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Probabilistic model checking (PMC) is a well-established method for the quantitative analysis of state based operational models such as Markov decision processes. Description logics (DLs) provide a well-suited formalism to describe and reason about knowledge and are used as basis for the web ontology language (OWL). We investigate how such knowledge described by DLs can be integrated into the PMC process, introducingontology-mediatedPMC. Specifically, we proposeontologized programsas a formalism that links ontologies to behaviors specified by probabilistic guarded commands, the de-facto standard input formalism for PMC tools such as Prism. Through DL reasoning, inconsistent states in the modeled system can be detected. We present three ways to resolve these inconsistencies, leading to different Markov decision process semantics. We analyze the computational complexity of checking whether an ontologized program is consistent under these semantics. Further, we present and implement a technique for the quantitative analysis of ontologized programs relying on standard DL reasoning and PMC tools. This way, we enable the application of PMC techniques to analyze knowledge-intensive systems.We evaluate our approach and implementation on amulti-server systemcase study,where different DL ontologies are used to provide specifications of different server platforms and situations the system is executed in.

Ontology-mediated querying (OMQ) provides a paradigm for query answering according to which users not only query records at the database but also query implicit information inferred from ontology. A key challenge in OMQ is that the implicit information may be infinite, which cannot be stored at the database and queried by off -the -shelf query engine. The commonly adopted technique to deal with infinite entailments is query rewriting, which, however, comes at the cost of query rewriting at runtime. In this work, the partial materialization method is proposed to ensure that the extension is always finite. The partial materialization technology does not rewrite query but instead computes partial consequences entailed by ontology before the online query. Besides, a query analysis algorithm is designed to ensure the completeness of querying rooted and Boolean conjunctive queries over partial materialization. We also soundly and incompletely expand our method to support highly expressive ontology language, OWL 2 DL. Finally, we further optimize the materialization efficiency by role rewriting algorithm and implement our approach as a prototype system SUMA by integrating off-the-shelf efficient SPARQL query engine. The experiments show that SUMA is complete on each test ontology and each test query, which is the same as Pellet and outperforms PAGOdA. Besides, SUMA is highly scalable on large datasets.

The project “Semantic Technologies for Situation Awareness” was concerned with detecting certain critical situations from data obtained by observing a complex hard- and software system, in order to trigger actions that allow this system to save energy. The general idea was to formalize situations as ontology-mediated queries, but in order to express the relevant situations, both the employed ontology language and the query language had to be extended. In this paper we sketch the general approach and then concentrate on reporting the formal results obtained for reasoning in these extensions, but do not describe the application that triggered these extensions in detail.

International audience; Two main families of ontology languages are considered in the context of data access, namely Horn description logics and existential rules. In this paper, we review the semantic relationships between these families in the light of the ontology-mediated query answering problem. To this end, we rely on the standard translation of description logics in first-order logic and on the notion of semantic emulation. We focus on description logics and classes of existential rules for which the con-junctive query answering problem has polynomial data complexity.

In the context of the Description Logic DL-Liteℛ≠, i.e., DL-Liteℛ without UNA and with inequality axioms, we address the problem of adding to unions of conjunctive queries (UCQs) one of the simplest forms of negation, namely, inequality. It is well known that answering conjunctive queries with unrestricted inequalities over DL-Liteℛ ontologies is in general undecidable. Therefore, we explore two strategies for recovering decidability, and, hopefully, tractability. Firstly, we weaken the ontology language, and consider the variant of DL-Liteℛ≠ corresponding to rdfs enriched with both inequality and disjointness axioms. Secondly, we weaken the query language, by preventing inequalities to be applied to existentially quantified variables, thus obtaining the class of queries named UCQ≠,bs. We prove that in the two cases, query answering is decidable, and we provide tight complexity bounds for the problem, both for data and combined complexity. Notably, the results show that answering UCQ≠,bs over DL-Liteℛ≠ ontologies is still in AC0 in data complexity.

