contexts and translation projects concerning the philosopher's writings.As for aesthetics, Pozzo notes that the history of philosophy can reflect on migrants' cultural and artistic creations. Historians of philosophy should thus start observing and interpreting phenomena created by... (shrink)

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and (...) relations dedicated to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

Intelligent defence support systems are confronted with the need to manage ever-increasing floods of data in a way that raises significant challenges because the data are described and presented using different terminologies and formats. How, on this basis, is it possible to reach a common understanding of the information content of these data among people and software agents? How is it possible to ensure that domain knowledge is reused in consistent fashion in a way that makes this (...) information available for integration and analysis? How can we support the identification, selection, composition, and orchestration of services based on such diverse data providing homogeneous support by a service-oriented architecture? This collection is devoted to the use of ontologies to answer questions such as these. (shrink)

We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of (...) data sources, types, models, and modalities (including text, images, audio, and signals). The result of applying this strategy to a given body of data is an evolving Dataspace that allows the application of a variety of integration and analytic processes to diverse data contents. We conceive semantic enhancement (SE) as a lightweight and flexible process that leverages the richness of the structured contents of the Dataspace without adding storage and processing burdens to what, in the intelligence domain, will be an already storage- and processing-heavy starting point. SE works not by changing the data to which it is applied, but rather by adding an extra semantic layer to this data. We sketch how the semantic enhancement approach can be applied consistently and in cumulative fashion to new data and data-models that enter the Dataspace. (shrink)

We develop a framework for assessing security market quality, relating five elements of market design to three metrics of market integrity and two metrics of market efficiency. We empirically implement this integrity–efficiency MQ framework by testing a hypothesis that trade-based ramping manipulation at the close raises execution costs on 24 security markets worldwide. Estimating a simultaneous equations model of ramping incidence, spreads, and the probability of deploying real-time surveillance, we show that quoted bid-ask spreads are positively related to the (...) incidence of MTC across seven liquidity deciles. The magnitude is economically significant; improving market integrity by cutting MTC in half reduces spreads 6–11 %. Allowing direct market access in conjunction with RTS, conducting auctions at the close, and developing regulations that require surveillance, all reduce MTC and thereby lower spreads, assuring better market integrity and enhancing market efficiency. Introducing circuit breakers or prohibiting shorts poses integrity–efficiency tradeoffs. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, (...) agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (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 article introduces the methodology of the ‘Ontology Explorer’, a semantic method and JavaScript-based open-source tool to analyse data models underpinning information systems. The Ontology Explorer has been devised and developed by the authors, who recognized a need to compare data models collected in different formats and used by diverse systems. The Ontology Explorer is distinctive firstly because it supports analyses of information systems that are not immediately comparable and, secondly, because it systematically and (...) quantitatively supports discursive analysis of ‘thin’ data models – also by detecting differences and absences through comparison. When applied to data models underpinning systems for population management, the Ontology Explorer enables the apprehension of how people are ‘inscribed’ in information systems: which assumptions are made about them, and which possibilities are excluded by design. The Ontology Explorer thus constitutes a methodology to capture authorities’ own imaginaries of populations and the ‘scripts’ through which they enact actual people. Furthermore, the method allows the comparison of scripts from diverse authorities. This is exemplified by illustrating its functioning with information systems for population management deployed at the European border. Our approach integrates a number of insights from early infrastructure studies and extends their methods and analytical depth to account for contemporary data infrastructures. By doing so, we hope to trigger a systematic discussion on how to extend those early methodical innovations at the semantic level to contemporary developments in digital methods. (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)

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)

This paper provides an account of the challenges and potentialities of a solidarity-based approach to data access and governance. To do that, it offers an infraethical understanding of solidarity that describes it as a structural moral enabler that can sustain collective action and risk taking. The paper ends with a brief discussion of health data access as a possible case study to test this approach.

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results (...) in publicly available databases. Such annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

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

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration (...) techniques such as ontology-based multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (shrink)

We address what is still a scarcity of general mathematical foundations for ontology-based semantic integration underlying current knowledge engineering methodologies in decentralised and distribut...

