WorldWideScience

Sample records for underlying reference ontology

  1. Formative evaluation of ontology learning methods for entity discovery by using existing ontologies as reference standards.

    Science.gov (United States)

    Liu, K; Mitchell, K J; Chapman, W W; Savova, G K; Sioutos, N; Rubin, D L; Crowley, R S

    2013-01-01

    Developing a two-step method for formative evaluation of statistical Ontology Learning (OL) algorithms that leverages existing biomedical ontologies as reference standards. In the first step optimum parameters are established. A 'gap list' of entities is generated by finding the set of entities present in a later version of the ontology that are not present in an earlier version of the ontology. A named entity recognition system is used to identify entities in a corpus of biomedical documents that are present in the 'gap list', generating a reference standard. The output of the algorithm (new entity candidates), produced by statistical methods, is subsequently compared against this reference standard. An OL method that performs perfectly will be able to learn all of the terms in this reference standard. Using evaluation metrics and precision-recall curves for different thresholds and parameters, we compute the optimum parameters for each method. In the second step, human judges with expertise in ontology development evaluate each candidate suggested by the algorithm configured with the optimum parameters previously established. These judgments are used to compute two performance metrics developed from our previous work: Entity Suggestion Rate (ESR) and Entity Acceptance Rate (EAR). Using this method, we evaluated two statistical OL methods for OL in two medical domains. For the pathology domain, we obtained 49% ESR, 28% EAR with the Lin method and 52% ESR, 39% EAR with the Church method. For the radiology domain, we obtain 87% ESA, 9% EAR using Lin method and 96% ESR, 16% EAR using Church method. This method is sufficiently general and flexible enough to permit comparison of any OL method for a specific corpus and ontology of interest.

  2. A reference ontology for harmonizing process-reference models

    Directory of Open Access Journals (Sweden)

    César Jesús Pardo-Calvache

    2014-01-01

    Full Text Available Desde hace un par de décadas, la calidad del proceso ha sido considerada como uno de los factores principales para la entrega de productos con alta calidad. Una gran variedad de modelos y estándares han surgido como solución a este problema, sin embargo, la implementación de varios modelos para que una empresa cumpla con múltiples requisitos de calidad no es una tarea fácil. La dificultad radica en la falta de directrices específicas y una representación homogénea que facilite el trabajo en esta línea de la ingeniería de software. Para hacer frente a esta situación, en este trabajo se presenta una ontología de modelos de referencia de procesos, llamado PrMO. Esta ontología define una Estructura Común de Elementos de Procesos (ECEP como medio para apoyar la armonización de las diferencias estructurales entre múltiples modelos. La armonización se lleva a cabo a través de la homogeneización de las estructuras de procesos de cada uno de los modelos. PrMO ha sido validada a través de la instanciación de la información contenida en diferentes modelos, tales como CMMI-(ACQ, DEV, ISO (9001, 27001, 27002, 20000- 2, ITIL, COBIT, RISK IT, Val IT, BASEL II, entre otros. Tanto la estructura común (ECEP y el método de homogeneización son presentados junto con un ejemplo de aplicación. Asimismo, se presenta una herramienta web que permite apoyar la homogeneización de los modelos, esto permite ilustrar mejor las ventajas de PrMO. La ontología propuesta podría ser de gran utilidad para las organizaciones y consultores que planean llevar a cabo la armonización de múltiples modelos.

  3. Towards a reference ontology of complex economic exchanges for Accounting Information Systems

    NARCIS (Netherlands)

    Blums, Ivar; Weigand, Hans; Matthes, Flores; Mendling, Jan; Rinderle-Ma, Stefanie

    Although the field of Accounting Information Systems (AIS) has a long tradition, there is still a lack of a widely adopted conceptualization. The Unified Foundational Ontology (UFO) and its Services sub- ontology (UFO-S) are regarded as grounding the engineering of a reference ontology for AIS. The

  4. The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

    Science.gov (United States)

    Cooper, Laurel; Meier, Austin; Laporte, Marie-Angélique; Elser, Justin L; Mungall, Chris; Sinn, Brandon T; Cavaliere, Dario; Carbon, Seth; Dunn, Nathan A; Smith, Barry; Qu, Botong; Preece, Justin; Zhang, Eugene; Todorovic, Sinisa; Gkoutos, Georgios; Doonan, John H; Stevenson, Dennis W; Arnaud, Elizabeth

    2018-01-01

    Abstract The Planteome project (http://www.planteome.org) 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. The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement. All the Planteome ontologies are publicly available and are maintained at the Planteome GitHub site (https://github.com/Planteome) for sharing, tracking revisions and new requests. The annotated data are freely accessible from the ontology browser (http://browser.planteome.org/amigo) and our data repository. PMID:29186578

  5. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

    Science.gov (United States)

    Hastings, Janna; de Matos, Paula; Dekker, Adriano; Ennis, Marcus; Harsha, Bhavana; Kale, Namrata; Muthukrishnan, Venkatesh; Owen, Gareth; Turner, Steve; Williams, Mark; Steinbeck, Christoph

    2013-01-01

    ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features. In addition to incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products and metabolites in many species. All database entries are now ‘is_a’ classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy. We have completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology. Furthermore, we have aligned our chemical classification with the classification of chemical-involving processes in the Gene Ontology (GO), and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated incorporating many additional biologically relevant compounds. We have incorporated additional data types including reference citations, and the species and component for metabolites. Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization. PMID:23180789

  6. How to keep a reference ontology relevant to the industry: A case study from the smart home

    NARCIS (Netherlands)

    Daniele, L.; Hartog, F. den; Roes, J.

    2016-01-01

    The Smart Appliance REFerence ontology (SAREF) is a shared model of consensus developed in close interaction with the industry to enable semantic interoperability for smart appliances. Smart appliances are intelligent and networked devices that accomplish some household functions, such as cleaning

  7. Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes

    Science.gov (United States)

    Ontology engineering and knowledge modeling for the plant sciences is expected to contribute to the understanding of the basis of plant traits that determine phenotypic expression in a given environment. Several crop- or clade-specific plant trait ontologies have been developed to describe plant tr...

  8. Ontological dependency

    NARCIS (Netherlands)

    Stamper, R.K.

    1996-01-01

    Successful ontological analysis depends upon having the right underlying theory. The work described here, exploring how to understand organisations as systems of social norms found that the familiar objectivist position did not work, eventually replacing it with a radically subjectivist ontology

  9. Ontology Merging as Social Choice: Judgment Aggregation under the Open World Assumption

    NARCIS (Netherlands)

    Porello, D.; Endriss, U.

    2014-01-01

    The problem of merging several ontologies has important applications in the Semantic Web, medical ontology engineering and other domains where information from several distinct sources needs to be integrated in a coherent manner. We propose to view ontology merging as a problem of social choice,

  10. Ontology or formal ontology

    Science.gov (United States)

    Žáček, Martin

    2017-07-01

    Ontology or formal ontology? Which word is correct? The aim of this article is to introduce correct terms and explain their basis. Ontology describes a particular area of interest (domain) in a formal way - defines the classes of objects that are in that area, and relationships that may exist between them. Meaning of ontology consists mainly in facilitating communication between people, improve collaboration of software systems and in the improvement of systems engineering. Ontology in all these areas offer the possibility of unification of view, maintaining consistency and unambiguity.

  11. The Harkening of the Infinite. On the Ontological Sense of Music in Reference to Schelling, Schopenhauer and Levinas´ Aesthetic Theories

    Directory of Open Access Journals (Sweden)

    Jaime Llorente

    2017-09-01

    Full Text Available The aim of the present study is to broach the question of the possible ontological and metaphysical meaning contained implicitly in the aesthetic reflection concerning the phenomenon of musical sonority. Starting from the consideration of the specific way of being of music understood as indeterminate ontological «event» separate from concrete objects, we shall examine the way in which the tension between the limit drawn by the world of defined things and the «un-limiting» power of sound is expressed in the context of aesthetic proposals on the essence of music made by F. W. J. Schelling, Arthur Schopenhauer and Emmanuel Levinas. These three meditations, each of them in its own way, coincide in pointing out a singular reference of the musical to the ontologically indefinite, the ab-solute and the boundless, that turn the experience of musical perception into a peculiar variant of harkening of the infinite.

  12. Ontology Repositories

    OpenAIRE

    Hartmann, J.; Palma, R.; Gómez-Pérez, A.

    2009-01-01

    The growing use and application of ontologies in the last years has led to an increased interest of researchers and practitioners in the development of ontologies, either from scratch o by reusing existing ones. ...

  13. Quantum ontologies

    International Nuclear Information System (INIS)

    Stapp, H.P.

    1988-12-01

    Quantum ontologies are conceptions of the constitution of the universe that are compatible with quantum theory. The ontological orientation is contrasted to the pragmatic orientation of science, and reasons are given for considering quantum ontologies both within science, and in broader contexts. The principal quantum ontologies are described and evaluated. Invited paper at conference: Bell's Theorem, Quantum Theory, and Conceptions of the Universe, George Mason University, October 20-21, 1988. 16 refs

  14. Referent tracking for treatment optimisation in schizophrenic patients: A case study in applying philosophical ontology to diagnostic algorithms.

    Science.gov (United States)

    Ceusters, Werner; Smith, Barry

    2006-09-01

    The IPAP Schizophrenia Algorithm was originally designed in the form of a flow-chart to help physicians optimise the treatment of schizophrenic patients in the spirit of guideline-based medicine. We take this algorithm as our starting point in investigating how artifacts of this sort can benefit from the facilities of high-quality ontologies. The IPAP algorithm exists thus far only in a form suitable for use by human beings. We draw on the resources of Basic Formal Ontology (BFO) in order to show how such an algorithm can be enhanced in such a way that it can be used in Semantic Web and related applications. We found that BFO provides a framework that is able to capture in a rigorous way all the types of entities represented in the IPAP Schizophrenia Algorithm in way which yields a computational tool that can be used by software agents to perform monitoring and control of schizophrenic patients. We discuss the issues involved in building an application ontology for this purpose, issues which are important for any Semantic Web application in the life science and healthcare domains.

  15. Ontology Evaluation

    OpenAIRE

    Vrandecic, Zdenko

    2010-01-01

    Ontology evaluation is the task of measuring the quality of an ontology. It enables us to answer the following main question: How to assess the quality of an ontology for the Web? In this thesis a theoretical framework and several methods breathing life into the framework are presented. The application to the above scenarios is explored, and the theoretical foundations are thoroughly grounded in the practical usage of the emerging Semantic Web.

  16. A novel algorithm for fully automated mapping of geospatial ontologies

    Science.gov (United States)

    Chaabane, Sana; Jaziri, Wassim

    2018-01-01

    Geospatial information is collected from different sources thus making spatial ontologies, built for the same geographic domain, heterogeneous; therefore, different and heterogeneous conceptualizations may coexist. Ontology integrating helps creating a common repository of the geospatial ontology and allows removing the heterogeneities between the existing ontologies. Ontology mapping is a process used in ontologies integrating and consists in finding correspondences between the source ontologies. This paper deals with the "mapping" process of geospatial ontologies which consist in applying an automated algorithm in finding the correspondences between concepts referring to the definitions of matching relationships. The proposed algorithm called "geographic ontologies mapping algorithm" defines three types of mapping: semantic, topological and spatial.

  17. GFVO: the Genomic Feature and Variation Ontology

    KAUST Repository

    Baran, Joachim

    2015-05-05

    Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.

  18. GFVO: the Genomic Feature and Variation Ontology

    Directory of Open Access Journals (Sweden)

    Joachim Baran

    2015-05-01

    Full Text Available Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA, GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations.Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations; examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0 and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.

  19. Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership

    Directory of Open Access Journals (Sweden)

    Ernesto eIacucci

    2012-02-01

    Full Text Available High-throughput molecular biology studies, such as microarray assays of gene expression, two-hybrid experiments for detecting protein interactions, or ChIP-Seq experiments for transcription factor binding, often result in an interesting set of genes—say, genes that are co-expressed or bound by the same factor. One way of understanding the biological meaning of such a set is to consider what processes or functions, as defined in an ontology, are over-represented (enriched or under-represented (depleted among genes in the set. Usually, the significance of enrichment or depletion scores is based on simple statistical models and on the membership of genes in different classifications. We consider the more general problem of computing p-values for arbitrary integer additive statistics, or weighted membership functions. Such membership functions can be used to represent, for example, prior knowledge on the role of certain genes or classifications, differential importance of different classifications or genes to the experimenter, hierarchical relationships between classifications, or different degrees of interestingness or evidence for specific genes. We describe a generic dynamic programming algorithm that can compute exact p-values for arbitrary integer additive statistics. We also describe several optimizations for important special cases, which can provide orders-of-magnitude speed up in the computations. We apply our methods to datasets describing oxidative phosphorylation and parturition and compare p-values based on computations of several different statistics for measuring enrichment. We find major differences between p-values resulting from these statistics, and that some statistics recover gold standard annotations of the data better than others. Our work establishes a theoretical and algorithmic basis for far richer notions of enrichment or depletion of gene sets with respect to gene ontologies than has previously been available.

  20. Semantics and metaphysics in informatics: toward an ontology of tasks.

    Science.gov (United States)

    Figdor, Carrie

    2011-04-01

    This article clarifies three principles that should guide the development of any cognitive ontology. First, that an adequate cognitive ontology depends essentially on an adequate task ontology; second, that the goal of developing a cognitive ontology is independent of the goal of finding neural implementations of the processes referred to in the ontology; and third, that cognitive ontologies are neutral regarding the metaphysical relationship between cognitive and neural processes. Copyright © 2011 Cognitive Science Society, Inc.

  1. PDON: Parkinson's disease ontology for representation and modeling of the Parkinson's disease knowledge domain.

    Science.gov (United States)

    Younesi, Erfan; Malhotra, Ashutosh; Gündel, Michaela; Scordis, Phil; Kodamullil, Alpha Tom; Page, Matt; Müller, Bernd; Springstubbe, Stephan; Wüllner, Ullrich; Scheller, Dieter; Hofmann-Apitius, Martin

    2015-09-22

    Despite the unprecedented and increasing amount of data, relatively little progress has been made in molecular characterization of mechanisms underlying Parkinson's disease. In the area of Parkinson's research, there is a pressing need to integrate various pieces of information into a meaningful context of presumed disease mechanism(s). Disease ontologies provide a novel means for organizing, integrating, and standardizing the knowledge domains specific to disease in a compact, formalized and computer-readable form and serve as a reference for knowledge exchange or systems modeling of disease mechanism. The Parkinson's disease ontology was built according to the life cycle of ontology building. Structural, functional, and expert evaluation of the ontology was performed to ensure the quality and usability of the ontology. A novelty metric has been introduced to measure the gain of new knowledge using the ontology. Finally, a cause-and-effect model was built around PINK1 and two gene expression studies from the Gene Expression Omnibus database were re-annotated to demonstrate the usability of the ontology. The Parkinson's disease ontology with a subclass-based taxonomic hierarchy covers the broad spectrum of major biomedical concepts from molecular to clinical features of the disease, and also reflects different views on disease features held by molecular biologists, clinicians and drug developers. The current version of the ontology contains 632 concepts, which are organized under nine views. The structural evaluation showed the balanced dispersion of concept classes throughout the ontology. The functional evaluation demonstrated that the ontology-driven literature search could gain novel knowledge not present in the reference Parkinson's knowledge map. The ontology was able to answer specific questions related to Parkinson's when evaluated by experts. Finally, the added value of the Parkinson's disease ontology is demonstrated by ontology-driven modeling of PINK1

  2. A Reference Architecture for Provisioning of Tools as a Service: Meta-Model, Ontologies and Design Elements

    DEFF Research Database (Denmark)

    Chauhan, Muhammad Aufeef; Babar, Muhammad Ali; Sheng, Quan Z.

    2016-01-01

    Software Architecture (SA) plays a critical role in designing, developing and evolving cloud-based platforms that can be used to provision different types of services to consumers on demand. In this paper, we present a Reference Architecture (RA) for designing cloud-based Tools as a service SPACE...... (TSPACE) for provisioning a bundled suite of tools by following the Software as a Service (SaaS) model. The reference architecture has been designed by leveraging information structuring approaches and by using well-known architecture design principles and patterns. The RA has been documented using view...

  3. SUGOI: automated ontology interchangeability

    CSIR Research Space (South Africa)

    Khan, ZC

    2015-04-01

    Full Text Available A foundational ontology can solve interoperability issues among the domain ontologies aligned to it. However, several foundational ontologies have been developed, hence such interoperability issues exist among domain ontologies. The novel SUGOI tool...

  4. The Ontology for Biomedical Investigations.

    Science.gov (United States)

    Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H; Bug, Bill; Chibucos, Marcus C; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H; Schober, Daniel; Smith, Barry; Soldatova, Larisa N; Stoeckert, Christian J; Taylor, Chris F; Torniai, Carlo; Turner, Jessica A; Vita, Randi; Whetzel, Patricia L; Zheng, Jie

    2016-01-01

    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed

  5. The Ontology for Biomedical Investigations.

    Directory of Open Access Journals (Sweden)

    Anita Bandrowski

    Full Text Available The Ontology for Biomedical Investigations (OBI is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI and Phenotype Attribute and Trait Ontology (PATO without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT. The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org providing details on the people, policies, and issues being

  6. Ontological interpretation of biomedical database content.

    Science.gov (United States)

    Santana da Silva, Filipe; Jansen, Ludger; Freitas, Fred; Schulz, Stefan

    2017-06-26

    Biological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a database record is often ambiguous. We address this problem by grounding implicit and explicit database content in a formal-ontological framework. By using a typical extract from the databases UniProt and Ensembl, annotated with content from GO, PR, ChEBI and NCBI Taxonomy, we created four ontological models (in OWL), which generate explicit, distinct interpretations under the BioTopLite2 (BTL2) upper-level ontology. The first three models interpret database entries as individuals (IND), defined classes (SUBC), and classes with dispositions (DISP), respectively; the fourth model (HYBR) is a combination of SUBC and DISP. For the evaluation of these four models, we consider (i) database content retrieval, using ontologies as query vocabulary; (ii) information completeness; and, (iii) DL complexity and decidability. The models were tested under these criteria against four competency questions (CQs). IND does not raise any ontological claim, besides asserting the existence of sample individuals and relations among them. Modelling patterns have to be created for each type of annotation referent. SUBC is interpreted regarding maximally fine-grained defined subclasses under the classes referred to by the data. DISP attempts to extract truly ontological statements from the database records, claiming the existence of dispositions. HYBR is a hybrid of SUBC and DISP and is more parsimonious regarding expressiveness and query answering complexity. For each of the four models, the four CQs were submitted as DL queries. This shows the ability to retrieve individuals with IND, and classes in SUBC and HYBR. DISP does not retrieve anything because the axioms with disposition are embedded in General Class Inclusion (GCI) statements. Ambiguity of biological database content is

  7. Development of an Ontology for Periodontitis.

    Science.gov (United States)

    Suzuki, Asami; Takai-Igarashi, Takako; Nakaya, Jun; Tanaka, Hiroshi

    2015-01-01

    In the clinical dentists and periodontal researchers' community, there is an obvious demand for a systems model capable of linking the clinical presentation of periodontitis to underlying molecular knowledge. A computer-readable representation of processes on disease development will give periodontal researchers opportunities to elucidate pathways and mechanisms of periodontitis. An ontology for periodontitis can be a model for integration of large variety of factors relating to a complex disease such as chronic inflammation in different organs accompanied by bone remodeling and immune system disorders, which has recently been referred to as osteoimmunology. Terms characteristic of descriptions related to the onset and progression of periodontitis were manually extracted from 194 review articles and PubMed abstracts by experts in periodontology. We specified all the relations between the extracted terms and constructed them into an ontology for periodontitis. We also investigated matching between classes of our ontology and that of Gene Ontology Biological Process. We developed an ontology for periodontitis called Periodontitis-Ontology (PeriO). The pathological progression of periodontitis is caused by complex, multi-factor interrelationships. PeriO consists of all the required concepts to represent the pathological progression and clinical treatment of periodontitis. The pathological processes were formalized with reference to Basic Formal Ontology and Relation Ontology, which accounts for participants in the processes realized by biological objects such as molecules and cells. We investigated the peculiarity of biological processes observed in pathological progression and medical treatments for the disease in comparison with Gene Ontology Biological Process (GO-BP) annotations. The results indicated that peculiarities of Perio existed in 1) granularity and context dependency of both the conceptualizations, and 2) causality intrinsic to the pathological processes

  8. Building ontologies with basic formal ontology

    CERN Document Server

    Arp, Robert; Spear, Andrew D.

    2015-01-01

    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 u...

  9. Overview of methodologies for building ontologies

    OpenAIRE

    Fernández-López, M.

    1999-01-01

    A few research groups are now proposing a series of steps and methodologies for developing ontologies. However, mainly due to the fact that Ontological Engineering is still a relatively immature discipline, each work group employs its own methodology. Our goal is to present the most representative methodologies used in ontology development and to perform an analysis of such methodologies against the same framework of reference. So, the goal of this paper is not to provide new insights about m...

  10. Ontological Surprises

    DEFF Research Database (Denmark)

    Leahu, Lucian

    2016-01-01

    This paper investigates how we might rethink design as the technological crafting of human-machine relations in the context of a machine learning technique called neural networks. It analyzes Google’s Inceptionism project, which uses neural networks for image recognition. The surprising output...... a hybrid approach where machine learning algorithms are used to identify objects as well as connections between them; finally, it argues for remaining open to ontological surprises in machine learning as they may enable the crafting of different relations with and through technologies....

  11. Engineering Ethics: Ontology and Politics

    OpenAIRE

    Conlon, Eddie

    2015-01-01

    Ontology...acts as both gatekeeper and bouncer for methodology” (Archer 1995: 22). This exploratory paper, through a focus on the relationship between structure and agency, examines the underlying social ontologies informing the teaching, and researching of the teaching, of engineering ethics. It argues that current approaches are deficient and that Critical Realism can provide the basis for a more robust and inclusive research agenda for understanding engineering practice and the teaching ...

  12. OntologyWidget – a reusable, embeddable widget for easily locating ontology terms

    Directory of Open Access Journals (Sweden)

    Skene JH Pate

    2007-09-01

    Full Text Available Abstract Background Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. Results We have produced a tool, OntologyWidget, which allows users to rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD, which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO website 1. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1 install Apache Tomcat 2 on one's web server, (2 download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3 create an html (HyperText Markup Language file that refers to the OntologyWidget using a simple, well-defined format. Conclusion We have developed Ontology

  13. The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

    Science.gov (United States)

    2013-01-01

    Background The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience. Description Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases. Conclusions In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community. PMID:24093723

  14. Fuel Crime Conceptualization through Specialization of Ontology for Investigation Management System

    Science.gov (United States)

    Cybulka, Jolanta

    We undertook the task of building the conceptual model of a particular economic offense, called "a fuel crime". This model is thought of as a part of a larger conceptualization, which comprises consensual semantics underlying the knowledge base of a system, aimed at supporting the teamwork of investigators of economic crimes. Because such a knowledge-based system represents a perspective on economic crimes, it should be carefully modeled. This can be done with the help of an expressive enough ontology. To achieve our goal we use the constructive descriptions and situations (c.DnS) design pattern, which enables us to construct an extensible, layered ontology in a top-down manner: c.DnS top layer is specialized by the reference ontology for investigation management system, that in turn, is specialized by the ontology of the fuel crime.

  15. An ontology-driven, diagnostic modeling system.

    Science.gov (United States)

    Haug, Peter J; Ferraro, Jeffrey P; Holmen, John; Wu, Xinzi; Mynam, Kumar; Ebert, Matthew; Dean, Nathan; Jones, Jason

    2013-06-01

    To present a system that uses knowledge stored in a medical ontology to automate the development of diagnostic decision support systems. To illustrate its function through an example focused on the development of a tool for diagnosing pneumonia. We developed a system that automates the creation of diagnostic decision-support applications. It relies on a medical ontology to direct the acquisition of clinic data from a clinical data warehouse and uses an automated analytic system to apply a sequence of machine learning algorithms that create applications for diagnostic screening. We refer to this system as the ontology-driven diagnostic modeling system (ODMS). We tested this system using samples of patient data collected in Salt Lake City emergency rooms and stored in Intermountain Healthcare's enterprise data warehouse. The system was used in the preliminary development steps of a tool to identify patients with pneumonia in the emergency department. This tool was compared with a manually created diagnostic tool derived from a curated dataset. The manually created tool is currently in clinical use. The automatically created tool had an area under the receiver operating characteristic curve of 0.920 (95% CI 0.916 to 0.924), compared with 0.944 (95% CI 0.942 to 0.947) for the manually created tool. Initial testing of the ODMS demonstrates promising accuracy for the highly automated results and illustrates the route to model improvement. The use of medical knowledge, embedded in ontologies, to direct the initial development of diagnostic computing systems appears feasible.

  16. Tackling the challenges of matching biomedical ontologies.

    Science.gov (United States)

    Faria, Daniel; Pesquita, Catia; Mott, Isabela; Martins, Catarina; Couto, Francisco M; Cruz, Isabel F

    2018-01-15

    Biomedical ontologies pose several challenges to ontology matching due both to the complexity of the biomedical domain and to the characteristics of the ontologies themselves. The biomedical tracks in the Ontology Matching Evaluation Initiative (OAEI) have spurred the development of matching systems able to tackle these challenges, and benchmarked their general performance. In this study, we dissect the strategies employed by matching systems to tackle the challenges of matching biomedical ontologies and gauge the impact of the challenges themselves on matching performance, using the AgreementMakerLight (AML) system as the platform for this study. We demonstrate that the linear complexity of the hash-based searching strategy implemented by most state-of-the-art ontology matching systems is essential for matching large biomedical ontologies efficiently. We show that accounting for all lexical annotations (e.g., labels and synonyms) in biomedical ontologies leads to a substantial improvement in F-measure over using only the primary name, and that accounting for the reliability of different types of annotations generally also leads to a marked improvement. Finally, we show that cross-references are a reliable source of information and that, when using biomedical ontologies as background knowledge, it is generally more reliable to use them as mediators than to perform lexical expansion. We anticipate that translating traditional matching algorithms to the hash-based searching paradigm will be a critical direction for the future development of the field. Improving the evaluation carried out in the biomedical tracks of the OAEI will also be important, as without proper reference alignments there is only so much that can be ascertained about matching systems or strategies. Nevertheless, it is clear that, to tackle the various challenges posed by biomedical ontologies, ontology matching systems must be able to efficiently combine multiple strategies into a mature matching

  17. The foundational ontology library ROMULUS

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-09-01

    Full Text Available A purpose of a foundational ontology is to solve interoperability issues among domain ontologies and they are used for ontology- driven conceptual data modelling. Multiple foundational ontologies have been developed in recent years, and most of them...

  18. An ontologically well-founded profile for UML conceptual models

    NARCIS (Netherlands)

    Guizzardi, G.; Wagner, Gerd; van Sinderen, Marten J.; Guarino, Nicola; Persson, Anne; Stirna, Janis

    2004-01-01

    UML class diagrams can be used as a language for expressing a conceptual model of a domain. In a series of papers [1,2,3] we have been using the General Ontological Language (GOL) and its underlying upper level ontology, proposed in [4,5], to evaluate the ontological correctness of a conceptual UML

  19. Margin based ontology sparse vector learning algorithm and applied in biology science.

    Science.gov (United States)

    Gao, Wei; Qudair Baig, Abdul; Ali, Haidar; Sajjad, Wasim; Reza Farahani, Mohammad

    2017-01-01

    In biology field, the ontology application relates to a large amount of genetic information and chemical information of molecular structure, which makes knowledge of ontology concepts convey much information. Therefore, in mathematical notation, the dimension of vector which corresponds to the ontology concept is often very large, and thus improves the higher requirements of ontology algorithm. Under this background, we consider the designing of ontology sparse vector algorithm and application in biology. In this paper, using knowledge of marginal likelihood and marginal distribution, the optimized strategy of marginal based ontology sparse vector learning algorithm is presented. Finally, the new algorithm is applied to gene ontology and plant ontology to verify its efficiency.

  20. Ontologies vs. Classification Systems

    DEFF Research Database (Denmark)

    Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

    2009-01-01

    What is an ontology compared to a classification system? Is a taxonomy a kind of classification system or a kind of ontology? These are questions that we meet when working with people from industry and public authorities, who need methods and tools for concept clarification, for developing meta...... data sets or for obtaining advanced search facilities. In this paper we will present an attempt at answering these questions. We will give a presentation of various types of ontologies and briefly introduce terminological ontologies. Furthermore we will argue that classification systems, e.g. product...... classification systems and meta data taxonomies, should be based on ontologies....

  1. Temporal Ontologies for Geoscience: Alignment Challenges

    Science.gov (United States)

    Cox, S. J. D.

    2014-12-01

    Time is a central concept in geoscience. Geologic histories are composed of sequences of geologic processes and events. Calibration of their timing ties a local history into a broader context, and enables correlation of events between locations. The geologic timescale is standardized in the International Chronostratigraphic Chart, which specifies interval names, and calibrations for the ages of the interval boundaries. Time is also a key concept in the world at large. A number of general purpose temporal ontologies have been developed, both stand-alone and as parts of general purpose or upper ontologies. A temporal ontology for geoscience should apply or extend a suitable general purpose temporal ontology. However, geologic time presents two challenges: Geology involves greater spans of time than in other temporal ontologies, inconsistent with the year-month-day/hour-minute-second formalization that is a basic assumption of most general purpose temporal schemes; The geologic timescale is a temporal topology. Its calibration in terms of an absolute (numeric) scale is a scientific issue in its own right supporting a significant community. In contrast, the general purpose temporal ontologies are premised on exact numeric values for temporal position, and do not allow for temporal topology as a primary structure. We have developed an ontology for the geologic timescale to account for these concerns. It uses the ISO 19108 distinctions between different types of temporal reference system, also linking to an explicit temporal topology model. Stratotypes used in the calibration process are modelled as sampling-features following the ISO 19156 Observations and Measurements model. A joint OGC-W3C harmonization project is underway, with standardization of the W3C OWL-Time ontology as one of its tasks. The insights gained from the geologic timescale ontology will assist in development of a general ontology capable of modelling a richer set of use-cases from geoscience.

  2. Statistical mechanics of ontology based annotations

    Science.gov (United States)

    Hoyle, David C.; Brass, Andrew

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.

  3. Differences among cell-structure ontologies: FMA, GO, & CCO.

    Science.gov (United States)

    Au, Alan P; Li, Xiang; Gennari, John H

    2006-01-01

    When different groups create models or ontologies of the same knowledge domain, this creates challenges for knowledge sharing. To identify these challenges, we compare cellular structure as modeled by the Foundational Model of Anatomy(FMA), the Gene Ontology (GO), and the Cell Component Ontology (CCO). These ontologies all model the physical anatomy of a cell, and we expected them to be similar in scope. However, we discovered that the actual differences among the mare substantial. These differences represent variations based on theory-driven vs. emergent construction,as well as differences in how small application ontologies like the CCO are created from reference ontologies. In this paper, we provide a description and analysis of these differences. By studying differences in language, granularity, breadth of coverage,and model organization, we hope to gain a better understanding of how to map between related ontologies.

  4. The Proteasix Ontology.

    Science.gov (United States)

    Arguello Casteleiro, Mercedes; Klein, Julie; Stevens, Robert

    2016-06-04

    The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides) The PxO re-uses parts of the Protein Ontology, the three Gene Ontology sub-ontologies, the Chemical Entities of Biological Interest Ontology, the Sequence Ontology and bespoke extensions to the PxO in support of a series of roles: 1. To describe the known proteases and their target cleaveage sites. 2. To enable the description of proteolytic cleaveage fragments as the outputs of observed and predicted proteolysis. 3. To use knowledge about the function, species and cellular location of a protease and protein substrate to support the prioritisation of proteases in observed and predicted proteolysis. The PxO is designed to describe the biological underpinnings of the generation of peptides. The peptide-centric PxO seeks to support the Proteasix tool by separating domain knowledge from the operational knowledge used in protease prediction by Proteasix and to support the confirmation of its analyses and results. The Proteasix Ontology may be found at: http://bioportal.bioontology.org/ontologies/PXO . This ontology is free and open for use by everyone.

  5. Extracting Cross-Ontology Weighted Association Rules from Gene Ontology Annotations.

    Science.gov (United States)

    Agapito, Giuseppe; Milano, Marianna; Guzzi, Pietro Hiram; Cannataro, Mario

    2016-01-01

    Gene Ontology (GO) is a structured repository of concepts (GO Terms) that are associated to one or more gene products through a process referred to as annotation. The analysis of annotated data is an important opportunity for bioinformatics. There are different approaches of analysis, among those, the use of association rules (AR) which provides useful knowledge, discovering biologically relevant associations between terms of GO, not previously known. In a previous work, we introduced GO-WAR (Gene Ontology-based Weighted Association Rules), a methodology for extracting weighted association rules from ontology-based annotated datasets. We here adapt the GO-WAR algorithm to mine cross-ontology association rules, i.e., rules that involve GO terms present in the three sub-ontologies of GO. We conduct a deep performance evaluation of GO-WAR by mining publicly available GO annotated datasets, showing how GO-WAR outperforms current state of the art approaches.

  6. The MMI Device Ontology: Enabling Sensor Integration

    Science.gov (United States)

    Rueda, C.; Galbraith, N.; Morris, R. A.; Bermudez, L. E.; Graybeal, J.; Arko, R. A.; Mmi Device Ontology Working Group

    2010-12-01

    The Marine Metadata Interoperability (MMI) project has developed an ontology for devices to describe sensors and sensor networks. This ontology is implemented in the W3C Web Ontology Language (OWL) and provides an extensible conceptual model and controlled vocabularies for describing heterogeneous instrument types, with different data characteristics, and their attributes. It can help users populate metadata records for sensors; associate devices with their platforms, deployments, measurement capabilities and restrictions; aid in discovery of sensor data, both historic and real-time; and improve the interoperability of observational oceanographic data sets. We developed the MMI Device Ontology following a community-based approach. By building on and integrating other models and ontologies from related disciplines, we sought to facilitate semantic interoperability while avoiding duplication. Key concepts and insights from various communities, including the Open Geospatial Consortium (eg., SensorML and Observations and Measurements specifications), Semantic Web for Earth and Environmental Terminology (SWEET), and W3C Semantic Sensor Network Incubator Group, have significantly enriched the development of the ontology. Individuals ranging from instrument designers, science data producers and consumers to ontology specialists and other technologists contributed to the work. Applications of the MMI Device Ontology are underway for several community use cases. These include vessel-mounted multibeam mapping sonars for the Rolling Deck to Repository (R2R) program and description of diverse instruments on deepwater Ocean Reference Stations for the OceanSITES program. These trials involve creation of records completely describing instruments, either by individual instances or by manufacturer and model. Individual terms in the MMI Device Ontology can be referenced with their corresponding Uniform Resource Identifiers (URIs) in sensor-related metadata specifications (e

  7. Margin based ontology sparse vector learning algorithm and applied in biology science

    OpenAIRE

    Gao, Wei; Qudair Baig, Abdul; Ali, Haidar; Sajjad, Wasim; Reza Farahani, Mohammad

    2016-01-01

    In biology field, the ontology application relates to a large amount of genetic information and chemical information of molecular structure, which makes knowledge of ontology concepts convey much information. Therefore, in mathematical notation, the dimension of vector which corresponds to the ontology concept is often very large, and thus improves the higher requirements of ontology algorithm. Under this background, we consider the designing of ontology sparse vector algorithm and applicatio...

  8. Constructive Ontology Engineering

    Science.gov (United States)

    Sousan, William L.

    2010-01-01

    The proliferation of the Semantic Web depends on ontologies for knowledge sharing, semantic annotation, data fusion, and descriptions of data for machine interpretation. However, ontologies are difficult to create and maintain. In addition, their structure and content may vary depending on the application and domain. Several methods described in…

  9. Ontologies vs. Classification Systems

    DEFF Research Database (Denmark)

    Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

    2009-01-01

    data sets or for obtaining advanced search facilities. In this paper we will present an attempt at answering these questions. We will give a presentation of various types of ontologies and briefly introduce terminological ontologies. Furthermore we will argue that classification systems, e.g. product...

  10. Ontology Sparse Vector Learning Algorithm for Ontology Similarity Measuring and Ontology Mapping via ADAL Technology

    Science.gov (United States)

    Gao, Wei; Zhu, Linli; Wang, Kaiyun

    2015-12-01

    Ontology, a model of knowledge representation and storage, has had extensive applications in pharmaceutics, social science, chemistry and biology. In the age of “big data”, the constructed concepts are often represented as higher-dimensional data by scholars, and thus the sparse learning techniques are introduced into ontology algorithms. In this paper, based on the alternating direction augmented Lagrangian method, we present an ontology optimization algorithm for ontological sparse vector learning, and a fast version of such ontology technologies. The optimal sparse vector is obtained by an iterative procedure, and the ontology function is then obtained from the sparse vector. Four simulation experiments show that our ontological sparse vector learning model has a higher precision ratio on plant ontology, humanoid robotics ontology, biology ontology and physics education ontology data for similarity measuring and ontology mapping applications.

  11. Ontological realism: A methodology for coordinated evolution of scientific ontologies.

    Science.gov (United States)

    Smith, Barry; Ceusters, Werner

    2010-11-15

    Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill's critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative.

  12. Conceptual querying through ontologies

    DEFF Research Database (Denmark)

    Andreasen, Troels; Bulskov, Henrik

    2009-01-01

    is motivated by an obvious need for users to survey huge volumes of objects in query answers. An ontology formalism and a special notion of-instantiated ontology" are introduced. The latter is a structure reflecting the content in the document collection in that; it is a restriction of a general world......We present here ail approach to conceptual querying where the aim is, given a collection of textual database objects or documents, to target an abstraction of the entire database content in terms of the concepts appearing in documents, rather than the documents in the collection. The approach...... knowledge ontology to the concepts instantiated in the collection. The notion of ontology-based similarity is briefly described, language constructs for direct navigation and retrieval of concepts in the ontology are discussed and approaches to conceptual summarization are presented....

  13. Evaluation of new reference genes in papaya for accurate transcript normalization under different experimental conditions.

    Directory of Open Access Journals (Sweden)

    Xiaoyang Zhu

    Full Text Available Real-time reverse transcription PCR (RT-qPCR is a preferred method for rapid and accurate quantification of gene expression studies. Appropriate application of RT-qPCR requires accurate normalization though the use of reference genes. As no single reference gene is universally suitable for all experiments, thus reference gene(s validation under different experimental conditions is crucial for RT-qPCR analysis. To date, only a few studies on reference genes have been done in other plants but none in papaya. In the present work, we selected 21 candidate reference genes, and evaluated their expression stability in 246 papaya fruit samples using three algorithms, geNorm, NormFinder and RefFinder. The samples consisted of 13 sets collected under different experimental conditions, including various tissues, different storage temperatures, different cultivars, developmental stages, postharvest ripening, modified atmosphere packaging, 1-methylcyclopropene (1-MCP treatment, hot water treatment, biotic stress and hormone treatment. Our results demonstrated that expression stability varied greatly between reference genes and that different suitable reference gene(s or combination of reference genes for normalization should be validated according to the experimental conditions. In general, the internal reference genes EIF (Eukaryotic initiation factor 4A, TBP1 (TATA binding protein 1 and TBP2 (TATA binding protein 2 genes had a good performance under most experimental conditions, whereas the most widely present used reference genes, ACTIN (Actin 2, 18S rRNA (18S ribosomal RNA and GAPDH (Glyceraldehyde-3-phosphate dehydrogenase were not suitable in many experimental conditions. In addition, two commonly used programs, geNorm and Normfinder, were proved sufficient for the validation. This work provides the first systematic analysis for the selection of superior reference genes for accurate transcript normalization in papaya under different experimental

  14. Building Integrated Ontological Knowledge Structures with Efficient Approximation Algorithms

    Science.gov (United States)

    2015-01-01

    The integration of ontologies builds knowledge structures which brings new understanding on existing terminologies and their associations. With the steady increase in the number of ontologies, automatic integration of ontologies is preferable over manual solutions in many applications. However, available works on ontology integration are largely heuristic without guarantees on the quality of the integration results. In this work, we focus on the integration of ontologies with hierarchical structures. We identified optimal structures in this problem and proposed optimal and efficient approximation algorithms for integrating a pair of ontologies. Furthermore, we extend the basic problem to address the integration of a large number of ontologies, and correspondingly we proposed an efficient approximation algorithm for integrating multiple ontologies. The empirical study on both real ontologies and synthetic data demonstrates the effectiveness of our proposed approaches. In addition, the results of integration between gene ontology and National Drug File Reference Terminology suggest that our method provides a novel way to perform association studies between biomedical terms. PMID:26550571

  15. Building Integrated Ontological Knowledge Structures with Efficient Approximation Algorithms

    Directory of Open Access Journals (Sweden)

    Yang Xiang

    2015-01-01

    Full Text Available The integration of ontologies builds knowledge structures which brings new understanding on existing terminologies and their associations. With the steady increase in the number of ontologies, automatic integration of ontologies is preferable over manual solutions in many applications. However, available works on ontology integration are largely heuristic without guarantees on the quality of the integration results. In this work, we focus on the integration of ontologies with hierarchical structures. We identified optimal structures in this problem and proposed optimal and efficient approximation algorithms for integrating a pair of ontologies. Furthermore, we extend the basic problem to address the integration of a large number of ontologies, and correspondingly we proposed an efficient approximation algorithm for integrating multiple ontologies. The empirical study on both real ontologies and synthetic data demonstrates the effectiveness of our proposed approaches. In addition, the results of integration between gene ontology and National Drug File Reference Terminology suggest that our method provides a novel way to perform association studies between biomedical terms.