An ontology language for ontology mediated query answering (OMQA-language) is universal for a family of OMQA-languages if it is the most expressive one among this family. In this paper, we focus on three families of tractable OMQA-languages, including first-order rewritable languages and languages whose data complexity of the query answering is in AC0 or PTIME. On the negative side, we prove that there is, in general, no universal language for each of these families of languages. On the positive side, we propose a novel property, the locality, to approximate the first-order rewritability, and show that there exists a language of disjunctive embedded dependencies that is universal for the family of OMQA-languages with locality. All of these results apply to OMQA with query languages such as conjunctive queries, unions of conjunctive queries and acyclic conjunctive queries., Comment: 10 pages, 1 figure, the full version of a paper accepted for AAAI 2020. Some typos have been corrected

In this tutorial, we learn how to set up and exploit the virtual knowledge graph (VKG) approach to access data stored in relational legacy systems and to enrich such data with domain knowledge coming from different heterogeneous (biomedical) resources. The VKG approach is based on an ontology that describes a domain of interest in terms of a vocabulary familiar to the user and exposes a high-level conceptual view of the data. Users can access the data by exploiting the conceptual view, and in this way they do not need to be aware of low-level storage details. They can easily integrate ontologies coming from different sources and can obtain richer answers thanks to the interaction between data and domain knowledge.

We present a machine-readable movement writing for sleight-of-hand moves with cards -- a "Labanotation of card magic." This scheme of movement writing contains 440 categories of motion, and appears to taxonomize all card sleights that have appeared in over 1500 publications. The movement writing is axiomatized in $\mathcal{SROIQ}$(D) Description Logic, and collected formally as an Ontology of Card Sleights, a computational ontology that extends the Basic Formal Ontology and the Information Artifact Ontology. The Ontology of Card Sleights is implemented in OWL DL, a Description Logic fragment of the Web Ontology Language. While ontologies have historically been used to classify at a less granular level, the algorithmic nature of card tricks allows us to transcribe a performer's actions step by step. We conclude by discussing design criteria we have used to ensure the ontology can be accessed and modified with a simple click-and-drag interface. This may allow database searches and performance transcriptions by users with card magic knowledge, but no ontology background., Comment: 8 pages. Preprint. Final version appeared in ICSC 2019. Copyright of final version is held by IEEE

Knowledge is an important asset that is easily lost. This loss process has a significant impact on plantation research organizations whose research takes a long time. This research aimed to develop an ontology model for recording knowledge about oil palm varieties. In order to save knowledge, in this research nine oil palm varieties were modeled into ontology using the Web Ontology Language (OWL). Any information in oil palm varieties can be sorted and grouped into classes, object properties, data properties, or data expressions. The relationship between data in oil palm varieties can be well represented using ontology. Based on the results from HermiT reasoners, the ontologies with 43 classes are consistent. Information in the ontology of oil palm varieties can be easily rediscovered using the description logic query (DL-Query). The model produced from this research can be used as an initial model in designing knowledge management systems and ontology-based oil palm expert systems.Keywords: ontology, OWL, oil palm seed, knowledge management

Interoperable ontologies already exist in the biomedical field, enabling scientists to communicate with minimum ambiguity. Unfortunately, ontology languages, in the semantic web, such as OW...

Information integration is great for military operations because the range of pertinent information sources is significantly distinct and dynamic. This article develops an intelligent knowledge treasure comprised of military resource ontology and procedures, as a learning model for better interoperability of heterogeneous resources of the Indian military. This model can interpret and learn the context of military information automatically, thereby facilitating the military commanders with decision making in several operations, such as command and control, teaching and training, military coalition, situation awareness and many more. To design the military resource ontology, this article specifies the core concepts of the ontology based on terms derived from heterogeneous resources. WWW standard ontology language, OWL has been used to codify the ontology. This article develops an intelligent tool—“QueryOnto”—as an interface to the military resource ontology that provides a commander decision support service and demonstrates how to apply the military ontology in practice. The developed ontology has been verified and validated with the best known approaches and metrics available. The presented model is helpful for military commanders to train their juniors in a systematic way and will provide an efficient web-based learning of different military tasks in future.

One of the most important goals in an organization is to have risks under an acceptance level along the time. All organizations are exposed to real-time security threats that could have an impact on their risk exposure levels harming the entire organization, their customers and their reputation. New emerging techniques, tactics and procedures (TTP) which remain undetected, the complexity and decentralization of organization assets, the great number of vulnerabilities proportional to the number of new type of devices (IoT) or still the high number of false positives, are only some examples of real risks for any organization. Risk management frameworks are not integrated and automated with near real-time (NRT) risk-related cybersecurity threat intelligence (CTI) information. The contribution of this paper is an integrated architecture based on the Web Ontology Language (OWL), a semantic reasoner and the use of Semantic Web Rule Language (SWRL) to approach a Dynamic Risk Assessment and Management (DRA/DRM) framework at all levels (operational, tactic and strategic). To enable such a dynamic, NRT and more realistic risk assessment and management processes, we created a new semantic version of STIX™v2.0 for cyber threat intelligence as it is becoming a de facto standard for structured threat information exchange. We selected an international leading organization in cybersecurity to demonstrate new dynamic ways to support decision making at all levels while being under attack. Semantic reasoners could be our ideal partners to fight against threats having risks under control along the time, for that, they need to understand the data. Our proposal uses an unprecedented mix of standards to cover all levels of a DRM and ensure easier adoption by users.