Consumer indirect misbehavior in access-based consumption is a significant challenge for enterprises. The literature is in short of a deep understanding of the antecedent conditions of consumer indirect misbehavior in this context and limited by inconsistent findings, calling for developing a holistic and integrative theoretical framework. This study integrates three commonly used theoretical perspectives in the consumer misbehavior literature to present holistic archetypes of consumer indirect misbehavior formation. In accordance with this theoretical objective, we adopted an emerging approach for (...) configurational analysis, i.e., fuzzy-set qualitative comparative analysis, to analyze the complex combinations of six influencing factors. We collected data using a scenario-based field survey of 264 experienced consumers of a popular bike-sharing service in China. The scenarios were developed based on relevant literature and a Delphi study. The fsQCA results reveal multiple configurations for high and low levels of consumer misbehavior intention. Specifically, perceived benefits and moral definition play important roles, while the effect of sanctions is highly dependent on other factors. These results lead us to derive three theoretical propositions for antecedent conditions leading to consumers’ indirect misbehavior intentions in access-based consumption. This study enriches our understanding of the causes of misbehavior and provides novel insights for management practitioners to take appropriate countermeasures. (shrink)

Recent advances in medical and information technologies, the availability of new types of medical data, the requirement of increasing numbers of study participants, as well as difficulties in recruitment and retention, all present serious problems for traditional models of specific and informed consent to medical research. However, these advances also enable novel ways to securely share and analyse data. This paper introduces one of these advances—blockchain technologies—and argues that they can be used to share medical data in (...) a secure and auditable fashion. In addition, some aspects of consent and data collection, as well as data access management and analysis, can be automated using blockchain-based smart contracts. This paper demonstrates how blockchain technologies can be used to further all three of the bioethical principles underlying consent requirements: the autonomy of patients, by giving them much greater control over their data; beneficence, by greatly facilitating medical research efficiency and by reducing biases and opportunities for errors; and justice, by enabling patients with rare or under-researched conditions to pseudonymously aggregate their data for analysis. Finally, we coin and describe the novel concept of prosent, by which we mean the blockchain-enabled ability of all stakeholders in the research process to pseudonymously and proactively consent to data release or exchange under specific conditions, such as trial completion. (shrink)