  16. The geographical ontology, LDAP, and the space information semantic grid

    Science.gov (United States)

    Cui, Wei; Li, Deren

    2005-10-01

    The research purpose is to discuss the development trend and theory of the semantic integration and interoperability of Geography Information Systems on the network ages and to point out that the geography ontology is the foregone conclusion of the development of the semantic-based integration and interoperability of Geography Information Systems. After analyzing the effect by using the various new technologies, the paper proposes new idea for the family of the ontology class based on the GIS knowledge built here. They are the basic ontology, the domain ontology and the application ontology and are very useful for the sharing and transferring of the semantic information between the complicated distributed systems and object abstracting. The main contributions of the paper are as follows: 1) For the first time taking the ontology and LDAP (Lightweight Directory Access Protocol) in creating and optimizing the architecture of Spatial Information Gird and accelerating the fusion of Geography Information System and other domain's information systems. 2) For the first time, introducing a hybrid method to build geography ontology. This hybrid method mixes the excellence of the independent domain expert and data mining. It improves the efficiency of the method of the domain expert and builds ontology semi-automatically. 3) For the first time, implementing the many-to-many relationship of integration ontology system by LDAP's reference and creating ontology-based virtual organization that could provide transparent service to guests.

  17. Practical ontologies for information professionals

    CERN Document Server

    AUTHOR|(CDS)2071712

    2016-01-01

    Practical Ontologies for Information Professionals provides an introduction to ontologies and their development, an essential tool for fighting back against information overload. The development of robust and widely used ontologies is an increasingly important tool in the fight against information overload. The publishing and sharing of explicit explanations for a wide variety of conceptualizations, in a machine readable format, has the power to both improve information retrieval and identify new knowledge. This new book provides an accessible introduction to the following: * What is an ontology? Defining the concept and why it is increasingly important to the information professional * Ontologies and the semantic web * Existing ontologies, such as SKOS, OWL, FOAF, schema.org, and the DBpedia Ontology * Adopting and building ontologies, showing how to avoid repetition of work and how to build a simple ontology with Protege * Interrogating semantic web ontologies * The future of ontologies and the role of the ...

  18. Ontological foundations for evolutionary economics: A Darwinian social ontology

    NARCIS (Netherlands)

    Stoelhorst, J.W.

    2008-01-01

    The purpose of this paper is to further the project of generalized Darwinism by developing a social ontology on the basis of a combined commitment to ontological continuity and ontological commonality. Three issues that are central to the development of a social ontology are addressed: (1) the

  19. The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.

    Science.gov (United States)

    Thacker, Robert W; Díaz, Maria Cristina; Kerner, Adeline; Vignes-Lebbe, Régine; Segerdell, Erik; Haendel, Melissa A; Mungall, Christopher J

    2014-01-01

    Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards. The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The ontology is available from http://purl.obolibrary.org/obo/poro.owl, or from the project homepage http://porifera-ontology.googlecode.com/. The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/. By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the ontology will focus on creating (1) ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the ontology is being extended to include features of fossil taxa.

  20. References

    OpenAIRE

    2018-01-01

    Aldridge, H., Kenway, P. and Born, T. (2015), ‘What Happened to Poverty Under the Coalition’. New Policy Institute. Armour, R. (2014) ‘Charity Shops Buck Trend’, http://thirdforcenews.org.uk,24 March 2014. Beatty, C. and Fothergill, S. (2016), The Uneven Impact of Welfare Reform. The Financial Losses to Places and People, Centre for Regional and Social Economic Research and Sheffield Hallam University, https://www4.shu.ac.uk/research/cresr/sites/shu.ac.uk/files/welfare-reform-2016_1.pdf Belfi...

  1. Perspectives on ontology learning

    CERN Document Server

    Lehmann, J

    2014-01-01

    Perspectives on Ontology Learning brings together researchers and practitioners from different communities − natural language processing, machine learning, and the semantic web − in order to give an interdisciplinary overview of recent advances in ontology learning.Starting with a comprehensive introduction to the theoretical foundations of ontology learning methods, the edited volume presents the state-of-the-start in automated knowledge acquisition and maintenance. It outlines future challenges in this area with a special focus on technologies suitable for pushing the boundaries beyond the c

  2. Appreciating ontological struggles

    DEFF Research Database (Denmark)

    Danholt, Peter

    Appreciating ontological struggles Peter Danholt, ass. prof., Information studies, Aarhus University In the west – most of us – take for granted that we inhabit a common world, which we share with 6 billion other human beings and multiple other living beings, animals and plants. As Annemarie Mol...... a condition in the world, but as the playing out of an ontological struggle, we become able to appreciate the situation and the treatment differently and in a manner that reconsiders treatment and disease in novel ways. Importantly, when the encounter is conceived of as an ontological struggle it becomes ever...

  3. Turning to Ontology in STS? Turning to STS through ‘Ontology’

    NARCIS (Netherlands)

    van Heur, B.; Leydesdorff, L.; Wyatt, S.

    2012-01-01

    We examine the evidence for the claim of an ‘ontological turn’ in science and technology studies (STS). Despite an increase in references to ‘ontology’ in STS since 1989, we show that there has not so much been an ontological turn as multiple discussions deploying the language of ontology,

  4. Best behaviour? Ontologies and the formal description of animal behaviour.

    Science.gov (United States)

    Gkoutos, Georgios V; Hoehndorf, Robert; Tsaprouni, Loukia; Schofield, Paul N

    2015-10-01

    The development of ontologies for describing animal behaviour has proved to be one of the most difficult of all scientific knowledge domains. Ranging from neurological processes to human emotions, the range and scope needed for such ontologies is highly challenging, but if data integration and computational tools such as automated reasoning are to be fully applied in this important area the underlying principles of these ontologies need to be better established and development needs detailed coordination. Whilst the state of scientific knowledge is always paramount in ontology and formal description framework design, this is a particular problem with neurobehavioural ontologies where our understanding of the relationship between behaviour and its underlying biophysical basis is currently in its infancy. In this commentary, we discuss some of the fundamental problems in designing and using behaviour ontologies, and present some of the best developed tools in this domain.

  5. Best behaviour? Ontologies and the formal description of animal behaviour

    KAUST Repository

    Gkoutos, Georgios V.

    2015-07-28

    The development of ontologies for describing animal behaviour has proved to be one of the most difficult of all scientific knowledge domains. Ranging from neurological processes to human emotions, the range and scope needed for such ontologies is highly challenging, but if data integration and computational tools such as automated reasoning are to be fully applied in this important area the underlying principles of these ontologies need to be better established and development needs detailed coordination. Whilst the state of scientific knowledge is always paramount in ontology and formal description framework design, this is a particular problem with neurobehavioural ontologies where our understanding of the relationship between behaviour and its underlying biophysical basis is currently in its infancy. In this commentary, we discuss some of the fundamental problems in designing and using behaviour ontologies, and present some of the best developed tools in this domain. © 2015 Springer Science+Business Media New York

  6. Data mining for ontology development.

    Energy Technology Data Exchange (ETDEWEB)

    Davidson, George S.; Strasburg, Jana (Pacific Northwest National Laboratory, Richland, WA); Stampf, David (Brookhaven National Laboratory, Upton, NY); Neymotin,Lev (Brookhaven National Laboratory, Upton, NY); Czajkowski, Carl (Brookhaven National Laboratory, Upton, NY); Shine, Eugene (Savannah River National Laboratory, Aiken, SC); Bollinger, James (Savannah River National Laboratory, Aiken, SC); Ghosh, Vinita (Brookhaven National Laboratory, Upton, NY); Sorokine, Alexandre (Oak Ridge National Laboratory, Oak Ridge, TN); Ferrell, Regina (Oak Ridge National Laboratory, Oak Ridge, TN); Ward, Richard (Oak Ridge National Laboratory, Oak Ridge, TN); Schoenwald, David Alan

    2010-06-01

    A multi-laboratory ontology construction effort during the summer and fall of 2009 prototyped an ontology for counterfeit semiconductor manufacturing. This effort included an ontology development team and an ontology validation methods team. Here the third team of the Ontology Project, the Data Analysis (DA) team reports on their approaches, the tools they used, and results for mining literature for terminology pertinent to counterfeit semiconductor manufacturing. A discussion of the value of ontology-based analysis is presented, with insights drawn from other ontology-based methods regularly used in the analysis of genomic experiments. Finally, suggestions for future work are offered.

  7. The design ontology

    DEFF Research Database (Denmark)

    Storga, Mario; Andreasen, Mogens Myrup; Marjanovic, Dorian

    2010-01-01

    The article presents the research of the nature, building and practical role of a Design Ontology as a potential framework for the more efficient product development (PD) data-, information- and knowledge- description, -explanation, -understanding and -reusing. In the methodology for development...... of the ontology two steps could be identified: empirical research and computer implementation. Empirical research has included domain documentation analysis (Genetic Design Model System developed by Mortensen 1999), identification of the key concepts and relations between them, and categorisation of the concepts...... and relations into taxonomies. As an epistemological foundation for the concepts formalisation, The Suggested Upper Merged Ontology (SUMO) proposed by IEEE, was reused. As the result of the previously described process, the ontology content has been categorised into six main subcategories divided between...

  8. Ontology of fractures

    Science.gov (United States)

    Zhong, Jian; Aydina, Atilla; McGuinness, Deborah L.

    2009-03-01

    Fractures are fundamental structures in the Earth's crust and they can impact many societal and industrial activities including oil and gas exploration and production, aquifer management, CO 2 sequestration, waste isolation, the stabilization of engineering structures, and assessing natural hazards (earthquakes, volcanoes, and landslides). Therefore, an ontology which organizes the concepts of fractures could help facilitate a sound education within, and communication among, the highly diverse professional and academic community interested in the problems cited above. We developed a process-based ontology that makes explicit specifications about fractures, their properties, and the deformation mechanisms which lead to their formation and evolution. Our ontology emphasizes the relationships among concepts such as the factors that influence the mechanism(s) responsible for the formation and evolution of specific fracture types. Our ontology is a valuable resource with a potential to applications in a number of fields utilizing recent advances in Information Technology, specifically for digital data and information in computers, grids, and Web services.

  9. Manufacturing ontology through templates

    Directory of Open Access Journals (Sweden)

    Diciuc Vlad

    2017-01-01

    Full Text Available The manufacturing industry contains a high volume of knowhow and of high value, much of it being held by key persons in the company. The passing of this know-how is the basis of manufacturing ontology. Among other methods like advanced filtering and algorithm based decision making, one way of handling the manufacturing ontology is via templates. The current paper tackles this approach and highlights the advantages concluding with some recommendations.

  10. Integrating phenotype ontologies with PhenomeNET

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel

    2017-12-19

    Background Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomical details being captured in clinical and model organism databases presents complex problems when attempting to match classes across species and across phenotypes as diverse as behaviour and neoplasia. We have previously developed PhenomeNET, a system for disease gene prioritization that includes as one of its components an ontology designed to integrate phenotype ontologies. While not applicable to matching arbitrary ontologies, PhenomeNET can be used to identify related phenotypes in different species, including human, mouse, zebrafish, nematode worm, fruit fly, and yeast. Results Here, we apply the PhenomeNET to identify related classes from two phenotype and two disease ontologies using automated reasoning. We demonstrate that we can identify a large number of mappings, some of which require automated reasoning and cannot easily be identified through lexical approaches alone. Combining automated reasoning with lexical matching further improves results in aligning ontologies. Conclusions PhenomeNET can be used to align and integrate phenotype ontologies. The results can be utilized for biomedical analyses in which phenomena observed in model organisms are used to identify causative genes and mutations underlying human disease.

  11. DMTO: a realistic ontology for standard diabetes mellitus treatment.

    Science.gov (United States)

    El-Sappagh, Shaker; Kwak, Daehan; Ali, Farman; Kwak, Kyung-Sup

    2018-02-06

    Treatment of type 2 diabetes mellitus (T2DM) is a complex problem. A clinical decision support system (CDSS) based on massive and distributed electronic health record data can facilitate the automation of this process and enhance its accuracy. The most important component of any CDSS is its knowledge base. This knowledge base can be formulated using ontologies. The formal description logic of ontology supports the inference of hidden knowledge. Building a complete, coherent, consistent, interoperable, and sharable ontology is a challenge. This paper introduces the first version of the newly constructed Diabetes Mellitus Treatment Ontology (DMTO) as a basis for shared-semantics, domain-specific, standard, machine-readable, and interoperable knowledge relevant to T2DM treatment. It is a comprehensive ontology and provides the highest coverage and the most complete picture of coded knowledge about T2DM patients' current conditions, previous profiles, and T2DM-related aspects, including complications, symptoms, lab tests, interactions, treatment plan (TP) frameworks, and glucose-related diseases and medications. It adheres to the design principles recommended by the Open Biomedical Ontologies Foundry and is based on ontological realism that follows the principles of the Basic Formal Ontology and the Ontology for General Medical Science. DMTO is implemented under Protégé 5.0 in Web Ontology Language (OWL) 2 format and is publicly available through the National Center for Biomedical Ontology's BioPortal at http://bioportal.bioontology.org/ontologies/DMTO . The current version of DMTO includes more than 10,700 classes, 277 relations, 39,425 annotations, 214 semantic rules, and 62,974 axioms. We provide proof of concept for this approach to modeling TPs. The ontology is able to collect and analyze most features of T2DM as well as customize chronic TPs with the most appropriate drugs, foods, and physical exercises. DMTO is ready to be used as a knowledge base for

  12. The Cognitive Paradigm Ontology: Design and Application

    Science.gov (United States)

    Laird, Angela R.

    2013-01-01

    We present the basic structure of the Cognitive Paradigm Ontology (CogPO) for human behavioral experiments. While the experimental psychology and cognitive neuroscience literature may refer to certain behavioral tasks by name (e.g., the Stroop paradigm or the Sternberg paradigm) or by function (a working memory task, a visual attention task), these paradigms can vary tremendously in the stimuli that are presented to the subject, the response expected from the subject, and the instructions given to the subject. Drawing from the taxonomy developed and used by the BrainMap project (www.brainmap.org) for almost two decades to describe key components of published functional imaging results, we have developed an ontology capable of representing certain characteristics of the cognitive paradigms used in the fMRI and PET literature. The Cognitive Paradigm Ontology is being developed to be compliant with the Basic Formal Ontology (BFO), and to harmonize where possible with larger ontologies such as RadLex, NeuroLex, or the Ontology of Biomedical Investigations (OBI). The key components of CogPO include the representation of experimental conditions focused on the stimuli presented, the instructions given, and the responses requested. The use of alternate and even competitive terminologies can often impede scientific discoveries. Categorization of paradigms according to stimulus, response, and instruction has been shown to allow advanced data retrieval techniques by searching for similarities and contrasts across multiple paradigm levels. The goal of CogPO is to develop, evaluate, and distribute a domain ontology of cognitive paradigms for application and use in the functional neuroimaging community. PMID:21643732

  13. Building an Ontology of Product/Service-Systems

    DEFF Research Database (Denmark)

    Pagoropoulos, Aris; Andersen, Jakob Axel Bejbro; Kjær, Louise Laumann

    2014-01-01

    a rich view of PSS as a strategy, also leaves some confusion as to what actually constitutes a PSS. The definition of a PSS ontology could provide the basis for a more systematic knowledge gathering within the field and facilitate the application of integrated solutions within the industry. Ontologies...... provide an effective tool for a knowledge management process, due to their semantic capabilities, interoperability and extendibility. A PSS ontology for domain conceptualisation is proposed that captures the underlying end-user value and relates to existing PSS offerings. The PSS ontology is subsequently...... integrated into an ontology for the maritime sector, in order to allow for the identification of the PSS implementation opportunities within the industry. A maritime ontology can help the industry to document and reuse tacit knowledge while facilitating the implementation and value assessment of PSS...

  14. NanoParticle Ontology for Cancer Nanotechnology Research

    Science.gov (United States)

    Thomas, Dennis G.; Pappu, Rohit V.; Baker, Nathan A.

    2010-01-01

    Data generated from cancer nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. In particular, ontologies that provide a unifying knowledge framework for annotating the data are required to facilitate the semantic integration, knowledge-based searching, unambiguous interpretation, mining and inferencing of the data using informatics methods. In this paper, we discuss the design and development of NanoParticle Ontology (NPO), which is developed within the framework of the Basic Formal Ontology (BFO), and implemented in the Ontology Web Language (OWL) using well-defined ontology design principles. The NPO was developed to represent knowledge underlying the preparation, chemical composition, and characterization of nanomaterials involved in cancer research. Public releases of the NPO are available through BioPortal website, maintained by the National Center for Biomedical Ontology. Mechanisms for editorial and governance processes are being developed for the maintenance, review, and growth of the NPO. PMID:20211274

  15. Reference genes for accurate transcript normalization in citrus genotypes under different experimental conditions.

    Directory of Open Access Journals (Sweden)

    Valéria Mafra

    Full Text Available Real-time reverse transcription PCR (RT-qPCR has emerged as an accurate and widely used technique for expression profiling of selected genes. However, obtaining reliable measurements depends on the selection of appropriate reference genes for gene expression normalization. The aim of this work was to assess the expression stability of 15 candidate genes to determine which set of reference genes is best suited for transcript normalization in citrus in different tissues and organs and leaves challenged with five pathogens (Alternaria alternata, Phytophthora parasitica, Xylella fastidiosa and Candidatus Liberibacter asiaticus. We tested traditional genes used for transcript normalization in citrus and orthologs of Arabidopsis thaliana genes described as superior reference genes based on transcriptome data. geNorm and NormFinder algorithms were used to find the best reference genes to normalize all samples and conditions tested. Additionally, each biotic stress was individually analyzed by geNorm. In general, FBOX (encoding a member of the F-box family and GAPC2 (GAPDH was the most stable candidate gene set assessed under the different conditions and subsets tested, while CYP (cyclophilin, TUB (tubulin and CtP (cathepsin were the least stably expressed genes found. Validation of the best suitable reference genes for normalizing the expression level of the WRKY70 transcription factor in leaves infected with Candidatus Liberibacter asiaticus showed that arbitrary use of reference genes without previous testing could lead to misinterpretation of data. Our results revealed FBOX, SAND (a SAND family protein, GAPC2 and UPL7 (ubiquitin protein ligase 7 to be superior reference genes, and we recommend their use in studies of gene expression in citrus species and relatives. This work constitutes the first systematic analysis for the selection of superior reference genes for transcript normalization in different citrus organs and under biotic stress.

  16. Open Biomedical Ontology-based Medline exploration

    Science.gov (United States)

    Xuan, Weijian; Dai, Manhong; Mirel, Barbara; Song, Jean; Athey, Brian; Watson, Stanley J; Meng, Fan

    2009-01-01

    Background Effective Medline database exploration is critical for the understanding of high throughput experimental results and the development of novel hypotheses about the mechanisms underlying the targeted biological processes. While existing solutions enhance Medline exploration through different approaches such as document clustering, network presentations of underlying conceptual relationships and the mapping of search results to MeSH and Gene Ontology trees, we believe the use of multiple ontologies from the Open Biomedical Ontology can greatly help researchers to explore literature from different perspectives as well as to quickly locate the most relevant Medline records for further investigation. Results We developed an ontology-based interactive Medline exploration solution called PubOnto to enable the interactive exploration and filtering of search results through the use of multiple ontologies from the OBO foundry. The PubOnto program is a rich internet application based on the FLEX platform. It contains a number of interactive tools, visualization capabilities, an open service architecture, and a customizable user interface. It is freely accessible at: . PMID:19426463

  17. Ontology Extraction Tools: An Empirical Study with Educators

    Science.gov (United States)

    Hatala, M.; Gasevic, D.; Siadaty, M.; Jovanovic, J.; Torniai, C.

    2012-01-01

    Recent research in Technology-Enhanced Learning (TEL) demonstrated several important benefits that semantic technologies can bring to the TEL domain. An underlying assumption for most of these research efforts is the existence of a domain ontology. The second unspoken assumption follows that educators will build domain ontologies for their…

  18. Ontology: ambiguity and accuracy

    Directory of Open Access Journals (Sweden)

    Marcelo Schiessl

    2012-08-01

    Full Text Available Ambiguity is a major obstacle to information retrieval. It is source of several researches in Information Science. Ontologies have been studied in order to solve problems related to ambiguities. Paradoxically, “ontology” term is also ambiguous and it is understood according to the use by the community. Philosophy and Computer Science seems to have the most accentuated difference related to the term sense. The former holds undisputed tradition and authority. The latter, in despite of being quite recent, holds an informal sense, but pragmatic. Information Science acts ranging from philosophical to computational approaches so as to get organized collections based on balance between users’ necessities and available information. The semantic web requires informational cycle automation and demands studies related to ontologies. Consequently, revisiting relevant approaches for the study of ontologies plays a relevant role as a way to provide useful ideas to researchers maintaining philosophical rigor, and convenience provided by computers.

  19. Ontological engineering versus metaphysics

    Science.gov (United States)

    Tataj, Emanuel; Tomanek, Roman; Mulawka, Jan

    2011-10-01

    It has been recognized that ontologies are a semantic version of world wide web and can be found in knowledge-based systems. A recent time survey of this field also suggest that practical artificial intelligence systems may be motivated by this research. Especially strong artificial intelligence as well as concept of homo computer can also benefit from their use. The main objective of this contribution is to present and review already created ontologies and identify the main advantages which derive such approach for knowledge management systems. We would like to present what ontological engineering borrows from metaphysics and what a feedback it can provide to natural language processing, simulations and modelling. The potential topics of further development from philosophical point of view is also underlined.

  20. Process attributes in bio-ontologies

    Directory of Open Access Journals (Sweden)

    Andrade André Q

    2012-08-01

    Full Text Available Abstract Background Biomedical processes can provide essential information about the (mal- functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Process branch. These processes often need to be described and categorised in terms of their attributes, such as rates or regularities. The adequate representation of such process attributes has been a contentious issue in bio-ontologies recently; and domain ontologies have correspondingly developed ad hoc workarounds that compromise interoperability and logical consistency. Results We present a design pattern for the representation of process attributes that is compatible with upper ontology frameworks such as BFO and BioTop. Our solution rests on two key tenets: firstly, that many of the sorts of process attributes which are biomedically interesting can be characterised by the ways that repeated parts of such processes constitute, in combination, an overall process; secondly, that entities for which a full logical definition can be assigned do not need to be treated as primitive within a formal ontology framework. We apply this approach to the challenge of modelling and automatically classifying examples of normal and abnormal rates and patterns of heart beating processes, and discuss the expressivity required in the underlying ontology representation language. We provide full definitions for process attributes at increasing levels of domain complexity. Conclusions We show that a logical definition of process attributes is feasible, though limited by the expressivity of DL languages so that the creation of primitives is still necessary. This finding may endorse current formal upper-ontology frameworks as a way of ensuring consistency, interoperability and clarity.

  1. Learning expressive ontologies

    CERN Document Server

    Völker, J

    2009-01-01

    This publication advances the state-of-the-art in ontology learning by presenting a set of novel approaches to the semi-automatic acquisition, refinement and evaluation of logically complex axiomatizations. It has been motivated by the fact that the realization of the semantic web envisioned by Tim Berners-Lee is still hampered by the lack of ontological resources, while at the same time more and more applications of semantic technologies emerge from fast-growing areas such as e-business or life sciences. Such knowledge-intensive applications, requiring large scale reasoning over complex domai

  2. Ontology Matching Across Domains

    Science.gov (United States)

    2010-05-01

    matching include GMO [1], Anchor-Prompt [2], and Similarity Flooding [3]. GMO is an iterative structural matcher, which uses RDF bipartite graphs to...AFRL under contract# FA8750-09-C-0058. References [1] Hu, W., Jian, N., Qu, Y., Wang, Y., “ GMO : a graph matching for ontologies”, in: Proceedings of

  3. Core Semantics for Public Ontologies

    National Research Council Canada - National Science Library

    Suni, Niranjan

    2005-01-01

    ... (schemas or ontologies) with respect to objects. The DARPA Agent Markup Language (DAML) through the use of ontologies provides a very powerful way to describe objects and their relationships to other objects...

  4. A Method for Building Personalized Ontology Summaries

    OpenAIRE

    Queiroz-Sousa, Paulo Orlando; Salgado, Ana Carolina; Pires, Carlos Eduardo

    2013-01-01

    In the context of ontology engineering, the ontology understanding is the basis for its further developmentand reuse. One intuitive eective approach to support ontology understanding is the process of ontology summarizationwhich highlights the most important concepts of an ontology. Ontology summarization identies an excerpt from anontology that contains the most relevant concepts and produces an abridged ontology. In this article, we present amethod for summarizing ontologies that represent ...

  5. Physical properties of biological entities: an introduction to the ontology of physics for biology.

    Directory of Open Access Journals (Sweden)

    Daniel L Cook

    Full Text Available As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities-molecules, cells, organs-are well-established, there are no principled ontologies of physical properties-energies, volumes, flow rates-of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB, a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration.

  6. Summarization by domain ontology navigation

    DEFF Research Database (Denmark)

    Andreasen, Troels; Bulskov, Henrik

    2013-01-01

    of the subject. In between these two extremes, conceptual summaries encompass selected concepts derived using background knowledge. We address in this paper an approach where conceptual summaries are provided through a conceptualization as given by an ontology. The ontology guiding the summarization can...... be a simple taxonomy or a generative domain ontology. A domain ontology can be provided by a preanalysis of a domain corpus and can be used to condense improved summaries that better reflects the conceptualization of a given domain....

  7. Using a Foundational Ontology for Reengineering a Software Enterprise Ontology

    Science.gov (United States)

    Perini Barcellos, Monalessa; de Almeida Falbo, Ricardo

    The knowledge about software organizations is considerably relevant to software engineers. The use of a common vocabulary for representing the useful knowledge about software organizations involved in software projects is important for several reasons, such as to support knowledge reuse and to allow communication and interoperability between tools. Domain ontologies can be used to define a common vocabulary for sharing and reuse of knowledge about some domain. Foundational ontologies can be used for evaluating and re-designing domain ontologies, giving to these real-world semantics. This paper presents an evaluating of a Software Enterprise Ontology that was reengineered using the Unified Foundation Ontology (UFO) as basis.

  8. Reliable reference gene selection for Cordyceps militaris gene expression studies under different developmental stages and media.

    Science.gov (United States)

    Lian, Tiantian; Yang, Tao; Liu, Guijun; Sun, Junde; Dong, Caihong

    2014-07-01

    Cordyceps militaris is considered a model organism for the study of Cordyceps species, which are highly prized in traditional Chinese medicine. Gene expression analysis has become more popular and important in studies of this fungus. Reference gene validation under different experimental conditions is crucial for RT-qPCR analysis. In this study, eight candidate reference genes, actin, cox5, gpd, rpb1, tef1, try, tub, and ubi, were selected and their expression stability was evaluated in C. militaris samples using four algorithms, genorm, normfinder, bestkeeper, and the comparative ∆Ct method. Three sets of samples, five different developmental stages cultured in wheat medium and pupae, and all the samples pool were included. The results showed that rpb1 was the best reference gene during all developmental stages examined, while the most common reference genes, actin and tub, were not suitable internal controls. Cox5 also performed poorly and was less stable in our analysis. The ranks of ubi and gpd were inconsistent in different sample sets by different methods. Our results provide guidelines for reference gene selection at different developmental stages and also represent a foundation for more accurate and widespread use of RT-qPCR in C. militaris gene expression analysis. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  9. Taking Critical Ontology Seriously

    DEFF Research Database (Denmark)

    Wigger, Angela; Horn, Laura

    2017-01-01

    privilege ontology over epistemology – that is, why we need to accept that social reality is constituted by complex power relations that evolve from a constant dialectical interplay of structure and agency over time, and that these power relations are revealed in both ideational and material dimensions...

  10. Dahlbeck and Pure Ontology

    Science.gov (United States)

    Mackenzie, Jim

    2016-01-01

    This article responds to Johan Dahlbeck's "Towards a pure ontology: Children's bodies and morality" ["Educational Philosophy and Theory," vol. 46 (1), 2014, pp. 8-23 (EJ1026561)]. His arguments from Nietzsche and Spinoza do not carry the weight he supposes, and the conclusions he draws from them about pedagogy would be…

  11. OWL Web Ontology Language

    NARCIS (Netherlands)

    Staab, S.; Studer, R.; Antoniou, Grigoris; Van Harmelen, Frank; Staab, S; Studer, R

    2004-01-01

    The OWL Web Ontology Language is designed for use by applications that need to process the content of information instead of just presenting information to humans. OWL facilitates greater machine interpretability of Web content than that supported by XML, RDF, and RDF Schema (RDF-S) by providing

  12. Ontological Order in Scientific Explanation | Park | Philosophical ...

    African Journals Online (AJOL)

    I argue that Stanford's proposal has a conceptual flaw. A conceptually sound explanation, I claim, respects the ontological order between properties. A dependent property is to be explained in terms of its underlying property, not the other way around. The applicability of this point goes well beyond the realm of the debate ...

  13. Epistemology and ontology in core ontologies: FOLaw and LRI-Core, two core ontologies for law

    NARCIS (Netherlands)

    Breukers, J.A.P.J.; Hoekstra, R.J.

    2004-01-01

    For more than a decade constructing ontologies for legal domains, we, at the Leibniz Center for Law, felt really the need to develop a core ontology for law that would enable us to re-use the common denominator of the various legal domains. In this paper we present two core ontologies for law. The

  14. Semi-automated ontology generation and evolution

    Science.gov (United States)

    Stirtzinger, Anthony P.; Anken, Craig S.

    2009-05-01

    Extending the notion of data models or object models, ontology can provide rich semantic definition not only to the meta-data but also to the instance data of domain knowledge, making these semantic definitions available in machine readable form. However, the generation of an effective ontology is a difficult task involving considerable labor and skill. This paper discusses an Ontology Generation and Evolution Processor (OGEP) aimed at automating this process, only requesting user input when un-resolvable ambiguous situations occur. OGEP directly attacks the main barrier which prevents automated (or self learning) ontology generation: the ability to understand the meaning of artifacts and the relationships the artifacts have to the domain space. OGEP leverages existing lexical to ontological mappings in the form of WordNet, and Suggested Upper Merged Ontology (SUMO) integrated with a semantic pattern-based structure referred to as the Semantic Grounding Mechanism (SGM) and implemented as a Corpus Reasoner. The OGEP processing is initiated by a Corpus Parser performing a lexical analysis of the corpus, reading in a document (or corpus) and preparing it for processing by annotating words and phrases. After the Corpus Parser is done, the Corpus Reasoner uses the parts of speech output to determine the semantic meaning of a word or phrase. The Corpus Reasoner is the crux of the OGEP system, analyzing, extrapolating, and evolving data from free text into cohesive semantic relationships. The Semantic Grounding Mechanism provides a basis for identifying and mapping semantic relationships. By blending together the WordNet lexicon and SUMO ontological layout, the SGM is given breadth and depth in its ability to extrapolate semantic relationships between domain entities. The combination of all these components results in an innovative approach to user assisted semantic-based ontology generation. This paper will describe the OGEP technology in the context of the architectural

  15. Benchmarking ontologies: bigger or better?

    Directory of Open Access Journals (Sweden)

    Lixia Yao

    2011-01-01

    Full Text Available A scientific ontology is a formal representation of knowledge within a domain, typically including central concepts, their properties, and relations. With the rise of computers and high-throughput data collection, ontologies have become essential to data mining and sharing across communities in the biomedical sciences. Powerful approaches exist for testing the internal consistency of an ontology, but not for assessing the fidelity of its domain representation. We introduce a family of metrics that describe the breadth and depth with which an ontology represents its knowledge domain. We then test these metrics using (1 four of the most common medical ontologies with respect to a corpus of medical documents and (2 seven of the most popular English thesauri with respect to three corpora that sample language from medicine, news, and novels. Here we show that our approach captures the quality of ontological representation and guides efforts to narrow the breach between ontology and collective discourse within a domain. Our results also demonstrate key features of medical ontologies, English thesauri, and discourse from different domains. Medical ontologies have a small intersection, as do English thesauri. Moreover, dialects characteristic of distinct domains vary strikingly as many of the same words are used quite differently in medicine, news, and novels. As ontologies are intended to mirror the state of knowledge, our methods to tighten the fit between ontology and domain will increase their relevance for new areas of biomedical science and improve the accuracy and power of inferences computed across them.

  16. Ontology-based Information Retrieval

    DEFF Research Database (Denmark)

    Styltsvig, Henrik Bulskov

    In this thesis, we will present methods for introducing ontologies in information retrieval. The main hypothesis is that the inclusion of conceptual knowledge such as ontologies in the information retrieval process can contribute to the solution of major problems currently found in information...... retrieval. This utilization of ontologies has a number of challenges. Our focus is on the use of similarity measures derived from the knowledge about relations between concepts in ontologies, the recognition of semantic information in texts and the mapping of this knowledge into the ontologies in use......, as well as how to fuse together the ideas of ontological similarity and ontological indexing into a realistic information retrieval scenario. To achieve the recognition of semantic knowledge in a text, shallow natural language processing is used during indexing that reveals knowledge to the level of noun...

  17. Margin based ontology sparse vector learning algorithm and applied in biology science

    Directory of Open Access Journals (Sweden)

    Wei Gao

    2017-01-01

    Full Text Available In biology field, the ontology application relates to a large amount of genetic information and chemical information of molecular structure, which makes knowledge of ontology concepts convey much information. Therefore, in mathematical notation, the dimension of vector which corresponds to the ontology concept is often very large, and thus improves the higher requirements of ontology algorithm. Under this background, we consider the designing of ontology sparse vector algorithm and application in biology. In this paper, using knowledge of marginal likelihood and marginal distribution, the optimized strategy of marginal based ontology sparse vector learning algorithm is presented. Finally, the new algorithm is applied to gene ontology and plant ontology to verify its efficiency.

  18. A broken symmetry ontology: Quantum mechanics as a broken symmetry

    International Nuclear Information System (INIS)

    Buschmann, J.E.

    1988-01-01

    The author proposes a new broken symmetry ontology to be used to analyze the quantum domain. This ontology is motivated and grounded in a critical epistemological analysis, and an analysis of the basic role of symmetry in physics. Concurrently, he is led to consider nonheterogeneous systems, whose logical state space contains equivalence relations not associated with the causal relation. This allows him to find a generalized principle of symmetry and a generalized symmetry-conservation formalisms. In particular, he clarifies the role of Noether's theorem in field theory. He shows how a broken symmetry ontology already operates in a description of the weak interactions. Finally, by showing how a broken symmetry ontology operates in the quantum domain, he accounts for the interpretational problem and the essential incompleteness of quantum mechanics. He proposes that the broken symmetry underlying this ontological domain is broken dilation invariance

  19. Kant and the romantic ontology

    Directory of Open Access Journals (Sweden)

    Prole Dragan

    2015-01-01

    Full Text Available In the first part of the paper, the author displays the specificities of the romantic concept of subjectivity. Based on the assumption that the Man is but a minute part of what he might be, the romantics emphasize on the imperative of infinite subjectivity. Giving up on the division of philosophical disciplines, the romantics request a unity of spirit in history. The relationship between Kant and romanticism is mostly deliberated under the auspices of the terms of anarchy and the nomadic spirit, which are pointed out by Kant in the beginning of the foreword to the first edition of the Critique of Pure Reason as the symptoms of the crisis of metaphysics. What Kant sees as a crisis, the romantics embrace as constitutive moments of subjectivity which aspire to soften the modern rifts by breaking up with all substance. Trying to develop a sketch of the ontology of existence, Friedrich Schlegel evokes Plato’s term ontos on, but ties it with the process of establishing the individual ideal, as opposed to the former link with the objective being. The author concludes that the ontology of existence with romantics is at the same time the metaphysics of subjectivity which cares mostly about originality, selfness and authenticity, about the integration of Kant’s term of dynamically sublime in the midst of the philosophical speech about the true being.

  20. Reference genes for gene expression studies in wheat flag leaves grown under different farming conditions

    Directory of Open Access Journals (Sweden)

    Cordeiro Raposo Fernando

    2011-09-01

    Full Text Available Abstract Background Internal control genes with highly uniform expression throughout the experimental conditions are required for accurate gene expression analysis as no universal reference genes exists. In this study, the expression stability of 24 candidate genes from Triticum aestivum cv. Cubus flag leaves grown under organic and conventional farming systems was evaluated in two locations in order to select suitable genes that can be used for normalization of real-time quantitative reverse-transcription PCR (RT-qPCR reactions. The genes were selected among the most common used reference genes as well as genes encoding proteins involved in several metabolic pathways. Findings Individual genes displayed different expression rates across all samples assayed. Applying geNorm, a set of three potential reference genes were suitable for normalization of RT-qPCR reactions in winter wheat flag leaves cv. Cubus: TaFNRII (ferredoxin-NADP(H oxidoreductase; AJ457980.1, ACT2 (actin 2; TC234027, and rrn26 (a putative homologue to RNA 26S gene; AL827977.1. In addition of these three genes that were also top-ranked by NormFinder, two extra genes: CYP18-2 (Cyclophilin A, AY456122.1 and TaWIN1 (14-3-3 like protein, AB042193 were most consistently stably expressed. Furthermore, we showed that TaFNRII, ACT2, and CYP18-2 are suitable for gene expression normalization in other two winter wheat varieties (Tommi and Centenaire grown under three treatments (organic, conventional and no nitrogen and a different environment than the one tested with cv. Cubus. Conclusions This study provides a new set of reference genes which should improve the accuracy of gene expression analyses when using wheat flag leaves as those related to the improvement of nitrogen use efficiency for cereal production.

  1. Completeness, supervenience and ontology

    International Nuclear Information System (INIS)

    Maudlin, Tim W E

    2007-01-01

    In 1935, Einstein, Podolsky and Rosen raised the issue of the completeness of the quantum description of a physical system. What they had in mind is whether or not the quantum description is informationally complete, in that all physical features of a system can be recovered from it. In a collapse theory such as the theory of Ghirardi, Rimini and Weber, the quantum wavefunction is informationally complete, and this has often been taken to suggest that according to that theory the wavefunction is all there is. If we distinguish the ontological completeness of a description from its informational completeness, we can see that the best interpretations of the GRW theory must postulate more physical ontology than just the wavefunction

  2. Cross-sectional-type weight reference values for village children under five years in Lesotho.

    Science.gov (United States)

    Cohen, N M; Clayden, A D; King, B

    1976-03-01

    Cross-sectional-type reference values for weight attained are described for village children under five years in rural Lesotho (formerly Basutoland). Weight measurements derive from observations on 1317 children attending an Under-Fives clinic; it is estimated that 60-70% of the children under five in the catchment area were represented. 4585 weighings on boys and 4826 weighings for girls are included in the analysis. Figures of weight-for-age of boys and girls are given separately as centile distributions suitable for use on Growth Charts. Lesotho 50 centile approximates to 3 centile of British children and slightly exceeds 80% Harvard standard. Weight attained for age is similar, in both sexes, to reports from other less-priviledged urban and rural areas, emphasizing the relative importance of environmental as compared to genetic influences in determining weight-for-age in early childhood. It is suggested that the construction of locally-derived growth reference values is both appropriate and practicable.

  3. Proceedings of a Sickle Cell Disease Ontology workshop — Towards the first comprehensive ontology for Sickle Cell Disease

    Directory of Open Access Journals (Sweden)

    Nicola Mulder

    2016-06-01

    The SCD community and H3ABioNet members joined forces at a recent SCD Ontology workshop to develop an ontology covering aspects of SCD under the classes: phenotype, diagnostics, therapeutics, quality of life, disease modifiers and disease stage. The aim of the workshop was for participants to contribute their expertise to development of the structure and contents of the SCD ontology. Here we describe the proceedings of the Sickle Cell Disease Ontology Workshop held in Cape Town South Africa in February 2016 and its outcomes. The objective of the workshop was to bring together experts in SCD from around the world to contribute their expertise to the development of various aspects of the SCD ontology.