The Web Ontology Language (OWL) is a widely used knowledge representation language for describing knowledge in application domains by using classes, properties, and individuals. Ontology classification is an important and widely used service that computes a taxonomy of all classes occurring in an ontology. It can require significant amounts of runtime, but most OWL reasoners do not support any kind of parallel processing. We present a novel thread-level parallel architecture for ontology classification, which is ideally suited for shared-memory SMP servers, but does not rely on locking techniques and thus avoids possible race conditions. We evaluated our prototype implementation with a set of real-world ontologies. Our experiments demonstrate a very good scalability resulting in a speedup that is linear to the number of available cores.

Computing technologies are increasingly dynamic and ubiquitous in everyday life nowadays. Context information plays a crucial role in such dynamically changing environments and the different types of contextual conditions bring new challenges to context-sensitive access control. This information mostly can be derived from the crisp sets. For example, we can utilize a crisp set to derive a patient and nurse are co-located in the general ward of the hospital or not. Some of the context information characterizations cannot be made using crisp sets, however, they are equally important in order to make access control decisions. Towards this end, this article proposes an approach to Context-Aware Access Control using Fuzzy logic (FCAAC) for data and information resources. We introduce a formal context model to represent the fuzzy and other contextual conditions. We also introduce a formal policy model to specify the policies by utilizing these conditions. Using our formal approach, we combine the fuzzy model with an ontology-based approach that captures such contextual conditions and incorporates them into the policies, utilizing the ontology languages and the fuzzy logic-based reasoning. We introduce a unified data ontology and its associated mapping ontology in terms of facilitating access control to cloud-based data resources. We justify the feasibility of our approach by demonstrating the practicality through a prototype implementation, several healthcare case studies and a usability study. Finally, we demonstrate an experimental evaluation in terms of query response time. The experiment results demonstrate the satisfactory performance of our proposed FCAAC approach.

Conjunctive query (CQ) answering over knowledge bases is an important reasoning task. However, with expressive ontology languages such as OWL, query answering is computationally very expensive. The PAGOdA system addresses this issue by using a tractable reasoner to compute lower and upper-bound approximations, falling back to a fully-fledged OWL reasoner only when these bounds don’t coincide. The effectiveness of this approach critically depends on the quality of the approximations, and in this paper we explore a technique for computing closer approximations via RSA, an ontology language that subsumes all the OWL 2 profiles while still maintaining tractability. We present a novel approximation of OWL 2 ontologies into RSA, and an algorithm to compute a closer (than PAGOdA) lower bound approximation using the RSA combined approach. We have implemented these algorithms in a prototypical CQ answering system, and we present a preliminary evaluation of our system that shows significant performance improvements w.r.t. PAGOdA.

Population-based cancer registry data provide a key epidemiological resource for monitoring cancer in defined populations. Validation of the data variables contributing to a common data set is necessary to remove statistical bias, the process is currently performed centrally. An ontology-based approach promises advantages in devolving the validation process to the registry level but the checks regarding multiple primary tumours have presented a hurdle. This work presents a solution by modelling the international rules for multiple primary cancers in description logic. Topography groupings described in the rules had to be further categorised in order to simplify the axioms. Description logic expressivity was constrained as far as possible for reasons of automatic reasoning performance. The axioms were consistently able to trap all the different types of scenarios signalling violation of the rules. Batch processing of many records were performed using the Web Ontology Language application programme interface. Performance issues were circumvented for large data sets using the software interface to perform the reasoning operations on the basis of the axioms encoded in the ontology. These results remove one remaining hurdle in developing a purely ontology-based solution for performing the European harmonised data-quality checks, with a number of inherent advantages including the formalisation and integration of the validation rules within the domain data model itself.

Summary Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset’s allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers’ discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide., Graphical abstract, Highlights Biomedical advances depend on the efficient and compliant re-use of sensitive human data The Data Use Ontology standardizes terms and definitions for consented data uses The Data Use Ontology facilitates discovery of, request for, and access to datasets Over 200,000 datasets worldwide have been annotated using the Data Use Ontology, The GA4GH Data Use Ontology (DUO) provides unambiguous, machine-readable standard language for consent forms and the data sharing policies they represent. Lawson et al. describe the DUO standard and implementations throughout the data access workflow to expedite data access while maintaining or improving compliant processes.