In recent years in Turkey, it has been attempted to ensure that students who need special education are educated through inclusion. In the meanwhile, it became important to reveal scientifically the educational theories on which the inclusive education is based and the approach of Islam towards inclusive education that somehow has an influence on our national education policy. This study aims to examine the educational theories on which the inclusive education is based and the Islamic approach towards inclusive (...) education. The data of the study was collected by literature review. As a result, it is possible to say that the underlying theories of inclusive education are integrated education theory, cognitive democrative theory and dysontogenesis theories. In addition, although there are no specific verses for inclusive education in the Qurʾān and the Sunnah, it can be said that Islam has an positive approach to the inclusive education in general. Depending on this result, formal education should be conducted in the context of the principle of “least restricted education environment”.Summary: It is a matter of controversy about how education that increases the potential of human beings can be given to people who differ from their peers and who need special education. In recent years, there have been two prominent views in literature on this issue: The first is the ‘discriminatory’ view, which advocates that individuals with special needs should receive education in special spaces with similar students. The second is the ‘integrative view’, which states that these students should receive inclusive education with their peers. This view defends that students with special needs should be educated in separate boarding/day special education schools and special education classes within the normal schools. Recently in Turkey it is aimed to provide education to the students who need special education mostly by means of inclusion as an alternative to the first group. For this education, which is held with the claim of a less restricted environment, the conditions of the students are constantly improved with new regulations.This study aims to reveal the theories that can be the basis of inclusive education and Islam's approach to inclusive education. In this study, I will try to find answers to the following questions.1. What are the educational theories and claims that can be the basis of inclusive education?2. What are the principles of inclusive education in the Qur’an and Sunnah?This study is important in terms of revealing general opinions that may be the basis of theoretical foundations of inclusive education and examining Islam’s approach to inclusive education. The study, which was prepared by examining the English and Turkish literature available within the scope of the possibilities, was designed with theoretical analysis method. Although ‘accessibility’, which is considered among the shortcomings of theoretical studies in literature, is an important limitation for this study, the fact that it constitutes a theoretical ground for future studies and fills an important gap in the literature determines the importance of the study.Integrated education theory, cognitive democratic theory and dyontogenesis theories can be regarded as the establishing theoretical foundations of inclusive education. Integrated education theory is based on Whitehead’s philosophy of education. This philosophy sees the individual as a whole. It does not intend to make people have a profession or make money by simply using their intelligence. Instead, it helps to ensure that both the individual and society as a whole are happy by helping them to make the most of their potential. This model is based on developing emotion, mind, body, and spirituality as a whole. The distinctness and sacredness of human life and the need to know about this sacredness are the main pillars of integrated education theory. In this model all people are seen equal. According to this theory, the “natural” as well as the “beautiful” is appreciated. Therefore, no one feels bad in such an environment because of its differences. Because of the value given to them, each individual’s love of learning and ideals remain alive. The individual makes use of his/her mind to make a connection between the meaning of life and the school.Cognitive democratic theory asserts that educational arrangements should be made to prevent any feelings of alienation, oppression, and insignificance by considering different groups in education. This theory, which emphasizes the phenomenon of democracy and citizenship, aims at social cohesion in the light of epistemological principles. The theory is based on the fact that social change and change in education support each other. According to the theory, the formation of democratic citizenship is only possible if the school environment is a place where students can internalize democratic values. This is achieved by equal consideration of each segment at different levels. According to this theory, elements such as classroom environment, discipline, program, rights, participation in decisions, educational activities should be organized according to democratic values. In such an environment, different special education students find a place for themselves.Vygotsky's dysontogenesis thesis is based on his theory of social learning. His theory provides a methodological framework for inclusion in special education. The theory states that information is obtained through social communication. In this theory, knowledge is an element that is acquired together with other people rather than something that happens in the human mind. According to this theory, instead of focusing on the brain (head), where social knowledge is formed, self, mind, emotion should be included in education. Also, disability is a social deviation rather than a biological disease. Social relations and the environment mostly shape this deviation. Therefore, the abnormal child approach that has become a place in the society should be abandoned. The theory opposes the concept of mental retardation. Because mental disability should be explained by the differences in mental development. According to this theory, mental retardation is a social problem; education should be provided with appropriate methods over the examples that can be experienced in a commonplace with their peers. Distracting the student from his/her normal peers due to his/her differences, creates negative social conditions and harms his/herself.As far as I have examined, there is no direct Qur’anic verse or phrase about inclusive education for the disabled. However, there are verses regarding the integration and solidarity of the society on righteousness. Principles for inclusive education can be drawn from these verses. The Prophet valued the disabled and settled the principles on how society should treat them. He frequently visited them, enabled them to employ appropriate jobs, determined the conditions of the economic order by considering them, and dignified them with honor. In other words, he tried to make provisions to prevent the disabled from being separated from society. For example he urged Zahir bin Itban to continue trade, asked Abdullah Ibn Umm Mektum to come to community prayers, thus he sought different ways to integrate disabled people into society. These practices can be seen as a positive outlook towards the mainstreaming education of today. In the period of the four great caliphs, practices for mainstreaming education continued. (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’, ‘ (...) class='Hi'>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)

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)

In many countries, such as Canada, the USA, England, and Australia, to graduate from a regulated profession such as nursing, students must complete a set of work‐integrated learning (WIL) hours and demonstrate their ability to safely perform physical skills and apply knowledge in relation to professional standards. For a disabled nursing student (DNS) undergoing training in higher education institutions (HEI), securing proper accommodations to participate effectively in WIL experiences has been difficult due to concerns related to risks to self and (...) patient safety. This study used critical discourse analysis to investigate the framing of risk and safety in association with providing DNS with accommodation in WIL. Our data were collected from an intensive codesign (group‐based discussion) session with participants (n = 16), including clinicians and DNS, from four institutions (two WIL‐sites and two HEI organizations). Using an iterative thematic approach based on Foucauldian framework, our analysis revealed three ways in which health professionals discursively framed risk and safety: (a) beliefs that a lack of disclosure by disabled students decreases patient safety and indicates poor self‐reflection, (b) concerns that accommodating students poses a risk to institutions offering WIL experiences and to the relationships between HEI and institutions offering WIL‐sites, and (c) a framing which challenges the dominant discourse by thinking about safety and risk more expansively. Our findings suggest the first two of these framings are ableist and function to enact barriers to access for DNSs in WIL, whereas the third framing serves the goal of inclusion. Recommendations to address the current ableist discourse within the Canadian nursing context are provided, which may also be applicable across other regulated health professions. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, (...) class='Hi'>data about languages may be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