  4. Insider Threat Indicator Ontology

    Science.gov (United States)

    2016-05-25

    Figure 12 shows a key with the symbols used to visualize the ontology. Figure 12: Diagram Key CMU/SEI-2016-TR-007 | SOFTWARE ENGINEERING...security guard is defined as an employee who guards, patrols, or monitors a premises to prevent theft, violence , or infractions of rules...malicious actions of an insider. Event Organization isVictimOrganizationOf hasWife hasSpouse This relates a married woman to her spouse. Person Person

  5. Tecnologia da informação e serviços de referência eletrônicos: uma proposta de aplicação baseada em chatterbots e ontologiasInformation technology and electronic reference services: an application proposal based in chatterbots and ontologies

    Directory of Open Access Journals (Sweden)

    Guilherme Ataíde Dias

    2007-01-01

    Full Text Available Discute os principais conceitos relacionados ao desenvolvimento de um sistema de referência eletrônico em unidades de informação através do uso da tecnologia de informação. Introduz o conceito de chatterbots, apresenta seus principais usos, gerações evolutivas e linguagens utilizadas na sua implementação. Conceitua ontologia de maneira geral e contextualiza seu significado na área da Ciência da Informação. Descreve a arquitetura do sistema DELPHOS, explicitando as etapas da construção da interface do usuário, processador AIML e bases de conhecimentos. Conclui sugerindo estudos futuros com o objetivo de avaliar as dinâmicas emergentes da interação dos usuários com o chatterbot e a possibilidade de construção de um perfil de usuário a partir das interações com o mesmo.Discusses the main concepts concerning to the development of an electronic reference system in an information unit through the use of information technology. The concepts related to the use of chatterbots are presented as well its main uses, evolutive generations and the languages used in its implementation. It is explained in a generalized way what it is an ontology and its meaning in the area of Information Science. The architecture of theDELPHOS system is explained and also the choices made concerning the construction of the user interface, AIML processor and the bases of knowledge. The paper ends suggesting a future study with the objective to evaluate the emergent dynamic relating the users’sinteraction with the chatterbot and the possibility building a user profile from the interactions with the chatterbot.

  6. An encoding methodology for medical knowledge using SNOMED CT ontology

    Directory of Open Access Journals (Sweden)

    Shaker El-Sappagh

    2016-07-01

    Full Text Available Knowledge-Intensive Case Based Reasoning (KI-CBR systems mainly depend on ontology. Using ontology as domain knowledge supports the implementation of semantically-intelligent case retrieval algorithms. The case-based knowledge must be encoded with the same concepts of the domain ontology. Standard medical ontologies, such as SNOMED CT (SCT, can play the role of domain ontology to enhance case representation and retrieval. This study has three stages. First, we propose an encoding methodology using SCT. Second, this methodology is used to encode the case-based knowledge. Third, all the used SCT concepts are collected in a reference set, and an OWL2 ontology of 550 pre-coordinated concepts is proposed. A diabetes diagnosis is chosen as a case study of our proposed framework. SCT is used to provide a pre-coordination concept coverage of ∼75% for diabetes diagnosis terms. Whereas, the uncovered concepts in SCT are proposed. The resulting OWL2 ontology will be used as domain knowledge representation in diabetes diagnosis CBR systems. The proposed framework is tested by using 60 real cases.

  7. A unified anatomy ontology of the vertebrate skeletal system.

    Directory of Open Access Journals (Sweden)

    Wasila M Dahdul

    Full Text Available The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO, to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish and multispecies (teleost, amphibian vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages, and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO, Gene Ontology (GO, Uberon, and Cell Ontology (CL, and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

  8. A unified anatomy ontology of the vertebrate skeletal system.

    Science.gov (United States)

    Dahdul, Wasila M; Balhoff, James P; Blackburn, David C; Diehl, Alexander D; Haendel, Melissa A; Hall, Brian K; Lapp, Hilmar; Lundberg, John G; Mungall, Christopher J; Ringwald, Martin; Segerdell, Erik; Van Slyke, Ceri E; Vickaryous, Matthew K; Westerfield, Monte; Mabee, Paula M

    2012-01-01

    The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

  9. Consistent Feature Extraction From Vector Fields: Combinatorial Representations and Analysis Under Local Reference Frames

    Energy Technology Data Exchange (ETDEWEB)

    Bhatia, Harsh [Univ. of Utah, Salt Lake City, UT (United States)

    2015-05-01

    This dissertation presents research on addressing some of the contemporary challenges in the analysis of vector fields—an important type of scientific data useful for representing a multitude of physical phenomena, such as wind flow and ocean currents. In particular, new theories and computational frameworks to enable consistent feature extraction from vector fields are presented. One of the most fundamental challenges in the analysis of vector fields is that their features are defined with respect to reference frames. Unfortunately, there is no single “correct” reference frame for analysis, and an unsuitable frame may cause features of interest to remain undetected, thus creating serious physical consequences. This work develops new reference frames that enable extraction of localized features that other techniques and frames fail to detect. As a result, these reference frames objectify the notion of “correctness” of features for certain goals by revealing the phenomena of importance from the underlying data. An important consequence of using these local frames is that the analysis of unsteady (time-varying) vector fields can be reduced to the analysis of sequences of steady (timeindependent) vector fields, which can be performed using simpler and scalable techniques that allow better data management by accessing the data on a per-time-step basis. Nevertheless, the state-of-the-art analysis of steady vector fields is not robust, as most techniques are numerical in nature. The residing numerical errors can violate consistency with the underlying theory by breaching important fundamental laws, which may lead to serious physical consequences. This dissertation considers consistency as the most fundamental characteristic of computational analysis that must always be preserved, and presents a new discrete theory that uses combinatorial representations and algorithms to provide consistency guarantees during vector field analysis along with the uncertainty

  10. How color difference formulas depend on reference pairs in the underlying constant stimuli experiment.

    Science.gov (United States)

    Kirchner, Eric; Dekker, Niels; Lucassen, Marcel; Njo, Lan; van der Lans, Ivo; Koeckhoven, Pim; Urban, Philipp; Huertas, Rafael

    2015-12-01

    For calculating color differences, the CIEDE2000 and CIE94 equations are widely used and recommended. These equations were derived more than a decade ago, based for a large part on the RIT-Dupont set of visual data. This data was collected from a series of psychophysical tests that use the method of constant stimuli. In this method, observers need to compare the color difference within a sample pair to that between a reference pair. In the current investigation, we show that the color difference equation significantly changes if reference pairs are chosen in the underlying visual experiments that differ from what was used when creating the RIT-Dupont dataset. The investigation is done using metallic paint samples representing two color centers, red and yellow-green. We show that the reproducibility differs for three different reference pairs, and that for modeling the visual data for the yellow-green color center, extra model terms are required as compared to the CIEDE2000 equation. Our results suggest that observers differ in their ability to mentally convert a color difference recognized in a sample pair into an equivalent color difference along the color difference direction represented by the reference pair. We also find that in these tests the tolerance to lightness differences is widened by a factor of 1.3 to 1.6, and that for the red color center the tolerance ellipsoid is rotated by 30° as compared to the CIEDE2000 equation. The latter observations are possibly due to the metallic texture in the samples used for the current experiment.

  11. Do higher-priced generic medicines enjoy a competitive advantage under reference pricing?

    Science.gov (United States)

    Puig-Junoy, Jaume

    2012-11-01

    In many countries with generic reference pricing, generic producers and distributors compete by means of undisclosed discounts offered to pharmacies in order to reduce acquisition costs and to induce them to dispense their generic to patients in preference over others. The objective of this article is to test the hypothesis that under prevailing reference pricing systems for generic medicines, those medicines sold at a higher consumer price may enjoy a competitive advantage. Real transaction prices for 179 generic medicines acquired by pharmacies in Spain have been used to calculate the discount rate on acquisition versus reimbursed costs to pharmacies. Two empirical hypotheses are tested: the discount rate at which pharmacies acquire generic medicines is higher for those pharmaceutical presentations for which there are more generic competitors; and, the discount rate at which pharmacies acquire generic medicines is higher for those pharmaceutical forms for which the consumer price has declined less in relation to the consumer price of the brand drug before generic entry (higher-priced generic medicines). An average discount rate of 39.3% on acquisition versus reimbursed costs to pharmacies has been observed. The magnitude of the discount positively depends on the number of competitors in the market. The higher the ratio of the consumer price of the generic to that of the brand drug prior to generic entry (i.e. the smaller the price reduction of the generic in relation to the brand drug), the larger the discount rate. Under reference pricing there is intense price competition among generic firms in the form of unusually high discounts to pharmacies on official ex-factory prices reimbursed to pharmacies. However, this effect is highly distorting because it favours those medicines with a higher relative price in relation to the brand price before generic entry.

  12. An Ontology for Software Engineering Education

    Science.gov (United States)

    Ling, Thong Chee; Jusoh, Yusmadi Yah; Adbullah, Rusli; Alwi, Nor Hayati

    2013-01-01

    Software agents communicate using ontology. It is important to build an ontology for specific domain such as Software Engineering Education. Building an ontology from scratch is not only hard, but also incur much time and cost. This study aims to propose an ontology through adaptation of the existing ontology which is originally built based on a…

  13. Nursing theories as nursing ontologies.

    Science.gov (United States)

    Flaming, Don

    2004-10-01

    By understanding the constructions of knowledge we currently label nursing theories as nursing ontologies, nurses can perceive these conceptualizations differently. Paul Ricoeur and Stephen White offer a conceptualization of ontology that differs from traditional, realist perspectives because they assume that a person's experience of a phenomenon (e.g., nursing) will change, but also maintain some stability. Discussing nursing ontologies, rather than nursing theories, might increase philosophy's status in nursing and may also more accurately reflect the experience of being a nurse.

  14. Semantic Similarity in Biomedical Ontologies

    OpenAIRE

    Pesquita, Catia; Faria, Daniel; Falc?o, Andr? O.; Lord, Phillip; Couto, Francisco M.

    2009-01-01

    In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degree of relatedness between two entities by the similarity in meaning of their annotations. The application of semantic similarity to biomedical ontologies is recent; nevertheless, several studies hav...

  15. Standardized description of scientific evidence using the Evidence Ontology (ECO).

    Science.gov (United States)

    Chibucos, Marcus C; Mungall, Christopher J; Balakrishnan, Rama; Christie, Karen R; Huntley, Rachael P; White, Owen; Blake, Judith A; Lewis, Suzanna E; Giglio, Michelle

    2014-01-01

    The Evidence Ontology (ECO) is a structured, controlled vocabulary for capturing evidence in biological research. ECO includes diverse terms for categorizing evidence that supports annotation assertions including experimental types, computational methods, author statements and curator inferences. Using ECO, annotation assertions can be distinguished according to the evidence they are based on such as those made by curators versus those automatically computed or those made via high-throughput data review versus single test experiments. Originally created for capturing evidence associated with Gene Ontology annotations, ECO is now used in other capacities by many additional annotation resources including UniProt, Mouse Genome Informatics, Saccharomyces Genome Database, PomBase, the Protein Information Resource and others. Information on the development and use of ECO can be found at http://evidenceontology.org. The ontology is freely available under Creative Commons license (CC BY-SA 3.0), and can be downloaded in both Open Biological Ontologies and Web Ontology Language formats at http://code.google.com/p/evidenceontology. Also at this site is a tracker for user submission of term requests and questions. ECO remains under active development in response to user-requested terms and in collaborations with other ontologies and database resources. Database URL: Evidence Ontology Web site: http://evidenceontology.org. © The Author(s) 2014. Published by Oxford University Press.

  16. Evaluation of an Andean common bean reference collection under drought stress Evaluation of an Andean common bean reference collection under drought stress

    Directory of Open Access Journals (Sweden)

    Pérez Vega Juan Carlos

    2011-04-01

    Full Text Available

    More than 60% of common bean (Phaseolus vulgaris L. production worldwide is impacted by the risk of drought. In this study, the goal was to evaluate 64 bush bean genotypes from the CIAT reference collection to identify possible sources of drought resistance in the Andean gene pool. Phenotypic traits such as yield, 100-seed weight (P100 and days to physiological maturity (Dpm were evaluated on selected accessions of this collection which was grown in an 8x8 lattice with two repetitions under three environments: intermittent drought (SI and irrigation (R in Palmira as well as early drought (ST in Darién, Colombia. The genotypes included 20 from the Nueva Granada 1 (NG1 sub-race, 19 from the Nueva Granada 2 (NG2 sub-race, 10 from race Peru (P, 14 Andean control genotypes and one Mesoamerican check. The variables were analyzed through a combined ANOVA across environments, while simple correlations between yield and others variables were determinate. The genotypes with better adaptation to drought showed higher yields, 100-seed weight and fewer days to physiological maturity. The coefficients of correlations among yield and 100-seed weight were significant and positive, while Dpm showed negative correlation. Fourteen genotypes were identified as drought tolerant: G4001, G5625, G6639, G16115, G17070, G18255, G21210 and G22247 from the NG1 sub-race; G5708, G14253, G18264 and LRK31 from the NG2 sub-race; and DRK47 and G22147 from race Peru.

  17. Toward an Ontology-Based Framework for Clinical Research Databases

    Science.gov (United States)

    Kong, Y. Megan; Dahlke, Carl; Xiang, Qun; Qian, Yu; Karp, David; Scheuermann, Richard H.

    2010-01-01

    Clinical research includes a wide range of study designs from focused observational studies to complex interventional studies with multiple study arms, treatment and assessment events, and specimen procurement procedures. Participant characteristics from case report forms need to be integrated with molecular characteristics from mechanistic experiments on procured specimens. In order to capture and manage this diverse array of data, we have developed the Ontology-Based eXtensible conceptual model (OBX) to serve as a framework for clinical research data in the Immunology Database and Analysis Portal (ImmPort). By designing OBX around the logical structure of the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI), we have found that a relatively simple conceptual model can represent the relatively complex domain of clinical research. In addition, the common framework provided by BFO makes it straightforward to develop data dictionaries based on reference and application ontologies from the OBO Foundry. PMID:20460173

  18. Exponential complexity and ontological theories of quantum mechanics

    International Nuclear Information System (INIS)

    Montina, A.

    2008-01-01

    Ontological theories of quantum mechanics describe a single system by means of well-defined classical variables and attribute the quantum uncertainties to our ignorance about the underlying reality represented by these variables. We consider the general class of ontological theories describing a quantum system by a set of variables with Markovian (either deterministic or stochastic) evolution. We provide proof that the number of continuous variables cannot be smaller than 2N-2, N being the Hilbert-space dimension. Thus, any ontological Markovian theory of quantum mechanics requires a number of variables which grows exponentially with the physical size. This result is relevant also in the framework of quantum Monte Carlo methods

  19. Ontology authoring with Forza

    CSIR Research Space (South Africa)

    Keet, CM

    2014-11-01

    Full Text Available step to make the construction of ontologies more agile and apt to the needs of organisations and business enterprises. Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided... is permitted. To copy otherwise, or re- publish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from Permissions@acm.org. CIKM’13, October 27 - November 01 2013, San Francisco, CA, USA...

  20. ONSET: Automated foundational ontology selection and explanation

    CSIR Research Space (South Africa)

    Khan, Z

    2012-10-01

    Full Text Available It has been shown that using a foundational ontology for domain ontology development is beneficial in theory and practice. However, developers have difficulty with choosing the appropriate foundational ontology, and why. In order to solve...

  1. Towards ontology based search and knowledgesharing using domain ontologies

    DEFF Research Database (Denmark)

    Zambach, Sine

    This paper reports on work in progress. We present work on domain specific verbs and their role as relations in domain ontologies. The domain ontology which is in focus for our research is modeled in cooperation with the Danish biotech company Novo Nordic. Two of the main purposes of domain...... ontologies for enterprises are as background for search and knowledge sharing used for e.g. multi lingual product development. Our aim is to use linguistic methods and logic to construct consistent ontologies that can be used in both a search perspective and as knowledge sharing.This focuses on identifying...... verbs for relations in the ontology modeling. For this work we use frequency lists from a biomedical text corpus of different genres as well as a study of the relations used in other biomedical text mining tools. In addition, we discuss how these relations can be used in broarder perspective....

  2. Ontological Analysis of Integrated Process Models: testing hypotheses

    Directory of Open Access Journals (Sweden)

    Michael Rosemann

    2001-11-01

    Full Text Available Integrated process modeling is achieving prominence in helping to document and manage business administration and IT processes in organizations. The ARIS framework is a popular example for a framework of integrated process modeling not least because it underlies the 800 or more reference models embedded in the world's most popular ERP package, SAP R/3. This paper demonstrates the usefulness of the Bunge-Wand-Weber (BWW representation model for evaluating modeling grammars such as those constituting ARIS. It reports some initial insights gained from pilot testing Green and Rosemann's (2000 evaluative propositions. Even when considering all five views of ARIS, modelers have problems representing business rules, the scope and boundary of systems, and decomposing models. However, even though it is completely ontologically redundant, users still find the function view useful in modeling.

  3. Ontology through a Mindfulness Process

    Science.gov (United States)

    Bearance, Deborah; Holmes, Kimberley

    2015-01-01

    Traditionally, when ontology is taught in a graduate studies course on social research, there is a tendency for this concept to be examined through the process of lectures and readings. Such an approach often leaves graduate students to grapple with a personal embodiment of this concept and to comprehend how ontology can ground their research.…

  4. Tracking Changes during Ontology Evolution

    NARCIS (Netherlands)

    Noy, Natalya F.; Kunnatur, Sandhya; Klein, Michel; Musen, Mark A.

    2004-01-01

    As ontology development becomes a collaborative process, developers face the problem of maintaining versions of ontologies akin to maintaining versions of software code or versions of documents in large projects. Traditional versioning systems enable users to compare versions, examine changes, and

  5. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

    Science.gov (United States)

    Whetzel, Patricia L; Noy, Natalya F; Shah, Nigam H; Alexander, Paul R; Nyulas, Csongor; Tudorache, Tania; Musen, Mark A

    2011-07-01

    The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

  6. Performance Evaluation of UPQC under Nonlinear Unbalanced Load Conditions Using Synchronous Reference Frame Based Control

    Science.gov (United States)

    Kota, Venkata Reddy; Vinnakoti, Sudheer

    2017-12-01

    Today, maintaining Power Quality (PQ) is very important in the growing competent world. With new equipments and devices, new challenges are also being put before power system operators. Unified Power Quality Conditioner (UPQC) is proposed to mitigate many power quality problems and to improve the performance of the power system. In this paper, an UPQC with Fuzzy Logic controller for capacitor voltage balancing is proposed in Synchronous Reference Frame (SRF) based control with Modified Phased Locked Loop (MPLL). The proposed controller with SRF-MPLL based control is tested under non-linear and unbalanced load conditions. The system is developed in Matlab/Simulink and its performance is analyzed under various conditions like non-linear, unbalanced load and polluted supply voltage including voltage sag/swells. Active and reactive power flow in the system, power factor and %THD of voltages and currents before and after compensation are also analyzed in this work. Results prove the applicability of the proposed scheme for power quality improvement. It is observed that the fuzzy controller gives better performance than PI controller with faster capacitor voltage balancing and also improves the dynamic performance of the system.

  7. Consideration of reference points for the management of renewable resources under an adaptive management paradigm

    Science.gov (United States)

    Irwin, Brian J.; Conroy, Michael J.

    2013-01-01

    The success of natural resource management depends on monitoring, assessment and enforcement. In support of these efforts, reference points (RPs) are often viewed as critical values of management-relevant indicators. This paper considers RPs from the standpoint of objective-driven decision making in dynamic resource systems, guided by principles of structured decision making (SDM) and adaptive resource management (AM). During the development of natural resource policy, RPs have been variously treated as either ‘targets’ or ‘triggers’. Under a SDM/AM paradigm, target RPs correspond approximately to value-based objectives, which may in turn be either of fundamental interest to stakeholders or intermediaries to other central objectives. By contrast, trigger RPs correspond to decision rules that are presumed to lead to desirable outcomes (such as the programme targets). Casting RPs as triggers or targets within a SDM framework is helpful towards clarifying why (or whether) a particular metric is appropriate. Further, the benefits of a SDM/AM process include elucidation of underlying untested assumptions that may reveal alternative metrics for use as RPs. Likewise, a structured decision-analytic framework may also reveal that failure to achieve management goals is not because the metrics are wrong, but because the decision-making process in which they are embedded is insufficiently robust to uncertainty, is not efficiently directed at producing a resource objective, or is incapable of adaptation to new knowledge.

  8. Development of Ontology and 3D Software for the Diseases of Spine

    Directory of Open Access Journals (Sweden)

    Seungbock Lee

    2015-01-01

    Full Text Available KISTI is carrying out an e-Spine project for spinal diseases to prepare for the aged society, so-called NAP. The purpose of the study is to build a spine ontology that represents the anatomical structure and disease information which is compatible with simulation model of KISTI. The final use of the ontology includes diagnosis of diseases and setting treatment directions by the clinicians. The ontology was represented using 3D software. Twenty diseases were selected to be represented after discussions with a spine specialist. Several ontology studies were reviewed, reference books were selected for each disease and were organized in MS Excel. All the contents were then reviewed by the specialists. Altova SemanticWorks and Protégé were used to code spine ontology with OWL Full model. Links to the images from KISTI and sample images of diseases were included in the ontology. The OWL ontology was also reviewed by the specialists again with Protégé. We represented unidirectional ontology from anatomical structure to disease, images, and treatment. The ontology was human understandable. It would be useful for the education of medical students or residents studying diseases of spine. But in order for the computer to understand the ontology, a new model with OWL DL or Lite is needed.

  9. Defining functional distances over Gene Ontology

    Directory of Open Access Journals (Sweden)

    del Pozo Angela

    2008-01-01

    Full Text Available Abstract Background A fundamental problem when trying to define the functional relationships between proteins is the difficulty in quantifying functional similarities, even when well-structured ontologies exist regarding the activity of proteins (i.e. 'gene ontology' -GO-. However, functional metrics can overcome the problems in the comparing and evaluating functional assignments and predictions. As a reference of proximity, previous approaches to compare GO terms considered linkage in terms of ontology weighted by a probability distribution that balances the non-uniform 'richness' of different parts of the Direct Acyclic Graph. Here, we have followed a different approach to quantify functional similarities between GO terms. Results We propose a new method to derive 'functional distances' between GO terms that is based on the simultaneous occurrence of terms in the same set of Interpro entries, instead of relying on the structure of the GO. The coincidence of GO terms reveals natural biological links between the GO functions and defines a distance model Df which fulfils the properties of a Metric Space. The distances obtained in this way can be represented as a hierarchical 'Functional Tree'. Conclusion The method proposed provides a new definition of distance that enables the similarity between GO terms to be quantified. Additionally, the 'Functional Tree' defines groups with biological meaning enhancing its utility for protein function comparison and prediction. Finally, this approach could be for function-based protein searches in databases, and for analysing the gene clusters produced by DNA array experiments.

  10. The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

    Science.gov (United States)

    Diehl, Alexander D; Meehan, Terrence F; Bradford, Yvonne M; Brush, Matthew H; Dahdul, Wasila M; Dougall, David S; He, Yongqun; Osumi-Sutherland, David; Ruttenberg, Alan; Sarntivijai, Sirarat; Van Slyke, Ceri E; Vasilevsky, Nicole A; Haendel, Melissa A; Blake, Judith A; Mungall, Christopher J

    2016-07-04

    The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. Recent work on the CL has focused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologies in coordination with the CL. For example, the Kidney and Urinary Pathway Ontology was used as a template to populate the CL with additional cell types. In addition, subtypes of the class 'cell in vitro' have received improved definitions and labels to provide for modularity with the representation of cells in the Cell Line Ontology and Reagent Ontology. Recent changes in the ontology development methodology for CL include a switch from OBO to OWL for the primary encoding of the ontology, and an increasing reliance on logical definitions for improved reasoning. The CL is now mandated as a metadata standard for large functional genomics and transcriptomics projects, and is used extensively for annotation, querying, and analyses of cell type specific data in sequencing consortia such as FANTOM5 and ENCODE, as well as for the NIAID ImmPort database and the Cell Image Library. The CL is also a vital component used in the modular construction of other biomedical ontologies-for example, the Gene Ontology and the cross-species anatomy ontology, Uberon, use CL to support the consistent representation of cell types across different levels of anatomical granularity, such as tissues and organs. The ongoing improvements to the CL make it a valuable resource to both the OBO Foundry community and the wider scientific community, and we continue to experience increased interest in the

  11. SSDOnt: An Ontology for Representing Single-Subject Design Studies.

    Science.gov (United States)

    Berges, Idoia; Bermúdez, Jesus; Illarramendi, Arantza

    2018-02-01

    Single-Subject Design is used in several areas such as education and biomedicine. However, no suited formal vocabulary exists for annotating the detailed configuration and the results of this type of research studies with the appropriate granularity for looking for information about them. Therefore, the search for those study designs relies heavily on a syntactical search on the abstract, keywords or full text of the publications about the study, which entails some limitations. To present SSDOnt, a specific purpose ontology for describing and annotating single-subject design studies, so that complex questions can be asked about them afterwards. The ontology was developed following the NeOn methodology. Once the requirements of the ontology were defined, a formal model was described in a Description Logic and later implemented in the ontology language OWL 2 DL. We show how the ontology provides a reference model with a suitable terminology for the annotation and searching of single-subject design studies and their main components, such as the phases, the intervention types, the outcomes and the results. Some mappings with terms of related ontologies have been established. We show as proof-of-concept that classes in the ontology can be easily extended to annotate more precise information about specific interventions and outcomes such as those related to autism. Moreover, we provide examples of some types of queries that can be posed to the ontology. SSDOnt has achieved the purpose of covering the descriptions of the domain of single-subject research studies. Schattauer GmbH.

  12. Ontology in association rules.

    Science.gov (United States)

    Ferraz, Inhaúma Neves; Garcia, Ana Cristina Bicharra

    2013-01-01

    Data mining has emerged to address the problem of transforming data into useful knowledge. Although most data mining techniques, such as the use of association rules, may substantially reduce the search effort over large data sets, often, the consequential outcomes surpass the amount of information humanly manageable. On the other hand, important association rules may be overlooked owing to the setting of the support threshold, which is a very subjective metric, but rooted in most data mining techniques. This paper presents a study on the effects, in terms of precision and recall, of using a data preparation technique, called SemPrune, which is built on domain ontology. SemPrune is intended for pre- and post-processing phases of data mining. Identifying generalization/specialization relations, as well as composition/decomposition relations, is the key to successfully applying SemPrune.

  13. Semantator: annotating clinical narratives with semantic web ontologies.

    Science.gov (United States)

    Song, Dezhao; Chute, Christopher G; Tao, Cui

    2012-01-01

    To facilitate clinical research, clinical data needs to be stored in a machine processable and understandable way. Manual annotating clinical data is time consuming. Automatic approaches (e.g., Natural Language Processing systems) have been adopted to convert such data into structured formats; however, the quality of such automatically extracted data may not always be satisfying. In this paper, we propose Semantator, a semi-automatic tool for document annotation with Semantic Web ontologies. With a loaded free text document and an ontology, Semantator supports the creation/deletion of ontology instances for any document fragment, linking/disconnecting instances with the properties in the ontology, and also enables automatic annotation by connecting to the NCBO annotator and cTAKES. By representing annotations in Semantic Web standards, Semantator supports reasoning based upon the underlying semantics of the owl:disjointWith and owl:equivalentClass predicates. We present discussions based on user experiences of using Semantator.

  14. Building a developmental toxicity ontology.

    Science.gov (United States)

    Baker, Nancy; Boobis, Alan; Burgoon, Lyle; Carney, Edward; Currie, Richard; Fritsche, Ellen; Knudsen, Thomas; Laffont, Madeleine; Piersma, Aldert H; Poole, Alan; Schneider, Steffen; Daston, George

    2018-04-03

    As more information is generated about modes of action for developmental toxicity and more data are generated using high-throughput and high-content technologies, it is becoming necessary to organize that information. This report discussed the need for a systematic representation of knowledge about developmental toxicity (i.e., an ontology) and proposes a method to build one based on knowledge of developmental biology and mode of action/ adverse outcome pathways in developmental toxicity. This report is the result of a consensus working group developing a plan to create an ontology for developmental toxicity that spans multiple levels of biological organization. This report provide a description of some of the challenges in building a developmental toxicity ontology and outlines a proposed methodology to meet those challenges. As the ontology is built on currently available web-based resources, a review of these resources is provided. Case studies on one of the most well-understood morphogens and developmental toxicants, retinoic acid, are presented as examples of how such an ontology might be developed. This report outlines an approach to construct a developmental toxicity ontology. Such an ontology will facilitate computer-based prediction of substances likely to induce human developmental toxicity. © 2018 Wiley Periodicals, Inc.

  15. Gene Ontology Consortium: going forward.

    Science.gov (United States)

    2015-01-01

    The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. The ontology of science teaching in the neoliberal era

    Science.gov (United States)

    Sharma, Ajay

    2017-12-01

    Because of ever stricter standards of accountability, science teachers are under an increasing and unrelenting pressure to demonstrate the effects of their teaching on student learning. Econometric perspectives of teacher quality have become normative in assessment of teachers' work for accountability purposes. These perspectives seek to normalize some key ontological assumptions about teachers and teaching, and thus play an important role in shaping our understanding of the work science teachers do as teachers in their classrooms. In this conceptual paper I examine the ontology of science teaching as embedded in econometric perspectives of teacher quality. Based on Foucault's articulation of neoliberalism as a discourse of governmentality in his `The Birth of Biopolitics' lectures, I suggest that this ontology corresponds well with the strong and substantivist ontology of work under neoliberalism, and thus could potentially be seen as reflection of the influence of neoliberal ideas in education. Implications of the mainstreaming of an ontology of teaching that is compatible with neoliberalism can be seen in increasing marketization of teaching, `teaching evangelism', and impoverished notions of learning and teaching. A shift of focus from teacher quality to quality of teaching and building conceptual models of teaching based on relational ontologies deserve to be explored as important steps in preserving critical and socially just conceptions of science teaching in neoliberal times.

  17. Unified Ontology for a Holonic Manufacturing System

    Directory of Open Access Journals (Sweden)

    I. Simón-Marmolejo

    2018-03-01

    Full Text Available Holonic manufacturing systems are formed by holons that are capable of behaving in an autonomous, cooperative, selforganized and reconfigurable way to adopt dierent structures under normal and emergency operating conditions. These holons possess: (1 a representation of the world in which they live, (2 a distributed and decentralized control unit, and (3 a coordination module. The object of interest of the present research is the conception of a unified ontology in manufacturing domain, that guarantees the requirements in the formalism of the knowledge model of a holonic system. Unlike the ontological models found in the literature, the proposed knowledge representation scheme integrates roles and behaviors, which are validated through a case study of a manufacturing cell from a university laboratory. The results show that by using a common vocabulary, it is possible to represent knowledge coherently so that all kinds of holons in a holarchy can exchange, share and retrieve information.

  18. Sample ontology, GOstat and ontology term enrichment - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available y to express samples in phase2.0 It is based on Cell Ontology, Disease Ontology a...nd Pan-vertebrate Uberon Ontology. The file format is OBO. Data file File name: Ontology File URL: ftp://ftp....biosciencedbc.jp/archive/fantom5/datafiles/LATEST/extra/Ontology/ File size: 1.8 MB Simple search URL - Dat

  19. Annotation modeling with formal ontologies: Implications for informal ontologies

    Science.gov (United States)

    Lumb, L. I.; Freemantle, J. R.; Lederman, J. I.; Aldridge, K. D.

    2009-04-01

    Knowledge representation is increasingly recognized as an important component of any cyberinfrastructure (CI). In order to expediently address scientific needs, geoscientists continue to leverage the standards and implementations emerging from the World Wide Web Consortium's (W3C) Semantic Web effort. In an ongoing investigation, previous efforts have been aimed towards the development of a semantic framework for the Global Geodynamics Project (GGP). In contrast to other efforts, the approach taken has emphasized the development of informal ontologies, i.e., ontologies that are derived from the successive extraction of Resource Description Framework (RDF) representations from eXtensible Markup Language (XML), and then Web Ontology Language (OWL) from RDF. To better understand the challenges and opportunities for incorporating annotations into the emerging semantic framework, the present effort focuses on knowledge-representation modeling involving formal ontologies. Although OWL's internal mechanism for annotation is constrained to ensure computational completeness and decidability, externally originating annotations based on the XML Pointer Language (XPointer) can easily violate these constraints. Thus, the effort of modeling with formal ontologies allows for recommendations applicable to the case of incorporating annotations into informal ontologies.

  20. Formal ontology for natural language processing and the integration of biomedical databases.

    Science.gov (United States)

    Simon, Jonathan; Dos Santos, Mariana; Fielding, James; Smith, Barry

    2006-01-01

    The central hypothesis underlying this communication is that the methodology and conceptual rigor of a philosophically inspired formal ontology can bring significant benefits in the development and maintenance of application ontologies [A. Flett, M. Dos Santos, W. Ceusters, Some Ontology Engineering Procedures and their Supporting Technologies, EKAW2002, 2003]. This hypothesis has been tested in the collaboration between Language and Computing (L&C), a company specializing in software for supporting natural language processing especially in the medical field, and the Institute for Formal Ontology and Medical Information Science (IFOMIS), an academic research institution concerned with the theoretical foundations of ontology. In the course of this collaboration L&C's ontology, LinKBase, which is designed to integrate and support reasoning across a plurality of external databases, has been subjected to a thorough auditing on the basis of the principles underlying IFOMIS's Basic Formal Ontology (BFO) [B. Smith, Basic Formal Ontology, 2002. http://ontology.buffalo.edu/bfo]. The goal is to transform a large terminology-based ontology into one with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase are standardized in the framework of first-order logic. In this paper we describe how this principles-based standardization has led to a greater degree of internal coherence of the LinKBase structure, and how it has facilitated the construction of mappings between external databases using LinKBase as translation hub. We argue that the collaboration here described represents a new phase in the quest to solve the so-called "Tower of Babel" problem of ontology integration [F. Montayne, J. Flanagan, Formal Ontology: The Foundation for Natural Language Processing, 2003. http://www.landcglobal.com/].

  1. Introducing defeasibility into OWL ontologies

    CSIR Research Space (South Africa)

    Casini, G

    2015-10-01

    Full Text Available comprehensively. A major barrier is the lack of naturally occurring ontologies with defeasible features - the ideal candidates for evaluation. Such data is unavailable due to absence of tool support for representing defeasible features. In the past, defeasible...

  2. A Mobile Army of Ontologies

    DEFF Research Database (Denmark)

    Juul, Jesper

    2015-01-01

    can be considered most useful for different ludo-analytical questions. Are there differences between the existential statuses of virtual videogame worlds, tangible board game worlds, and the mundane? Can the experience of the player be used to explain the existence of the (video)game artifact? How do......Presentation at the Ludo-ontologies panel. Do we need ludo-ontologies, and what are they? In this event several scholars of games and videogames discuss these questions from a variety of perspectives. What different game and videogame ontologies exist and could exist, and why they are important...... for game and videogame research? The round table is designed to promote ludo-ontological dialogue in order to make these questions visible and debated. A series of short presentations (approximately 10 minutes each) will be followed by an intense debate through freeform dialogue. After the industrial...

  3. Austrian height and body proportion references for children aged 4 to under 19 years.

    Science.gov (United States)

    Gleiss, Andreas; Lassi, Michael; Blümel, Peter; Borkenstein, Martin; Kapelari, Klaus; Mayer, Michael; Schemper, Michael; Häusler, Gabriele

    2013-07-01

    Previous studies have demonstrated differences between national and the WHO reference curves in children older than 5 years. Moreover, reference curves for body proportions (sitting height, subischial leg length and their ratio) based on state-of-the-art statistics are not available. To develop reference curves for height and body proportions for use in Austria and compare the curves with WHO reference curves. To estimate and statistically investigate extreme percentiles. A sample of ∼14 500 children between 4-19 years of age was drawn via schooling institutions, stratified by provinces according to age- and sex-specific population proportions. GAMLSS models were used for a flexible estimation of percentile curves. After the age of 5 years national reference curves are more suitable than the WHO reference curves for clinical use in Austria. These height curves are very similar to the German reference curves published recently. Therefore, these reference curves for criteria of body proportions are recommended for use in other populations. Further validation studies are needed to establish whether the recently recommended -2.5 and -3.0 SD for height are a sensitive and specific cut-off in the diagnostic work-up for children with a suspected growth disorder using this new Austrian height chart.

  4. Finding the best visualization of an ontology

    DEFF Research Database (Denmark)

    Fabritius, Christina Valentin; Madsen, Nadia Lyngaa; Clausen, Jens

    2004-01-01

    An ontology is a classification model for a given domain. In information retrieval ontologies are used to perform broad searches. An ontology can be visualized as nodes and edges. Each node represents an element and each edge a relation between a parent and a child element. Working with an ontology...... should be feasible for on-line processing and what-if analysis of ontologies....

  5. Finding the best visualization of an ontology

    DEFF Research Database (Denmark)

    Fabritius, Christina; Madsen, Nadia; Clausen, Jens

    2006-01-01

    An ontology is a classification model for a given domain.In information retrieval ontologies are used to perform broad searches.An ontology can be visualized as nodes and edges. Each node represents an element and each edge a relation between a parent and a child element. Working with an ontology...... should be feasible for on-line processing and what-if analysis of ontologies....

  6. Enhanced Search Method for Ontology Classification

    OpenAIRE

    Je Min Kim; Soon Hyen Kwon; Young Tack Park

    2012-01-01

    The web ontology language (OWL) has become a W3C recommendation to publish and share ontologies on the semantic web. In order to infer implicit information (classification, satisfiability and realization) of OWL ontology, a number of OWL reasoners have been introduced. Ontology classification is to compute a partial ordering or hierarchy of named concepts in the ontology using the subsumption testing. Most of the reasoners use both top-down and bottom-up searches using subsumption testing for...

  7. Transport Calculations for the reference configuration under neutral bean injection in TJ-II

    International Nuclear Information System (INIS)

    Guasp, J.; Castejon, F.; Liniers, M.

    1999-01-01

    Transport calculations for the Reference Configuration under Neutral Beam Injection in TJ-II are discussed. For all these analysis the Transport Code PROCTR has been used but, in reason of the complex geometry of TJ-II, some modifications to the code have been needed, not only for the absorption, losses and deposition radial profile evaluations, but also for the treatment of the transition between ECRH and NBI or the fit of Transport Coefficients to the different Scaling Laws. The attained centralβ values for high density ( central value around 11 x 10''13 cm''3), in steady, range between a minimum of 1.9% for the GRB law up to 3.6% or 4.2% for those laws that show an explicit dependence with the rotational transform (ISS and LGS), with an intermediate value of 2.8% for the LHD case. Global energy confinement times range between 3.9 and 8.8 ms for the two extreme cases and 5.6 ms for LHD. As well ions as electrons are clearly in the plateau regime, in contrast to the ECRH phase where the electrons are well inside the 1/ν regime, dominated by helical ripple effects. The effect of impurities is to decrease slightly the absorption and the attainable β levels, but only for Zeff values higher than 4 this degradation becomes important. For the stationary state the density remains always below the semiempirical limit, independently of the Zeff value. Even along the first stages of injection, where absorption can be rather low, the limit is not reached, at least for Zeff < 4, so that radioactive collapse along this critical phase should not to be expected. (Author) 14 refs

  8. Modeling issues & choices in the data mining optimization ontology

    CSIR Research Space (South Africa)

    Keet, CM

    2013-05-01

    Full Text Available We describe the Data Mining Optimization Ontology (DMOP), which was developed to support informed decision-making at various choice points of the knowledge discovery (KD) process. It can be used as a reference by data miners, but its primary purpose...