This chapter presents the ontology for Multi-Paradigm Modelling (MPM) specfied using the Web Ontology Language (OWL) as introduced in Chapter 2 . A thorough state of the art on MPM's core notions including multi-formalism and model management approaches, languages and tools is presented. In particular, model management approaches have been characterized according to their modularity and incremental execution properties as required to scale for the large complex CPSs we face today. Based on this state of the art, an outline of the MPM ontology is developed by introducing its main classes and properties. The validation of the ontology is presented by showing how it can adequatly model the two case studies briefly introduced in Chapter 2 .

OWL 2 QL is a standard profile of the OWL 2 ontology language, specifically tailored to Ontology-Based Data Management. Inspired by recent work on higher-order Description Logics, in this paper we present a new semantics for OWL 2 QL ontologies, called Metamodeling Semantics (MS), and show that, in contrast to the official Direct Semantics (DS) for OWL 2 , it allows exploiting the metamodeling capabilities natively offered by the OWL 2 punning. We then extend unions of conjunctive queries with both metavariables, and the possibility of using TBox atoms, with the purpose of expressing meaningful metalevel queries. We first show that under MS both satisfiability checking and answering queries including only ABox atoms, have the same complexity as under DS. Second, we investigate the problem of answering general metaqueries, and single out a new source of complexity coming from the combined presence of a specific type of incompleteness in the ontology, and of TBox axioms among the query atoms. Then we focus on a specific class of ontologies, called TBox-complete, where there is no incompleteness in the TBox axioms, and show that general metaquery answering in this case has again the same complexity as under DS. Finally, we move to general ontologies and show that answering general metaqueries is coNP-complete with respect to ontology complexity, Π 2 p -complete with respect to combined complexity, and remains AC 0 with respect to ABox complexity.

During recent years, globalization has had an impact on the competitive capacity of industries, forcing them to integrate their productive processes with other, geographically distributed, facilities. This requires the information systems that support such processes to interoperate. Significant attention has been paid to the development of ontology-based solutions, which are meant to tackle issues from inconsistency to semantic interoperability and knowledge reusability. This paper looks into how the available technology, models and ontology-based solutions might interact within the manufacturing industry environment to achieve semantic interoperability among industrial information systems. Through a systematic literature review, this paper has aimed to identify the most relevant elements to consider in the development of an ontology-based solution and how these solutions are being deployed in industry. The research analyzed 54 studies in alignment with the specific requirements of our research questions. The most relevant results show that ontology-based solutions can be set up using OWL as the ontology language, Protégé as the ontology modeling tool, Jena as the application programming interface to interact with the built ontology, and different standards from the International Organization for Standardization Technical Committee 184, Subcommittee 4 or 5, to get the foundational concepts, axioms, and relationships to develop the knowledge base. We believe that the findings of this study make an important contribution to practitioners and researchers as they provide useful information about different projects and choices involved in undertaking projects in the field of industrial ontology application. Fil: Fraga, Alvaro Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentina Fil: Vegetti, Maria Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentina Fil: Leone, Horacio Pascual. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentina

Multiple ontology languages have been developed over the years, which brings afore two key components: how to select the appropriate language for the task at hand and language design itself. This engineering step entails examining the ontological ‘commitments’ embedded into the language, which, in turn, demands for an insight into what the effects of philosophical viewpoints may be on the design of a representation language. But what are the sort of commitments one should be able to choose from that have an underlying philosophical point of view, and which philosophical stances have a knock-on effect on the specification or selection of an ontology language? In this paper, we provide a first step towards answering these questions. We identify and analyse ontological commitments embedded in logics, or that could be, and show that they have been taken in well-known ontology languages. This contributes to reflecting on the language as enabler or inhibitor to formally characterising an ontology or an ontological investigation, as well as the design of new ontology languages following the proposed design process.

Finding a logical formula that separates positive and negative examples given in the form of labeled data items is fundamental in applications such as concept learning, reverse engineering of database queries, and generating referring expressions. In this paper, we investigate the existence of a separating formula for incomplete data in the presence of an ontology. Both for the ontology language and the separation language, we concentrate on first-order logic and three important fragments thereof: the description logic ALCI, the guarded fragment, and the two-variable fragment. We consider several forms of separability that differ in the treatment of negative examples and in whether or not they admit the use of additional helper symbols to achieve separation. We characterize separability in a model-theoretic way, compare the separating power of the different languages, and determine the computational complexity of separability as a decision problem.

