Ontological realism is a philosophical stance that provides a definitional framework for ontologies and is referred to by various applied ontologists. From a computer science perspective, ontologies are often associated with formal languages for the representation of ontologies like the Web Ontology Language (OWL). It has, however, not been made explicit how the realist framework is related to the representation formalism. We analyse how the representational units of OWL can be used for modelling realist ontologies. While OWL is (...) sufficiently close to the realist framework of ontologies to describe them, there are categories in OWL that are alien to realist ontologies or duplicate categories in realist ontologies. This clarification allows separating talk about ontologies in general from talk about their specific representation. (shrink)

Ontology languages for the Semantic Web have their strengths and weaknesses, in particular in the light of deploying them for biological and medical information systems. We survey and compare the Description Logics-based OWL languages, and the DL-Lite and DLR families of languages. Language choices that an ontology developer has to make are, among others, expressivity with n-ary relations (where n > 2) and more role properties versus ontology usage for data-intensive tasks. Guidelines are suggested to facilitate (...) choosing the language best fitted for a task. (shrink)

The paper gives ontologies in the Web Ontology Language (OWL) for Legal Case-based Reasoning (LCBR) systems, giving explicit, formal, and general specifications of a conceptualisation LCBR. Ontologies for different systems allows comparison and contrast between them. OWL ontologies are standardised, machine-readable formats that support automated processing with Semantic Web applications. Intermediate concepts, concepts between base-level concepts and higher level concepts, are central in LCBR. The main issues and their relevance to ontological reasoning and to LCBR are discussed. Two (...) LCBR systems (AS-CATO, which is based on CATO, and IBP) are analysed in terms of basic and intermediate concepts. Central components of the OWL ontologies for these systems are presented, pointing out differences and similarities. The main novelty of the paper is the ontological analysis and representation in OWL of LCBR systems. The paper also emphasises the important issues concerning the representation and reasoning of intermediate concepts. (shrink)

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

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

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.

Web legal information retrieval systems need the capability to reason with the knowledge modeled by legal ontologies. Using this knowledge it is possible to represent and to make inferences about the semantic content of legal documents. In this paper a methodology for applying NLP techniques to automatically create a legal ontology is proposed. The ontology is defined in the OWL semantic web language and it is used in a logic programming framework, EVOLP+ISCO, to allow users to query (...) the semantic content of the documents. ISCO allows an easy and efficient integration of declarative, object-oriented and constraint-based programming techniques with the capability to create connections with external databases. EVOLP is a dynamic logic programming framework allowing the definition of rules for actions and events. An application of the proposed methodology to the legal web information retrieval system of the Portuguese Attorney General’s Office is described. (shrink)

Computational models of affect (CMAS), in their most common form, cannot take into account the qualitative (phenomenal) dimension of affect itself. Their expressivity can be extended, thus promoting the much sought-after standardization in the most theory-neutral way, using OWL (Web Ontology Language) and machine learning techniques. OWL is an expressive formal language, as well as an established open standard, and can be used to describe the models, possibly including qualitative entities at the fundamental level. The supervised machine (...) learning techniques allow the direct learning and application of models described as OWL ontologies. Thanks to human supervision (e.g. using datasets labeled by a human user), they can take into account the qualitative dimension of affect when the models warrant it. To further promote the aforementioned standardization, the task of classifying texts according to their affective content (known in computer science as "sentiment analysis") can be recommended as a way to assess the performance of the models. It is a multifaceted task, in which usually divergent fields as philosophy, psychology and computer science meet. Moreover, since it is a very current task in computer science, there are many resources available to facilitate the development of a standard benchmark for CMAS. (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)

As it emerged from philosophical analyses and cognitive research, most concepts exhibit typicality effects, and resist to the efforts of defining them in terms of necessary and sufficient conditions. This holds also in the case of many medical concepts. This is a problem for the design of computer science ontologies, since knowledge representation formalisms commonly adopted in this field (such as, in the first place, the Web Ontology Language - OWL) do not allow for the representation of concepts (...) in terms of typical traits. The need of representing concepts in terms of typical traits concerns almost every domain of real world knowledge, including medical domains. In particular, in this article we take into account the domain of mental disorders, starting from the DSM-5 descriptions of some specific disorders. We favour a hybrid approach to concept representation, in which ontology oriented formalisms are combined to a geometric representation of knowledge based on conceptual space. As a preliminary step to apply our proposal to mental disorder concepts, we started to develop an OWL ontology of the schizophrenia spectrum, which is as close as possible to the DSM-5 descriptions. (shrink)