  9. Probabilistic Ontology Architecture for a Terrorist Identification Decision Support System

    Science.gov (United States)

    2014-06-01

    34 International Journal of Human-Computer Studies, pp. 907-928, 1995. [14] Grigoris Antoniou and Frank Van Harmelen, "Web Ontology Language: OWL," in...developerworks / webservices/library/ws-soa-ref-arch/ [23] Johan Eltes , The Reference Architecture - a foundation for successful projects, 2004

  10. Musical Ontology: Critical, not Metaphysical

    Directory of Open Access Journals (Sweden)

    Jonathan A. Neufeld

    2014-01-01

    Full Text Available The ontology of musical works often sets the boundaries within which evaluation of musical works and performances takes place. Questions of ontology are therefore often taken to be prior to and apart from the evaluative questions considered by either performers as they present works to audiences or an audience’s critical reflection on a performance. In this paper I argue that, while the ontology of musical works may well set the boundaries of legitimate evaluation, ontological questions should not be considered as prior to or apart from critical evaluation. Rather, ontological claims are a type of critical evaluation made within musical practices. I argue that philosophers of music might learn from the debate in political philosophy about the difficulty of setting the limits of public reason in a way that remains open to a plurality of legitimate evaluative perspectives. Just as pre-political or metaphysical identification of the boundaries of public reason fail to accommodate the fact of pluralism in contemporary democratic politics, so too does a metaphysical identification of the boundaries of legitimate evaluation of musical works and performances fail to accommodate the fact of pluralism in contemporary musical practices. I apply John Rawls’s formulation of political liberalism, arguing that musical ontology should be critical, not metaphysical.

  11. Ontological knowledge structure of intuitive biology

    Science.gov (United States)

    Martin, Suzanne Michele

    It has become increasingly important for individuals to understand infections disease, as there has been a tremendous rise in viral and bacterial disease. This research examines systematic misconceptions regarding the characteristics of viruses and bacteria present in individuals previously educated in biological sciences at a college level. 90 pre-nursing students were administered the Knowledge Acquisition Device (KAD) which consists of 100 True/False items that included statements about the possible attributes of four entities: bacteria, virus, amoeba, and protein. Thirty pre-nursing students, who incorrectly stated that viruses were alive, were randomly assigned to three conditions. (1) exposed to information about the ontological nature of viruses, (2) Information about viruses, (3) control. In the condition that addressed the ontological nature of a virus, all of those participants were able to classify viruses correctly as not alive; however any items that required inferences, such as viruses come in male and female forms or viruses breed with each other to make baby viruses were still incorrectly answered by all conditions in the posttest. It appears that functional knowledge, ex. If a virus is alive or dead, or how it is structured, is not enough for an individual to have a full and accurate understanding of viruses. Ontological knowledge information may alter the functional knowledge but underlying inferences remain systematically incorrect.

  12. Selection of suitable endogenous reference genes for qPCR in kidney and hypothalamus of rats under testosterone influence.

    Science.gov (United States)

    Gholami, Khadijeh; Loh, Su Yi; Salleh, Naguib; Lam, Sau Kuen; Hoe, See Ziau

    2017-01-01

    Real-time quantitative PCR (qPCR) is the most reliable and accurate technique for analyses of gene expression. Endogenous reference genes are being used to normalize qPCR data even though their expression may vary under different conditions and in different tissues. Nonetheless, verification of expression of reference genes in selected studied tissue is essential in order to accurately assess the level of expression of target genes of interest. Therefore, in this study, we attempted to examine six commonly used reference genes in order to identify the gene being expressed most constantly under the influence of testosterone in the kidneys and hypothalamus. The reference genes include glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin beta (ACTB), beta-2 microglobulin (B2m), hypoxanthine phosphoribosyltransferase 1 (HPRT), peptidylprolylisomerase A (Ppia) and hydroxymethylbilane synthase (Hmbs). The cycle threshold (Ct) value for each gene was determined and data obtained were analyzed using the software programs NormFinder, geNorm, BestKeeper, and rank aggregation. Results showed that Hmbs and Ppia genes were the most stably expressed in the hypothalamus. Meanwhile, in kidneys, Hmbs and GAPDH appeared to be the most constant genes. In conclusion, variations in expression levels of reference genes occur in kidneys and hypothalamus under similar conditions; thus, it is important to verify reference gene levels in these tissues prior to commencing any studies.

  13. AISO: Annotation of Image Segments with Ontologies.

    Science.gov (United States)

    Lingutla, Nikhil Tej; Preece, Justin; Todorovic, Sinisa; Cooper, Laurel; Moore, Laura; Jaiswal, Pankaj

    2014-01-01

    Large quantities of digital images are now generated for biological collections, including those developed in projects premised on the high-throughput screening of genome-phenome experiments. These images often carry annotations on taxonomy and observable features, such as anatomical structures and phenotype variations often recorded in response to the environmental factors under which the organisms were sampled. At present, most of these annotations are described in free text, may involve limited use of non-standard vocabularies, and rarely specify precise coordinates of features on the image plane such that a computer vision algorithm could identify, extract and annotate them. Therefore, researchers and curators need a tool that can identify and demarcate features in an image plane and allow their annotation with semantically contextual ontology terms. Such a tool would generate data useful for inter and intra-specific comparison and encourage the integration of curation standards. In the future, quality annotated image segments may provide training data sets for developing machine learning applications for automated image annotation. We developed a novel image segmentation and annotation software application, "Annotation of Image Segments with Ontologies" (AISO). The tool enables researchers and curators to delineate portions of an image into multiple highlighted segments and annotate them with an ontology-based controlled vocabulary. AISO is a freely available Java-based desktop application and runs on multiple platforms. It can be downloaded at http://www.plantontology.org/software/AISO. AISO enables curators and researchers to annotate digital images with ontology terms in a manner which ensures the future computational value of the annotated images. We foresee uses for such data-encoded image annotations in biological data mining, machine learning, predictive annotation, semantic inference, and comparative analyses.

  14. ``Force,'' ontology, and language

    Science.gov (United States)

    Brookes, David T.; Etkina, Eugenia

    2009-06-01

    We introduce a linguistic framework through which one can interpret systematically students’ understanding of and reasoning about force and motion. Some researchers have suggested that students have robust misconceptions or alternative frameworks grounded in everyday experience. Others have pointed out the inconsistency of students’ responses and presented a phenomenological explanation for what is observed, namely, knowledge in pieces. We wish to present a view that builds on and unifies aspects of this prior research. Our argument is that many students’ difficulties with force and motion are primarily due to a combination of linguistic and ontological difficulties. It is possible that students are primarily engaged in trying to define and categorize the meaning of the term “force” as spoken about by physicists. We found that this process of negotiation of meaning is remarkably similar to that engaged in by physicists in history. In this paper we will describe a study of the historical record that reveals an analogous process of meaning negotiation, spanning multiple centuries. Using methods from cognitive linguistics and systemic functional grammar, we will present an analysis of the force and motion literature, focusing on prior studies with interview data. We will then discuss the implications of our findings for physics instruction.

  15. Hydro-mechanical behaviour of two reference Belgian clay formations under non-isothermal conditions

    International Nuclear Information System (INIS)

    Lima, A.; Romero, E.; Gens, A.; Li, X.L.

    2012-01-01

    Document available in extended abstract form only. Two deep clay formations are being investigated in Belgium in connection with the design of a repository for 'High-Level Radioactive Waste': Boom clay BC at Mol (located between 160 and 270 m depths), considered the reference host formation, and Ypresian clay YC at Kallo (located between 300 and 450 m depths) as an alternative one. A comprehensive experimental programme has been carried out on these materials to explore water permeability at different temperatures and sample orientations, as well as to analyse volume change behaviour on loading/unloading at different temperatures and sample orientations (including pre and post-yield compressibility, yield properties and volume changes on drained thermal loading). Table 1 summarises some properties of BC and YC. Figure 1 presents the pore size distribution PSD curves of both clays obtained by mercury intrusion porosimetry. They display contrasting features (bi-modal pore network in YP with larger dominant pore sizes). Larger water permeability values are expected on YC as indicated in Table 1 and Figure 2, not only as a consequence of its higher void ratio but also due to these double porosity features. Water retention properties, of particular concern on sample retrieval from large depths, are also affected due to desaturation processes that are associated with the double porosity network of YP and its effects on air-entry value (a lower initial suction is measured on YP, despite being retrieved from larger depths). Figure 2 shows vertical and horizontal water permeability results under constant volume conditions and different temperatures. BC and YC display small anisotropy at sample scale - permeability is slightly larger on horizontal direction-. With regard to temperature effects, the figure shows that water permeability dependency on temperature in YC is slightly higher than the water viscosity prediction for both orientations. Instead BC displayed a thermal

  16. Expression stabilities of candidate reference genes for RT-qPCR under different stress conditions in soybean.

    Directory of Open Access Journals (Sweden)

    Shuhua Ma

    Full Text Available Due to its accuracy, sensitivity and high throughput, real time quantitative PCR (RT-qPCR has been widely used in analysing gene expression. The quality of data from such analyses is affected by the quality of reference genes used. Expression stabilities for nine candidate reference genes widely used in soybean were evaluated under different stresses in this study. Our results showed that EF1A and ACT11 were the best under salinity stress, TUB4, TUA5 and EF1A were the best under drought stress, ACT11 and UKN2 were the best under dark treatment, and EF1B and UKN2 were the best under virus infection. EF1B and UKN2 were the top two genes which can be reliably used in all of the stress conditions assessed.

  17. A bibliometric and visual analysis of global geo-ontology research

    Science.gov (United States)

    Li, Lin; Liu, Yu; Zhu, Haihong; Ying, Shen; Luo, Qinyao; Luo, Heng; Kuai, Xi; Xia, Hui; Shen, Hang

    2017-02-01

    In this paper, the results of a bibliometric and visual analysis of geo-ontology research articles collected from the Web of Science (WOS) database between 1999 and 2014 are presented. The numbers of national institutions and published papers are visualized and a global research heat map is drawn, illustrating an overview of global geo-ontology research. In addition, we present a chord diagram of countries and perform a visual cluster analysis of a knowledge co-citation network of references, disclosing potential academic communities and identifying key points, main research areas, and future research trends. The International Journal of Geographical Information Science, Progress in Human Geography, and Computers & Geosciences are the most active journals. The USA makes the largest contributions to geo-ontology research by virtue of its highest numbers of independent and collaborative papers, and its dominance was also confirmed in the country chord diagram. The majority of institutions are in the USA, Western Europe, and Eastern Asia. Wuhan University, University of Munster, and the Chinese Academy of Sciences are notable geo-ontology institutions. Keywords such as "Semantic Web," "GIS," and "space" have attracted a great deal of attention. "Semantic granularity in ontology-driven geographic information systems, "Ontologies in support of activities in geographical space" and "A translation approach to portable ontology specifications" have the highest cited centrality. Geographical space, computer-human interaction, and ontology cognition are the three main research areas of geo-ontology. The semantic mismatch between the producers and users of ontology data as well as error propagation in interdisciplinary and cross-linguistic data reuse needs to be solved. In addition, the development of geo-ontology modeling primitives based on OWL (Web Ontology Language)and finding methods to automatically rework data in Semantic Web are needed. Furthermore, the topological

  18. InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk.

    Science.gov (United States)

    Cheng, Liang; Jiang, Yue; Ju, Hong; Sun, Jie; Peng, Jiajie; Zhou, Meng; Hu, Yang

    2018-01-19

    Since the establishment of the first biomedical ontology Gene Ontology (GO), the number of biomedical ontology has increased dramatically. Nowadays over 300 ontologies have been built including extensively used Disease Ontology (DO) and Human Phenotype Ontology (HPO). Because of the advantage of identifying novel relationships between terms, calculating similarity between ontology terms is one of the major tasks in this research area. Though similarities between terms within each ontology have been studied with in silico methods, term similarities across different ontologies were not investigated as deeply. The latest method took advantage of gene functional interaction network (GFIN) to explore such inter-ontology similarities of terms. However, it only used gene interactions and failed to make full use of the connectivity among gene nodes of the network. In addition, all existent methods are particularly designed for GO and their performances on the extended ontology community remain unknown. We proposed a method InfAcrOnt to infer similarities between terms across ontologies utilizing the entire GFIN. InfAcrOnt builds a term-gene-gene network which comprised ontology annotations and GFIN, and acquires similarities between terms across ontologies through modeling the information flow within the network by random walk. In our benchmark experiments on sub-ontologies of GO, InfAcrOnt achieves a high average area under the receiver operating characteristic curve (AUC) (0.9322 and 0.9309) and low standard deviations (1.8746e-6 and 3.0977e-6) in both human and yeast benchmark datasets exhibiting superior performance. Meanwhile, comparisons of InfAcrOnt results and prior knowledge on pair-wise DO-HPO terms and pair-wise DO-GO terms show high correlations. The experiment results show that InfAcrOnt significantly improves the performance of inferring similarities between terms across ontologies in benchmark set.

  19. Product line based ontology reuse in context-aware e-business environment

    DEFF Research Database (Denmark)

    Zhang, Weishan; Kunz, Thomas

    2006-01-01

    Improving the reusability of ontology is recognized as increasingly important due to the prevalence of OWL research and applications. But there exists no convincing methodology and tool support in this direction yet. In this paper, we apply ideas from the research and practice with software product...... lines in order to explore this issue. The ontology is developed and managed according to the commonalities and variabilities underlying a specific problem domain. Meta-ontology is used in order to improve the reusability, evolve-ability and customizability of ontology. Another advantage is being able...... to generate needed ontology with the created meta-ontology implemented with XVCL (XML based Variant Configuration Language) technology. We demonstrate our product line based reuse approach with an example B2C application....

  20. PROUST’S ARTISTIC ONTOLOGY : A Comparison of Merleau-Ponty’s and Deleuze’s Readings of Proust’s Recherche

    Directory of Open Access Journals (Sweden)

    Judith Wambacq

    2013-12-01

    Full Text Available In this article, I examine how Merleau-Ponty and Deleuze read Proust. It is not only remarkable that Merleau-Ponty and Deleuze refer to exactly the same passages of the Recherche, but they also read them in a similar way. This is all the more striking because Merleau-Ponty and Deleuze are usually subsumed under different schools of thought. This article sketches the artistic ontology both philosophers see illustrated in the Recherche.

  1. Identification of Appropriate Reference Genes for Normalization of miRNA Expression in Grafted Watermelon Plants under Different Nutrient Stresses.

    Science.gov (United States)

    Wu, Weifang; Deng, Qin; Shi, Pibiao; Yang, Jinghua; Hu, Zhongyuan; Zhang, Mingfang

    2016-01-01

    Watermelon (Citrullus lanatus) is a globally important crop belonging to the family Cucurbitaceae. The grafting technique is commonly used to improve its tolerance to stress, as well as to enhance its nutrient uptake and utilization. It is believed that miRNA is most likely involved in its nutrient-starvation response as a graft-transportable signal. The quantitative real-time reverse transcriptase polymerase chain reaction is the preferred method for miRNA functional analysis, in which reliable reference genes for normalization are crucial to ensure the accuracy. The purpose of this study was to select appropriate reference genes in scion (watermelon) and rootstocks (squash and bottle gourd) of grafted watermelon plants under normal growth conditions and nutrient stresses (nitrogen and phosphorus starvation). Under nutrient starvation, geNorm identified miR167c and miR167f as two most stable genes in both watermelon leaves and squash roots. miR166b was recommended by both geNorm and NormFinder as the best reference in bottle gourd roots under nutrient limitation. Expression of a new Cucurbitaceae miRNA, miR85, was used to validate the reliability of candidate reference genes under nutrient starvation. Moreover, by comparing several target genes expression in qRT-PCR analysis with those in RNA-seq data, miR166b and miR167c were proved to be the most suitable reference genes to normalize miRNA expression under normal growth condition in scion and rootstock tissues, respectively. This study represents the first comprehensive survey of the stability of miRNA reference genes in Cucurbitaceae and provides valuable information for investigating more accurate miRNA expression involving grafted watermelon plants.

  2. Invariance as a Tool for Ontology of Information

    Directory of Open Access Journals (Sweden)

    Marcin J. Schroeder

    2016-03-01

    Full Text Available Attempts to answer questions regarding the ontological status of information are frequently based on the assumption that information should be placed within an already existing framework of concepts of established ontological statuses related to science, in particular to physics. However, many concepts of physics have undetermined or questionable ontological foundations. We can look for a solution in the recognition of the fundamental role of invariance with respect to a change of reference frame and to other transformations as a criterion for objective existence. The importance of invariance (symmetry as a criterion for a primary ontological status can be identified in the methodology of physics from its beginnings in the work of Galileo, to modern classifications of elementary particles. Thus, the study of the invariance of the theoretical description of information is proposed as the first step towards ontology of information. With the exception of only a few works among publications which set the paradigm of information studies, the issues of invariance were neglected. Orthodox analysis of information lacks conceptual framework for the study of invariance. The present paper shows how invariance can be formalized for the definition of information and, accompanying it, mathematical formalism proposed by the author in his earlier publications.

  3. Identification of candidate reference genes in perennial ryegrass for quantitative RT-PCR under various abiotic stress conditions.

    Directory of Open Access Journals (Sweden)

    Linkai Huang

    Full Text Available BACKGROUND: Quantitative real-time reverse-transcriptase PCR (qRT-PCR is an important technique for analyzing differences in gene expression due to its sensitivity, accuracy and specificity. However, the stability of the expression of reference genes is necessary to ensure accurate qRT-PCR assessment of expression in genes of interest. Perennial ryegrass (Lolium perenne L. is important forage and turf grass species in temperate regions, but the expression stability of its reference genes under various stresses has not been well-studied. METHODOLOGY/PRINCIPAL FINDINGS: In this study, 11 candidate reference genes were evaluated for use as controls in qRT-PCR to quantify gene expression in perennial ryegrass under drought, high salinity, heat, waterlogging, and ABA (abscisic acid treatments. Four approaches--Delta CT, geNorm, BestKeeper and Normfinder were used to determine the stability of expression in these reference genes. The results are consistent with the idea that the best reference genes depend on the stress treatment under investigation. Eukaryotic initiation factor 4 alpha (eIF4A, Transcription elongation factor 1 (TEF1 and Tat binding protein-1 (TBP-1 were the three most stably expressed genes under drought stress and were also the three best genes for studying salt stress. eIF4A, TBP-1, and Ubiquitin-conjugating enzyme (E2 were the most suitable reference genes to study heat stress, while eIF4A, TEF1, and E2 were the three best reference genes for studying the effects of ABA. Finally, Ubiquitin (UBQ, TEF1, and eIF4A were the three best reference genes for waterlogging treatments. CONCLUSIONS/SIGNIFICANCE: These results will be helpful in choosing the best reference genes for use in studies related to various abiotic stresses in perennial ryegrass. The stability of expression in these reference genes will enable better normalization and quantification of the transcript levels for studies of gene expression in such studies.

  4. Evaluation of candidate reference genes for normalization of quantitative RT-PCR in soybean tissues under various abiotic stress conditions.

    Directory of Open Access Journals (Sweden)

    Dung Tien Le

    Full Text Available Quantitative RT-PCR can be a very sensitive and powerful technique for measuring differential gene expression. Changes in gene expression induced by abiotic stresses are complex and multifaceted, which make determining stably expressed genes for data normalization difficult. To identify the most suitable reference genes for abiotic stress studies in soybean, 13 candidate genes collected from literature were evaluated for stability of expression under dehydration, high salinity, cold and ABA (abscisic acid treatments using delta CT and geNorm approaches. Validation of reference genes indicated that the best reference genes are tissue- and stress-dependent. With respect to dehydration treatment, the Fbox/ABC, Fbox/60s gene pairs were found to have the highest expression stability in the root and shoot tissues of soybean seedlings, respectively. Fbox and 60s genes are the most suitable reference genes across dehydrated root and shoot tissues. Under salt stress the ELF1b/IDE and Fbox/ELF1b are the most stably expressed gene pairs in roots and shoots, respectively, while 60s/Fbox is the best gene pair in both tissues. For studying cold stress in roots or shoots, IDE/60s and Fbox/Act27 are good reference gene pairs, respectively. With regard to gene expression analysis under ABA treatment in either roots, shoots or across these tissues, 60s/ELF1b, ELF1b/Fbox and 60s/ELF1b are the most suitable reference genes, respectively. The expression of ELF1b/60s, 60s/Fbox and 60s/Fbox genes was most stable in roots, shoots and both tissues, respectively, under various stresses studied. Among the genes tested, 60s was found to be the best reference gene in different tissues and under various stress conditions. The highly ranked reference genes identified from this study were proved to be capable of detecting subtle differences in expression rates that otherwise would be missed if a less stable reference gene was used.

  5. Evaluation of putative reference genes for quantitative real-time PCR normalization in Lilium regale during development and under stress

    Science.gov (United States)

    Zhang, Ming-Fang

    2016-01-01

    Normalization to reference genes is the most common method to avoid bias in real-time quantitative PCR (qPCR), which has been widely used for quantification of gene expression. Despite several studies on gene expression, Lilium, and particularly L. regale, has not been fully investigated regarding the evaluation of reference genes suitable for normalization. In this study, nine putative reference genes, namely 18S rRNA, ACT, BHLH, CLA, CYP, EF1, GAPDH, SAND and TIP41, were analyzed for accurate quantitative PCR normalization at different developmental stages and under different stress conditions, including biotic (Botrytis elliptica), drought, salinity, cold and heat stress. All these genes showed a wide variation in their Cq (quantification Cycle) values, and their stabilities were calculated by geNorm, NormFinder and BestKeeper. In a combination of the results from the three algorithms, BHLH was superior to the other candidates when all the experimental treatments were analyzed together; CLA and EF1 were also recommended by two of the three algorithms. As for specific conditions, EF1 under various developmental stages, SAND under biotic stress, CYP/GAPDH under drought stress, and TIP41 under salinity stress were generally considered suitable. All the algorithms agreed on the stability of SAND and GAPDH under cold stress, while only CYP was selected under heat stress by all of them. Additionally, the selection of optimal reference genes under biotic stress was further verified by analyzing the expression level of LrLOX in leaves inoculated with B. elliptica. Our study would be beneficial for future studies on gene expression and molecular breeding of Lilium. PMID:27019788

  6. Use of the CIM Ontology

    Energy Technology Data Exchange (ETDEWEB)

    Neumann, Scott; Britton, Jay; Devos, Arnold N.; Widergren, Steven E.

    2006-02-08

    There are many uses for the Common Information Model (CIM), an ontology that is being standardized through Technical Committee 57 of the International Electrotechnical Commission (IEC TC57). The most common uses to date have included application modeling, information exchanges, information management and systems integration. As one should expect, there are many issues that become apparent when the CIM ontology is applied to any one use. Some of these issues are shortcomings within the current draft of the CIM, and others are a consequence of the different ways in which the CIM can be applied using different technologies. As the CIM ontology will and should evolve, there are several dangers that need to be recognized. One is overall consistency and impact upon applications when extending the CIM for a specific need. Another is that a tight coupling of the CIM to specific technologies could limit the value of the CIM in the longer term as an ontology, which becomes a larger issue over time as new technologies emerge. The integration of systems is one specific area of interest for application of the CIM ontology. This is an area dominated by the use of XML for the definition of messages. While this is certainly true when using Enterprise Application Integration (EAI) products, it is even more true with the movement towards the use of Web Services (WS), Service-Oriented Architectures (SOA) and Enterprise Service Buses (ESB) for integration. This general IT industry trend is consistent with trends seen within the IEC TC57 scope of power system management and associated information exchange. The challenge for TC57 is how to best leverage the CIM ontology using the various XML technologies and standards for integration. This paper will provide examples of how the CIM ontology is used and describe some specific issues that should be addressed within the CIM in order to increase its usefulness as an ontology. It will also describe some of the issues and challenges that will

  7. Ontology Language to Support Description of Experiment Control System Semantics, Collaborative Knowledge-Base Design and Ontology Reuse

    International Nuclear Information System (INIS)

    Gyurjyan, Vardan; Abbott, D.; Heyes, G.; Jastrzembski, E.; Moffit, B.; Timmer, C.; Wolin, E.

    2009-01-01

    In this paper we discuss the control domain specific ontology that is built on top of the domain-neutral Resource Definition Framework (RDF). Specifically, we will discuss the relevant set of ontology concepts along with the relationships among them in order to describe experiment control components and generic event-based state machines. Control Oriented Ontology Language (COOL) is a meta-data modeling language that provides generic means for representation of physics experiment control processes and components, and their relationships, rules and axioms. It provides a semantic reference frame that is useful for automating the communication of information for configuration, deployment and operation. COOL has been successfully used to develop a complete and dynamic knowledge-base for experiment control systems, developed using the AFECS framework.

  8. Ontology Language to Support Description of Experiment Control System Semantics, Collaborative Knowledge-Base Design and Ontology Reuse

    Energy Technology Data Exchange (ETDEWEB)

    Vardan Gyurjyan, D Abbott, G Heyes, E Jastrzembski, B Moffit, C Timmer, E Wolin

    2009-10-01

    In this paper we discuss the control domain specific ontology that is built on top of the domain-neutral Resource Definition Framework (RDF). Specifically, we will discuss the relevant set of ontology concepts along with the relationships among them in order to describe experiment control components and generic event-based state machines. Control Oriented Ontology Language (COOL) is a meta-data modeling language that provides generic means for representation of physics experiment control processes and components, and their relationships, rules and axioms. It provides a semantic reference frame that is useful for automating the communication of information for configuration, deployment and operation. COOL has been successfully used to develop a complete and dynamic knowledge-base for experiment control systems, developed using the AFECS framework.

  9. A Review on Current Reference Calculation of Three-Phase Grid-Connected PV Converters under Grid Faults

    DEFF Research Database (Denmark)

    Afshari, Ehsan; Moradi, Gholam Reza; Yang, Yongheng

    2017-01-01

    of the most important issues that should be coped with for a reliable operation of grid-connected converters under unbalanced grid faults. Accordingly, this paper reviews the existing CRC methods and presents a current reference generation method, which can have 16 unique modes. Issues are also investigated...

  10. Comparing categories among geographic ontologies

    Science.gov (United States)

    Kavouras, Marinos; Kokla, Margarita; Tomai, Eleni

    2005-03-01

    Numerous attempts have been made to generate semantic "mappings" between different ontologies, or create aligned/integrated ones. An essential step towards their success is the ability to compare the categories involved. This paper introduces a systematic methodology for comparing categories met in geographic ontologies. The methodology explores/extracts semantic information provided by categories' definitions. The first step towards this goal is the recognition of syntactic and lexical patterns in definitions, which help to identify (a) semantic properties such as purpose, location, cover, and (b) semantic relations such as hypernym, part of, has-parts, etc. At the second step, a similarity measure among categories is applied, in order to explore how (the) extracted properties and relations interrelate. This framework enables us to (a) better understand the impact of context in cross-ontology "mappings", (b) evaluate the "quality" of definitions as to whether they respect mere ontological aspects (such as unambiguous taxonomies), and (c) deal more effectively with the problem of semantic translation among geographic ontologies.

  11. The values underlying the Draft Common Frame of Reference: what role for fairness and 'social justice'?

    NARCIS (Netherlands)

    Hesselink, M.W.

    2008-01-01

    This study provides an in-depth analysis of the provisions of the draft Common Frame of Reference (DCFR), in order to assess if the DCFR perceives contract law only as a tool for regulating private law relations between equally strong parties or if it contains elements of 'social justice' in favour

  12. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

    Science.gov (United States)

    2013-01-01

    Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341

  13. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

    Science.gov (United States)

    Hill, David P; Adams, Nico; Bada, Mike; Batchelor, Colin; Berardini, Tanya Z; Dietze, Heiko; Drabkin, Harold J; Ennis, Marcus; Foulger, Rebecca E; Harris, Midori A; Hastings, Janna; Kale, Namrata S; de Matos, Paula; Mungall, Christopher J; Owen, Gareth; Roncaglia, Paola; Steinbeck, Christoph; Turner, Steve; Lomax, Jane

    2013-07-29

    The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl.

  14. Inferring ontology graph structures using OWL reasoning.

    Science.gov (United States)

    Rodríguez-García, Miguel Ángel; Hoehndorf, Robert

    2018-01-05

    Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies' semantic content remains a challenge. We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph . Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

  15. Inferring ontology graph structures using OWL reasoning

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel

    2018-01-05

    Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies\\' semantic content remains a challenge.We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies\\' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph .Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

  16. Complex Topographic Feature Ontology Patterns

    Science.gov (United States)

    Varanka, Dalia E.; Jerris, Thomas J.

    2015-01-01

    Semantic ontologies are examined as effective data models for the representation of complex topographic feature types. Complex feature types are viewed as integrated relations between basic features for a basic purpose. In the context of topographic science, such component assemblages are supported by resource systems and found on the local landscape. Ontologies are organized within six thematic modules of a domain ontology called Topography that includes within its sphere basic feature types, resource systems, and landscape types. Context is constructed not only as a spatial and temporal setting, but a setting also based on environmental processes. Types of spatial relations that exist between components include location, generative processes, and description. An example is offered in a complex feature type ‘mine.’ The identification and extraction of complex feature types are an area for future research.

  17. An ontology for sensor networks

    Science.gov (United States)

    Compton, Michael; Neuhaus, Holger; Bermudez, Luis; Cox, Simon

    2010-05-01

    Sensors and networks of sensors are important ways of monitoring and digitizing reality. As the number and size of sensor networks grows, so too does the amount of data collected. Users of such networks typically need to discover the sensors and data that fit their needs without necessarily understanding the complexities of the network itself. The burden on users is eased if the network and its data are expressed in terms of concepts familiar to the users and their job functions, rather than in terms of the network or how it was designed. Furthermore, the task of collecting and combining data from multiple sensor networks is made easier if metadata about the data and the networks is stored in a format and conceptual models that is amenable to machine reasoning and inference. While the OGC's (Open Geospatial Consortium) SWE (Sensor Web Enablement) standards provide for the description and access to data and metadata for sensors, they do not provide facilities for abstraction, categorization, and reasoning consistent with standard technologies. Once sensors and networks are described using rich semantics (that is, by using logic to describe the sensors, the domain of interest, and the measurements) then reasoning and classification can be used to analyse and categorise data, relate measurements with similar information content, and manage, query and task sensors. This will enable types of automated processing and logical assurance built on OGC standards. The W3C SSN-XG (Semantic Sensor Networks Incubator Group) is producing a generic ontology to describe sensors, their environment and the measurements they make. The ontology provides definitions for the structure of sensors and observations, leaving the details of the observed domain unspecified. This allows abstract representations of real world entities, which are not observed directly but through their observable qualities. Domain semantics, units of measurement, time and time series, and location and mobility

  18. Markov Chain Ontology Analysis (MCOA

    Directory of Open Access Journals (Sweden)

    Frost H

    2012-02-01

    Full Text Available Abstract Background Biomedical ontologies have become an increasingly critical lens through which researchers analyze the genomic, clinical and bibliographic data that fuels scientific research. Of particular relevance are methods, such as enrichment analysis, that quantify the importance of ontology classes relative to a collection of domain data. Current analytical techniques, however, remain limited in their ability to handle many important types of structural complexity encountered in real biological systems including class overlaps, continuously valued data, inter-instance relationships, non-hierarchical relationships between classes, semantic distance and sparse data. Results In this paper, we describe a methodology called Markov Chain Ontology Analysis (MCOA and illustrate its use through a MCOA-based enrichment analysis application based on a generative model of gene activation. MCOA models the classes in an ontology, the instances from an associated dataset and all directional inter-class, class-to-instance and inter-instance relationships as a single finite ergodic Markov chain. The adjusted transition probability matrix for this Markov chain enables the calculation of eigenvector values that quantify the importance of each ontology class relative to other classes and the associated data set members. On both controlled Gene Ontology (GO data sets created with Escherichia coli, Drosophila melanogaster and Homo sapiens annotations and real gene expression data extracted from the Gene Expression Omnibus (GEO, the MCOA enrichment analysis approach provides the best performance of comparable state-of-the-art methods. Conclusion A methodology based on Markov chain models and network analytic metrics can help detect the relevant signal within large, highly interdependent and noisy data sets and, for applications such as enrichment analysis, has been shown to generate superior performance on both real and simulated data relative to existing

  19. Markov Chain Ontology Analysis (MCOA).

    Science.gov (United States)

    Frost, H Robert; McCray, Alexa T

    2012-02-03

    Biomedical ontologies have become an increasingly critical lens through which researchers analyze the genomic, clinical and bibliographic data that fuels scientific research. Of particular relevance are methods, such as enrichment analysis, that quantify the importance of ontology classes relative to a collection of domain data. Current analytical techniques, however, remain limited in their ability to handle many important types of structural complexity encountered in real biological systems including class overlaps, continuously valued data, inter-instance relationships, non-hierarchical relationships between classes, semantic distance and sparse data. In this paper, we describe a methodology called Markov Chain Ontology Analysis (MCOA) and illustrate its use through a MCOA-based enrichment analysis application based on a generative model of gene activation. MCOA models the classes in an ontology, the instances from an associated dataset and all directional inter-class, class-to-instance and inter-instance relationships as a single finite ergodic Markov chain. The adjusted transition probability matrix for this Markov chain enables the calculation of eigenvector values that quantify the importance of each ontology class relative to other classes and the associated data set members. On both controlled Gene Ontology (GO) data sets created with Escherichia coli, Drosophila melanogaster and Homo sapiens annotations and real gene expression data extracted from the Gene Expression Omnibus (GEO), the MCOA enrichment analysis approach provides the best performance of comparable state-of-the-art methods. A methodology based on Markov chain models and network analytic metrics can help detect the relevant signal within large, highly interdependent and noisy data sets and, for applications such as enrichment analysis, has been shown to generate superior performance on both real and simulated data relative to existing state-of-the-art approaches.

  20. Knowledge retrieval from PubMed abstracts and electronic medical records with the Multiple Sclerosis Ontology.

    Science.gov (United States)

    Malhotra, Ashutosh; Gündel, Michaela; Rajput, Abdul Mateen; Mevissen, Heinz-Theodor; Saiz, Albert; Pastor, Xavier; Lozano-Rubi, Raimundo; Martinez-Lapiscina, Elena H; Martinez-Lapsicina, Elena H; Zubizarreta, Irati; Mueller, Bernd; Kotelnikova, Ekaterina; Toldo, Luca; Hofmann-Apitius, Martin; Villoslada, Pablo

    2015-01-01

    In order to retrieve useful information from scientific literature and electronic medical records (EMR) we developed an ontology specific for Multiple Sclerosis (MS). The MS Ontology was created using scientific literature and expert review under the Protégé OWL environment. We developed a dictionary with semantic synonyms and translations to different languages for mining EMR. The MS Ontology was integrated with other ontologies and dictionaries (diseases/comorbidities, gene/protein, pathways, drug) into the text-mining tool SCAIView. We analyzed the EMRs from 624 patients with MS using the MS ontology dictionary in order to identify drug usage and comorbidities in MS. Testing competency questions and functional evaluation using F statistics further validated the usefulness of MS ontology. Validation of the lexicalized ontology by means of named entity recognition-based methods showed an adequate performance (F score = 0.73). The MS Ontology retrieved 80% of the genes associated with MS from scientific abstracts and identified additional pathways targeted by approved disease-modifying drugs (e.g. apoptosis pathways associated with mitoxantrone, rituximab and fingolimod). The analysis of the EMR from patients with MS identified current usage of disease modifying drugs and symptomatic therapy as well as comorbidities, which are in agreement with recent reports. The MS Ontology provides a semantic framework that is able to automatically extract information from both scientific literature and EMR from patients with MS, revealing new pathogenesis insights as well as new clinical information.

  1. Knowledge retrieval from PubMed abstracts and electronic medical records with the Multiple Sclerosis Ontology.

    Directory of Open Access Journals (Sweden)

    Ashutosh Malhotra

    Full Text Available In order to retrieve useful information from scientific literature and electronic medical records (EMR we developed an ontology specific for Multiple Sclerosis (MS.The MS Ontology was created using scientific literature and expert review under the Protégé OWL environment. We developed a dictionary with semantic synonyms and translations to different languages for mining EMR. The MS Ontology was integrated with other ontologies and dictionaries (diseases/comorbidities, gene/protein, pathways, drug into the text-mining tool SCAIView. We analyzed the EMRs from 624 patients with MS using the MS ontology dictionary in order to identify drug usage and comorbidities in MS. Testing competency questions and functional evaluation using F statistics further validated the usefulness of MS ontology.Validation of the lexicalized ontology by means of named entity recognition-based methods showed an adequate performance (F score = 0.73. The MS Ontology retrieved 80% of the genes associated with MS from scientific abstracts and identified additional pathways targeted by approved disease-modifying drugs (e.g. apoptosis pathways associated with mitoxantrone, rituximab and fingolimod. The analysis of the EMR from patients with MS identified current usage of disease modifying drugs and symptomatic therapy as well as comorbidities, which are in agreement with recent reports.The MS Ontology provides a semantic framework that is able to automatically extract information from both scientific literature and EMR from patients with MS, revealing new pathogenesis insights as well as new clinical information.

  2. Gene Ontology-Based Analysis of Zebrafish Omics Data Using the Web Tool Comparative Gene Ontology.

    Science.gov (United States)

    Ebrahimie, Esmaeil; Fruzangohar, Mario; Moussavi Nik, Seyyed Hani; Newman, Morgan

    2017-10-01

    Gene Ontology (GO) analysis is a powerful tool in systems biology, which uses a defined nomenclature to annotate genes/proteins within three categories: "Molecular Function," "Biological Process," and "Cellular Component." GO analysis can assist in revealing functional mechanisms underlying observed patterns in transcriptomic, genomic, and proteomic data. The already extensive and increasing use of zebrafish for modeling genetic and other diseases highlights the need to develop a GO analytical tool for this organism. The web tool Comparative GO was originally developed for GO analysis of bacterial data in 2013 ( www.comparativego.com ). We have now upgraded and elaborated this web tool for analysis of zebrafish genetic data using GOs and annotations from the Gene Ontology Consortium.

  3. Multimedia ontology representation and applications

    CERN Document Server

    Chaudhury, Santanu; Ghosh, Hiranmay

    2015-01-01

    The result of more than 15 years of collective research, Multimedia Ontology: Representation and Applications provides a theoretical foundation for understanding the nature of media data and the principles involved in its interpretation. The book presents a unified approach to recent advances in multimedia and explains how a multimedia ontology can fill the semantic gap between concepts and the media world. It relays real-life examples of implementations in different domains to illustrate how this gap can be filled.The book contains information that helps with building semantic, content-based

  4. Root justifications for ontology repair

    CSIR Research Space (South Africa)

    Moodley, K

    2011-08-01

    Full Text Available stream_source_info Moodley_2011.pdf.txt stream_content_type text/plain stream_size 32328 Content-Encoding ISO-8859-1 stream_name Moodley_2011.pdf.txt Content-Type text/plain; charset=ISO-8859-1 Root Justi cations... the ontology, based on the no- tion of root justi cations [8, 9]. In Section 5, we discuss the implementation of a Prot eg e3 plugin which demonstrates our approach to ontology repair. In this section we also discuss some experimental results comparing...

  5. Platonic wholes and quantum ontology

    CERN Document Server

    Woszczek, Marek

    2015-01-01

    The subject of the book is a reconsideration of the internalistic model of composition of the Platonic type, more radical than traditional, post-Aristotelian externalistic compositionism, and its application in the field of the ontology of quantum theory. At the centre of quantum ontology is nonseparability. Quantum wholes are atemporal wholes governed by internalistic logic and they are primitive, global physical entities, requiring an extreme relativization of the fundamental notions of mechanics. That ensures quantum theory to be fully consistent with the relativistic causal structure, with

  6. Technique for designing a domain ontology

    OpenAIRE

    Palagin, A. V.; Petrenko, N. G.; Malakhov, K. S.

    2018-01-01

    The article describes the technique for designing a domain ontology, shows the flowchart of algorithm design and example of constructing a fragment of the ontology of the subject area of Computer Science is considered.

  7. Ontologies, Knowledge Bases and Knowledge Management

    National Research Council Canada - National Science Library

    Chalupsky, Hans

    2002-01-01

    ...) an application called Strategy Development Assistant (SDA) that uses that ontology. The JFACC ontology served as a basis for knowledge sharing among several applications in the domain of air campaign planning...

  8. A Bayesian Network Approach to Ontology Mapping

    National Research Council Canada - National Science Library

    Pan, Rong; Ding, Zhongli; Yu, Yang; Peng, Yun

    2005-01-01

    .... In this approach, the source and target ontologies are first translated into Bayesian networks (BN); the concept mapping between the two ontologies are treated as evidential reasoning between the two translated BNs...

  9. Ontology Learning - Suggesting Associations from Text

    OpenAIRE

    Kvarv, Gøran Sveia

    2007-01-01

    In many applications, large-scale ontologies have to be constructed and maintained. A manual construction of an ontology is a time consuming and resource demanding process, often involving some domain experts. It would therefore be beneficial to support this process with tools that automates the construction of an ontology. This master thesis has examined the use of association rules for suggesting associations between words in text. In ontology learning, concepts are often extracted from d...