We describe the development and envisioned use case applications of a comprehensive insider threat ontology—“Sociotechnical and Organizational Factors for Insider Threat” (SOFIT)—that comprises more than 300 indicators of technical, behavioral, and organizational factors. Requirements, design, and engineering development for the Web Ontology Language (OWL) implementation of the SOFIT knowledge base are reviewed; additional relationships among constructs are defined that extend the representation beyond a simple taxonomic hierarchy and that enable inferences for qualitative and quantitative threat assessment. We show how queries may be constructed to support these inferences and threat assessments. Several major application concepts are reviewed to show how the ontology may be used by the insider threat research and operational communities. To this end, the SOFIT knowledge base may be shared with stakeholders to advance research and practice for proactive insider threat mitigation.

To date, widely implemented and full-featured query languages for building models in their native exchange formats do not exist. While interesting proposals exist for querying Industry Foundation Classes (IFC) models, their functionality is often incomplete and their semantics not precisely defined. With the introduction of the ifcOWL ontology as an equivalent to the IFC schema in the Web Ontology Language (OWL), an option to represent such models in RDF (Resource Description Framework, a general information modeling method) is provided, and such models can be queried using SPARQL (SPARQL Protocol and RDF Query Language). The size of data sets in complex building projects, however, renders the use of clear-text encoded RDF infeasible in many cases. A SPARQL implementation, compatible with ifcOWL, is proposed, directly atop a standardized binary serialization format for IFC building models. This novel format is the binary equivalent of traditional IFC serialization formats but with more compact storage and less overhead than the graph serialization in RDF. The format is based on ISO 10303-26 and relies on an open standard for organizing large amounts of data: Hierarchical Data Format version 5 (HDF5). Due to hierarchical partitioning and fixed-length records, only small subsets of the data are read to answer queries, improving efficiency. A prototypical implementation of the query engine is provided in the Python programming language. In several realistic use cases, the proposed system performs equivalent to or better than the state of the art in SPARQL querying on building models. For large datasets, the proposed storage format results in files that are 2–3 times smaller than the current, most concise, RDF databases while offering a platform-neutral, containerized exchange file.

This paper introduces a novel, semantics-informed geologic mapping process, whose application domain is the production of a synthetic geologic map of a large administrative region. A number of approaches concerning the expression of geologic knowledge through UML schemata and ontologies have been around for more than a decade. These approaches have yielded resources that concern specific domains, such as, e.g., lithology. We develop a conceptual model that aims at building a digital encoding of several domains of geologic knowledge, in order to support the interoperability of the sources. We apply the devised terminological base to the classification of the elements of a geologic map of the Italian Western Alps and northern Apennines (Piemonte region). The digitally encoded knowledge base is a merged set of ontologies, called OntoGeonous. The encoding process identifies the objects of the semantic encoding, the geologic units, gathers the relevant information about such objects from authoritative resources, such as GeoSciML (giving priority to the application schemata reported in the INSPIRE Encoding Cookbook), and expresses the statements by means of axioms encoded in the Web Ontology Language (OWL). To support interoperability, OntoGeonous interlinks the general concepts by referring to the upper part level of ontology SWEET (developed by NASA), and imports knowledge that is already encoded in ontological format (e.g., ontology Simple Lithology). Machine-readable knowledge allows for consistency checking and for classification of the geological map data through algorithms of automatic reasoning.

To achieve efficient development of high-quality product, manufacturing constraints must be fully taken into account at the early design stage. However, designers lack in-depth knowledge of manufacturing and production. Many time-consuming iterations of design changes are required between designers and manufacturing engineers. In order to minimize this knowledge gap, this paper presents an ontology-based product design framework for manufacturability verification and knowledge reuse to support the sharing and reuse of design and manufacturing knowledge. It aims at providing advices and feedback of restraints of manufacturing processes to the designers during the design process. The proposed framework consists of three major layers which include a foundation layer, a domain layer, and an instance layer. We use the Web Ontology Language (OWL), a standard of ontology representation language, to formalize the foundation layer. It contains the core product model and the standard ISO 10303 AP224 application protocol. The domain layer comprises extensional concepts and relationships for design and manufacturing integration and a rule base for manufacturability verification, which is represented in Semantic Web Rule Language (SWRL). In the instance layer, an inference engine is developed based on ontology and rule inference. It provides recommendations of manufacturability. Two case studies are provided as application examples to demonstrate the effectiveness of the framework.