Health‐related data uses and data sharing have been in the spotlight for a while. Since the beginning of the big data era, massive data mining and its inherent possibilities have only increased the debate about what the limits are. Data governance is a relevant aspect addressed in ethics guidelines. In this context, the European project BRIDGE Health (BRidging Information and Data Generation for Evidence‐based Health policy and research) strove to achieve a comprehensive, integrated (...) and sustainable EU health‐information system. One of the aims of the project was to evaluate the requirements to construct a data‐linkage infrastructure for the secure management of health information. In a blueprint provided for this infrastructure, the topics ethics and the intimately related governance occupied a whole section, where the recent ethics guidelines by the Council for International Organizations of Medical Sciences (CIOMS) and the World Medical Association (WMA) were referenced. We explore what has changed in the latest versions of the ethics documents adopted by CIOMS and WMA regarding the management of health data and human tissues, the appropriateness of their application in new forms of research and infrastructures as the proposed in the BRIDGE Health project, and whether society should be so concerned about this topic, in the digital era of social exchange. (shrink)

We present a reference model for finding evidence of discrimination in datasets of historical decision records in socially sensitive tasks, including access to credit, mortgage, insurance, labor market and other benefits. We formalize the process of direct and indirect discrimination discovery in a rule-based framework, by modelling protected-by-law groups, such as minorities or disadvantaged segments, and contexts where discrimination occurs. Classification rules, extracted from the historical records, allow for unveiling contexts of unlawful discrimination, where the degree of burden over (...) protected-by-law groups is evaluated by formalizing existing norms and regulations in terms of quantitative measures. The measures are defined as functions of the contingency table of a classification rule, and their statistical significance is assessed, relying on a large body of statistical inference methods for proportions. Key legal concepts and reasonings are then used to drive the analysis on the set of classification rules, with the aim of discovering patterns of discrimination, either direct or indirect. Analyses of affirmative action, favoritism and argumentation against discrimination allegations are also modelled in the proposed framework. Finally, we present an implementation, called LP2DD, of the overall reference model that integrates induction, through data mining classification rule extraction, and deduction, through a computational logic implementation of the analytical tools. The LP2DD system is put at work on the analysis of a dataset of credit decision records. (shrink)

Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some (...) will find self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. Ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But the ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, ontologies such as the GO are in different respects comparable to scientific theories, to scientific databases, and to scientific journal publications. Such a view implies a new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a new approach to the evaluation of ontologies and to the training of ontologists. (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)

Formal ontologies are nowadays widely considered a standard tool for knowledge representation and reasoning in the Semantic Web. In this context, they are expected to play an important role in helping automated processes to access information. Namely: they are expected to provide a formal structure able to explicate the relationships between different concepts/terms, thus allowing intelligent agents to interpret, correctly, the semantics of the web resources improving the performances of the search technologies. Here we take into account a problem regarding (...) Knowledge Representation in general, and ontology based representations in particular; namely: the fact that knowledge modeling seems to be constrained between conflicting requirements, such as compositionality, on the one hand and the need to represent prototypical information on the other. In particular, most common sense concepts seem not to be captured by the stringent semantics expressed by such formalisms as, for example, Description Logics (which are the formalisms on which the ontology languages have been built). The aim of this work is to analyse this problem, suggesting a possible solution suitable for formal ontologies and semantic web representations. The questions guiding this research, in fact, have been: is it possible to provide a formal representational framework which, for the same concept, combines both the classical modelling view (accounting for compositional information) and defeasible, prototypical knowledge ? Is it possible to propose a modelling architecture able to provide different type of reasoning (e.g. classical deductive reasoning for the compositional component and a non monotonic reasoning for the prototypical one)? We suggest a possible answer to these questions proposing a modelling framework able to represent, within the semantic web languages, a multilevel representation of conceptual information, integrating both classical and non classical (typicality based) information. Within this framework we hypothesise, at least in principle, the coexistence of multiple reasoning processes involving the different levels of representation. (shrink)