  10. Validation of reference genes from Eucalyptus spp. under different stress conditions

    Science.gov (United States)

    2012-01-01

    Background The genus Eucalyptus consists of approximately 600 species and subspecies and has a physiological plasticity that allows some species to propagate in different regions of the world. Eucalyptus is a major source of cellulose for paper manufacturing, and its cultivation is limited by weather conditions, particularly water stress and low temperatures. Gene expression studies using quantitative reverse transcription polymerase chain reaction (qPCR) require reference genes, which must have stable expression to facilitate the comparison of the results from analyses using different species, tissues, and treatments. Such studies have been limited in eucalyptus. Results Eucalyptus globulus Labill, Eucalyptus urograndis (hybrid from Eucalyptus urophylla S.T. Blake X Eucalyptus grandis Hill ex-Maiden) and E. uroglobulus (hybrid from E. urograndis X E. globulus) were subjected to different treatments, including water deficiency and stress recovery, low temperatures, presence or absence of light, and their respective controls. Except for treatment with light, which examined the seedling hypocotyl or apical portion of the stem, the expression analyses were conducted in the apical and basal parts of the stem. To select the best pair of genes, the bioinformatics tools GeNorm and NormFinder were compared. Comprehensive analyses that did not differentiate between species, treatments, or tissue types, showed that IDH (isocitrate dehydrogenase), SAND (SAND protein), ACT (actin), and A-Tub (α-tubulin) genes were the most stable. IDH was the most stable gene in all of the treatments. Conclusion Comparing these results with those of other studies on eucalyptus, we concluded that five genes are stable in different species and experimental conditions: IDH, SAND, ACT, A-Tub, and UBQ (ubiquitin). It is usually recommended a minimum of two reference genes is expression analysis; therefore, we propose that IDH and two others genes among the five identified genes in this study

  11. Validation of reference genes from Eucalyptus spp. under different stress conditions

    Directory of Open Access Journals (Sweden)

    Moura Jullyana Cristina Magalhães Silva

    2012-11-01

    Full Text Available Abstract Background The genus Eucalyptus consists of approximately 600 species and subspecies and has a physiological plasticity that allows some species to propagate in different regions of the world. Eucalyptus is a major source of cellulose for paper manufacturing, and its cultivation is limited by weather conditions, particularly water stress and low temperatures. Gene expression studies using quantitative reverse transcription polymerase chain reaction (qPCR require reference genes, which must have stable expression to facilitate the comparison of the results from analyses using different species, tissues, and treatments. Such studies have been limited in eucalyptus. Results Eucalyptus globulus Labill, Eucalyptus urograndis (hybrid from Eucalyptus urophylla S.T. Blake X Eucalyptus grandis Hill ex-Maiden and E. uroglobulus (hybrid from E. urograndis X E. globulus were subjected to different treatments, including water deficiency and stress recovery, low temperatures, presence or absence of light, and their respective controls. Except for treatment with light, which examined the seedling hypocotyl or apical portion of the stem, the expression analyses were conducted in the apical and basal parts of the stem. To select the best pair of genes, the bioinformatics tools GeNorm and NormFinder were compared. Comprehensive analyses that did not differentiate between species, treatments, or tissue types, showed that IDH (isocitrate dehydrogenase, SAND (SAND protein, ACT (actin, and A-Tub (α-tubulin genes were the most stable. IDH was the most stable gene in all of the treatments. Conclusion Comparing these results with those of other studies on eucalyptus, we concluded that five genes are stable in different species and experimental conditions: IDH, SAND, ACT, A-Tub, and UBQ (ubiquitin. It is usually recommended a minimum of two reference genes is expression analysis; therefore, we propose that IDH and two others genes among the five identified

  12. Validation of reference genes from Eucalyptus spp. under different stress conditions.

    Science.gov (United States)

    Moura, Jullyana Cristina Magalhães Silva; Araújo, Pedro; Brito, Michael dos Santos; Souza, Uiara Romero; Viana, Juliana de Oliveira Fernandes; Mazzafera, Paulo

    2012-11-14

    The genus Eucalyptus consists of approximately 600 species and subspecies and has a physiological plasticity that allows some species to propagate in different regions of the world. Eucalyptus is a major source of cellulose for paper manufacturing, and its cultivation is limited by weather conditions, particularly water stress and low temperatures. Gene expression studies using quantitative reverse transcription polymerase chain reaction (qPCR) require reference genes, which must have stable expression to facilitate the comparison of the results from analyses using different species, tissues, and treatments. Such studies have been limited in eucalyptus. Eucalyptus globulus Labill, Eucalyptus urograndis (hybrid from Eucalyptus urophylla S.T. Blake X Eucalyptus grandis Hill ex-Maiden) and E. uroglobulus (hybrid from E. urograndis X E. globulus) were subjected to different treatments, including water deficiency and stress recovery, low temperatures, presence or absence of light, and their respective controls. Except for treatment with light, which examined the seedling hypocotyl or apical portion of the stem, the expression analyses were conducted in the apical and basal parts of the stem. To select the best pair of genes, the bioinformatics tools GeNorm and NormFinder were compared. Comprehensive analyses that did not differentiate between species, treatments, or tissue types, showed that IDH (isocitrate dehydrogenase), SAND (SAND protein), ACT (actin), and A-Tub (α-tubulin) genes were the most stable. IDH was the most stable gene in all of the treatments. Comparing these results with those of other studies on eucalyptus, we concluded that five genes are stable in different species and experimental conditions: IDH, SAND, ACT, A-Tub, and UBQ (ubiquitin). It is usually recommended a minimum of two reference genes is expression analysis; therefore, we propose that IDH and two others genes among the five identified genes in this study should be used as reference genes

  13. ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease.

    Science.gov (United States)

    Malhotra, Ashutosh; Younesi, Erfan; Gündel, Michaela; Müller, Bernd; Heneka, Michael T; Hofmann-Apitius, Martin

    2014-03-01

    Biomedical ontologies offer the capability to structure and represent domain-specific knowledge semantically. Disease-specific ontologies can facilitate knowledge exchange across multiple disciplines, and ontology-driven mining approaches can generate great value for modeling disease mechanisms. However, in the case of neurodegenerative diseases such as Alzheimer's disease, there is a lack of formal representation of the relevant knowledge domain. Alzheimer's disease ontology (ADO) is constructed in accordance to the ontology building life cycle. The Protégé OWL editor was used as a tool for building ADO in Ontology Web Language format. ADO was developed with the purpose of containing information relevant to four main biological views-preclinical, clinical, etiological, and molecular/cellular mechanisms-and was enriched by adding synonyms and references. Validation of the lexicalized ontology by means of named entity recognition-based methods showed a satisfactory performance (F score = 72%). In addition to structural and functional evaluation, a clinical expert in the field performed a manual evaluation and curation of ADO. Through integration of ADO into an information retrieval environment, we show that the ontology supports semantic search in scientific text. The usefulness of ADO is authenticated by dedicated use case scenarios. Development of ADO as an open ADO is a first attempt to organize information related to Alzheimer's disease in a formalized, structured manner. We demonstrate that ADO is able to capture both established and scattered knowledge existing in scientific text. Copyright © 2014 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

  14. Evaluation of an andean common bean reference collection under drought stress

    OpenAIRE

    Pérez Vega, Juan Carlos; Blair, Matthew W.; Monserrate, Fredy; Ligarreto Moreno, Gustavo Adolfo

    2012-01-01

    More than 60% of common bean (Phaseolus vulgaris L.) production worldwide is impacted by the risk of drought. In this study, the goal was to evaluate 64 bush bean genotypes from the CIAT reference collection to identify possible sources of drought resistance in the Andean gene pool. Phenotypic traits such as yield, 100-seed weight (P100) and days to physiological maturity (Dpm) were evaluated on selected accessions of this collection which was grown in an 8x8 lattice with two repetitions unde...

  15. Aspects of ontology visualization and integration

    NARCIS (Netherlands)

    Dmitrieva, Joelia Borisovna

    2011-01-01

    In this thesis we will describe and discuss methodologies for ontology visualization and integration. Two visualization methods will be elaborated. In one method the ontology is visualized with the node-link technique, and with the other method the ontology is visualized with the containment

  16. development of ontological knowledge representation: learning ...

    African Journals Online (AJOL)

    Preferred Customer

    This group of authors describes use of ontologies for knowledge organization in a given domain. In the context of computer science, ontologies have been applied in the field of artificial intelligence in order to facilitate knowledge sharing and reuse of acquired knowledge (15). Soon, ontologies have gained great popularity.

  17. Sample evaluation of ontology-matching systems

    NARCIS (Netherlands)

    Hage, W.R. van; Isaac, A.; Aleksovski, Z.

    2007-01-01

    Ontology matching exists to solve practical problems. Hence, methodologies to find and evaluate solutions for ontology matching should be centered on practical problems. In this paper we propose two statistically-founded evaluation techniques to assess ontology-matching performance that are based on

  18. The Ontology of Power and Its Interpretation in the Economics

    Directory of Open Access Journals (Sweden)

    Miriasov Iurii O.

    2016-04-01

    Full Text Available The article is concerned with considering the ontological foundations of the modern economic theory, which determine both directly the subject area of research and the methodological approaches to its studying. Differentiation of scientific ontologies, i.e. perceptions of reality, leads to differences in explaining the large circle of issues, in particular, differences in the interpretation of the concept of power in the economic science. Studying and generalizing principles of the neoclassical mainstream together with the methodologically related directions provides characterization of the substant scientific ontology as «empirical realism». An alternative can be the ontology of «critical realism», according to which power acts as a system characteristic of economic relations, identifying the underlying trends and directions of system evolution. It has been displayed that certain provisions of the Marxism research program, such as class structure, market, social competition are consistent with the critical realism ontology and can serve as a prospect for studying the essential problems of economic development and transformation of society. In particular, they can be applied while studying the role of capital as a factor of power in the national and global competition.

  19. A reference stress approach for the characterisation of the creep failure of dissimilar welds under isothermal conditions

    International Nuclear Information System (INIS)

    Nicholson, R.D.; Williams, J.A.

    1988-11-01

    In high temperature power plant, welds between austenitic and ferritic steels are required to operate under plant conditions for up to 250,000h. The experience and failure modes for such joints are briefly surveyed in this report. A semi-empirical reference stress approach is used to define the failure life of joints under isothermal conditions. The reference stress is based on a previously published form for multiaxial creep fracture of homogeneous materials but modified to include an additional factor to reflect the complex strains present close to the interface in a dissimilar weld. This reference stress can be modified to give approximate bounds characterised by the equivalent stress or the axial stress on the weld. The reference stress, when applied to the 21/4Cr1Mo:Type 316 welded component data base, gives conservative results for the test data available although conservatism is low for the 9Cr1Mo:Alloy 600 combination. The existing data base for welded components is limited. More data are needed covering a wider range of stress ratios and incorporating bending loads. (author)

  20. Sistem Promosi Pariwisata Menggunakan Ontologi

    Directory of Open Access Journals (Sweden)

    Adi Kurniawan

    2013-03-01

    Full Text Available Pariwisata merupakan sektor yang penting di Indonesia. World Tourism Organization (WTO meramalkan pada tahun  2019,  bahwa  industri pariwisata Asia Pasifik akan mengalami perkembangan yang menjanjikan terutama dari segi pendapatan. Sistem  promosi pariwisata berbasis konteks yang ada hanya mengakomodasi pelancong yang sudah memiliki rencana dengan jelas (pelancong terencana, sedangkan pelancong yang sekedar ingin menjelajahi kota, berjalan-jalan  atau menghabiskan waktu luang (pelancong dadakan belum ada yang mengakomodasi. Salah satu solusi tersebut adalah dengan menggunakan teknologi piranti bergerak dan ontologi.  Piranti bergerak memudahkan pelancong untuk mendapatkan informasi kapanpun dan dimanapun. Sedangkan penggunaan ontologi akan mempermudah penyajian informasi yang lebih relevan kepada pelancong. Ontologi dalam konteks studi ini adalah ontologi probabilitas dengan pendekatan bayesian network. Pengujian sistem dibagi menjadi dua bagian yaitu uji validitas kebutuhan sistem dengan menggunakan perkaka Requirements Traceability Matrixs (RTM dan pengujian sistem purwarupa dengan pengujian kotak hitam. Secara umum, fungsionalitas sistem berjalan baik dan sesuai dengan rancangan sistem.

  1. Ontology for the Intelligence Analyst

    Science.gov (United States)

    2012-12-01

    an artillery tractor that runs on wheels ⎣ tracked artillery tractor =def: an artillery tractor that runs on caterpillar track 20...in response to identified situational needs of analysts, and architectural requirements are designed to ensure coherent evolution of the SE resource...Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology, 25 (11), November 2007, 1251-1255. 13

  2. Gene Ontology annotations and resources.

    Science.gov (United States)

    Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

  3. Ontological problems of contemporary linguistics

    Directory of Open Access Journals (Sweden)

    А В Бондаренко

    2009-03-01

    Full Text Available The article studies linguistic ontology problems such as evolution of essential-existential views of language, interrelation within Being-Language-Man triad, linguistics gnosiological principles, language essence localization, and «expression» as language metalinguistic unit as well as architectonics of language personality et alia.

  4. CLO : The cell line ontology

    NARCIS (Netherlands)

    Sarntivijai, Sirarat; Lin, Yu; Xiang, Zuoshuang; Meehan, Terrence F.; Diehl, Alexander D.; Vempati, Uma D.; Schuerer, Stephan C.; Pang, Chao; Malone, James; Parkinson, Helen; Liu, Yue; Takatsuki, Terue; Saijo, Kaoru; Masuya, Hiroshi; Nakamura, Yukio; Brush, Matthew H.; Haendel, Melissa A.; Zheng, Jie; Stoeckert, Christian J.; Peters, Bjoern; Mungall, Christopher J.; Carey, Thomas E.; States, David J.; Athey, Brian D.; He, Yongqun

    2014-01-01

    Background: Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO

  5. Anytime classification by ontology approximation

    NARCIS (Netherlands)

    Schlobach, S.; Blaauw, E.; El Kebir, M.; Ten Teije, A.; Van Harmelen, F.; Bortoli, S.; Hobbelman, M.C.; Millian, K.; Ren, Y.; Stam, S.; Thomassen, P.; Van Het Schip, R.; Van Willigem, W.

    2007-01-01

    Reasoning with large or complex ontologies is one of the bottle-necks of the Semantic Web. In this paper we present an anytime algorithm for classification based on approximate subsumption. We give the formal definitions for approximate subsumption, and show its monotonicity and soundness; we show

  6. Quantum physics and relational ontology

    Energy Technology Data Exchange (ETDEWEB)

    Cordovil, Joao [Center of Philosophy of Sciences of University of Lisbon (Portugal)

    2013-07-01

    The discovery of the quantum domain of reality put a serious ontological challenge, a challenge that is still well present in the recent developments of Quantum Physics. Physics was conceived from an atomistic conception of the world, reducing it, in all its diversity, to two types of entities: simple, individual and immutable entities (atoms, in metaphysical sense) and composite entities, resulting solely from combinations. Linear combinations, additive, indifferent to the structure or to the context. However, the discovery of wave-particle dualism and the developments in Quantum Field Theories and in Quantum Nonlinear Physical, showed that quantum entities are not, in metaphysical sense, neither simple, nor merely the result of linear (or additive) combinations. In other words, the ontological foundations of Physics revealed as inadequate to account for the nature of quantum entities. Then a fundamental challenge arises: How to think the ontic nature of these entities? In my view, this challenge appeals to a relational and dynamist ontology of physical entities. This is the central hypothesis of this communication. In this sense, this communication has two main intentions: 1) positively characterize this relational and dynamist ontology; 2) show some elements of its metaphysical suitability to contemporary Quantum Physics.

  7. Constitutive rules, language, and ontology

    NARCIS (Netherlands)

    Hindriks, Frank

    It is a commonplace within philosophy that the ontology of institutions can be captured in terms of constitutive rules. What exactly such rules are, however, is not well understood. They are usually contrasted to regulative rules: constitutive rules (such as the rules of chess) make institutional

  8. Underlying data for derived emergency reference levels. Post-Chernobyl action

    International Nuclear Information System (INIS)

    Sinnaeve, J.; Gerber, G.

    1991-01-01

    After an accidental release of radioactive material to the atmosphere leading to significant off-site contamination, various countermeasures are needed to reduce the radiation exposure of the population. These may include measures to reduce the consumption of contaminated foodstuffs. This report is concerned with the underlying information required for calculating when and if such countermeasures as regards foodstuffs should be introduced. The work in this report was sponsored by the Commission of the European Communities as one of a series of post-Chernobyl actions under its radiation protection programme

  9. Semantic similarity in biomedical ontologies.

    Directory of Open Access Journals (Sweden)

    Catia Pesquita

    2009-07-01

    Full Text Available In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degree of relatedness between two entities by the similarity in meaning of their annotations. The application of semantic similarity to biomedical ontologies is recent; nevertheless, several studies have been published in the last few years describing and evaluating diverse approaches. Semantic similarity has become a valuable tool for validating the results drawn from biomedical studies such as gene clustering, gene expression data analysis, prediction and validation of molecular interactions, and disease gene prioritization. We review semantic similarity measures applied to biomedical ontologies and propose their classification according to the strategies they employ: node-based versus edge-based and pairwise versus groupwise. We also present comparative assessment studies and discuss the implications of their results. We survey the existing implementations of semantic similarity measures, and we describe examples of applications to biomedical research. This will clarify how biomedical researchers can benefit from semantic similarity measures and help them choose the approach most suitable for their studies.Biomedical ontologies are evolving toward increased coverage, formality, and integration, and their use for annotation is increasingly becoming a focus of both effort by biomedical experts and application of automated annotation procedures to create corpora of higher quality and completeness than are currently available. Given that semantic similarity measures are directly dependent on these evolutions, we can expect to see them gaining more relevance and even becoming as essential as sequence similarity is today in biomedical research.

  10. Semantic similarity in biomedical ontologies.

    Science.gov (United States)

    Pesquita, Catia; Faria, Daniel; Falcão, André O; Lord, Phillip; Couto, Francisco M

    2009-07-01

    In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degree of relatedness between two entities by the similarity in meaning of their annotations. The application of semantic similarity to biomedical ontologies is recent; nevertheless, several studies have been published in the last few years describing and evaluating diverse approaches. Semantic similarity has become a valuable tool for validating the results drawn from biomedical studies such as gene clustering, gene expression data analysis, prediction and validation of molecular interactions, and disease gene prioritization. We review semantic similarity measures applied to biomedical ontologies and propose their classification according to the strategies they employ: node-based versus edge-based and pairwise versus groupwise. We also present comparative assessment studies and discuss the implications of their results. We survey the existing implementations of semantic similarity measures, and we describe examples of applications to biomedical research. This will clarify how biomedical researchers can benefit from semantic similarity measures and help them choose the approach most suitable for their studies.Biomedical ontologies are evolving toward increased coverage, formality, and integration, and their use for annotation is increasingly becoming a focus of both effort by biomedical experts and application of automated annotation procedures to create corpora of higher quality and completeness than are currently available. Given that semantic similarity measures are directly dependent on these evolutions, we can expect to see them gaining more relevance and even becoming as essential as sequence similarity is today in biomedical research.

  11. Ontological, Epistemological and Methodological Assumptions: Qualitative versus Quantitative

    Science.gov (United States)

    Ahmed, Abdelhamid

    2008-01-01

    The review to follow is a comparative analysis of two studies conducted in the field of TESOL in Education published in "TESOL QUARTERLY." The aspects to be compared are as follows. First, a brief description of each study will be presented. Second, the ontological, epistemological and methodological assumptions underlying each study…

  12. Gradient Learning Algorithms for Ontology Computing

    Science.gov (United States)

    Gao, Wei; Zhu, Linli

    2014-01-01

    The gradient learning model has been raising great attention in view of its promising perspectives for applications in statistics, data dimensionality reducing, and other specific fields. In this paper, we raise a new gradient learning model for ontology similarity measuring and ontology mapping in multidividing setting. The sample error in this setting is given by virtue of the hypothesis space and the trick of ontology dividing operator. Finally, two experiments presented on plant and humanoid robotics field verify the efficiency of the new computation model for ontology similarity measure and ontology mapping applications in multidividing setting. PMID:25530752

  13. Gradient learning algorithms for ontology computing.

    Science.gov (United States)

    Gao, Wei; Zhu, Linli

    2014-01-01

    The gradient learning model has been raising great attention in view of its promising perspectives for applications in statistics, data dimensionality reducing, and other specific fields. In this paper, we raise a new gradient learning model for ontology similarity measuring and ontology mapping in multidividing setting. The sample error in this setting is given by virtue of the hypothesis space and the trick of ontology dividing operator. Finally, two experiments presented on plant and humanoid robotics field verify the efficiency of the new computation model for ontology similarity measure and ontology mapping applications in multidividing setting.

  14. Gradient Learning Algorithms for Ontology Computing

    Directory of Open Access Journals (Sweden)

    Wei Gao

    2014-01-01

    Full Text Available The gradient learning model has been raising great attention in view of its promising perspectives for applications in statistics, data dimensionality reducing, and other specific fields. In this paper, we raise a new gradient learning model for ontology similarity measuring and ontology mapping in multidividing setting. The sample error in this setting is given by virtue of the hypothesis space and the trick of ontology dividing operator. Finally, two experiments presented on plant and humanoid robotics field verify the efficiency of the new computation model for ontology similarity measure and ontology mapping applications in multidividing setting.

  15. Ontologies as integrative tools for plant science.

    Science.gov (United States)

    Walls, Ramona L; Athreya, Balaji; Cooper, Laurel; Elser, Justin; Gandolfo, Maria A; Jaiswal, Pankaj; Mungall, Christopher J; Preece, Justin; Rensing, Stefan; Smith, Barry; Stevenson, Dennis W

    2012-08-01

    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). 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. 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.

  16. Development of a Korean reference HLW disposal system under the Korean representative geologic conditions

    International Nuclear Information System (INIS)

    Choi, Heui-Joo; Lee, Jong Youl; Choi, Jongwon

    2007-01-01

    The development of a Korean Reference disposal System for the spent fuels from PWR and CANDU reactors is outlined in this paper. Around 36,000 tU of spent fuels are being projected based on the lifetimes of 28 nuclear power reactors in Korea. Since the site for the geological disposal has not yet been decided, a hypothetical site with representative Korean geologic conditions is proposed for the conceptual design of the repository. The disposal rates of the spent fuels are determined according to the total operation time of 55 years. The canisters are optimized by considering natural Korean conditions, and the buffer is designed with domestic Ca-bentonite. The depth of the repository is determined to be 500 m below the ground's surface. The canister separation distances are determined through a thermal analysis. The main features of the repository are presented from the layout to the closure. A computer program has been developed to calculate and analyze the volume and the area of the disposal system to help in the cost analysis. The final output of the design is presented as a unit disposal cost, US $315 /kgU. (authors)

  17. Discovering beaten paths in collaborative ontology-engineering projects using Markov chains.

    Science.gov (United States)

    Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A; Noy, Natalya F

    2014-10-01

    Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology

  18. ¿Ontología u Ontologías?

    OpenAIRE

    Vélez León, Paulo

    2015-01-01

    En recientes décadas se ha observado un renovado interés por algunos de los temas clásicos de la ontología, desde áreas de conocimiento externas a la filosofía, sin embargo, este renacimiento ontológico ha «estimulado» una multiplicidad y diversidad de teorías y concepciones «ontológicas» que ha dado como consecuencia una proliferación de «ontologías» y de interminables batallas para determinar qué tipo de «entidades» estudian sus respectivos «dominios», que a su vez se consideran autónomos e...

  19. ¿Ontología u Ontologías?

    OpenAIRE

    Vélez León, Paulo

    2015-01-01

    [ES] En recientes décadas se ha observado un renovado interés por algunos de los temas clásicos de la ontología, desde áreas de conocimiento externas a la filosofía, sin embargo, este renacimiento ontológico ha «estimulado» una multiplicidad y diversidad de teorías y concepciones «ontológicas» que ha dado como consecuencia una proliferación de «ontologías» y de interminables batallas para determinar qué tipo de «entidades» estudian sus respectivos «dominios», que a su vez se consideran autóno...

  20. Building a biomedical ontology recommender web service

    Directory of Open Access Journals (Sweden)

    Jonquet Clement

    2010-06-01

    Full Text Available Abstract Background Researchers in biomedical informatics use ontologies and terminologies to annotate their data in order to facilitate data integration and translational discoveries. As the use of ontologies for annotation of biomedical datasets has risen, a common challenge is to identify ontologies that are best suited to annotating specific datasets. The number and variety of biomedical ontologies is large, and it is cumbersome for a researcher to figure out which ontology to use. Methods We present the Biomedical Ontology Recommender web service. The system uses textual metadata or a set of keywords describing a domain of interest and suggests appropriate ontologies for annotating or representing the data. The service makes a decision based on three criteria. The first one is coverage, or the ontologies that provide most terms covering the input text. The second is connectivity, or the ontologies that are most often mapped to by other ontologies. The final criterion is size, or the number of concepts in the ontologies. The service scores the ontologies as a function of scores of the annotations created using the National Center for Biomedical Ontology (NCBO Annotator web service. We used all the ontologies from the UMLS Metathesaurus and the NCBO BioPortal. Results We compare and contrast our Recommender by an exhaustive functional comparison to previously published efforts. We evaluate and discuss the results of several recommendation heuristics in the context of three real world use cases. The best recommendations heuristics, rated ‘very relevant’ by expert evaluators, are the ones based on coverage and connectivity criteria. The Recommender service (alpha version is available to the community and is embedded into BioPortal.

  1. A relative frame of reference underlies reversed depth perception in anticorrelated random-dot stereograms.

    Science.gov (United States)

    Aoki, Shuntaro C; Shiozaki, Hiroshi M; Fujita, Ichiro

    2017-10-01

    Binocular disparity is represented by interocular cross-correlation of visual images in the striate and some extrastriate cortices. This correlation-based representation produces reversed depth perception in a binocularly anticorrelated random-dot stereogram (aRDS) when it is accompanied by an adjacent correlated RDS (cRDS). Removal of the cRDS or spatial separation between the aRDS and cRDS abolishes reversed depth perception. However, how an immediate plane supports reversed depth perception is unclear. One possible explanation is that the correlation-based representation generates reversed depth based on the relative disparity between the aRDS and cRDS rather than the absolute disparity of the aRDS. Here, we psychophysically tested this hypothesis. We found that participants perceived reversed depth in an aRDS with zero absolute disparity when it was surrounded by a cRDS with nonzero absolute disparity (i.e., nonzero relative disparity), suggesting a role of relative disparity on the depth reversal. In addition, manipulation of the absolute disparities of the central aRDS and surrounding cRDS caused depth perception to reverse with respect to the depth of the surround. Further, depth reversal persisted after swapping the locations of the two RDSs. A model of relative-disparity encoding explains all these results. We conclude that reversed depth perception in aRDSs occurs in a relative frame of reference and suggest that the visual system contains correlation-based representation that encodes relative disparity.

  2. Diffusive Barrier and Getter Under Waste Packages VA Reference Design Feature Evaluations

    Energy Technology Data Exchange (ETDEWEB)

    MacNeil, K.

    1999-05-24

    This technical document evaluates those aspects of the diffusive barrier and getter features which have the potential for enhancing the performance of the Viability Assessment Reference Design and are also directly related to the key attributes for the repository safety strategy of that design. The effects of advection, hydrodynamic dispersion, and diffusion on the radionuclide migration rates through the diffusive barrier were determined through the application of the one-dimensional, advection/dispersion/diffusion equation. The results showed that because advective flow described by the advection-dispersion equation dominates, the diffusive barrier feature alone would not be effective in retarding migration of radiocuclides. However, if the diffusive barrier were combined with one or more features that reduced the potential for advection, then transport of radionuclides would be dominated by diffusion and their migration from the EBS would be impeded. Apatite was chosen as the getter material used for this report. Two getter configurations were developed, Case 1 and Case 2. As in the evaluation of the diffusive barrier, the effects of advection, hydrodynamic dispersion, and diffusion on the migration of radionuclides through the getter are evaluated. However, in addition to these mechanisms, the one-dimensional advection/dispersion/diffusion model is modified to include the effect of sorption on radionuclide migration rates through the sorptive medium (getter). As a result of sorption, the longitudinal dispersion coefficient, and the average linear velocity are effectively reduced by the retardation factor. The retardation factor is a function of the getter material's dry bulk density, sorption coefficient and moisture content. The results of the evaluation showed that a significant delay in breakthrough through the getter can be achieved if the thickness of the getter barrier is increased.

  3. Ontology-based specification, identification and analysis of perioperative risks.

    Science.gov (United States)

    Uciteli, Alexandr; Neumann, Juliane; Tahar, Kais; Saleh, Kutaiba; Stucke, Stephan; Faulbrück-Röhr, Sebastian; Kaeding, André; Specht, Martin; Schmidt, Tobias; Neumuth, Thomas; Besting, Andreas; Stegemann, Dominik; Portheine, Frank; Herre, Heinrich

    2017-09-06

    Medical personnel in hospitals often works under great physical and mental strain. In medical decision-making, errors can never be completely ruled out. Several studies have shown that between 50 and 60% of adverse events could have been avoided through better organization, more attention or more effective security procedures. Critical situations especially arise during interdisciplinary collaboration and the use of complex medical technology, for example during surgical interventions and in perioperative settings (the period of time before, during and after surgical intervention). In this paper, we present an ontology and an ontology-based software system, which can identify risks across medical processes and supports the avoidance of errors in particular in the perioperative setting. We developed a practicable definition of the risk notion, which is easily understandable by the medical staff and is usable for the software tools. Based on this definition, we developed a Risk Identification Ontology (RIO) and used it for the specification and the identification of perioperative risks. An agent system was developed, which gathers risk-relevant data during the whole perioperative treatment process from various sources and provides it for risk identification and analysis in a centralized fashion. The results of such an analysis are provided to the medical personnel in form of context-sensitive hints and alerts. For the identification of the ontologically specified risks, we developed an ontology-based software module, called Ontology-based Risk Detector (OntoRiDe). About 20 risks relating to cochlear implantation (CI) have already been implemented. Comprehensive testing has indicated the correctness of the data acquisition, risk identification and analysis components, as well as the web-based visualization of results.

  4. The Quest to Solve Problems That Don’t Exist: Thought Artifacts in Contemporary Ontology

    Directory of Open Access Journals (Sweden)

    Kastrup Bernardo

    2017-10-01

    Full Text Available Questions about the nature of reality and consciousness remain unresolved in philosophy today, but not for lack of hypotheses. Ontologies as varied as physicalism, microexperientialism and cosmopsychism enrich the philosophical menu. Each of these ontologies faces a seemingly fundamental problem: under physicalism, for instance, we have the ‘hard problem of consciousness,’ whereas under microexperientialism we have the ‘subject combination problem.’ I argue that these problems are thought artifacts, having no grounding in empirical reality. In a manner akin to semantic paradoxes, they exist only in the internal logico-conceptual structure of their respective ontologies.

  5. Revealing ontological commitments by magic.

    Science.gov (United States)

    Griffiths, Thomas L

    2015-03-01

    Considering the appeal of different magical transformations exposes some systematic asymmetries. For example, it is more interesting to transform a vase into a rose than a rose into a vase. An experiment in which people judged how interesting they found different magic tricks showed that these asymmetries reflect the direction a transformation moves in an ontological hierarchy: transformations in the direction of animacy and intelligence are favored over the opposite. A second and third experiment demonstrated that judgments of the plausibility of machines that perform the same transformations do not show the same asymmetries, but judgments of the interestingness of such machines do. A formal argument relates this sense of interestingness to evidence for an alternative to our current physical theory, with magic tricks being a particularly pure source of such evidence. These results suggest that people's intuitions about magic tricks can reveal the ontological commitments that underlie human cognition. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. The Usability-Error Ontology

    DEFF Research Database (Denmark)

    Elkin, Peter L.; Beuscart-zephir, Marie-Catherine; Pelayo, Sylvia

    2013-01-01

    in patients coming to harm. Often the root cause analysis of these adverse events can be traced back to Usability Errors in the Health Information Technology (HIT) or its interaction with users. Interoperability of the documentation of HIT related Usability Errors in a consistent fashion can improve our...... ability to do systematic reviews and meta-analyses. In an effort to support improved and more interoperable data capture regarding Usability Errors, we have created the Usability Error Ontology (UEO) as a classification method for representing knowledge regarding Usability Errors. We expect the UEO...... will grow over time to support an increasing number of HIT system types. In this manuscript, we present this Ontology of Usability Error Types and specifically address Computerized Physician Order Entry (CPOE), Electronic Health Records (EHR) and Revenue Cycle HIT systems....

  7. Mechanical response of FFTF reference and P1 cladding tubes under transient heating

    International Nuclear Information System (INIS)

    Youngahl, C.A.; Ariman, T.; Lepacek, B.E.

    1977-01-01

    Burst tests of Type 316 stainless steel cladding tube samples subjected to increasing temperature and relatively constant internal pressure were conducted to assist in the pretest analysis of the P1 experiment performed in the Sodium Loop Safety Facility. This paper reports and analyzes the burst test results and those of subsequent transient heating work. The use of a modified extensometer in obtaining mechanical response data for stainless steel in the high temperature range is illustrated, some of such data is provided, and the potential of further experiments and analysis is indicated. Tubing of the same design as Fast Flux Test Facility (FFTF) cladding (20% cold worked, 0.230 in. OD, 15 mil wall) was tested as-received and after annealing or electrolytic thinning. P1 tubing (38% cold worked, 0.230 in. OD, 10 mil wall) was tested before and after aging under conditions anticipated in the P1 reactor experiment. The P1 cladding was designed to simulate FFTF tubing that had experienced irradiation embrittlement and attack by cesium oxide and sodium impurities

  8. BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

    Science.gov (United States)

    Moreno, Pablo; Beisken, Stephan; Harsha, Bhavana; Muthukrishnan, Venkatesh; Tudose, Ilinca; Dekker, Adriano; Dornfeldt, Stefanie; Taruttis, Franziska; Grosse, Ivo; Hastings, Janna; Neumann, Steffen; Steinbeck, Christoph

    2015-02-21

    Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis. We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

  9. Building an ontology for cyberterrorism

    CSIR Research Space (South Africa)

    Veerasamy, N

    2012-07-01

    Full Text Available . As defined in this research, a cyberterrorism attack consists of a high-level motivation that is religious, social or political. The individual/group can furthermore be classified as having a specific driving force depending of the level of extremism... or revolutionary thinking. Thus, the ontology will take into consideration the motivating characteristics that play a significant role in contributing towards the definition of cyberterrorism. Overall, this paper promotes the understanding of the field...

  10. Ontology Maintenance using Textual Analysis

    Directory of Open Access Journals (Sweden)

    Yassine Gargouri

    2003-10-01

    Full Text Available Ontologies are continuously confronted to evolution problem. Due to the complexity of the changes to be made, a maintenance process, at least a semi-automatic one, is more and more necessary to facilitate this task and to ensure its reliability. In this paper, we propose a maintenance ontology model for a domain, whose originality is to be language independent and based on a sequence of text processing in order to extract highly related terms from corpus. Initially, we deploy the document classification technique using GRAMEXCO to generate classes of texts segments having a similar information type and identify their shared lexicon, agreed as highly related to a unique topic. This technique allows a first general and robust exploration of the corpus. Further, we apply the Latent Semantic Indexing method to extract from this shared lexicon, the most associated terms that has to be seriously considered by an expert to eventually confirm their relevance and thus updating the current ontology. Finally, we show how the complementarity between these two techniques, based on cognitive foundation, constitutes a powerful refinement process.

  11. Development of a Ground Vehicle Maneuver Ontology to Support the Common Operational Picture

    National Research Council Canada - National Science Library

    Richmond, Paul W; Blais, Curtis L; Goerger, Niki C

    2006-01-01

    .... This paper describes both the Mobility-COP, from which warfighters can assess the ability of forces to maneuver effectively under multiple environmental and tactical conditions, and a formal ontology...

  12. Levothyroxine soft capsules demonstrate bioequivalent pharmacokinetic exposure with the European reference tablets in healthy volunteers under fasting conditions.

    Science.gov (United States)

    Al-Numani, Dina; Scarsi, Claudia; Ducharme, Murray P

    2016-02-01

    To assess the bioequivalence (BE) potential under fasting conditions between levothyroxine soft capsules and the European reference tablet formulation. Two studies were conducted to assess the BE potential as per European regulations. Study 1 was a two-way crossover BE study comparing a high strength of levothyroxine soft capsules versus levothyroxine tablets (200 μg), while study 2 was a three-way crossover dosage form proportionality study between low, medium, and high strengths of soft capsules. 70 healthy adult subjects participated in the two studies. Each treatment consisted of a 600-μg dose of levothyroxine sodium, administered under fasting conditions. Blood samples were collected for levothyroxine (T4) assay prior to dosing and up to 72 hours post dose. A washout of 35 days separated treatments in each study. Pharmacokinetics was assessed using noncompartmental methods. A total of 61 subjects completed the studies. Baseline-adjusted total T4 ratios (test/reference) and 90% confidence intervals (CIs) between soft capsules and tablets were within 80.00 - 125.00%. Comparison of the three strengths of soft capsules indicated pharmacokinetic equivalence between them (ratios and 90% CIs were contained within 80.00 - 125.00%). Overall, levothyroxine sodium was well tolerated with all products when given as single oral doses of 600 μg, except for 1 serious adverse event of secondary bacteremia reported in study 2, deemed not to be related to treatment. Levothyroxine soft capsules meet BE criteria in terms of systemic exposure when compared to a European reference tablet under fasting conditions in healthy volunteers.

  13. Use of ontology in the retrieval of information in digital collections of newspapers

    Directory of Open Access Journals (Sweden)

    Luana Carla de Moura dos Santos

    2017-10-01

    Full Text Available Introduction: It aims at modeling an ontology of the soccer field for the treatment of diachronic and synchronic variations of the language; Objective: To support the retrieval of information in digital collections of newspapers. Methodology: This is an applied research, using as basis a digital journal collection. It uses the methodology OntoForInfoScience, de Mendonça (2015 to develop the ontology of the soccer field. Information collection was carried out on domain reference materials and newspaper news. Chronologically, the established cut covers terminology used between 1900 to 2015, a period that contemplates the existence of football clubs in Brazil. The ontology was formalized in logical language with the help of the editor Protegé. As a way of evaluating the developed ontology, competence issues were elaborated that were executed in SPARQL language. To verify the use of the ontology in environments composed by printed and digital newspapers, demonstrative searches were carried out in a real collection. Results: The analysis of the results showed that without the use of the ontology in the digital collections of newspapers, the information retrieval is exhaustive and retrieves documents that are not relevant due to the absence of relationships between the terms that form the domain. Conclusion: With the inclusion of the ontology, the search for information can dispense with both the user's literacy, because with the relationships formed, it is not necessary to perform numerous searches to retrieve equivalent concepts and expressions.

  14. Database Concepts in a Domain Ontology

    Directory of Open Access Journals (Sweden)

    Gorskis Henrihs

    2017-12-01

    Full Text Available There are multiple approaches for mapping from a domain ontology to a database in the task of ontology-based data access. For that purpose, external mapping documents are most commonly used. These documents describe how the data necessary for the description of ontology individuals and other values, are to be obtained from the database. The present paper investigates the use of special database concepts. These concepts are not separated from the domain ontology; they are mixed with domain concepts to form a combined application ontology. By creating natural relationships between database concepts and domain concepts, mapping can be implemented more easily and with a specific purpose. The paper also investigates how the use of such database concepts in addition to domain concepts impacts ontology building and data retrieval.