Though many kinds of multi-agent systems based on argumentation have been proposed where only rule-based knowledge is taken into account, they have been unable to handle the ontological knowledge so far. In our daily life, however, there are a lot of human argumentation where both ontological and rule knowledges are used. For example, in e-commerce, a seller and a buyer usually use ontologies about products along with their respective strategic rules for buying and selling. Recent progress of the Semantic Web (...) technology provides expressive ontology languages. In this paper, we demonstrate integration of the Semantic Web reasoning and argument-based reasoning. We have implemented the integrated system such that Logic of Multiple-valued Argumentation-based agent system (specialized to two values { f, t }) can be accessible to the Semantic Web reasoning established as the description logic reasoning system, given ontologies expressed by OWL DL or its notational variant the DL SHOIN (D). An interesting argumentation result using both ontologies and rules about the university curriculum is shown as an example executed by our system. (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)

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)

The semantic web ontology languages RDFS and OWL are widely used but limited in both their expressivity and their support for modularity and integrated documentation. Expressivity, modularity, and documentation of formal knowledge have always been important issues in the MKM community. Therefore, we try to improve these ontology languages by well-tried MKM techniques. Concretely, we propose OM- Doc as an alternative. We show how OMDoc can be made compatible with semantic web ontology languages, focusing on knowledge representation, (...) modular design, documentation, and metadata. We evaluate our technology by re-implementing the Friend-of-a-friend (FOAF) ontology and applying it in a novel metadata framework for technical documents (including ontologies). (shrink)

Legal codes, such as the Uniform Commercial Code (UCC) examined in this article, are good points of entry for AI and ontology work because of their more straightforward adaptability to relationship linking and rules-based encoding. However, approaches relying on encoding solely on formal code structure are incomplete, missing the rich experience of practitioner expertise that identifies key relationships and decision criteria often supplied by experienced practitioners and process experts from various disciplines (e.g., sociology, political economics, logistics, operations research). This (...) research focuses on the UCC because it transcends the limitations of a formal code, functioning essentially as a composite. AI work can benefit from real-world codes like the UCC, which are essentially formal codes enlightened from a more realistic experience-base from centuries of development in international commercial transactions settings. This paper then describes our initial work in converting an expert system on the U.S. law governing the sale of goods from Article II of the Uniform Commercial Code (UCC), into a knowledge-based system using the Web Ontology Language OWL. (shrink)

Background: In order to improve ontology quality, tool- and language-related tutorials are not sufficient. Care must be taken to provide optimized curricula for teaching the representational language in the context of a semantically rich upper level ontology. The constraints provided by rigid top and upper level models assure that the ontologies built are not only logically consistent but also adequately represent the domain of discourse and align to explicitly outlined ontological principles. Finally such a curriculum must (...) take into account the pre-existing skills and knowledge of the target audience. -/- Objective: To develop a well-structured curriculum aligned to the particular requirements of life science professionals, in order to enable them to create logically sound, domain adequate and predicable ontologies using the Web Ontology Language (OWL) in Protégè. -/- Methods: Content selection for the curriculum was based on the literature, pre-existing tutorials, and a guideline for good ontology development (i.e ontology design enhancing domain adequacy, sustainability and interoperability) that drew on the authors previous experiences with large ontology development projects. Learning objectives were formulated according to a needs assessment of the targeted learners, who were students trained in life sciences with basic knowledge and practical skills in computer science. As instructional format we choose an approach with a high amount of practical exercises. The curriculum was first implemented with 24 Students and 7 lecturers/ tutors over 5 full days. The curriculum was evaluated by gathering the participants feedback via a questionnaire. -/- Results: Curricular development produced 16 modules of approximately 2 hours each, which covered basic principles of Applied Ontology, description logic syntax and semantics, as well as best design practices outlined in ontology design patterns and variants of the BioTop upper ontology. An opinion survey based on questionnaires indicated that the participants took advantage from the teaching strategies applied, as they indicated good knowledge gain and acknowledged the relevance of the modules. The difficulty was rated slightly lower. -/- Conclusion: The development of teaching material for principled ontology design and best practices is of crucial importance in order to enhance the quality of biomedical ontologies. Here, we present a curriculum for a week long workshop, leveraging on current educational principles, focusing on interactive hands-on exercises, group interactions, and problem-oriented learning. Whereas evaluation clearly showed the success of this approach, in particular regarding student’s satisfaction, the objective measurement of traceable effects on the quality of the generated ontology, although of much higher interest, has just started. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Knowledge representation is a central issue for Artificial Intelligence and the Semantic Web. In particular, the problem of representing n-ary relations in RDF-based languages such as RDFS or OWL by no means is an obvious one. With respect to previous attempts, we show why the solutions proposed by the well known W3C Working Group Note on n-ary relations are not satisfactory on several scores. We then present our abstract model for representing n-ary relations as directed labeled graphs, and we show (...) how this model gives rise to a new ontological pattern for the representation of such relations in the Semantic Web. To this end, we define PROL. PROL is an ontological language designed to express any n-ary fact as a parametric pattern, which turns out to be a special RDF graph. The vocabulary of PROL is defined by a simple RDFS ontology. We argue that the parametric pattern may be particularly beneficial in the context of the Semantic Web, in virtue of its high expressive power, technical simplicity, and faithful meaning rendition. Examples are also provided. (shrink)