In this paper we introduce Eddy, a new open-source tool for the graphical editing of OWL~2 ontologies. Eddy is specifically designed for creating ontologies in Graphol, a completely visual ontology language that is equivalent to OWL~2. Thus, in Eddy ontologies are easily drawn as diagrams, rather than written as sets of formulas, as commonly happens in popular ontology design and engineering environments. This makes Eddy particularly suited for usage by people who are more familiar with diagramatic languages for conceptual modeling rather than with typical ontology formalisms, as is often required in non-academic and industrial contexts. Eddy provides intuitive functionalities for specifying Graphol diagrams, guarantees their syntactic correctness, and allows for exporting them in standard OWL 2 syntax. A user evaluation study we conducted shows that Eddy is perceived as an easy and intuitive tool for ontology specification.

Autonomous systems consist of agents that have access to interpretable information allowing them to make intelligent decisions. This requires the systems to have a good semantic knowledge base. A good semantic knowledge repository has to be backed by a well-defined domain ontology. For the sake of decidability, ontology languages do not provide the required expressiveness. Rules present an efficient support thereby enabling even better decision making. Their complexity and their exponentially growing number imply the need for an automatic management. In this paper, we introduce a new method for the automatic dependency extraction among rule bases associated to ontologies. This is founded on a novel technique of dependency extraction. A prototype of our proposal was implemented and applied on two different rule bases associated to ontologies from different domains. Our results succeeded in increasing the number of the extracted dependency relationships.

Semantic technologies have emerged as a prominent research area within Big Earth Data. These technologies have provided significant benefits for data discovery and integration. Yet, the formality of the Semantic Web, in languages such as the Web Ontology Language (OWL), does not always integrate well with the numerical, statistical, and geometric methods of the geosciences. Two prominent challenges in this area are how to semantically model individual measurements and what to do when geoscience needs are not addressed by languages such as OWL. This has led to a fragmented Big Earth Data community with either no solution or incompatible semantic solutions. We use an oceanographic example to highlight the limitations and challenges surrounding the semantic encoding of observations and the use of semantics during analysis. We then present potential solutions to each challenge showing that a full end-to-end application of semantic technologies is not only feasible, but beneficial to Big Earth Data.

The article describes the process of creating a Finnish language FrameNet or FinnFN, based on the original English language FrameNet hosted at the International Computer Science Institute in Berkeley, California. We outline the goals and results relating to the FinnFN project and especially to the creation of the FinnFrame corpus. The main aim of the project was to test the universal applicability of frame semantics by annotating real Finnish using the same frames and annotation conventions as in the original Berkeley FrameNet project. From Finnish newspaper corpora, 40,721 sentences were automatically retrieved and manually annotated as example sentences evoking certain frames. This became the FinnFrame corpus. Applying the Berkeley FrameNet annotation conventions to the Finnish language required some modifications due to Finnish morphology, and a convention for annotating individual morphemes within words was introduced for phenomena such as compounding, comparatives and case endings. Various questions about cultural salience across the two languages arose during the project, but problematic situations occurred only in a few examples, which we also discuss in the article. The article shows that, barring a few minor instances, the universality hypothesis of frames is largely confirmed for languages as different as Finnish and English.

International audience; Objective: Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies. Methods: From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated " role-filler " constraints. We also propose an algorithm for performing local closed world reasoning in simple situations. Results: We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning. Conclusion: Owlready has been successfully used in a medical research project. It has been published as Open-Source software and then used by many other researchers. Future developments will focus on the support of vagueness and additional non-monotonic reasoning feature, and automatic dialog box generation.

In the context of the Semantic Web, fuzzy extensions to OWL (the W3C standard ontology language) and Description Logics (DLs, the logical foundation of OWL) have been extensively investigated, and there are many real fuzzy DL ontology knowledge bases. Therefore, how to store fuzzy DL ontology knowledge bases has become an important issue. In this paper, we propose an approach and implement a tool for storing fuzzy DL ontology knowledge bases in fuzzy relational databases. Our chosen formalism is a fuzzy extension of the very expressive DL SHOIN(D), which is the main logical foundation of the standard ontology language OWL, so that our storage approach can store not only fuzzy DL-knowledge bases but also fuzzy ontology knowledge bases. Firstly, we give a formal definition of fuzzy DL-knowledge bases. In the definition, we consider the constructors of both fuzzy SHOIN(D) DL and fuzzy OWL ontology and add some common fuzzy datatypes (e.g., trapezoidal values, interval values, approximate values, and labels) into the knowledge bases. On this basis, we propose an approach which can store fuzzy DL-knowledge bases in fuzzy relational databases, and provide an example to well explain the approach. The correctness and quality of the storage approach are proved and analyzed. Furthermore, following the proposed approach, we implemented a prototype tool, which can automatically store fuzzy DL-knowledge bases. Finally, we make a discussion about the query problem and make a comparison with the existing works.