  15. An ontology approach to comparative phenomics in plants.

    Science.gov (United States)

    Oellrich, Anika; Walls, Ramona L; Cannon, Ethalinda Ks; Cannon, Steven B; Cooper, Laurel; Gardiner, Jack; Gkoutos, Georgios V; Harper, Lisa; He, Mingze; Hoehndorf, Robert; Jaiswal, Pankaj; Kalberer, Scott R; Lloyd, John P; Meinke, David; Menda, Naama; Moore, Laura; Nelson, Rex T; Pujar, Anuradha; Lawrence, Carolyn J; Huala, Eva

    2015-01-01

    Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a small scale, comprehensive queries and analyses that span a broad set of reference species, research disciplines, and knowledge domains continue to be severely limited by the absence of a common semantic framework. We developed a workflow to curate and standardize existing phenotype datasets for six plant species, encompassing both model species and crop plants with established genetic resources. Our effort focused on mutant phenotypes associated with genes of known sequence in Arabidopsis thaliana (L.) Heynh. (Arabidopsis), Zea mays L. subsp. mays (maize), Medicago truncatula Gaertn. (barrel medic or Medicago), Oryza sativa L. (rice), Glycine max (L.) Merr. (soybean), and Solanum lycopersicum L. (tomato). We applied the same ontologies, annotation standards, formats, and best practices across all six species, thereby ensuring that the shared dataset could be used for cross-species querying and semantic similarity analyses. Curated phenotypes were first converted into a common format using taxonomically broad ontologies such as the Plant Ontology, Gene Ontology, and Phenotype and Trait Ontology. We then compared ontology-based phenotypic descriptions with an existing classification system for plant phenotypes and evaluated our semantic similarity dataset for its ability to enhance predictions of gene families, protein functions, and shared metabolic pathways that underlie informative plant phenotypes. The use of ontologies, annotation standards, shared formats, and best practices for cross-taxon phenotype data analyses represents a novel approach to plant phenomics that enhances the utility of

  16. An ontology approach to comparative phenomics in plants

    KAUST Repository

    Oellrich, Anika

    2015-02-25

    Background: Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a small scale, comprehensive queries and analyses that span a broad set of reference species, research disciplines, and knowledge domains continue to be severely limited by the absence of a common semantic framework. Results: We developed a workflow to curate and standardize existing phenotype datasets for six plant species, encompassing both model species and crop plants with established genetic resources. Our effort focused on mutant phenotypes associated with genes of known sequence in Arabidopsis thaliana (L.) Heynh. (Arabidopsis), Zea mays L. subsp. mays (maize), Medicago truncatula Gaertn. (barrel medic or Medicago), Oryza sativa L. (rice), Glycine max (L.) Merr. (soybean), and Solanum lycopersicum L. (tomato). We applied the same ontologies, annotation standards, formats, and best practices across all six species, thereby ensuring that the shared dataset could be used for cross-species querying and semantic similarity analyses. Curated phenotypes were first converted into a common format using taxonomically broad ontologies such as the Plant Ontology, Gene Ontology, and Phenotype and Trait Ontology. We then compared ontology-based phenotypic descriptions with an existing classification system for plant phenotypes and evaluated our semantic similarity dataset for its ability to enhance predictions of gene families, protein functions, and shared metabolic pathways that underlie informative plant phenotypes. Conclusions: The use of ontologies, annotation standards, shared formats, and best practices for cross-taxon phenotype data analyses represents a novel approach to plant phenomics

  17. Dataset Curation through Renders and Ontology Matching

    Science.gov (United States)

    2015-09-01

    Dataset Curation through Renders and Ontology Matching Yair Movshovitz-Attias CMU-CS-15-119 September 2015 School of Computer Science Computer...REPORT TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Dataset Curation through Renders and Ontology Matching 5a...mapped to an ontology of geographical entities, we are able to extract multiple relevant labels per image. For the viewpoint estimation problem, by

  18. Tools of knowledge representation: Thesauri versus ontologies

    Directory of Open Access Journals (Sweden)

    Antonio García Jiménez

    2004-01-01

    Full Text Available The ontologies as valid tools of knowledge representation are analysed, by means of the presentation of different aspects that conform this emergent reality. Below, one of the most relevant goals in this paper is to connect ontologies with thesaurus, in order to determine their features in common, their differences and the possibilities of conversion. Finally, from viewpoint of Library and Information Science, the future implications because of generalization of the ontologies are presented

  19. Versioning System for Distributed Ontology Development

    Science.gov (United States)

    2016-03-15

    E. Jiménez-Ruiz, B. Cuenca Grau, Y. Zhou, and I. Horrocks, “Large-Scale Interactive Ontology Matching: Algorithms and Implementation,” in Proc. of...Horrocks, and R. Berlanga, “Supporting Concurrent Ontology Development: Framework, Algorithms and Tool,” Data & Knowledge Engineering, vol. 70, Issue 1...Distributed Ontology Development S.K. Damodaran 15 March 2016 This material is based on work supported by the Assistant Secretary of Defense for

  20. Cohesion Metrics for Ontology Design and Application

    OpenAIRE

    Haining Yao; Anthony M. Orme; Letha Etzkorn

    2005-01-01

    Recently, domain specific ontology development has been driven by research on the Semantic Web. Ontologies have been suggested for use in many application areas targeted by the Semantic Web, such as dynamic web service composition and general web service matching. Fundamental characteristics of these ontologies must be determined in order to effectively make use of them: for example, Sirin, Hendler and Parsia have suggested that determining fundamental characteristics...

  1. Semoogle - An Ontology Based Search Engine

    OpenAIRE

    Aghajani, Nooshin

    2012-01-01

    In this thesis, we present a prototype for search engine to show how such a semantic search application based on ontology techniques contributes to save time for user, and improve the quality of relevant search results compared to a traditional search engine. This system is built as a query improvement module, which uses ontology and sorts the results search based on four predefined categories. The first and important part of the implementation of search engine prototype is to apply ontology ...

  2. Applications and Uses of Dental Ontologies

    OpenAIRE

    Smart, Paul R.; Sadraie, Marjan

    2012-01-01

    The development of a number of large-scale semantically-rich ontologies for biomedicine attests to the interest of life science researchers and clinicians in Semantic Web technologies. To date, however, the dental profession has lagged behind other areas of biomedicine in developing a commonly accepted, standardized ontology to support the representation of dental knowledge and information. This paper attempts to identify some of the potential uses of dental ontologies as part of an effort to...

  3. Representations of spacetime: Formalism and ontological commitment

    Science.gov (United States)

    Bain, Jonathan Stanley

    This dissertation consists of two parts. The first is on the relation between formalism and ontological commitment in the context of theories of spacetime, and the second is on scientific realism. The first part begins with a look at how the substantivalist/relationist debate over the ontological status of spacetime has been influenced by a particular mathematical formalism, that of tensor analysis on differential manifolds (TADM). This formalism has motivated the substantivalist position known as manifold substantivalism. Chapter 1 focuses on the hole argument which maintains that manifold substantivalism is incompatible with determinism. I claim that the realist motivations underlying manifold substantivalism can be upheld, and the hole argument avoided, by adopting structural realism with respect to spacetime. In this context, this is the claim that it is the structure that spacetime points enter into that warrants belief and not the points themselves. In Chapter 2, an elimination principle is defined by means of which a distinction can be made between surplus structure and essential structure with respect to formulations of a theory in two distinct mathematical formulations and some prior ontological commitments. This principle is then used to demonstrate that manifold points may be considered surplus structure in the formulation of field theories. This suggests that, if we are disposed to read field theories literally, then, at most, it should be the essential structure common to all alternative formulations of such theories that should be taken literally. I also investigate how the adoption of alternative formalisms informs other issues in the philosophy of spacetime. Chapter 3 offers a realist position which takes a semantic moral from the preceding investigation and an epistemic moral from work done on reliability. The semantic moral advises us to read only the essential structure of our theories literally. The epistemic moral shows us that such structure

  4. Towards Process-Ontology: A Critical Study of Substance-Ontological Premises

    DEFF Research Database (Denmark)

    Seibt, Johanna

    The thesis proposes therapeutic revision of fundamental assumptions in contemporary ontological thought. I show that non of the prevalent theories of objects, by virtue of certain implicit substance-ontological assumptions provides a viable account of the numerical, qualitative, and trans-tempora......-ontological presuppositions, I finally explore the result of rejecting all of them and sketch a scheme basic on dynamic masses which promises to yield coherent explanation of the ontological features of those complex processes that we commonly call objects....

  5. Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.

    Science.gov (United States)

    Xiang, Zuoshuang; Zheng, Jie; Lin, Yu; He, Yongqun

    2015-01-01

    It is time-consuming to build an ontology with many terms and axioms. Thus it is desired to automate the process of ontology development. Ontology Design Patterns (ODPs) provide a reusable solution to solve a recurrent modeling problem in the context of ontology engineering. Because ontology terms often follow specific ODPs, the Ontology for Biomedical Investigations (OBI) developers proposed a Quick Term Templates (QTTs) process targeted at generating new ontology classes following the same pattern, using term templates in a spreadsheet format. Inspired by the ODPs and QTTs, the Ontorat web application is developed to automatically generate new ontology terms, annotations of terms, and logical axioms based on a specific ODP(s). The inputs of an Ontorat execution include axiom expression settings, an input data file, ID generation settings, and a target ontology (optional). The axiom expression settings can be saved as a predesigned Ontorat setting format text file for reuse. The input data file is generated based on a template file created by a specific ODP (text or Excel format). Ontorat is an efficient tool for ontology expansion. Different use cases are described. For example, Ontorat was applied to automatically generate over 1,000 Japan RIKEN cell line cell terms with both logical axioms and rich annotation axioms in the Cell Line Ontology (CLO). Approximately 800 licensed animal vaccines were represented and annotated in the Vaccine Ontology (VO) by Ontorat. The OBI team used Ontorat to add assay and device terms required by ENCODE project. Ontorat was also used to add missing annotations to all existing Biobank specific terms in the Biobank Ontology. A collection of ODPs and templates with examples are provided on the Ontorat website and can be reused to facilitate ontology development. With ever increasing ontology development and applications, Ontorat provides a timely platform for generating and annotating a large number of ontology terms by following

  6. An Upper-Ontology-Based Approach for Automatic Construction of IOT Ontology

    OpenAIRE

    Yuan Xu; Chunhong Zhang; Yang Ji

    2014-01-01

    Ontology gives us a reliable group of concepts and the relations between concepts in an IOT system. It does not only save words of format but also accurately transfers semantic data between human users and the computers. Hence, the usefulness of resources in IOT system depends on whether the domain ontology can be constructed effectively and correctly. In this paper we propose an automated method to construct the IOT ontology. First, we explain the necessity of introducing ontology automatic ...

  7. Vaccine and Drug Ontology Studies (VDOS 2014).

    Science.gov (United States)

    Tao, Cui; He, Yongqun; Arabandi, Sivaram

    2016-01-01

    The "Vaccine and Drug Ontology Studies" (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have been critical to prevent and treat human and animal diseases. Work in both (drugs and vaccines) areas is closely related - from preclinical research and development to manufacturing, clinical trials, government approval and regulation, and post-licensure usage surveillance and monitoring. Over the last decade, tremendous efforts have been made in the biomedical ontology community to ontologically represent various areas associated with vaccines and drugs - extending existing clinical terminology systems such as SNOMED, RxNorm, NDF-RT, and MedDRA, developing new models such as the Vaccine Ontology (VO) and Ontology of Adverse Events (OAE), vernacular medical terminologies such as the Consumer Health Vocabulary (CHV). The VDOS workshop series provides a platform for discussing innovative solutions as well as the challenges in the development and applications of biomedical ontologies for representing and analyzing drugs and vaccines, their administration, host immune responses, adverse events, and other related topics. The five full-length papers included in this 2014 thematic issue focus on two main themes: (i) General vaccine/drug-related ontology development and exploration, and (ii) Interaction and network-related ontology studies.

  8. Electricity Markets Ontology to Support MASCEM's Simulations

    DEFF Research Database (Denmark)

    Santos, Gabriel; Pinto, Tiago; Vale, Zita

    2016-01-01

    the several issues related to these systems, including the involved players that act in this domain. To take better advantage of these systems, their integration is mandatory. The main contribution of this paper is the development of the Electricity Markets Ontology, which integrates the essential concepts...... necessary to interpret all the available information related to electricity markets, while enabling an easier cooperation and adequate communication between related systems. Additionally, the concepts and rules defined by this ontology can be extended and complemented according to the needs of other...... simulation and real systems in this area. Each system's particular ontology must import the proposed ontology, thus enabling the effective interoperability between independent systems....

  9. The NASA Air Traffic Management Ontology (atmonto)

    Data.gov (United States)

    National Aeronautics and Space Administration — The NASA ATM (Air Traffic Management) Ontology describes classes, properties, and relationships relevant to the domain of air traffic management, and represents...

  10. Ontology Enabled Generation of Embedded Web Services

    DEFF Research Database (Denmark)

    Hansen, Klaus Marius; Zhang, Weishan; Soares, Goncalo Teofilo Afonso Pinheiro

    2008-01-01

    and software platforms, and of devices state and context changes. To address these challenges, we developed a Web service compiler, Limbo, in which Web Ontology Language (OWL) ontologies are used to make the Limbo compiler aware of its compilation context, such as targeted hardware and software. At the same...... time, knowledge on device details, platform dependencies, and resource/power consumption is built into the supporting ontologies, which are used to configure Limbo for generating resource efficient web service code. A state machine ontology is used to generate stub code to facilitate handling of state...

  11. The current landscape of pitfalls in Ontologies

    CSIR Research Space (South Africa)

    Keet, CM

    2013-09-01

    Full Text Available 2Ontology Engineering Group, Departamento de Inteligencia Artificial, Universidad Polite´cnica de Madrid, Madrid, Spain keet@ukzn.ac.za, {mcsuarez,mpoveda}@fi.upm.es Keywords: Ontology Development : Ontology Quality : Pitfall Abstract: A growing... in Ontologies C. Maria Keet1, Mari Carmen Sua´rez-Figueroa2 and Marı´a Poveda-Villalo´n2 1School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, and UKZN/CSIR-Meraka Centre for Artificial Intelligence Research, Durban, South Africa...

  12. Components for Ontology Driven Information Push

    National Research Council Canada - National Science Library

    Hart, Lewis L

    2005-01-01

    .... Four primary applications were developed AND supported by these technologies. Duet was developed to support visualization, application and management of ontologies using the UML/MOF engineering standard...

  13. Logical development of the cell ontology.

    Science.gov (United States)

    Meehan, Terrence F; Masci, Anna Maria; Abdulla, Amina; Cowell, Lindsay G; Blake, Judith A; Mungall, Christopher J; Diehl, Alexander D

    2011-01-05

    The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and assist with classification. Here we report on the generation of computable definitions for the hematopoietic cell types in the CL. Computable definitions for over 340 CL classes have been created using a genus-differentia approach. These define cell types according to multiple axes of classification such as the protein complexes found on the surface of a cell type, the biological processes participated in by a cell type, or the phenotypic characteristics associated with a cell type. We employed automated reasoners to verify the ontology and to reveal mistakes in manual curation. The implementation of this process exposed areas in the ontology where new cell type classes were needed to accommodate species-specific expression of cellular markers. Our use of reasoners also inferred new relationships within the CL, and between the CL and the contributing ontologies. This restructured ontology can be used to identify immune cells by flow cytometry, supports sophisticated biological queries involving cells, and helps generate new hypotheses about cell function based on similarities to other cell types. Use of computable definitions enhances the development of the CL and supports the interoperability of OBO ontologies.

  14. Logical Development of the Cell Ontology

    Directory of Open Access Journals (Sweden)

    Blake Judith A

    2011-01-01

    Full Text Available Abstract Background The Cell Ontology (CL is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and assist with classification. Here we report on the generation of computable definitions for the hematopoietic cell types in the CL. Results Computable definitions for over 340 CL classes have been created using a genus-differentia approach. These define cell types according to multiple axes of classification such as the protein complexes found on the surface of a cell type, the biological processes participated in by a cell type, or the phenotypic characteristics associated with a cell type. We employed automated reasoners to verify the ontology and to reveal mistakes in manual curation. The implementation of this process exposed areas in the ontology where new cell type classes were needed to accommodate species-specific expression of cellular markers. Our use of reasoners also inferred new relationships within the CL, and between the CL and the contributing ontologies. This restructured ontology can be used to identify immune cells by flow cytometry, supports sophisticated biological queries involving cells, and helps generate new hypotheses about cell function based on similarities to other cell types. Conclusion Use of computable definitions enhances the development of the CL and supports the interoperability of OBO ontologies.

  15. Surreptitious, Evolving and Participative Ontology Development: An End-User Oriented Ontology Development Methodology

    Science.gov (United States)

    Bachore, Zelalem

    2012-01-01

    Ontology not only is considered to be the backbone of the semantic web but also plays a significant role in distributed and heterogeneous information systems. However, ontology still faces limited application and adoption to date. One of the major problems is that prevailing engineering-oriented methodologies for building ontologies do not…

  16. How Ontologies are Made: Studying the Hidden Social Dynamics Behind Collaborative Ontology Engineering Projects

    Science.gov (United States)

    Strohmaier, Markus; Walk, Simon; Pöschko, Jan; Lamprecht, Daniel; Tudorache, Tania; Nyulas, Csongor; Musen, Mark A.; Noy, Natalya F.

    2013-01-01

    Traditionally, evaluation methods in the field of semantic technologies have focused on the end result of ontology engineering efforts, mainly, on evaluating ontologies and their corresponding qualities and characteristics. This focus has led to the development of a whole arsenal of ontology-evaluation techniques that investigate the quality of ontologies as a product. In this paper, we aim to shed light on the process of ontology engineering construction by introducing and applying a set of measures to analyze hidden social dynamics. We argue that especially for ontologies which are constructed collaboratively, understanding the social processes that have led to its construction is critical not only in understanding but consequently also in evaluating the ontology. With the work presented in this paper, we aim to expose the texture of collaborative ontology engineering processes that is otherwise left invisible. Using historical change-log data, we unveil qualitative differences and commonalities between different collaborative ontology engineering projects. Explaining and understanding these differences will help us to better comprehend the role and importance of social factors in collaborative ontology engineering projects. We hope that our analysis will spur a new line of evaluation techniques that view ontologies not as the static result of deliberations among domain experts, but as a dynamic, collaborative and iterative process that needs to be understood, evaluated and managed in itself. We believe that advances in this direction would help our community to expand the existing arsenal of ontology evaluation techniques towards more holistic approaches. PMID:24311994

  17. Where to Publish and Find Ontologies? A Survey of Ontology Libraries

    Science.gov (United States)

    d'Aquin, Mathieu; Noy, Natalya F.

    2011-01-01

    One of the key promises of the Semantic Web is its potential to enable and facilitate data interoperability. The ability of data providers and application developers to share and reuse ontologies is a critical component of this data interoperability: if different applications and data sources use the same set of well defined terms for describing their domain and data, it will be much easier for them to “talk” to one another. Ontology libraries are the systems that collect ontologies from different sources and facilitate the tasks of finding, exploring, and using these ontologies. Thus ontology libraries can serve as a link in enabling diverse users and applications to discover, evaluate, use, and publish ontologies. In this paper, we provide a survey of the growing—and surprisingly diverse—landscape of ontology libraries. We highlight how the varying scope and intended use of the libraries a ects their features, content, and potential exploitation in applications. From reviewing eleven ontology libraries, we identify a core set of questions that ontology practitioners and users should consider in choosing an ontology library for finding ontologies or publishing their own. We also discuss the research challenges that emerge from this survey, for the developers of ontology libraries to address. PMID:22408576

  18. Towards Ontology-Driven Information Systems: Guidelines to the Creation of New Methodologies to Build Ontologies

    Science.gov (United States)

    Soares, Andrey

    2009-01-01

    This research targeted the area of Ontology-Driven Information Systems, where ontology plays a central role both at development time and at run time of Information Systems (IS). In particular, the research focused on the process of building domain ontologies for IS modeling. The motivation behind the research was the fact that researchers have…

  19. How Ontologies are Made: Studying the Hidden Social Dynamics Behind Collaborative Ontology Engineering Projects.

    Science.gov (United States)

    Strohmaier, Markus; Walk, Simon; Pöschko, Jan; Lamprecht, Daniel; Tudorache, Tania; Nyulas, Csongor; Musen, Mark A; Noy, Natalya F

    2013-05-01

    Traditionally, evaluation methods in the field of semantic technologies have focused on the end result of ontology engineering efforts, mainly, on evaluating ontologies and their corresponding qualities and characteristics. This focus has led to the development of a whole arsenal of ontology-evaluation techniques that investigate the quality of ontologies as a product . In this paper, we aim to shed light on the process of ontology engineering construction by introducing and applying a set of measures to analyze hidden social dynamics. We argue that especially for ontologies which are constructed collaboratively, understanding the social processes that have led to its construction is critical not only in understanding but consequently also in evaluating the ontology. With the work presented in this paper, we aim to expose the texture of collaborative ontology engineering processes that is otherwise left invisible. Using historical change-log data, we unveil qualitative differences and commonalities between different collaborative ontology engineering projects. Explaining and understanding these differences will help us to better comprehend the role and importance of social factors in collaborative ontology engineering projects. We hope that our analysis will spur a new line of evaluation techniques that view ontologies not as the static result of deliberations among domain experts, but as a dynamic, collaborative and iterative process that needs to be understood, evaluated and managed in itself. We believe that advances in this direction would help our community to expand the existing arsenal of ontology evaluation techniques towards more holistic approaches.

  20. Describing localized diseases in medical ontology: an FMA-based algorithm.

    Science.gov (United States)

    Charlet, Jean; Mazuel, Laurent; Declerck, Gunnar; Miroux, Patrick; Gayet, Pierre

    2014-01-01

    OntolUrgences is a termino-ontological resource developed to index and retrieve information in electronic Emergency Medical Record. In this project, we improved the ontology coverage to accommodate both anatomical and pathophysiological concepts in emergency medicine. This work lead to the automatic addition of 3,470 concepts and their underlying semantic formalization. In our method, we reuse and select the anatomical concepts relevant to emergency from FMA: To capture the anatomical specific concepts, (i) we involved Emergency practitioners and identified the key concepts from this domain; (ii) we applied an automatic algorithm to define the semantic relationships and integrated the result in the existing ontology.

  1. NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

    Science.gov (United States)

    Martínez-Romero, Marcos; Jonquet, Clement; O'Connor, Martin J; Graybeal, John; Pazos, Alejandro; Musen, Mark A

    2017-06-07

    Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios. Ontology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability

  2. Concepts, ontologies, and knowledge representation

    CERN Document Server

    Jakus, Grega; Omerovic, Sanida; Tomažic, Sašo

    2013-01-01

    Recording knowledge in a common framework that would make it possible to seamlessly share global knowledge remains an important challenge for researchers. This brief examines several ideas about the representation of knowledge addressing this challenge. A widespread general agreement is followed that states uniform knowledge representation should be achievable by using ontologies populated with concepts. A separate chapter is dedicated to each of the three introduced topics, following a uniform outline: definition, organization, and use. This brief is intended for those who want to get to know

  3. Nosology, ontology and promiscuous realism.

    Science.gov (United States)

    Binney, Nicholas

    2015-06-01

    Medics may consider worrying about their metaphysics and ontology to be a waste of time. I will argue here that this is not the case. Promiscuous realism is a metaphysical position which holds that multiple, equally valid, classification schemes should be applied to objects (such as patients) to capture different aspects of their complex and heterogeneous nature. As medics at the bedside may need to capture different aspects of their patients' problems, they may need to use multiple classification schemes (multiple nosologies), and thus consider adopting a different metaphysics to the one commonly in use. © 2014 John Wiley & Sons, Ltd.

  4. Semantic similarity between ontologies at different scales

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qingpeng; Haglin, David J.

    2016-04-01

    In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.

  5. Ontology modeling for generation of clinical pathways

    Directory of Open Access Journals (Sweden)

    Jasmine Tehrani

    2012-12-01

    Full Text Available Purpose: Increasing costs of health care, fuelled by demand for high quality, cost-effective healthcare has drove hospitals to streamline their patient care delivery systems. One such systematic approach is the adaptation of Clinical Pathways (CP as a tool to increase the quality of healthcare delivery. However, most organizations still rely on are paper-based pathway guidelines or specifications, which have limitations in process management and as a result can influence patient safety outcomes. In this paper, we present a method for generating clinical pathways based on organizational semiotics by capturing knowledge from syntactic, semantic and pragmatic to social level. Design/methodology/approach: The proposed modeling approach to generation of CPs adopts organizational semiotics and enables the generation of semantically rich representation of CP knowledge. Semantic Analysis Method (SAM is applied to explicitly represent the semantics of the concepts, their relationships and patterns of behavior in terms of an ontology chart. Norm Analysis Method (NAM is adopted to identify and formally specify patterns of behavior and rules that govern the actions identified on the ontology chart. Information collected during semantic and norm analysis is integrated to guide the generation of CPs using best practice represented in BPMN thus enabling the automation of CP. Findings: This research confirms the necessity of taking into consideration social aspects in designing information systems and automating CP. The complexity of healthcare processes can be best tackled by analyzing stakeholders, which we treat as social agents, their goals and patterns of action within the agent network. Originality/value: The current modeling methods describe CPs from a structural aspect comprising activities, properties and interrelationships. However, these methods lack a mechanism to describe possible patterns of human behavior and the conditions under which the

  6. Mobile computing with special reference to readability task under the impact of vibration, colour combination and gender.

    Science.gov (United States)

    Mallick, Zulquernain; Siddiquee, Arshad Noor; Haleem, Abid

    2008-12-01

    The last 20 years have seen a tremendous growth in the field of computing with special reference to mobile computing. Ergonomic issues pertaining to this theme remains unexplored. With special reference to readability in mobile computing, an experimental research was conducted to study the gender effect on human performance under the impact of vibration in a human computer interaction environment. Fourteen subjects (7 males and 7 females) participated in the study. Three independent variables, namely gender, level of vibration and screen text/background colour, were selected for the experimental investigation while the dependent variable was the number of characters read per minute. The data collected were analyzed statistically through an experimental design for repeated measures. Results indicated that gender as an organismic variable, the level of vibration and screen text/background colour revealed statistically significant differences. However, the second order interaction was found to be statistically non-significant. These findings are discussed in light of the previous studies undertaken on the topic.

  7. Merged ontology for engineering design: Contrasting empirical and theoretical approaches to develop engineering ontologies

    DEFF Research Database (Denmark)

    Ahmed, Saeema; Storga, M

    2009-01-01

    This paper presents a comparison of two previous and separate efforts to develop an ontology in the engineering design domain, together with an ontology proposal from which ontologies for a specific application may be derived. The research contrasts an empirical, user-centered approach to develop...... that is theoretically sound and another that is applicable, is recognized and argued. Finally, the merged ontology for engineering design is proposed as a template ontology that can be tailored by researchers and practitioners for a specific context....

  8. A commitment-based reference ontology for services

    NARCIS (Netherlands)

    Nardi, Julio Cesar; de Almeida Falbo, Ricardo; Andrade Almeida, João; Guizzardi, G.; Ferreira Pires, Luis; van Sinderen, Marten J.; Guarino, Nicola; Fonseca, Claudenir Morais

    2015-01-01

    The concept of “service‿ has been characterized by different disciplines and by different authors from various points of view. This variety of characterizations has emerged because although this notion seems intuitive, it is far from trivial, with many interrelated perspectives. Given their

  9. Representing virus-host interactions and other multi-organism processes in the Gene Ontology.

    Science.gov (United States)

    Foulger, R E; Osumi-Sutherland, D; McIntosh, B K; Hulo, C; Masson, P; Poux, S; Le Mercier, P; Lomax, J

    2015-07-28

    The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms. To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms. Building on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.

  10. Escaping the behavioural 'spin' of evidence-based psychiatry: Merleau-Ponty's ontology of truth.

    Science.gov (United States)

    Morstyn, Ron

    2013-08-01

    To explore the limitations of the concept of 'truth' in the ontology of evidence-based psychiatry and to provide expanded ontological foundations for psychiatric practice based instead on the ontology of the French existential-phenomenologist, Maurice Merleau-Ponty. Evidence-based medicine is founded on a 'scientific' ontology of 'causality', which equates 'truth' with effecting statistically-significant changes in objective measures of disease by a specified treatment. Because of the absence of biological markers of disease in psychiatry, evidence-based psychiatry equates 'truth' with effecting changes in observable psychometric measures of behaviour. This is the same ontology underlying marketing 'spin' and all attempts to effect pre-determined behavioural change. In contrast, Merleau-Ponty's ontology rejects causality and mind/body duality, and views 'truth' as the expression of our deepest embodied feeling and perception of the world, which establishes all our thinking, and on which all our thinking relies, including 'scientific' thinking. Merleau-Ponty's ontology is therefore a preferable foundation for psychiatric practice, because it allows psychiatrists to consider the 'truth' of clinically important, but non-measurable, aspects of psychiatry while not excluding 'scientific' thinking, but recognising its limitations and potential for misuse.

  11. Australia’s National Health Programs: An Ontological Mapping

    Directory of Open Access Journals (Sweden)

    Arkalgud Ramaprasad

    2016-11-01

    Full Text Available Australia has a large number of health program initiatives whose comprehensive assessment will help refine and redefine priorities by highlighting areas of emphasis, under-emphasis, and non-emphasis. The objectives of our research are to: (a systematically map all the programs onto an ontological framework, and (b systemically analyse their relative emphases at different levels of granularity. We mapped all the health program initiatives onto an ontology with five dimensions, namely: (a Policy-scope, (b Policy-focus, (c Outcomes, (d Type of care, and (e Population served. Each dimension is expanded into a taxonomy of its constituent elements. Each combination of elements from the five dimensions is a possible policy initiative component. There are 30,030 possible components encapsulated in the ontology. It includes, for example: (a National financial policies on accessibility of preventive care for family, and (b Local-urban regulatory policies on cost of palliative care for individual-aged. Four of the authors mapped all of Australia’s health programs and initiatives on to the ontology. Visualizations of the data are used to highlight the relative emphases in the program initiatives. The dominant emphasis of the program initiatives is: [National] [educational, personnel-physician, information] policies on [accessibility, quality] of [preventive, wellness] care for the [community]. However, although (a information is emphasized technology is not; and (b accessibility and quality are emphasized cost, satisfaction, and quality are not. The ontology and the results of the mapping can help systematically reassess and redirect the relative emphases of the programs and initiatives from a systemic perspective.

  12. The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.

    Science.gov (United States)

    He, Yongqun; Xiang, Zuoshuang; Zheng, Jie; Lin, Yu; Overton, James A; Ong, Edison

    2018-01-12

    Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).

  13. Ontologies and Information Systems: A Literature Survey

    Science.gov (United States)

    2011-06-01

    Falcon-AO (LMO + GMO ) [146], and RiMOM [317]. Meta-matching systems include APFEL [76] and eTuner [286]. There also exist frameworks that provide a set...Jian, N., Qu, Y. and Wang, Q. 2005. GMO : A graph matching for ontologies. In Proceedings of the K-CAPWorkshop on Integrating Ontologies, Banff

  14. Critical Ontology for an Enactive Music Pedagogy

    Science.gov (United States)

    van der Schyff, Dylan; Schiavio, Andrea; Elliott, David J.

    2016-01-01

    An enactive approach to music education is explored through the lens of critical ontology. Assumptions central to Western academic music culture are critically discussed; and the concept of "ontological education" is introduced as an alternative framework. We argue that this orientation embraces more primordial ways of knowing and being,…

  15. Recent changes in the Building Topology Ontology

    DEFF Research Database (Denmark)

    Rasmussen, Mads Holten; Pauwels, Pieter; Lefrancois, Maxime

    The Building Topology Ontology (BOT) was in early 2017 suggested to the W3C community group for Linked Building Data as a simple ontology covering the core concepts of a building. Since it was first announced it has been extended to cover a building site, elements hosted by other elements, zones...

  16. Ontological Engineering for the Cadastral Domain

    DEFF Research Database (Denmark)

    Stubkjær, Erik; Stuckenschmidt, Heiner

    2000-01-01

    that characterizes established academic disciplines, like geodesy. Many university courses address more application oriented fields, like cadastral law, and spatial planning, and they may benefit from the ontological engineering approach. The paper provides an introduction to the field of ontological engineering...... by means of examples from the cadastral domain....

  17. Development of ontological knowledge representation: learning ...

    African Journals Online (AJOL)

    This paper presents the development of an ontological knowledge organization and representation, and explains how application of appropriate methods for its visualization can lead to meaningful learning. We have applied systemic diagrams (SD) as a method of visualizing ontological knowledge organization.

  18. Social Groups, Explanation and Ontological Holism | Sheehy ...

    African Journals Online (AJOL)

    Ontological holism is the thesis that social groups are best understood as composite material particulars. At a high level of taxonomic classification groups such as mobs, tribes and nations are the same kind of thing as organisms and artefacts. This holism is opposed by ontological individualism, which maintains that in our ...

  19. Integrity and change in modular ontologies

    NARCIS (Netherlands)

    Stuckenschmidt, Heiner; Klein, Michel

    2003-01-01

    The benefits of modular representations arc well known from many areas of computer science. In this paper, we concentrate on the benefits of modular ontologies with respect to local containment of terminological reasoning. We define an architecture for modular ontologies that supports local

  20. An Ontology Design Pattern for Digital Video

    OpenAIRE

    Mitzias, Panagiotis; Riga, Marina; Waddington, Simon; Kontopoulos, Efstratios; Meditskos, Georgios; Laurenson, Pip; Kompatsiaris, Ioannis

    2015-01-01

    The paper proposes an Ontology Design Pattern (ODP) for modelling digital video resources, which was developed in the context of the PERICLES domain ontologies for Art & Media. The ODP can be found at this address: http://ontologydesignpatterns.org/wiki/Submissions:DigitalVideo

  1. Developing Ontological Background Knowledge for Biomedicine

    OpenAIRE

    Beißwanger, Anna Elena

    2013-01-01

    Biomedicine is an impressively fast developing, interdisciplinary field of research. To control the growing volumes of biomedical data, ontologies are increasingly used as common organization structures. Biomedical ontologies describe domain knowledge in a formal, computationally accessible way. They serve as controlled vocabularies and background knowledge in applications dealing with the integration, analysis and retrieval of heterogeneous types of data. The development of...

  2. Automating Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.

    2006-01-22

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  3. Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.

    2006-06-06

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  4. Selection of reliable reference genes for gene expression analysis under abiotic stresses in the desert biomass willow, Salix psammophila

    Directory of Open Access Journals (Sweden)

    Jianbo Li

    2016-10-01

    Full Text Available Salix psammophila is a desert shrub willow that has extraordinary adaptation to abiotic stresses and plays an important role in maintaining local ecosystems. Moreover, S. psammophila is regarded as a promising biomass feedstock because of its high biomass yields and short rotation coppice cycle. However, few suitable reference genes (RGs for quantitative real-time polymerase chain reaction (qRT-PCR constrain the study on normalization of gene expression in S. psammophila until now. Here, we investigated the expression stabilities of 14 candidate RGs across tissue types and under four abiotic stress treatments, including heat, cold, salt and drought treatments. After calculation of PCR efficiencies, three different software, NormFinder, geNorm, and BestKeeper were employed to analyze systematically the qRT-PCR data, and the outputs were merged by RankAggreg software. The optimal reference genes selected for gene expression analysis were EF1□□ (Elongation factor-1 alpha and OTU (OTU-like cysteine protease family protein for different tissue types, UBC (Ubiquitin-conjugating enzyme E2 and LTA4H (Leukotriene A-4 hydrolase homologue for heat treatment, HIS (Histone superfamily protein H3 and ARF2 (ADP-ribosylation factor 2 for cold treatment, OTU and ACT7 (Actin 7 for salt treatment, UBC and LTA4H for drought treatment. The expression of UBC, ARF2 and VHAC (V-type proton ATPase subunit C varied the least across tissue types and under abiotic stresses. Furthermore, the relative genes expression profiles of one tissue-specific gene WOX1a (WUSCHEL-related homeobox 1a, and four stress-inducible genes, including Hsf-A2 (Heat shock transcription factors A2, CBF3 (C-repeat binding factor 3, HKT1 (High-Affinity K+ Transporter 1 and GST (Glutathione S-transferase, were conducted to confirm the validity of the reference genes in this study. These results provided an important RGs application guideline for gene expression characterization in S. psammophila.

  5. ONTOGRABBING: Extracting Information from Texts Using Generative Ontologies

    DEFF Research Database (Denmark)

    Nilsson, Jørgen Fischer; Szymczak, Bartlomiej Antoni; Jensen, P.A.

    2009-01-01

    We describe principles for extracting information from texts using a so-called generative ontology in combination with syntactic analysis. Generative ontologies are introduced as semantic domains for natural language phrases. Generative ontologies extend ordinary finite ontologies with rules...... for producing recursively shaped terms representing the ontological content (ontological semantics) of NL noun phrases and other phrases. We focus here on achieving a robust, often only partial, ontology-driven parsing of and ascription of semantics to a sentence in the text corpus. The aim of the ontological...

  6. The Role of Ontologies in Schema-based Program Synthesis

    Science.gov (United States)

    Bures, Tomas; Denney, Ewen; Fischer, Bernd; Nistor, Eugen C.

    2004-01-01

    Program synthesis is the process of automatically deriving executable code from (non-executable) high-level specifications. It is more flexible and powerful than conventional code generation techniques that simply translate algorithmic specifications into lower-level code or only create code skeletons from structural specifications (such as UML class diagrams). Key to building a successful synthesis system is specializing to an appropriate application domain. The AUTOBAYES and AUTOFILTER systems, under development at NASA Ames, operate in the two domains of data analysis and state estimation, respectively. The central concept of both systems is the schema, a representation of reusable computational knowledge. This can take various forms, including high-level algorithm templates, code optimizations, datatype refinements, or architectural information. A schema also contains applicability conditions that are used to determine when it can be applied safely. These conditions can refer to the initial specification, to intermediate results, or to elements of the partially-instantiated code. Schema-based synthesis uses AI technology to recursively apply schemas to gradually refine a specification into executable code. This process proceeds in two main phases. A front-end gradually transforms the problem specification into a program represented in an abstract intermediate code. A backend then compiles this further down into a concrete target programming language of choice. A core engine applies schemas on the initial problem specification, then uses the output of those schemas as the input for other schemas, until the full implementation is generated. Since there might be different schemas that implement different solutions to the same problem this process can generate an entire solution tree. AUTOBAYES and AUTOFILTER have reached the level of maturity where they enable users to solve interesting application problems, e.g., the analysis of Hubble Space Telescope images

  7. PERKEMBANGAN ONTOLOGI DALAM FILSAFAT ISLAM

    Directory of Open Access Journals (Sweden)

    Fathul Mufid

    2013-09-01

    Full Text Available THE ONTOLOGY DEVELOPMENTS IN ISLAMIC PHILOSOPHY. The primary basis in the study of ontology is what it is, where it exists and, what the truth is. The fundamental and profound of these issues, so that people are faced with different answers. The first question, “what is there”, gives different answers according to their beliefs. Monism, which is only one and that one was spirit and ideas, then gave the flow of spiritualism and idealism. But if that one is full of material, then gave materialism. Dualism, that is round two, for example, body and soul, it gives the existentialism flow. Pluralism, that is composed of  many elements, there is something that cannot be known, then gave the flow of agnosticism. The second problem, “where it exists”, the answer is that dwells in the world of  ideas, abstract, fixed and immutable. That is living in the world of  ideas that are concrete and individual, so that the truth is limited and changeable. The third issue, “what the truth is”, if  the truth is eternal and immortal, then it is God. However, if the truth is capricious, then the problem is how to change it and what determines the change. Keywords: Ontology, Philosophy, Existence, Essence, Metaphysics. Dasar  utama  dalam  kajian  ontologi  adalah  apa  yang  ada,  di mana yang ada dan, apa itu kebenaran. Sedemikian mendasar dan mendalamnya persoalan-persoalan ini, sehingga manusia dihadapkan pada  jawaban-jawaban  yang  berbeda.  Persoalan  pertama,  “apa yang ada”, memberikan jawaban yang berbeda-beda sesuai dengan keyakinan mereka. Monisme, yang ada hanya satu dan yang satu itu serba spirit dan ide, maka melahirkan aliran spiritualisme dan idealisme. Tetapi jika yang satu itu serba materi, maka melahirkan materialisme.  Dualisme,  yang  ada  serba  dua,  misalnya  jiwa  dan raga, maka lahirlah aliran eksistensialisme. Pluralisme, yang ada terdiri atas banyak unsur, yang ada adalah sesuatu yang tidak dapat

  8. Evaluation and validation of housekeeping genes as reference for gene expression studies in pigeonpea (Cajanus cajan) under drought stress conditions.