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

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

In the context of the emerging Semantic Web and the quest for a common logical framework underpinning its architecture, the relation of rule-based languages such as Answer Set Programming (ASP) and ontology languages such as the Web Ontology Language (OWL) has attracted a lot of attention in the literature over the past years. With its roots in Deductive Databases and Datalog though, ASP shares much more commonality with another Semantic Web standard, namely the Simple Protocol and RDF (...) Query Language (SPARQL). In this paper, we take the recent approval of the SPARQL1.1 standard by the World Wide Web consortium (W3C) as an opportunity to introduce this standard to the Logic Programming community by providing a translation of SPARQL1.1 into ASP. In this translation, we explain and highlight peculiarities of the new W3C standard. Along the way, we survey existing literature on foundations of SPARQL and SPARQL1.1, and also combinations of SPARQL with ontology and rules languages. Thereby, apart from providing the means to implement and support SPARQL natively within Logic Programming engines and particularly ASP engines, we hope to pave the way for further research on a common logical framework for Semantic Web languages, including query languages, from an ASP point of view. (shrink)

The Leibniz Center for Law is involved in the project Digitale Uitwisseling Ruimtelijke Plannen [DURP (http://www.vrom.nl/durp); digital exchange of spatial plans] which develops a XML-based digital exchange format for spatial regulations. Involvement in the DURP project offers new possibilities to study a legal area that hasn’t yet been studied to the extent it deserves in the field of Computer Science & Law. We studied and criticised the work of the DURP project and the Dutch Ministry of internal affairs on metadata (...) for regulatory documents, and made an inventory of issues related to legal knowledge representation that it felt were not sufficiently covered by current initiatives in the Geographic Information Systems (GIS) field. This inventory was an input to the DURP standardisation effort. In a second phase of the project we extended the METALex XML schema (cf. Boer et al. 2002; Boer et al. 2003) for ‚regular’ legal sources that we developed in the past for geospatial regulatory information, in order to support exchange of spatial regulations, including the associated geospatial information in the form of maps. We developed a prototype application and demonstrated how the spatial planning information in GML can be combined with XML with only minimal changes, using the Web Ontology Language (OWL). This paper describes our experiences. (shrink)

Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara (...) distinção entre os quatro tipos de representação, de forma a oferecer uma base mais racional para o uso das ontologias e artefatos relacionados no avanço da integração de dados e interoperabilidade de sistemas de raciocínio associados. Destacamos que apenas uma pequena porção de fatos cientificamente relevantes em áreas como a biomedicina pode ser adequadamente representada por ontologias formais, quando estas últimas são concebidas como representações de tipos de entidades. Particularmente, a tentativa de codificar conhecimento padrão ou probabilístico pela utilização de ontologias assim concebidas é fadada à produção de modelos não intencionais e errôneos. (shrink)