In recent years, business process modeling has increasingly drawn the attention of enterprises. As a result of the wide use of business processes, redundancy problems have arisen and researchers introduced the variability management, in order to enhance the business process reuse. The most approach used in this context is the Configurable Process Model solution, which consists in representing the variable and the fixed parts together in a unique model. Due to the increasing number of variants, the configurable models become complex and incomprehensible, and their quality is therefore impacted. Most of research work is limited to the syntactic quality of process variants. The approach presented in this paper aims at providing a novel method towards syntactic verification and semantic validation of configurable process models based on ontology languages. We define validation rules for assessing the quality of configurable process models. An example in the e-healthcare domain illustrates the main steps of our approach.

SoftwareX 12, 100571 (2020). doi:10.1016/j.softx.2020.100571, Published by Elsevier, Amsterdam [u.a.]

Knowledge bases (KBs) are not static entities: new information constantly appears and some of the previous knowledge becomes obsolete. In order to reflect this evolution of knowledge, KBs should be expanded with the new knowledge and contracted from the obsolete one. This problem is well-studied for propositional but much less for first-order KBs. In this work we investigate knowledge expansion and contraction for KBs expressed in DL-Lite, a family of description logics (DLs) that underlie the tractable fragment OWL 2 QL of the Web Ontology Language OWL 2. We start with a novel knowledge evolution framework and natural postulates that evolution should respect, and compare our postulates to the well-established AGM postulates. We then review well-known model and formula-based approaches for expansion and contraction for propositional theories and show how they can be adapted to the case of DL-Lite. In particular, we show intrinsic limitations of model-based approaches: besides the fact that some of them do not respect the postulates we have established, they ignore the structural properties of KBs. This leads to undesired properties of evolution results: evolution of DL-Lite KBs cannot be captured in DL-Lite. Moreover, we show that well-known formula-based approaches are also not appropriate for DL-Lite expansion and contraction: they either have a high complexity of computation, or they produce logical theories that cannot be expressed in DL-Lite. Thus, we propose a novel formula-based approach that respects our principles and for which evolution is expressible in DL-Lite. For this approach we also propose polynomial time deterministic algorithms to compute evolution of DL-Lite KBs when evolution affects only factual data.

In this paper, we propose a new mapping technique from the OMG’s UML modeling language into the Web Ontology Language (OWL) to serve the Semantic Web. UML (Unified Modeling Language) is widely accepted and used as a standardized modeling language in Object-Oriented Analysis (OOA) and Design (OOD) approach by domain experts to model real-world objects in software development. On the other hand, the conceptualization, which is represented in OWL, is designed to process the content of information rather than just present the information. Therefore, the matter of migrating UML to OWL is becoming an energetic research domain. OWL (Web Ontology Language) is a Semantic Web language designed for defining ontologies on the Web. An ontology is a formal specification naming and definition of shared data. This technique describes how to map UML Models into OWL and allows us to keep semantic of UML sequence diagrams such as messages, the sequence of messages, guard invariant, etc. to make data of UML sequence diagrams machine-readable.

A second opinion about cancer stage is crucial when clinicians assess patient treatment progress. Staging is a process that takes into account description, location, characteristics, and possible metastasis of tumors in a patient. It should follow standards, such as the TNM Classification of Malignant Tumors. However, in clinical practice, the implementation of this process can be tedious and error prone. In order to alleviate these problems, we intend to assist radiologists by providing a second opinion in the evaluation of cancer stage. For doing this, we developed a TNM classifier based on semantic annotations, made by radiologists, using the ePAD tool. It transforms the annotations (stored using the AIM format), using axioms and rules, into AIM4-O ontology instances. From then, it automatically calculates the liver TNM cancer stage. The AIM4-O ontology was developed, as part of this work, to represent annotations in the Web Ontology Language (OWL). A dataset of 51 liver radiology reports with staging data, from NCI’s Genomic Data Commons (GDC), were used to evaluate our classifier. When compared with the stages attributed by physicians, the classifier stages had a precision of 85.7% and recall of 81.0%. In addition, 3 radiologists from 2 different institutions manually reviewed a random sample of 4 of the 51 records and agreed with the tool staging. AIM4-O was also evaluated with good results. Our classifier can be integrated into AIM aware imaging tools, such as ePAD, to offer a second opinion about staging as part of the cancer treatment workflow.