    Science.gov (United States)

    Sinha, Pallavi; Singh, Vikas K; Suryanarayana, V; Krishnamurthy, L; Saxena, Rachit K; Varshney, Rajeev K

    2015-01-01

    Gene expression analysis using quantitative real-time PCR (qRT-PCR) is a very sensitive technique and its sensitivity depends on the stable performance of reference gene(s) used in the study. A number of housekeeping genes have been used in various expression studies in many crops however, their expression were found to be inconsistent under different stress conditions. As a result, species specific housekeeping genes have been recommended for different expression studies in several crop species. However, such specific housekeeping genes have not been reported in the case of pigeonpea (Cajanus cajan) despite the fact that genome sequence has become available for the crop. To identify the stable housekeeping genes in pigeonpea for expression analysis under drought stress conditions, the relative expression variations of 10 commonly used housekeeping genes (EF1α, UBQ10, GAPDH, 18SrRNA, 25SrRNA, TUB6, ACT1, IF4α, UBC and HSP90) were studied on root, stem and leaves tissues of Asha (ICPL 87119). Three statistical algorithms geNorm, NormFinder and BestKeeper were used to define the stability of candidate genes. geNorm analysis identified IF4α and TUB6 as the most stable housekeeping genes however, NormFinder analysis determined IF4α and HSP90 as the most stable housekeeping genes under drought stress conditions. Subsequently validation of the identified candidate genes was undertaken in qRT-PCR based gene expression analysis of uspA gene which plays an important role for drought stress conditions in pigeonpea. The relative quantification of the uspA gene varied according to the internal controls (stable and least stable genes), thus highlighting the importance of the choice of as well as validation of internal controls in such experiments. The identified stable and validated housekeeping genes will facilitate gene expression studies in pigeonpea especially under drought stress conditions.

  9. XML, Ontologies, and Their Clinical Applications.

    Science.gov (United States)

    Yu, Chunjiang; Shen, Bairong

    2016-01-01

    The development of information technology has resulted in its penetration into every area of clinical research. Various clinical systems have been developed, which produce increasing volumes of clinical data. However, saving, exchanging, querying, and exploiting these data are challenging issues. The development of Extensible Markup Language (XML) has allowed the generation of flexible information formats to facilitate the electronic sharing of structured data via networks, and it has been used widely for clinical data processing. In particular, XML is very useful in the fields of data standardization, data exchange, and data integration. Moreover, ontologies have been attracting increased attention in various clinical fields in recent years. An ontology is the basic level of a knowledge representation scheme, and various ontology repositories have been developed, such as Gene Ontology and BioPortal. The creation of these standardized repositories greatly facilitates clinical research in related fields. In this chapter, we discuss the basic concepts of XML and ontologies, as well as their clinical applications.

  10. Ontology modeling in physical asset integrity management

    CERN Document Server

    Yacout, Soumaya

    2015-01-01

    This book presents cutting-edge applications of, and up-to-date research on, ontology engineering techniques in the physical asset integrity domain. Though a survey of state-of-the-art theory and methods on ontology engineering, the authors emphasize essential topics including data integration modeling, knowledge representation, and semantic interpretation. The book also reflects novel topics dealing with the advanced problems of physical asset integrity applications such as heterogeneity, data inconsistency, and interoperability existing in design and utilization. With a distinctive focus on applications relevant in heavy industry, Ontology Modeling in Physical Asset Integrity Management is ideal for practicing industrial and mechanical engineers working in the field, as well as researchers and graduate concerned with ontology engineering in physical systems life cycles. This book also: Introduces practicing engineers, research scientists, and graduate students to ontology engineering as a modeling techniqu...

  11. Film and Skepticism: Stanley Cavell on the Ontology of Film

    OpenAIRE

    Trifonova, Temenuga

    2017-01-01

    The present essay analyzes the reflections on the ontology of cinema in the works of Stanley Cavell. In particular, it highlights the way in which Cavell foresees in the philosophy of ordinary language as in Hollywood comedy, as many forms of that effort of redemption from the human condition which he calls skepticism, understood not so much as a philosophical position but rather as an underlying condition, as a reaction to the knowledge conceived as human knowledge, that is, experienced as p...

  12. Quality control of radiotherapy centres in the Slovak Republic: a dosimetry intercomparison of photon and electron beams under reference conditions

    International Nuclear Information System (INIS)

    Gomola, I.; Kralik, G.; Laginova, V.; Van Dam, J.

    2001-01-01

    The aim of this paper is a dosimetry intercomparison of photon and electron beams under reference conditions as well as quality control of radiotherapy centres in the Slovak Republic. The results obtained in the first check shows that only about 60% of beams are within the acceptance limit. The reasons of discrepancies were traced, in some cases by an on site visit of experts from the NRC, and unacceptable deviations were corrected. The results clearly demonstrate the usefulness of the external dosimetry checks performed with the mailed thermoluminescent dosimeters. Standard deviation of the distribution of the results decreased from SD=4.3% to SD=I.8% for checked photon beams and from SD=8.6% to SD=2.4% for electron beams, respectively, at the end of the project. The dosimetry audits which are performed in regular intervals significantly decreasing a possibility of mistreatment (under-dosage or over-dosage ) of patients due to wrong calibration of radiation therapy beams. In order to keep the reached level of dosimetry precision, it is necessary to establish the external audit in radiotherapy at the national level based on postal TLD dosimetry by transferring the know-how from the international program on quality assurance in radiotherapy dosimetry with the assistance of the IAEA. (authors)

  13. Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri.

    Directory of Open Access Journals (Sweden)

    Lucia Manni

    Full Text Available Ontologies provide an important resource to integrate information. For developmental biology and comparative anatomy studies, ontologies of a species are used to formalize and annotate data that are related to anatomical structures, their lineage and timing of development. Here, we have constructed the first ontology for anatomy and asexual development (blastogenesis of a bilaterian, the colonial tunicate Botryllus schlosseri. Tunicates, like Botryllus schlosseri, are non-vertebrates and the only chordate taxon species that reproduce both sexually and asexually. Their tadpole larval stage possesses structures characteristic of all chordates, i.e. a notochord, a dorsal neural tube, and gill slits. Larvae settle and metamorphose into individuals that are either solitary or colonial. The latter reproduce both sexually and asexually and these two reproductive modes lead to essentially the same adult body plan. The Botryllus schlosseri Ontology of Development and Anatomy (BODA will facilitate the comparison between both types of development. BODA uses the rules defined by the Open Biomedical Ontologies Foundry. It is based on studies that investigate the anatomy, blastogenesis and regeneration of this organism. BODA features allow the users to easily search and identify anatomical structures in the colony, to define the developmental stage, and to follow the morphogenetic events of a tissue and/or organ of interest throughout asexual development. We invite the scientific community to use this resource as a reference for the anatomy and developmental ontology of B. schlosseri and encourage recommendations for updates and improvements.

  14. Ontology-based semantic information technology for safeguards: opportunities and challenges

    International Nuclear Information System (INIS)

    McDaniel, Michael

    2014-01-01

    The challenge of efficiently handling large volumes of heterogeneous information is a barrier to more effective safeguards implementation. With the emergence of new technologies for generating and collecting information this is an issue common to many industries and problem domains. Several diverse information‑intensive fields are developing and adopting ontology‑based semantic information technology solutions to address issues of information integration, federation and interoperability. Ontology, in this context, refers to the formal specification of the content, structure, and logic of knowledge within a domain of interest. Ontology‑based semantic information technologies have the potential to impact nearly every level of safeguards implementation, from information collection and integration, to personnel training and knowledge retention, to planning and analysis. However, substantial challenges remain before the full benefits of semantic technology can be realized. Perhaps the most significant challenge is the development of a nuclear fuel cycle ontology. For safeguards, existing knowledge resources such as the IAEA’s Physical Model and established upper level ontologies can be used as starting points for ontology development, but a concerted effort must be taken by the safeguards community for such an activity to be successful. This paper provides a brief background of ontologies and semantic information technology, demonstrates how these technologies are used in other areas, offers examples of how ontologies can be applied to safeguards, and discusses the challenges of developing and implementing this technology as well as a possible path forward.

  15. Ontologies and tag-statistics

    International Nuclear Information System (INIS)

    Tibély, Gergely; Vicsek, Tamás; Pollner, Péter; Palla, Gergely

    2012-01-01

    Due to the increasing popularity of collaborative tagging systems, the research on tagged networks, hypergraphs, ontologies, folksonomies and other related concepts is becoming an important interdisciplinary area with great potential and relevance for practical applications. In most collaborative tagging systems the tagging by the users is completely ‘flat’, while in some cases they are allowed to define a shallow hierarchy for their own tags. However, usually no overall hierarchical organization of the tags is given, and one of the interesting challenges of this area is to provide an algorithm generating the ontology of the tags from the available data. In contrast, there are also other types of tagged networks available for research, where the tags are already organized into a directed acyclic graph (DAG), encapsulating the ‘is a sub-category of’ type of hierarchy between each other. In this paper, we study how this DAG affects the statistical distribution of tags on the nodes marked by the tags in various real networks. The motivation for this research was the fact that understanding the tagging based on a known hierarchy can help in revealing the hidden hierarchy of tags in collaborative tagging systems. We analyse the relation between the tag-frequency and the position of the tag in the DAG in two large sub-networks of the English Wikipedia and a protein-protein interaction network. We also study the tag co-occurrence statistics by introducing a two-dimensional (2D) tag-distance distribution preserving both the difference in the levels and the absolute distance in the DAG for the co-occurring pairs of tags. Our most interesting finding is that the local relevance of tags in the DAG (i.e. their rank or significance as characterized by, e.g., the length of the branches starting from them) is much more important than their global distance from the root. Furthermore, we also introduce a simple tagging model based on random walks on the DAG, capable of

  16. Ontologies and tag-statistics

    Science.gov (United States)

    Tibély, Gergely; Pollner, Péter; Vicsek, Tamás; Palla, Gergely

    2012-05-01

    Due to the increasing popularity of collaborative tagging systems, the research on tagged networks, hypergraphs, ontologies, folksonomies and other related concepts is becoming an important interdisciplinary area with great potential and relevance for practical applications. In most collaborative tagging systems the tagging by the users is completely ‘flat’, while in some cases they are allowed to define a shallow hierarchy for their own tags. However, usually no overall hierarchical organization of the tags is given, and one of the interesting challenges of this area is to provide an algorithm generating the ontology of the tags from the available data. In contrast, there are also other types of tagged networks available for research, where the tags are already organized into a directed acyclic graph (DAG), encapsulating the ‘is a sub-category of’ type of hierarchy between each other. In this paper, we study how this DAG affects the statistical distribution of tags on the nodes marked by the tags in various real networks. The motivation for this research was the fact that understanding the tagging based on a known hierarchy can help in revealing the hidden hierarchy of tags in collaborative tagging systems. We analyse the relation between the tag-frequency and the position of the tag in the DAG in two large sub-networks of the English Wikipedia and a protein-protein interaction network. We also study the tag co-occurrence statistics by introducing a two-dimensional (2D) tag-distance distribution preserving both the difference in the levels and the absolute distance in the DAG for the co-occurring pairs of tags. Our most interesting finding is that the local relevance of tags in the DAG (i.e. their rank or significance as characterized by, e.g., the length of the branches starting from them) is much more important than their global distance from the root. Furthermore, we also introduce a simple tagging model based on random walks on the DAG, capable of

  17. ANTHROPOLOGICAL COMPONENT OF DESCARTES’ ONTOLOGY

    Directory of Open Access Journals (Sweden)

    Anatolii M. Malivskyi

    2014-06-01

    Full Text Available The purpose of the article is to outline and comprehend the Descartes’ theory about anthropological component of ontology as the most important part of his philosophy. The accomplishment of this purpose covers the successive solution of the following tasks: 1 review of the research literature concerning the problem of human’s presence and the individual nature of truth; 2 emphasize the ambivalence of the basic intention of his legacy; 3 justify the thesis about constitutivity of human’s presence and comprehend passions as the form of disclosure of ontology’s anthropological component. Methodology. The use of the euristic potential of phenomenology, postpositivism and postmodernism makes it possible to emphasize the multiple-layer and multiple-meaning classical philosophy works, to comprehend the limitation and scarcity of the naïve-enlightening vision of human nature and to look for a new reception of European classics that provides the overcoming of established nihilism and pessimism concerning the interpretation of human nature. Scientific novelty. It is the first time that anthropological component of Descartes’ ontology became an object of particular attention. It previously lacked attention because of following main reasons: 1 traditional underestimating of the fact of Descartes’ legacy incompleteness as an unrealized anthropological project and 2 lack of proper attention to the individual nature of truth. The premise for its constructive overcoming is the attention to ambivalence of the basic intention and the significance of ethics in the philosopher’s legacy. His texts and research literature allow confirming the constitutive nature of human’s presence and passions as the key form of disclosure of the ontology anthropological component. Conclusions. The established tradition of interpretation the Descartes’ philosophizing nature as the filiation process of impersonal knowledge loses its cogency these days. The

  18. Anthropological Component of Descartes’ Ontology

    Directory of Open Access Journals (Sweden)

    Anatolii M. Malivskyi

    2014-06-01

    Full Text Available The purpose of the article is to outline and comprehend the Descartes’ theory about anthropological component of ontology as the most important part of his philosophy. The accomplishment of this purpose covers the successive solution of the following tasks: 1 review of the research literature concerning the problem of human’s presence and the individual nature of truth; 2 emphasize the ambivalence of the basic intention of his legacy; 3 justify the thesis about constitutivity of human’s presence and comprehend passions as the form of disclosure of ontology’s anthropological component. Methodology. The use of the euristic potential of phenomenology, postpositivism and postmodernism makes it possible to emphasize the multiple-layer and multiple-meaning classical philosophy works, to comprehend the limitation and scarcity of the naïve-enlightening vision of human nature and to look for a new reception of European classics that provides the overcoming of established nihilism and pessimism concerning the interpretation of human nature. Scientific novelty. It is the first time that anthropological component of Descartes’ ontology became an object of particular attention. It previously lacked attention because of following main reasons: 1 traditional underestimating of the fact of Descartes’ legacy incompleteness as an unrealized anthropological project and 2 lack of proper attention to the individual nature of truth. The premise for its constructive overcoming is the attention to ambivalence of the basic intention and the significance of ethics in the philosopher’s legacy. His texts and research literature allow confirming the constitutive nature of human’s presence and passions as the key form of disclosure of the ontology anthropological component. Conclusions. The established tradition of interpretation the Descartes’ philosophizing nature as the filiation process of impersonal knowledge loses its cogency these days. The

  19. Ontology-Based Information Behaviour to Improve Web Search

    Directory of Open Access Journals (Sweden)

    Silvia Calegari

    2010-10-01

    Full Text Available Web Search Engines provide a huge number of answers in response to a user query, many of which are not relevant, whereas some of the most relevant ones may not be found. In the literature several approaches have been proposed in order to help a user to find the information relevant to his/her real needs on the Web. To achieve this goal the individual Information Behavior can been analyzed to ’keep’ track of the user’s interests. Keeping information is a type of Information Behavior, and in several works researchers have referred to it as the study on what people do during a search on the Web. Generally, the user’s actions (e.g., how the user moves from one Web page to another, or her/his download of a document, etc. are recorded in Web logs. This paper reports on research activities which aim to exploit the information extracted from Web logs (or query logs in personalized user ontologies, with the objective to support the user in the process of discovering Web information relevant to her/his information needs. Personalized ontologies are used to improve the quality of Web search by applying two main techniques: query reformulation and re-ranking of query evaluation results. In this paper we analyze various methodologies presented in the literature aimed at using personalized ontologies, defined on the basis of the observation of Information Behaviour to help the user in finding relevant information.

  20. Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.

    Science.gov (United States)

    Nigam, Rajni; Munzenmaier, Diane H; Worthey, Elizabeth A; Dwinell, Melinda R; Shimoyama, Mary; Jacob, Howard J

    2013-11-22

    The Rat Genome Database (RGD) ( http://rgd.mcw.edu/) is the premier site for comprehensive data on the different strains of the laboratory rat (Rattus norvegicus). The strain data are collected from various publications, direct submissions from individual researchers, and rat providers worldwide. Rat strain, substrain designation and nomenclature follow the Guidelines for Nomenclature of Mouse and Rat Strains, instituted by the International Committee on Standardized Genetic Nomenclature for Mice. While symbols and names aid in identifying strains correctly, the flat nature of this information prohibits easy search and retrieval, as well as other data mining functions. In order to improve these functionalities, particularly in ontology-based tools, the Rat Strain Ontology (RS) was developed. The Rat Strain Ontology (RS) reflects the breeding history, parental background, and genetic manipulation of rat strains. This controlled vocabulary organizes strains by type: inbred, outbred, chromosome altered, congenic, mutant and so on. In addition, under the chromosome altered category, strains are organized by chromosome, and further by type of manipulations, such as mutant or congenic. This allows users to easily retrieve strains of interest with modifications in specific genomic regions. The ontology was developed using the Open Biological and Biomedical Ontology (OBO) file format, and is organized on the Directed Acyclic Graph (DAG) structure. Rat Strain Ontology IDs are included as part of the strain report (RS: ######). As rat researchers are often unaware of the number of substrains or altered strains within a breeding line, this vocabulary now provides an easy way to retrieve all substrains and accompanying information. Its usefulness is particularly evident in tools such as the PhenoMiner at RGD, where users can now easily retrieve phenotype measurement data for related strains, strains with similar backgrounds or those with similar introgressed regions. This

  1. Formal ontologies in biomedical knowledge representation.

    Science.gov (United States)

    Schulz, S; Jansen, L

    2013-01-01

    Medical decision support and other intelligent applications in the life sciences depend on increasing amounts of digital information. Knowledge bases as well as formal ontologies are being used to organize biomedical knowledge and data. However, these two kinds of artefacts are not always clearly distinguished. Whereas the popular RDF(S) standard provides an intuitive triple-based representation, it is semantically weak. Description logics based ontology languages like OWL-DL carry a clear-cut semantics, but they are computationally expensive, and they are often misinterpreted to encode all kinds of statements, including those which are not ontological. We distinguish four kinds of statements needed to comprehensively represent domain knowledge: universal statements, terminological statements, statements about particulars and contingent statements. We argue that the task of formal ontologies is solely to represent universal statements, while the non-ontological kinds of statements can nevertheless be connected with ontological representations. To illustrate these four types of representations, we use a running example from parasitology. We finally formulate recommendations for semantically adequate ontologies that can efficiently be used as a stable framework for more context-dependent biomedical knowledge representation and reasoning applications like clinical decision support systems.

  2. Ontology-Based Multiple Choice Question Generation

    Directory of Open Access Journals (Sweden)

    Maha Al-Yahya

    2014-01-01

    Full Text Available With recent advancements in Semantic Web technologies, a new trend in MCQ item generation has emerged through the use of ontologies. Ontologies are knowledge representation structures that formally describe entities in a domain and their relationships, thus enabling automated inference and reasoning. Ontology-based MCQ item generation is still in its infancy, but substantial research efforts are being made in the field. However, the applicability of these models for use in an educational setting has not been thoroughly evaluated. In this paper, we present an experimental evaluation of an ontology-based MCQ item generation system known as OntoQue. The evaluation was conducted using two different domain ontologies. The findings of this study show that ontology-based MCQ generation systems produce satisfactory MCQ items to a certain extent. However, the evaluation also revealed a number of shortcomings with current ontology-based MCQ item generation systems with regard to the educational significance of an automatically constructed MCQ item, the knowledge level it addresses, and its language structure. Furthermore, for the task to be successful in producing high-quality MCQ items for learning assessments, this study suggests a novel, holistic view that incorporates learning content, learning objectives, lexical knowledge, and scenarios into a single cohesive framework.

  3. APPLICATION OF COMPUTER SYSTEMS ONTOLOGY IN THE PROCESS OF FUTURE ENGINEER AND EDUCATOR’S PRACTICAL ACTIVITY

    Directory of Open Access Journals (Sweden)

    Сергій Козіброда

    2014-04-01

    Full Text Available This article develops the problem of the use of computer systems ontology in the professional activity of future engineers and teachers in the sphere of computer technology. The tasks of automated exchange of formal model descriptions as a main factor of a research performing in the sphere of ontology use have been grounded. The expediency of use of the ontology of computer systems in the following fields of intending engineers and teachers’ training: artificial intelligence, interface, natural language processing, question-answer systems, classification of goods and services semantic mark-up of text, modelling organizational structure of enterprises, systems of reference information (NSI.

  4. Nuclear Nonproliferation Ontology Assessment Team Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Strasburg, Jana D.; Hohimer, Ryan E.

    2012-01-01

    Final Report for the NA22 Simulations, Algorithm and Modeling (SAM) Ontology Assessment Team's efforts from FY09-FY11. The Ontology Assessment Team began in May 2009 and concluded in September 2011. During this two-year time frame, the Ontology Assessment team had two objectives: (1) Assessing the utility of knowledge representation and semantic technologies for addressing nuclear nonproliferation challenges; and (2) Developing ontological support tools that would provide a framework for integrating across the Simulation, Algorithm and Modeling (SAM) program. The SAM Program was going through a large assessment and strategic planning effort during this time and as a result, the relative importance of these two objectives changed, altering the focus of the Ontology Assessment Team. In the end, the team conducted an assessment of the state of art, created an annotated bibliography, and developed a series of ontological support tools, demonstrations and presentations. A total of more than 35 individuals from 12 different research institutions participated in the Ontology Assessment Team. These included subject matter experts in several nuclear nonproliferation-related domains as well as experts in semantic technologies. Despite the diverse backgrounds and perspectives, the Ontology Assessment team functioned very well together and aspects could serve as a model for future inter-laboratory collaborations and working groups. While the team encountered several challenges and learned many lessons along the way, the Ontology Assessment effort was ultimately a success that led to several multi-lab research projects and opened up a new area of scientific exploration within the Office of Nuclear Nonproliferation and Verification.

  5. Underlying diseases in dogs referred to a veterinary teaching hospital because of dyspnea: 229 cases (2003-2007).

    Science.gov (United States)

    Fonfara, Sonja; de la Heras Alegret, Lourdes; German, Alexander J; Blackwood, Laura; Dukes-McEwan, Joanna; M Noble, P-J; Burrow, Rachel D

    2011-11-01

    To identify the most frequent underlying diseases in dogs examined because of dyspnea and determine whether signalment, clinical signs, and duration of clinical signs might help guide assessment of the underlying condition and prognosis. Retrospective case series. 229 dogs with dyspnea. Case records of dogs referred for dyspnea were reviewed and grouped according to location or etiology (upper airway, lower respiratory tract, pleural space, cardiac diseases, or obesity and stress). Signalment, clinical signs at initial examination, treatment, and survival time were analyzed. Upper airway (n = 74 [32%]) and lower respiratory tract (76 [33%]) disease were the most common diagnoses, followed by pleural space (44 [19%]) and cardiac (27 [12%]) diseases. Dogs with upper airway and pleural space disease were significantly younger than dogs with lower respiratory tract and cardiac diseases. Dogs with lower respiratory tract and associated systemic diseases were significantly less likely to be discharged from the hospital. Dogs with diseases that were treated surgically had a significantly better outcome than did medically treated patients, which were significantly more likely to be examined on an emergency basis with short duration of clinical signs. In dogs examined because of dyspnea, young dogs may be examined more frequently with breed-associated upper respiratory tract obstruction or pleural space disease after trauma, whereas older dogs may be seen more commonly with progressive lower respiratory tract or acquired cardiac diseases. Nontraumatic acute onset dyspnea is often associated with a poor prognosis, but stabilization, especially in patients with cardiac disease, is possible. Obesity can be an important contributing or exacerbating factor in dyspneic dogs.

  6. owlcpp: a C++ library for working with OWL ontologies.

    Science.gov (United States)

    Levin, Mikhail K; Cowell, Lindsay G

    2015-01-01

    The increasing use of ontologies highlights the need for a library for working with ontologies that is efficient, accessible from various programming languages, and compatible with common computational platforms. We developed owlcpp, a library for storing and searching RDF triples, parsing RDF/XML documents, converting triples into OWL axioms, and reasoning. The library is written in ISO-compliant C++ to facilitate efficiency, portability, and accessibility from other programming languages. Internally, owlcpp uses the Raptor RDF Syntax library for parsing RDF/XML and the FaCT++ library for reasoning. The current version of owlcpp is supported under Linux, OSX, and Windows platforms and provides an API for Python. The results of our evaluation show that, compared to other commonly used libraries, owlcpp is significantly more efficient in terms of memory usage and searching RDF triple stores. owlcpp performs strict parsing and detects errors ignored by other libraries, thus reducing the possibility of incorrect semantic interpretation of ontologies. owlcpp is available at http://owl-cpp.sf.net/ under the Boost Software License, Version 1.0.

  7. A novel method of calibrating a MEMS inertial reference unit on a turntable under limited working conditions

    Science.gov (United States)

    Lu, Jiazhen; Liang, Shufang; Yang, Yanqiang

    2017-10-01

    Micro-electro-mechanical systems (MEMS) inertial measurement devices tend to be widely used in inertial navigation systems and have quickly emerged on the market due to their characteristics of low cost, high reliability and small size. Calibration is the most effective way to remove the deterministic error of an inertial reference unit (IRU), which in this paper consists of three orthogonally mounted MEMS gyros. However, common testing methods in the lab cannot predict the corresponding errors precisely when the turntable’s working condition is restricted. In this paper, the turntable can only provide a relatively small rotation angle. Moreover, the errors must be compensated exactly because of the great effect caused by the high angular velocity of the craft. To deal with this question, a new method is proposed to evaluate the MEMS IRU’s performance. In the calibration procedure, a one-axis table that can rotate a limited angle in the form of a sine function is utilized to provide the MEMS IRU’s angular velocity. A new algorithm based on Fourier series is designed to calculate the misalignment and scale factor errors. The proposed method is tested in a set of experiments, and the calibration results are compared to a traditional calibration method performed under normal working conditions to verify their correctness. In addition, a verification test in the given rotation speed is implemented for further demonstration.

  8. Hierarchical Analysis of the Omega Ontology

    Energy Technology Data Exchange (ETDEWEB)

    Joslyn, Cliff A.; Paulson, Patrick R.

    2009-12-01

    Initial delivery for mathematical analysis of the Omega Ontology. We provide an analysis of the hierarchical structure of a version of the Omega Ontology currently in use within the US Government. After providing an initial statistical analysis of the distribution of all link types in the ontology, we then provide a detailed order theoretical analysis of each of the four main hierarchical links present. This order theoretical analysis includes the distribution of components and their properties, their parent/child and multiple inheritance structure, and the distribution of their vertical ranks.

  9. Designing Network-based Business Model Ontology

    DEFF Research Database (Denmark)

    Hashemi Nekoo, Ali Reza; Ashourizadeh, Shayegheh; Zarei, Behrouz

    2015-01-01

    is going to propose e-business model ontology from the network point of view and its application in real world. The suggested ontology for network-based businesses is composed of individuals` characteristics and what kind of resources they own. also, their connections and pre-conceptions of connections...... such as shared-mental model and trust. However, it mostly covers previous business model elements. To confirm the applicability of this ontology, it has been implemented in business angel network and showed how it works....

  10. St. Thomas and the hilemorfic ontology

    Directory of Open Access Journals (Sweden)

    Lawrence Dewan, O.P.

    2009-06-01

    Full Text Available This article presents the relevancy of Aristotle’s hylemorphic ontology.Aristotle himself highlighted the importance and astonishing complexityof the problem of prime matter’s ontological status and he presenting thesolution in his doctrine of hylemorphism. As Saint Thomas Aquinasnoted, it is a crucial issue for philosophy because all four, hilemorfism,logic, physics and metaphysics, stand or fall depending on a correctunderstanding of the ontology of prime matter and of the kind of causalrelationship which exist between prime matter and substantial form ingenerable and corruptible substance.

  11. Product line based ontology development for semantic web service

    DEFF Research Database (Denmark)

    Zhang, Weishan; Kunz, Thomas

    2006-01-01

    Ontology is recognized as a key technology for the success of the Semantic Web. Building reusable and evolve-able ontologies in order to cope with ontology evolution and requirement changes is increasingly important. But the existing methodologies and tools fail to support effective ontology reus...

  12. Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.

    Science.gov (United States)

    Amith, Muhammad; He, Zhe; Bian, Jiang; Lossio-Ventura, Juan Antonio; Tao, Cui

    2018-04-01

    With the proliferation of heterogeneous health care data in the last three decades, biomedical ontologies and controlled biomedical terminologies play a more and more important role in knowledge representation and management, data integration, natural language processing, as well as decision support for health information systems and biomedical research. Biomedical ontologies and controlled terminologies are intended to assure interoperability. Nevertheless, the quality of biomedical ontologies has hindered their applicability and subsequent adoption in real-world applications. Ontology evaluation is an integral part of ontology development and maintenance. In the biomedicine domain, ontology evaluation is often conducted by third parties as a quality assurance (or auditing) effort that focuses on identifying modeling errors and inconsistencies. In this work, we first organized four categorical schemes of ontology evaluation methods in the existing literature to create an integrated taxonomy. Further, to understand the ontology evaluation practice in the biomedicine domain, we reviewed a sample of 200 ontologies from the National Center for Biomedical Ontology (NCBO) BioPortal-the largest repository for biomedical ontologies-and observed that only 15 of these ontologies have documented evaluation in their corresponding inception papers. We then surveyed the recent quality assurance approaches for biomedical ontologies and their use. We also mapped these quality assurance approaches to the ontology evaluation criteria. It is our anticipation that ontology evaluation and quality assurance approaches will be more widely adopted in the development life cycle of biomedical ontologies. Copyright © 2018 Elsevier Inc. All rights reserved.

  13. A Knowledge Engineering Approach to Develop Domain Ontology

    Science.gov (United States)

    Yun, Hongyan; Xu, Jianliang; Xiong, Jing; Wei, Moji

    2011-01-01

    Ontologies are one of the most popular and widespread means of knowledge representation and reuse. A few research groups have proposed a series of methodologies for developing their own standard ontologies. However, because this ontological construction concerns special fields, there is no standard method to build domain ontology. In this paper,…

  14. Uberon: towards a comprehensive multi-species anatomy ontology

    OpenAIRE

    Melissa A. Haendel; Georgios G. Gkoutos; Suzanna E. Lewis; Chris Mungall

    2009-01-01

    The lack of a single unified species-neutral ontology covering the anatomy of a variety of metazoans is a hindrance to translating model organism research to human health. We have developed an Uber-anatomy ontology to fill this need, filling the gap between the CARO upper-level ontology and species-specific anatomical ontologies.

  15. Ontology Evolution: Not the Same as Schema Evolution

    NARCIS (Netherlands)

    Noy, Natalya F.; Klein, Michel

    2004-01-01

    As ontology development becomes a more ubiquitous and collaborative process, ontology versioning and evolution becomes an important area of ontology research. The many similarities between database-schema evolution and ontology evolution will allow us to build on the extensive research in schema

  16. Ontological View-Driven Semantic Integration in Collaborative Networks

    Science.gov (United States)

    Xue, Yunjiao; Ghenniwa, Hamada H.; Shen, Weiming

    In collaborative enterprise networks, semantic heterogeneity is an important factor that hinders collaboration of various information systems. Ontology-driven semantic integration is an important category of solutions for the semantic integration problem. However, in many domains, there are no explicit and formal ontologies available. This paper proposes to adopt ontological views to address such challenges. It investigates the theoretical foundation of ontologies and ontological views. It presents a framework as a solution, based on the theoretical foundation, including the architecture of a semantic integration enabled environment, the modeling and representation of ontological views, and the semantic equivalence relationship discovered from the ontological views.

  17. Construct Primary Education Semantic Ontology Library Based Mind Mapping

    Directory of Open Access Journals (Sweden)

    Hu Dong-Hong

    2016-01-01

    Full Text Available Researches conducted for Mind mapping application in primary education semantic ontology, while considering unique characteristics of primary education, found there were rare widely used ontology libraries and few connections between ontology libraries for information sharing and reuse. In addition, primary semantic ontology library lack precise definitions of the semantics. This paper proposed a solution based on cluster structure derived from mind mapping by providing logical description of the ontologies to precisely define semantics; Meanwhile, tags were adapted to associate different ontologies to form ontology library.

  18. A Process for Engineer Domain Ontology: An Experience in Developing Business Analysis Ontology

    Directory of Open Access Journals (Sweden)

    Irena ATANASOVA

    2011-01-01

    Full Text Available During the last years several works have been aimed to improve ontology technological as-pects, like representation language and inference mechanisms. This paper presents a discussion on the process and product of an experience in developing ontology for the public sector whose organization requires a strong knowledge management. This process is applied to engineer and develop ontology for Business analysis domain.

  19. Modulated evaluation metrics for drug-based ontologies.

    Science.gov (United States)

    Amith, Muhammad; Tao, Cui

    2017-04-24

    Research for ontology evaluation is scarce. If biomedical ontological datasets and knowledgebases are to be widely used, there needs to be quality control and evaluation for the content and structure of the ontology. This paper introduces how to effectively utilize a semiotic-inspired approach to ontology evaluation, specifically towards drug-related ontologies hosted on the National Center for Biomedical Ontology BioPortal. Using the semiotic-based evaluation framework for drug-based ontologies, we adjusted the quality metrics based on the semiotic features of drug ontologies. Then, we compared the quality scores before and after tailoring. The scores revealed a more precise measurement and a closer distribution compared to the before-tailoring. The results of this study reveal that a tailored semiotic evaluation produced a more meaningful and accurate assessment of drug-based ontologies, lending to the possible usefulness of semiotics in ontology evaluation.

  20. An empirical analysis of ontology reuse in BioPortal.

    Science.gov (United States)

    Ochs, Christopher; Perl, Yehoshua; Geller, James; Arabandi, Sivaram; Tudorache, Tania; Musen, Mark A

    2017-07-01

    Biomedical ontologies often reuse content (i.e., classes and properties) from other ontologies. Content reuse enables a consistent representation of a domain and reusing content can save an ontology author significant time and effort. Prior studies have investigated the existence of reused terms among the ontologies in the NCBO BioPortal, but as of yet there has not been a study investigating how the ontologies in BioPortal utilize reused content in the modeling of their own content. In this study we investigate how 355 ontologies hosted in the NCBO BioPortal reuse content from other ontologies for the purposes of creating new ontology content. We identified 197 ontologies that reuse content. Among these ontologies, 108 utilize reused classes in the modeling of their own classes and 116 utilize reused properties in class restrictions. Current utilization of reuse and quality issues related to reuse are discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Ontology Evaluation:Consideration of Criteria, Approaches and Layers

    Directory of Open Access Journals (Sweden)

    Akram Fathian Dastgerdi

    2012-03-01

    Full Text Available Ontology is commonly used as a structure capturing knowledge about a certain area via providing relevant concepts and relations between them. Nowadays, because of the increase in designing ontologies in different domains, it is important to describe some criteria for selecting the most appropriate ontology. The purpose of this paper is to discuss the ontology evaluation criteria, approaches and layers. At first, different evaluation stages in ontology evaluation were explained. Then the most important approaches to ontology evaluation were described: included gold standard, task-based, data-driven and criteria based evaluation. Another part of this paper was about ontology evaluation criteria such as those mentioned by experts of ontology domain as well as the criteria that proposed by US National Center for ontological Research. Lastly, the levels of ontology evaluation, involved lexical, vocabulary, or data layer, hierarchy or taxonomy layer, other semantic relations layer, context or application level, syntactic level, structure, architecture and design layer were characterized.

  2. Applications of Ontologies in Collaborative Software Development

    Science.gov (United States)

    Happel, Hans-Jörg; Maalej, Walid; Seedorf, Stefan

    Making distributed teams more efficient is one main goal of Collaborative Software Development (CSD) research. To this end, ontologies, which are models that capture a shared understanding of a specific domain, provide key benefits. Ontologies have formal, machine-interpretable semantics that allow to define semantic mappings for heterogeneous data and to infer implicit knowledge at run-time. Extending development infrastructures and software architectures with ontologies (of problem and solution domains) will address coordination and knowledge sharing challenges in activities such as documentation, requirements specificationrequirements specification , component reuse, error handling, and test case management. The purpose of this article is to provide systematic account of how ontologies can be applied in CSD, and to describe benefits of both existing applications such as "semantic wikissemantic wikis " as well as visionary scenarios such as a "Software Engineering Semantic Websemantic web ".

  3. Phenomenological and ontological models in natural science

    Czech Academy of Sciences Publication Activity Database

    Lokajíček, Miloš

    2007-01-01

    Roč. 4, - (2007), s. 657-669 ISSN 1733-8026 Institutional research plan: CEZ:AV0Z10100502 Keywords : science in new age * mathematical models * microscopic world * ontological reflection Subject RIV: AA - Philosophy ; Religion

  4. The Russian Quest for Ontological Security

    DEFF Research Database (Denmark)

    Pedersen, Jonas Gejl

    This paper argues that Russia’s decision to militarily intervene in the Kosovo crisis (1999) arose out of ontological, alongside material, insecurity. Whereas states’ material security essentially deals with national survival, ontological security concerns safety of the ‘national Self......’. By supplementing the existing theories of geopolitics and regime security with the conceptual lens of ontological security, my interpretivist case study demonstrates why Russia, despite great risk and material costs, decided to militarily intervene and traces how Russian senses of ‘national Self’ were...... how Russia’s material security decreased while its sense of ontological security increased. Thus, the intensified Russo-Western antagonism following intervention opened a ‘window of opportunity’ for Russian elite to reconstruct a more self-confident sense of ‘Russian Self’. The paper contributes...

  5. Using an ontology for network attack planning

    CSIR Research Space (South Africa)

    Van Heerden, R

    2016-09-01

    Full Text Available The modern complexity of network attacks and their counter-measures (cyber operations) requires detailed planning. This paper presents a Network Attack Planning ontology which is aimed at providing support for planning such network operations within...

  6. A Bayesian Network Approach to Ontology Mapping

    National Research Council Canada - National Science Library

    Pan, Rong; Ding, Zhongli; Yu, Yang; Peng, Yun

    2005-01-01

    This paper presents our ongoing effort on developing a principled methodology for automatic ontology mapping based on BayesOWL, a probabilistic framework we developed for modeling uncertainty in semantic web...

  7. Learning Ontology from Object-Relational Database

    Directory of Open Access Journals (Sweden)

    Kaulins Andrejs

    2015-12-01

    Full Text Available This article describes a method of transformation of object-relational model into ontology. The offered method uses learning rules for such complex data types as object tables and collections – arrays of a variable size, as well as nested tables. Object types and their transformation into ontologies are insufficiently considered in scientific literature. This fact served as motivation for the authors to investigate this issue and to write the article on this matter. In the beginning, we acquaint the reader with complex data types and object-oriented databases. Then we describe an algorithm of transformation of complex data types into ontologies. At the end of the article, some examples of ontologies described in the OWL language are given.

  8. An Ontology for Insider Threat Indicators Development and Applications

    Science.gov (United States)

    2014-11-01

    G. Antoniou and F. Van Harmelen, "Web ontology language: Owl," in Handbook on ontologies , ed: Springer, 2004, pp. 67-92 ...An Ontology for Insider Threat Indicators Development and Applications Daniel L. Costa, Matthew L. Collins, Samuel J. Perl, Michael J. Albrethsen...cert.org Abstract—We describe our ongoing development of an insider threat indicator ontology . Our ontology is intended to serve as a standardized

  9. The Semantic Mapping of Archival Metadata to the CIDOC CRM Ontology

    Science.gov (United States)

    Bountouri, Lina; Gergatsoulis, Manolis

    2011-01-01

    In this article we analyze the main semantics of archival description, expressed through Encoded Archival Description (EAD). Our main target is to map the semantics of EAD to the CIDOC Conceptual Reference Model (CIDOC CRM) ontology as part of a wider integration architecture of cultural heritage metadata. Through this analysis, it is concluded…

  10. Grid Synchronization of Wind Turbine Converters under Transient Grid Faults using a Double Synchronous Reference Frame PLL

    DEFF Research Database (Denmark)

    Teodorescu, Remus; Blaabjerg, Frede; Rodriguez, P.

    2008-01-01

    This work employs the Double Synchronous Reference Frame PLL (DSRF-PLL) as an effective method for grid synchronization of WT's power converters in the presence of transient faults in the grid. The DSRF-PLL exploits a dual synchronous reference frame voltage characterization, adding a decoupling ...

  11. Making methodology a matter of process ontology

    DEFF Research Database (Denmark)

    Revsbæk, Line

    2016-01-01

    This paper presents a practice of doing qualitative interview analysis from the insights of the process ontology in G. H. Mead’s Philosophy of the Present (1932). The paper presents two cases of analyzing in the present while listening to recorded interview material eliciting researcher’s case...... study and otherwise related experiences creating case narratives inclusive of researcher’s reflexive voice. The paper presents an auto-ethnographic approach to data analysis based on process theory ontology....

  12. "Worlds otherwise": Archaeology, anthropology, and ontological difference

    OpenAIRE

    Alberti, Ben; Fowles, Severin; Holbraad, Martin; Marshall, Yvonne; Whitmore, Chris

    2011-01-01

    The debate concerning ontology is heating up in the social sciences. How is this impacting anthropology and archaeology? What contributions can these disciplines make? Following a session at the 2010 Theoretical Archaeology Group conference at Brown University (“‘Worlds Otherwise’: Archaeology, Theory, and Ontological Difference,” convened by Ben Alberti and Yvonne Marshall), a group of archaeologists and anthropologists have continued to discuss the merits, possibilities, and problems of an ...