Along with the rapid development of remote sensing satellites and sensor network technology, vast amounts of remote sensing imagery and in situ observations have been accumulated. Further, various researchers and agencies have released a variety of thematic image products. These heterogeneous observations are therefore difficult to utilize comprehensively. In this study, an ontology-based framework for integrating remote sensing imagery, image products, and in situ observations was developed. It was extended based on the Semantic Sensor Network (SSN) ontology in the Web Ontology Language (OWL). The detailed process of ontology construction and rule establishment was demonstrated. Combined with some actual remote sensing imagery, image products, and in situ observations, semantic queries based on DL Query and SPARQL were conducted to establish the rationality and feasibility of the ontology and framework.

This study aims to improve the interoperability between models of geospatial information from the applications domains of Geographic Information Systems (GIS), Intelligent Transport Systems (ITS) and Building Information Models (BIM). A state-of-the-art analysis showed that the Unified Modelling Language (UML) and Model-Driven Architecture (MDA) are used for modelling information in a geospatial context in all three domains, but with different approaches and levels of formality. A structure of formal UML profiles for modelling of geospatial information in GIS, ITS and BIM is suggested and tested for implementation. The Core Geospatial Profile (GCP) and general encoding profiles for the Geography Markup Language (GML) and the Web Ontology Language (OWL) are based on adapted concepts from ISO/TC 211 standards. Community specific profiles for conceptual models and encodings are based on UML profiles and the use of UML for specific information models in the three application domains. The studies and related research showed that the structure of UML profiles could be implemented and used for information modelling in the UML software Enterprise Architect and that existing profiles and information models could be adapted into the framework. Integration of information models in a common approach based on MDA and UML establishes a fundament for improved interoperability through a shared understanding of the digital representation of the real world. © Author(s) 2020. This work is distributed under the Creative Commons Attribution 4.0 License.

Background Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms. For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protégé ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool. Results ROBOT (a recursive acronym for “ROBOT is an OBO Tool”) is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks. These commands can be combined into larger workflows using a separate task execution system such as GNU Make, and workflows can be automatically executed within continuous integration systems. Conclusions ROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions. It packages common high-level ontology development functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows. This helps ontology developers to efficiently create, maintain, and release high-quality ontologies, so that they can spend more time focusing on development tasks. It also helps guarantee that released ontologies are free of certain types of logical errors and conform to standard quality control checks, increasing the overall robustness and efficiency of the ontology development lifecycle.

We present WebProt\'eg\'e, a tool to develop ontologies represented in the Web Ontology Language (OWL). WebProt\'eg\'e is a cloud-based application that allows users to collaboratively edit OWL ontologies, and it is available for use at https://webprotege.stanford.edu. WebProt\'ege\'e currently hosts more than 68,000 OWL ontology projects and has over 50,000 user accounts. In this paper, we detail the main new features of the latest version of WebProt\'eg\'e.

Scrap steel reverse supply chain service system is a typical complex system. The realization of the service activities involves a large number of service resources. And there are multiple relationships between atomic service activities and service resources. To realize the search matching between complex service resources and service activity demand in scrap steel reverse supply chain service, the modelling method of service resource information in scrap steel reverse supply chain based on ontology is proposed. After analysing the classification method of service resource, the ontology information model of service resources and service activities is constructed. Then the search matching between service demander and service resource provider is transformed into the mapping between service resource ontology and service activity ontology to solve. Finally, the ontology model of specific instance is established, and the Semantic Web ontology language OWL is used. The model is proved to be correct and feasible by describing the instance service resource ontology and service activity ontology.

Supporters of languages planned for international communication, like Esperanto, often claim that these languages are less complex and therefore easy to learn as compared to natural languages. To what extent does this claim have empirical support? In this contribution, planned languages will be presented from the perspective of learnability. In particular, the question of language complexity will be addressed. Almost all planned languages show a high degree of morphological regularity, obtained by a drastic reduction of allomorphy and suppletion. While these morphological traits can help learners acquire the basics of the planned language more easily as compared to standard natural languages, other factors should be taken into account in order to assess the learnability of these languages, in particular their sociolinguistic status.