  13. Ontologies, Agents and the Grid: An Overview

    OpenAIRE

    Drozdowicz, Michal; Ganzha, Maria; Paprzycki, Marcin; Olejnik, Richard; Lirkov, Ivan; Telegin, P.; Senobari, M.

    2009-01-01

    23 pages; One of the important claims that permeate the current view of information management is that ontological demarcation of data and semantic information processing are going to allow us to infuse "intelligence" into information systems. Separately, it is claimed that software agents, combined with ontologies will be the foundation ofWeb 4.0. In our work we are developing an agent-team-based resource management and brokering infrastructure for computational grids. The proposed meta-leve...

  14. Concerning the Importance of Ontological Issues for Cultural Psychology: a Reply to Comments.

    Science.gov (United States)

    Mironenko, Irina A

    2017-09-01

    The paper continues the "ontological" discussion in IBPS, addressing the question of the importance of ontological issues for contemporary development of cultural psychology. The language psychological science speaks is considered as an ontological issue and a most topical one for cultural psychology, aiming at "constructing a psychology that is universal while being culture-inclusive" (Valsiner 2009, p.2). Ontological issues could stay implicit and neglected, as long as the 'etant, "the mode of being", "the particularities" were discussed within the circle of adherents of one and the same school, who implicitly had in mind the same 'entre. However, as soon as the discussion involves representatives of different schools, ontological issues become crucial for mutual understanding and meanings of the words have to be explicated. Same words like "psyche", "subjectivity", "social", "culture", etc., - often mean different things when they are pronounces or written by representatives of different theoretical trends. The discussion of the 'etant without clear indicating of the 'entre under consideration is likely to turn into a Babel. Global modernity requires constant efforts and insistent desire for mutual understanding across the diversified global scientific community. Thus, creative collaboration in epistemological developments has to ground on clear comprehension of the ontological stances of the debaters.

  15. Ontology of Bio-Medical Educational Objectives (OBEO: ein Vorschlag für eine Ontologie medizinischer Lernziele / A proposal for an Ontology of Bio-Medical Educational Objectives (OBEO

    Directory of Open Access Journals (Sweden)

    Boeker, Martin

    2010-01-01

    Full Text Available Objectives: The Ontology of Bio-Medical Educational Objectives (OBEO is a formal ontology for the annotation of educational objective catalogues and learning object resources to improve their usability. OBEO has been designed to allow semantic retrieval and navigation of educational objectives as well as the solution of questions in regard to consistency, sequence and correctness of educational objectives in databases. Methods: To specify OBEO various educational objective taxonomies and catalogues were analyzed and a requirements analysis was performed. OBEO was developed on the foundation of the top-level ontology Descriptive Ontology for Linguistic and Cognitive Engineering (DOLCE and the upper-level ontology BioTop. It was implemented in the Web Ontology Language (OWL. Medical content is bound by links to reference terminologies and ontologies. Results: OBEO provides classes and relations for the correct and almost complete representation of educational objectives. OBEO formalizes the relations between educational objective specifications and the concrete actions which realize them as well as the medical contents which are bound to them. Although OBEO uses only few own classes and relations, its complexity is already extensive. Conclusion: OBEO is a prototypical tool to annotate existing and developing educational objective catalogues and learning object resources for their better usability. OBEO has to be further developed and improved in regard to the representation of medical content in educational objectives and the inclusion of curricular context of educational objectives. The formal representation of OBEO enables the retrieval and navigation of annotated data in regard to content.

  16. The Development of Ontology from Multiple Databases

    Science.gov (United States)

    Kasim, Shahreen; Aswa Omar, Nurul; Fudzee, Mohd Farhan Md; Azhar Ramli, Azizul; Aizi Salamat, Mohamad; Mahdin, Hairulnizam

    2017-08-01

    The area of halal industry is the fastest growing global business across the world. The halal food industry is thus crucial for Muslims all over the world as it serves to ensure them that the food items they consume daily are syariah compliant. Currently, ontology has been widely used in computer sciences area such as web on the heterogeneous information processing, semantic web, and information retrieval. However, ontology has still not been used widely in the halal industry. Today, Muslim community still have problem to verify halal status for products in the market especially foods consisting of E number. This research tried to solve problem in validating the halal status from various halal sources. There are various chemical ontology from multilple databases found to help this ontology development. The E numbers in this chemical ontology are codes for chemicals that can be used as food additives. With this E numbers ontology, Muslim community could identify and verify the halal status effectively for halal products in the market.

  17. An ontology for major histocompatibility restriction.

    Science.gov (United States)

    Vita, Randi; Overton, James A; Seymour, Emily; Sidney, John; Kaufman, Jim; Tallmadge, Rebecca L; Ellis, Shirley; Hammond, John; Butcher, Geoff W; Sette, Alessandro; Peters, Bjoern

    2016-01-01

    MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s) of MHC molecule involved in a specific immune recognition context. No consistent nomenclature exists across different vertebrate species. To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology and created an ontology to represent MHC molecules as they relate to immunological experiments. This ontology models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multi-chain proteins, and establishes evidence codes for MHC restriction. Where available, this work is based on existing ontologies from the OBO foundry. Overall, representing MHC molecules provides a challenging and practically important test case for ontology building, and could serve as an example of how to integrate other ontology building efforts into web resources.

  18. Inferring gene ontologies from pairwise similarity data

    Science.gov (United States)

    Kramer, Michael; Dutkowski, Janusz; Yu, Michael; Bafna, Vineet; Ideker, Trey

    2014-01-01

    Motivation: While the manually curated Gene Ontology (GO) is widely used, inferring a GO directly from -omics data is a compelling new problem. Recognizing that ontologies are a directed acyclic graph (DAG) of terms and hierarchical relations, algorithms are needed that: analyze a full matrix of gene–gene pairwise similarities from -omics data;infer true hierarchical structure in these data rather than enforcing hierarchy as a computational artifact; andrespect biological pleiotropy, by which a term in the hierarchy can relate to multiple higher level terms. Methods addressing these requirements are just beginning to emerge—none has been evaluated for GO inference. Methods: We consider two algorithms [Clique Extracted Ontology (CliXO), LocalFitness] that uniquely satisfy these requirements, compared with methods including standard clustering. CliXO is a new approach that finds maximal cliques in a network induced by progressive thresholding of a similarity matrix. We evaluate each method’s ability to reconstruct the GO biological process ontology from a similarity matrix based on (a) semantic similarities for GO itself or (b) three -omics datasets for yeast. Results: For task (a) using semantic similarity, CliXO accurately reconstructs GO (>99% precision, recall) and outperforms other approaches (Ontology) and better than LocalFitness or standard clustering (20–25% precision, recall). Conclusion: This study provides algorithmic foundation for building gene ontologies by capturing hierarchical and pleiotropic structure embedded in biomolecular data. Contact: tideker@ucsd.edu PMID:24932003

  19. On the ontological emergence from quantum regime

    Energy Technology Data Exchange (ETDEWEB)

    Luty, Damian [Adam Mickiewicz University, Poznan (Poland)

    2014-07-01

    There are several views on the relation between quantum physics and theory of relativity (especially General Relativity, GR). A popular perspective is this: GR with its macroscopic gravitational effects will turn out to be a limit of a more fundamental theory which should consider discrete physics and not deal with continuity (like theory of relativity). Thus, GR will emerge from a more basic theory, which should be quantum-like. One could call this an epistemic emergence view towards fundamental theories. The question is, given that scientific realism is valid: should emergence be a fundamental notion in our ontological view about the evolving, physical Universe? Is there an ontological emergence fully compatible with the notion of fundamentality? I argue that if we want to defend ontological emergence (from quantum to macroscopic regime) as something fundamental, we will arrive at the position of metaphysics of dispositions (and I argue, why this is undesirable), or conclude, that we cannot square fully fundamental ontology with the notion of emergence, and that we have to accept an ontological pluralism relativised to a certain scale. I defend the latter proposition, showing, that epistemic emergence doesn't entail (logically) ontological emergence.

  20. Expression Stabilities of Candidate Reference Genes for RT-qPCR in Chinese Jujube (Ziziphus jujuba Mill. under a Variety of Conditions.

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    Jiaodi Bu

    Full Text Available Reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR is a powerful method for evaluating patterns of gene expression. Jujube whole-genome sequencing has been completed, and analysis of gene function, an important part of any follow-up study, requires the appropriate selection of reference genes. Indeed, suitable reference gene selection for RT-qPCR is critical for accurate normalization of target gene expression. In this study, the software packages geNorm and NormFinder were employed to examine the expression stabilities of nine candidate reference genes under a variety of conditions. Actin-depolymerizing factor 1 (ACT1, Histone-H3 (His3, and Polyadenylate-binding protein-interacting protein (PAIP were determined to be the most stably expressed genes during five stages of fruit development and ACT1, SiR-Fd, BTF3, and Tubulin alpha chain (TUA across different tissues/organs. Whereas ACT1, Basic Transcription factor 3 (BTF3, Glyceraldehyde-3-phosphate dehydrogenase (GADPH, and PAIP were the most stable under dark conditions. ACT1, PAIP, BTF3, and Elongation factor 1- gamma (EF1γ were the most stably expressed genes under phytoplasma infection. Among these genes, SiR-Fd and PAIP are here first reported as stable reference genes. When normalized using these most stable reference genes, the expression patterns of four target genes were found to be in accordance with physiological data, indicating that the reference genes selected in our study are suitable for use in such analyses. This study provides appropriate reference genes and corresponding primers for further RT-qPCR studies in Chinese jujube and emphasizes the importance of validating reference genes for gene expression analysis under variable experimental conditions.

  1. Using Ontologies in Cybersecurity Field

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    Tiberiu Marian GEORGESCU

    2017-01-01

    Full Text Available This paper is an exploratory research which aims to improve the cybersecurity field by means of semantic web technologies. The authors present a framework which uses Semantic Web technologies to automatically extract and analyse text in natural language available online. The system provides results that are further analysed by cybersecurity experts to detect black hat hackers’ activities. The authors examine several characteristics of how hacking communities communicate and collaborate online and how much information can be obtained by analysing different types of internet text communication channels. Having online sources as input data, the model proposed extracts and analyses natural language that relates with cybersecurity field, with the aid of ontologies. The main objective is to generate information about possible black hat hacking actions, which later can be analysed punctually by experts. This paper describes the data flow of the framework and it proposes technological solutions so that the model can be applied. In their future work, the authors plan to implement the framework described as a system software application.

  2. COHeRE: Cross-Ontology Hierarchical Relation Examination for Ontology Quality Assurance.

    Science.gov (United States)

    Cui, Licong

    Biomedical ontologies play a vital role in healthcare information management, data integration, and decision support. Ontology quality assurance (OQA) is an indispensable part of the ontology engineering cycle. Most existing OQA methods are based on the knowledge provided within the targeted ontology. This paper proposes a novel cross-ontology analysis method, Cross-Ontology Hierarchical Relation Examination (COHeRE), to detect inconsistencies and possible errors in hierarchical relations across multiple ontologies. COHeRE leverages the Unified Medical Language System (UMLS) knowledge source and the MapReduce cloud computing technique for systematic, large-scale ontology quality assurance work. COHeRE consists of three main steps with the UMLS concepts and relations as the input. First, the relations claimed in source vocabularies are filtered and aggregated for each pair of concepts. Second, inconsistent relations are detected if a concept pair is related by different types of relations in different source vocabularies. Finally, the uncovered inconsistent relations are voted according to their number of occurrences across different source vocabularies. The voting result together with the inconsistent relations serve as the output of COHeRE for possible ontological change. The highest votes provide initial suggestion on how such inconsistencies might be fixed. In UMLS, 138,987 concept pairs were found to have inconsistent relationships across multiple source vocabularies. 40 inconsistent concept pairs involving hierarchical relationships were randomly selected and manually reviewed by a human expert. 95.8% of the inconsistent relations involved in these concept pairs indeed exist in their source vocabularies rather than being introduced by mistake in the UMLS integration process. 73.7% of the concept pairs with suggested relationship were agreed by the human expert. The effectiveness of COHeRE indicates that UMLS provides a promising environment to enhance

  3. Ontology and anthropology of interanimality: Merleau-Ponty from Tim ingold's perspective

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    Ana Cristina Ramírez Barreto

    2010-01-01

    Full Text Available This essay explores Tim Ingold’s anthropological theory following his references to Merleau-Ponty and the concept of interanimality/interagentivity. It poses some ideas of Ingold’s “poetics of dwelling”, which he highlights from ethnographies of hunter-gatherer peoples, and how these ideas are linked to an ontological consideration which does not dissociate body and person, body and mind, nature and culture, animality and humanity. The paper reviews animal literature in Merleau-Ponty’s philosophy, and Ingold’s critique of “Anthropology of the senses”. It also gives critical clues for the ethical and political implications of this ontology.

  4. Prediction of Change in Prescription Ingredient Costs and Co-payment Rates under a Reference Pricing System in South Korea.

    Science.gov (United States)

    Heo, Ji Haeng; Rascati, Karen L; Lee, Eui-Kyung

    2017-05-01

    The reference pricing system (RPS) establishes reference prices within interchangeable reference groupings. For drugs priced higher than the reference point, patients pay the difference between the reference price and the total price. To predict potential changes in prescription ingredient costs and co-payment rates after implementation of an RPS in South Korea. Korean National Health Insurance claims data were used as a baseline to develop possible RPS models. Five components of a potential RPS policy were varied: reference groupings, reference pricing methods, co-pay reduction programs, manufacturer price reductions, and increased drug substitutions. The potential changes for prescription ingredient costs and co-payment rates were predicted for the various scenarios. It was predicted that transferring the difference (total price minus reference price) from the insurer to patients would reduce ingredient costs from 1.4% to 22.8% for the third-party payer (government), but patient co-payment rates would increase from a baseline of 20.4% to 22.0% using chemical groupings and to 25.0% using therapeutic groupings. Savings rates in prescription ingredient costs (government and patient combined) were predicted to range from 1.6% to 13.7% depending on various scenarios. Although the co-payment rate would increase, a 15% price reduction by manufacturers coupled with a substitution rate of 30% would result in a decrease in the co-payment amount (change in absolute dollars vs. change in rates). Our models predicted that the implementation of RPS in South Korea would lead to savings in ingredient costs for the third-party payer and co-payments for patients with potential scenarios. Copyright © 2017 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

  5. New concepts for building vocabulary for cell image ontologies

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    Plant Anne L

    2011-12-01

    Full Text Available Abstract Background There are significant challenges associated with the building of ontologies for cell biology experiments including the large numbers of terms and their synonyms. These challenges make it difficult to simultaneously query data from multiple experiments or ontologies. If vocabulary terms were consistently used and reused across and within ontologies, queries would be possible through shared terms. One approach to achieving this is to strictly control the terms used in ontologies in the form of a pre-defined schema, but this approach limits the individual researcher's ability to create new terms when needed to describe new experiments. Results Here, we propose the use of a limited number of highly reusable common root terms, and rules for an experimentalist to locally expand terms by adding more specific terms under more general root terms to form specific new vocabulary hierarchies that can be used to build ontologies. We illustrate the application of the method to build vocabularies and a prototype database for cell images that uses a visual data-tree of terms to facilitate sophisticated queries based on a experimental parameters. We demonstrate how the terminology might be extended by adding new vocabulary terms into the hierarchy of terms in an evolving process. In this approach, image data and metadata are handled separately, so we also describe a robust file-naming scheme to unambiguously identify image and other files associated with each metadata value. The prototype database http://sbd.nist.gov/ consists of more than 2000 images of cells and benchmark materials, and 163 metadata terms that describe experimental details, including many details about cell culture and handling. Image files of interest can be retrieved, and their data can be compared, by choosing one or more relevant metadata values as search terms. Metadata values for any dataset can be compared with corresponding values of another dataset through logical

  6. New concepts for building vocabulary for cell image ontologies.

    Science.gov (United States)

    Plant, Anne L; Elliott, John T; Bhat, Talapady N

    2011-12-21

    There are significant challenges associated with the building of ontologies for cell biology experiments including the large numbers of terms and their synonyms. These challenges make it difficult to simultaneously query data from multiple experiments or ontologies. If vocabulary terms were consistently used and reused across and within ontologies, queries would be possible through shared terms. One approach to achieving this is to strictly control the terms used in ontologies in the form of a pre-defined schema, but this approach limits the individual researcher's ability to create new terms when needed to describe new experiments. Here, we propose the use of a limited number of highly reusable common root terms, and rules for an experimentalist to locally expand terms by adding more specific terms under more general root terms to form specific new vocabulary hierarchies that can be used to build ontologies. We illustrate the application of the method to build vocabularies and a prototype database for cell images that uses a visual data-tree of terms to facilitate sophisticated queries based on a experimental parameters. We demonstrate how the terminology might be extended by adding new vocabulary terms into the hierarchy of terms in an evolving process. In this approach, image data and metadata are handled separately, so we also describe a robust file-naming scheme to unambiguously identify image and other files associated with each metadata value. The prototype database http://sbd.nist.gov/ consists of more than 2000 images of cells and benchmark materials, and 163 metadata terms that describe experimental details, including many details about cell culture and handling. Image files of interest can be retrieved, and their data can be compared, by choosing one or more relevant metadata values as search terms. Metadata values for any dataset can be compared with corresponding values of another dataset through logical operations. Organizing metadata for cell imaging

  7. Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning.

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    Robert Hoehndorf

    Full Text Available Researchers design ontologies as a means to accurately annotate and integrate experimental data across heterogeneous and disparate data- and knowledge bases. Formal ontologies make the semantics of terms and relations explicit such that automated reasoning can be used to verify the consistency of knowledge. However, many biomedical ontologies do not sufficiently formalize the semantics of their relations and are therefore limited with respect to automated reasoning for large scale data integration and knowledge discovery. We describe a method to improve automated reasoning over biomedical ontologies and identify several thousand contradictory class definitions. Our approach aligns terms in biomedical ontologies with foundational classes in a top-level ontology and formalizes composite relations as class expressions. We describe the semi-automated repair of contradictions and demonstrate expressive queries over interoperable ontologies. Our work forms an important cornerstone for data integration, automatic inference and knowledge discovery based on formal representations of knowledge. Our results and analysis software are available at http://bioonto.de/pmwiki.php/Main/ReasonableOntologies.

  8. Ontology Mapping Neural Network: An Approach to Learning and Inferring Correspondences among Ontologies

    Science.gov (United States)

    Peng, Yefei

    2010-01-01

    An ontology mapping neural network (OMNN) is proposed in order to learn and infer correspondences among ontologies. It extends the Identical Elements Neural Network (IENN)'s ability to represent and map complex relationships. The learning dynamics of simultaneous (interlaced) training of similar tasks interact at the shared connections of the…

  9. Using an ontology pattern stack to engineer a core ontology of Accounting Information Systems

    NARCIS (Netherlands)

    Blums, Ivar; Weigand, Hans

    Although the field of Accounting Information Systems (AIS) has a long tradition, there is still a lack of a widely adopted conceptualization. In this paper, The UFO ontology patterns are regarded for application by analogy and extension in the engineering of a core ontology for AIS. The new IASB

  10. Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base.

    Science.gov (United States)

    Ai, Jiye; Smith, Barry; Wong, David T

    2010-06-03

    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.

  11. OIntEd: online ontology instance editor enabling a new approach to ontology development

    NARCIS (Netherlands)

    Wibisono, A.; Koning, R.; Grosso, P.; Belloum, A.; Bubak, M.; de Laat, C.

    2013-01-01

    Ontology development involves people with different background knowledge and expertise. It is an elaborate process, where sophisticated tools for experienced knowledge engineers are available. However, domain experts need simple tools that they can use to focus on ontology instantiation. In this

  12. The relevance of geoethics to under-developed and developing Nations wth special reference to India.i

    Science.gov (United States)

    Desikachari, Vasudevan

    2015-04-01

    Relevance of Geoethics to underdeveloped And developing Nations, with special reference to India ------- The application of ethical principles to results of scientific investigations which will have direct impact on the well being of human kind is well amplified by medical sciences (eg.,the laws governing testing of new medications and anti-viral vaccination on humans and their subsequent usage to preserve and protect humanity), and its application to Geoscience, which is very important,however, is very recent.Geoscientific investigations involve such wide and varying aspects of our mother Earth that most of it find applications directly to the welfare and development of civilized society, such as mining of natural resources,like coal,minerals and building stones;exploration for petroleum and natural gas;or geo-engineering investigations for major civil engineering projects like construction of dams,tunnels or work related to mitigation of effects of natural hazards (earthquakes,tsunamis or landslides).The Geoscientists, since their work will contribute to the resource development and economic progress of a country,will have to be very conscientious in parting their knowledge to user agency.This involves,true and practical reporting of data without succumbing to corrupt practices or doing away tendency to over-emphasising the results to the point of creating unnecessary panic to public.In all these geoscientific investigations therefore ethics plays a vital role.For, instance,both the loss of life and property in the 2001 earthquake of Gujerat,India could have been kept at a minimum if the planning authorities had applied their mind to designs for construction of houses for city dwellers, based on geological investigation of rocks,soils and geologic structures of the area.As Pointed out succinctly by Lambert(2014),since corruption plays a negative role in formulating geologic results in developing/underdeveloping countries,combating this using a forceful geoethical

  13. A 2013 workshop: vaccine and drug ontology studies (VDOS 2013).

    Science.gov (United States)

    Tao, Cui; He, Yongqun; Arabandi, Sivaram

    2014-03-20

    The 2013 "Vaccine and Drug Ontology Studies" (VDOS 2013) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have contributed to dramatic improvements in public health worldwide. Over the last decade, tremendous efforts have been made in the biomedical ontology community to ontologically represent various areas associated with vaccines and drugs - extending existing clinical terminology systems such as SNOMED, RxNorm, NDF-RT, and MedDRA, as well as developing new models such as Vaccine Ontology. The VDOS workshop series provides a platform for discussing innovative solutions as well as the challenges in the development and applications of biomedical ontologies for representing and analyzing drugs and vaccines, their administration, host immune responses, adverse events, and other related topics. The six full-length papers included in this thematic issue focuses on three main areas: (i) ontology development and representation, (ii) ontology mapping, maintaining and auditing, and (iii) ontology applications.

  14. An open annotation ontology for science on web 3.0.

    Science.gov (United States)

    Ciccarese, Paolo; Ocana, Marco; Garcia Castro, Leyla Jael; Das, Sudeshna; Clark, Tim

    2011-05-17

    There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables "stand-off" or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO's Google Code page: http://code.google.com/p/annotation-ontology/ . The Annotation Ontology meets critical requirements for

  15. Construction of Fuzzy Ontologies from Fuzzy UML Models

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    Fu Zhang

    2013-05-01

    Full Text Available The success and proliferation of the Semantic Web depends heavily on construction of Web ontologies. However, classical ontology construction approaches are not sufficient for handling imprecise and uncertain information that is commonly found in many application domains. Therefore, great efforts on construction of fuzzy ontologies have been made in recent years. In this paper, we propose a formal approach and develop an automated tool for constructing fuzzy ontologies from fuzzy UML models. , we propose formalization methods of fuzzy UML models and fuzzy ontologies, where fuzzy UML models and fuzzy ontologies can be represented and interpreted by their respective formal definitions and semantic interpretation methods. , we propose an approach for constructing fuzzy ontologies from fuzzy UML models, i.e., transforming fuzzy UML models (including the structure and instance information of fuzzy UML models into fuzzy ontologies. , following the proposed approach, we implement a prototype transformation tool called that can construct fuzzy ontologies from fuzzy UML models. Constructing fuzzy ontologies from fuzzy UML models will facilitate the development of Web ontologies. , in order to show that the constructed fuzzy ontologies may be useful for reasoning on fuzzy UML models, we investigate how to reason on fuzzy UML models based on the constructed fuzzy ontologies, and it turns out that the reasoning tasks of fuzzy UML models can be checked by means of the reasoning mechanism of fuzzy ontologies.

  16. Validation of Suitable Reference Genes for RT-qPCR Data in Achyranthes bidentata Blume under Different Experimental Conditions

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    Jinting Li

    2017-05-01

    Full Text Available Real-time quantitative polymerase chain reaction (RT-qPCR is a sensitive technique for gene expression studies. However, choosing the appropriate reference gene is essential to obtain reliable results for RT-qPCR assays. In the present work, the expression of eight candidate reference genes, EF1-α (elongation factor 1-α, GAPDH (glyceraldehyde 3-phosphate dehydrogenase, UBC (ubiquitin-conjugating enzyme, UBQ (polyubiquitin, ACT (actin, β-TUB (β-tubulin, APT1 (adenine phosphoribosyltransferase 1, and 18S rRNA (18S ribosomal RNA, was evaluated in Achyranthes bidentata samples using two algorithms, geNorm and NormFinder. The samples were classified into groups according to developmental stages, various tissues, stresses (cold, heat, drought, NaCl, and hormone treatments (MeJA, IBA, SA. Suitable combination of reference genes for RT-qPCR normalization should be applied according to different experimental conditions. In this study, EF1-α, UBC, and ACT genes were verified as the suitable reference genes across all tested samples. To validate the suitability of the reference genes, we evaluated the relative expression of CAS, which is a gene that may be involved in phytosterol synthesis. Our results provide the foundation for gene expression analysis in A. bidentata and other species of Amaranthaceae.

  17. Brucellosis Ontology (IDOBRU as an extension of the Infectious Disease Ontology

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    Lin Yu

    2011-10-01

    Full Text Available Abstract Background Caused by intracellular Gram-negative bacteria Brucella spp., brucellosis is the most common bacterial zoonotic disease. Extensive studies in brucellosis have yielded a large number of publications and data covering various topics ranging from basic Brucella genetic study to vaccine clinical trials. To support data interoperability and reasoning, a community-based brucellosis-specific biomedical ontology is needed. Results The Brucellosis Ontology (IDOBRU: http://sourceforge.net/projects/idobru, a biomedical ontology in the brucellosis domain, is an extension ontology of the core Infectious Disease Ontology (IDO-core and follows OBO Foundry principles. Currently IDOBRU contains 1503 ontology terms, which includes 739 Brucella-specific terms, 414 IDO-core terms, and 350 terms imported from 10 existing ontologies. IDOBRU has been used to model different aspects of brucellosis, including host infection, zoonotic disease transmission, symptoms, virulence factors and pathogenesis, diagnosis, intentional release, vaccine prevention, and treatment. Case studies are typically used in our IDOBRU modeling. For example, diurnal temperature variation in Brucella patients, a Brucella-specific PCR method, and a WHO-recommended brucellosis treatment were selected as use cases to model brucellosis symptom, diagnosis, and treatment, respectively. Developed using OWL, IDOBRU supports OWL-based ontological reasoning. For example, by performing a Description Logic (DL query in the OWL editor Protégé 4 or a SPARQL query in an IDOBRU SPARQL server, a check of Brucella virulence factors showed that eight of them are known protective antigens based on the biological knowledge captured within the ontology. Conclusions IDOBRU is the first reported bacterial infectious disease ontology developed to represent different disease aspects in a formal logical format. It serves as a brucellosis knowledgebase and supports brucellosis data integration and

  18. Ion Channel ElectroPhysiology Ontology (ICEPO) - a case study of text mining assisted ontology development.

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    Elayavilli, Ravikumar Komandur; Liu, Hongfang

    2016-01-01

    Computational modeling of biological cascades is of great interest to quantitative biologists. Biomedical text has been a rich source for quantitative information. Gathering quantitative parameters and values from biomedical text is one significant challenge in the early steps of computational modeling as it involves huge manual effort. While automatically extracting such quantitative information from bio-medical text may offer some relief, lack of ontological representation for a subdomain serves as impedance in normalizing textual extractions to a standard representation. This may render textual extractions less meaningful to the domain experts. In this work, we propose a rule-based approach to automatically extract relations involving quantitative data from biomedical text describing ion channel electrophysiology. We further translated the quantitative assertions extracted through text mining to a formal representation that may help in constructing ontology for ion channel events using a rule based approach. We have developed Ion Channel ElectroPhysiology Ontology (ICEPO) by integrating the information represented in closely related ontologies such as, Cell Physiology Ontology (CPO), and Cardiac Electro Physiology Ontology (CPEO) and the knowledge provided by domain experts. The rule-based system achieved an overall F-measure of 68.93% in extracting the quantitative data assertions system on an independently annotated blind data set. We further made an initial attempt in formalizing the quantitative data assertions extracted from the biomedical text into a formal representation that offers potential to facilitate the integration of text mining into ontological workflow, a novel aspect of this study. This work is a case study where we created a platform that provides formal interaction between ontology development and text mining. We have achieved partial success in extracting quantitative assertions from the biomedical text and formalizing them in ontological

  19. Leave-two-out stability of ontology learning algorithm

    International Nuclear Information System (INIS)

    Wu, Jianzhang; Yu, Xiao; Zhu, Linli; Gao, Wei

    2016-01-01

    Ontology is a semantic analysis and calculation model, which has been applied to many subjects. Ontology similarity calculation and ontology mapping are employed as machine learning approaches. The purpose of this paper is to study the leave-two-out stability of ontology learning algorithm. Several leave-two-out stabilities are defined in ontology learning setting and the relationship among these stabilities are presented. Furthermore, the results manifested reveal that leave-two-out stability is a sufficient and necessary condition for ontology learning algorithm.

  20. Validating EHR clinical models using ontology patterns.

    Science.gov (United States)

    Martínez-Costa, Catalina; Schulz, Stefan

    2017-12-01

    Clinical models are artefacts that specify how information is structured in electronic health records (EHRs). However, the makeup of clinical models is not guided by any formal constraint beyond a semantically vague information model. We address this gap by advocating ontology design patterns as a mechanism that makes the semantics of clinical models explicit. This paper demonstrates how ontology design patterns can validate existing clinical models using SHACL. Based on the Clinical Information Modelling Initiative (CIMI), we show how ontology patterns detect both modeling and terminology binding errors in CIMI models. SHACL, a W3C constraint language for the validation of RDF graphs, builds on the concept of "Shape", a description of data in terms of expected cardinalities, datatypes and other restrictions. SHACL, as opposed to OWL, subscribes to the Closed World Assumption (CWA) and is therefore more suitable for the validation of clinical models. We have demonstrated the feasibility of the approach by manually describing the correspondences between six CIMI clinical models represented in RDF and two SHACL ontology design patterns. Using a Java-based SHACL implementation, we found at least eleven modeling and binding errors within these CIMI models. This demonstrates the usefulness of ontology design patterns not only as a modeling tool but also as a tool for validation. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. An Architectural Approach for Building Medical Ontologies

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    Mircea Adrian FOCŞA

    2016-07-01

    Full Text Available Starting from a use case scenario related to the Electronic Medical Record (EMR information retrieval, this paper proposes several design principles for an ontology-based EMR system, which will allow the physician to perform a semantic search about a specific body structure or zone/space (affected, explored or treated. The research starts from analyzing the information requirements of the family doctors related to the medical history of their patients. By interviewing a group of family doctors, a set of common questions have been identified and modeled as one generic question. The key terms from this generic question then became the building blocks of an ontology, which was further built incrementally and constantly adjusted depending on the query response (design pattern by querying. Elements from other terminologies/ontologies have been reused thus facilitating interoperability with similar constructions. As a result of this research, we tested and proposed for adoption several basic modeling principles for medical ontologies, among them, the particularities of part-whole relations for body regions/spaces and anatomical components, the requirements for propagation of the medical activities from one class to an upper or subsequent class. These modeling principles have a good degree of generality and could be taken into consideration for building any medical ontology.

  2. Construction of Formal Ontology on Computer

    Directory of Open Access Journals (Sweden)

    Yelda FIRAT

    2013-01-01

    Full Text Available From a general point of view, the defined reality models by using a formal language are called formal ontology. These general purposeful models can be also used in the special fields of application. Because ontologies are large-scale by their nature, they have the potential of hosting errors and deficiencies in case they are generated by human labor. Besides, an ontology formed such a way will be difficult to be adapted to a application specific. In this study, an application of a computerized formal ontology formation saved from probable problems which are likely to arise using human labor will be introduced. In the application, semantic analysis of Turkish has been targetted as a special application field using corpus-based marking method in the framework of formal concept analysis. Beside the applications of these kinds of natural language processing formal ontologies are used considerably in the field of education as they present the information in the way of semantic structures clearly and meaningfully. The most important reasons of this are the use of the information technologies such as expansion of constructivist approach and the concept maps used for educational reasons.

  3. Annotating breast cancer microarray samples using ontologies

    Science.gov (United States)

    Liu, Hongfang; Li, Xin; Yoon, Victoria; Clarke, Robert

    2008-01-01

    As the most common cancer among women, breast cancer results from the accumulation of mutations in essential genes. Recent advance in high-throughput gene expression microarray technology has inspired researchers to use the technology to assist breast cancer diagnosis, prognosis, and treatment prediction. However, the high dimensionality of microarray experiments and public access of data from many experiments have caused inconsistencies which initiated the development of controlled terminologies and ontologies for annotating microarray experiments, such as the standard microarray Gene Expression Data (MGED) ontology (MO). In this paper, we developed BCM-CO, an ontology tailored specifically for indexing clinical annotations of breast cancer microarray samples from the NCI Thesaurus. Our research showed that the coverage of NCI Thesaurus is very limited with respect to i) terms used by researchers to describe breast cancer histology (covering 22 out of 48 histology terms); ii) breast cancer cell lines (covering one out of 12 cell lines); and iii) classes corresponding to the breast cancer grading and staging. By incorporating a wider range of those terms into BCM-CO, we were able to indexed breast cancer microarray samples from GEO using BCM-CO and MGED ontology and developed a prototype system with web interface that allows the retrieval of microarray data based on the ontology annotations. PMID:18999108

  4. Evaluating the effects of alternative forest management plans under various physiographic settings using historical records as a reference

    Science.gov (United States)

    Yangjian Zhang; Hong S. He; Stephen R. Shifley; Jian Yang; Brian J. Palik

    2011-01-01

    Using historical General Land Office record as a reference, this study employed a landscape-scale disturbance and succession model to estimate the future cumulative effects of six alternative management plans on the tree species composition for various physiographic settings for the Mark Twain National Forest in Missouri. The results indicate that over a 200-year...

  5. Iluminator of the wide earth; Unbribable judge; Strong weapon of the Gods: Intuitive ontology and divine epithets in Assyro-Babylonian religious texts

    DEFF Research Database (Denmark)

    Westh, Peter

    2011-01-01

    to their conceptual content and underlying ontology, and a quantitative analysis of their use and distribution within the corpus is performed. On this background, some of the predictions made by Pascal Boyer regarding the role of evolved, intuitive ontologies in the formation and transmission of religious concepts...

  6. Ontology mapping and data discovery for the translational investigator.

    Science.gov (United States)

    Wynden, Rob; Weiner, Mark G; Sim, Ida; Gabriel, Davera; Casale, Marco; Carini, Simona; Hastings, Shannon; Ervin, David; Tu, Samson; Gennari, John H; Anderson, Nick; Mobed, Ketty; Lakshminarayanan, Prakash; Massary, Maggie; Cucina, Russ J

    2010-03-01

    An integrated data repository (IDR) containing aggregations of clinical, biomedical, economic, administrative, and public health data is a key component of an overall translational research infrastructure. But most available data repositories are designed using standard data warehouse architecture that employs arbitrary data encoding standards, making queries across disparate repositories difficult. In response to these shortcomings we have designed a Health Ontology Mapper (HOM) that translates terminologies into formal data encoding standards without altering the underlying source data. We believe the HOM system promotes inter-institutional data sharing and research collaboration, and will ultimately lower the barrier to developing and using an IDR.

  7. ON THE POSSIBILITY OF APHILOSOPHICAL ONTOLOGY OF EVIL

    Directory of Open Access Journals (Sweden)

    ADAM DOBRZYNSKI

    2010-10-01

    Full Text Available The author attempts to analyze various responses to the problem of evil, demon-strating, that the majority of the philosophical attempts at constructing ontology of evil (or at least trying to «justify» its existence do not hold water. Evil is considered under the aspects of chaos, as the absence of good (privatio boni, or as ignorance. Dealing with evil from the social perspective is considered as a general trend in modern research. Lastly, the question of the possible expediency or utility of evil is treated from the meta-physical, aesthetic, ethical, dialectic and phenomenological point of view.

  8. An Approach for Composing Services Based on Environment Ontology

    Directory of Open Access Journals (Sweden)

    Guangjun Cai

    2013-01-01

    Full Text Available Service-oriented computing is revolutionizing the modern computing paradigms with its aim to boost software reuse and enable business agility. Under this paradigm, new services are fabricated by composing available services. The problem arises as how to effectively and efficiently compose heterogeneous services facing the high complexity of service composition. Based on environment ontology, this paper introduces a requirement-driven service composition approach. We propose the algorithms to decompose the requirement, the rules to deduct the relation between services, and the algorithm for composing service. The empirical results and the comparison with other services’ composition methodologies show that this approach is feasible and efficient.

  9. Ontology-enriched Visualization of Human Anatomy

    Energy Technology Data Exchange (ETDEWEB)

    Pouchard, LC

    2005-12-20

    The project focuses on the problem of presenting a human anatomical 3D model associated with other types of human systemic information ranging from physiological to anatomical information while navigating the 3D model. We propose a solution that integrates a visual 3D interface and navigation features with the display of structured information contained in an ontology of anatomy where the structures of the human body are formally and semantically linked. The displayed and annotated anatomy serves as a visual entry point into a patient's anatomy, medical indicators and other information. The ontology of medical information provides labeling to the highlighted anatomical parts in the 3D display. Because of the logical organization and links between anatomical objects found in the ontology and associated 3D model, the analysis of a structure by a physician is greatly enhanced. Navigation within the 3D visualization and between this visualization and objects representing anatomical concepts within the model is also featured.

  10. Toward a formal ontology for narrative

    Directory of Open Access Journals (Sweden)

    Ciotti, Fabio

    2016-03-01

    Full Text Available In this paper the rationale and the first draft of a formal ontology for modeling narrative texts are presented. Building on the semiotic and structuralist narratology, and on the work carried out in the late 1980s by Giuseppe Gigliozzi in Italy, the focus of my research are the concepts of character and of narrative world/space. This formal model is expressed in the OWL 2 ontology language. The main reason to adopt a formal modeling approach is that I consider the purely probabilistic-quantitative methods (now widespread in digital literary studies inadequate. An ontology, on one hand provides a tool for the analysis of strictly literary texts. On the other hand (though beyond the scope of the present work, its formalization can also represent a significant contribution towards grounding the application of storytelling methods outside of scholarly contexts.

  11. Matching disease and phenotype ontologies in the ontology alignment evaluation initiative.

    Science.gov (United States)

    Harrow, Ian; Jiménez-Ruiz, Ernesto; Splendiani, Andrea; Romacker, Martin; Woollard, Peter; Markel, Scott; Alam-Faruque, Yasmin; Koch, Martin; Malone, James; Waaler, Arild

    2017-12-02

    The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery and understanding the genetics of disease. Eleven systems (out of 21 OAEI participating systems) were able to cope with at least one of the tasks in the Disease and Phenotype track. AML, FCA-Map, LogMap(Bio) and PhenoMF systems produced the top results for ontology matching in comparison to consensus alignments. The results against manually curated mappings proved to be more difficult most likely because these mapping sets comprised mostly subsumption relationships rather than equivalence. Manual assessment of unique equivalence mappings showed that AML, LogMap(Bio) and PhenoMF systems have the highest precision results. Four systems gave the highest performance for matching disease and phenotype ontologies. These systems coped well with the detection of equivalence matches, but struggled to detect semantic similarity. This deserves more attention in the future development of ontology matching systems. The findings of this evaluation show that such systems could help to automate equivalence matching in the workflow of curators, who maintain ontology mapping services in numerous domains such as disease and phenotype.

  12. Selection of reference genes suitable for normalization of qPCR data under abiotic stresses in bioenergy crop Arundo donax L.

    Science.gov (United States)

    Poli, Michele; Salvi, Silvio; Li, Mingai; Varotto, Claudio

    2017-09-06

    Suitable reference gene selection in qRT-PCR is a key pre-requisite to produce reliable data in gene expression analyses. In this study, novel primers for six commonly used reference genes (AC1, TLF, Act2, TUB α, EF-1α and GAPDH) plus two new candidates (pDUF221 and RPN6) were designed and comparatively tested for expression stability under abiotic stresses (osmotic, heavy metal and heat shock) in shoot, root and their combination of Arundo donax L., a raising non-food energy crop. Expression stability rankings from the most to the least stable gene in each condition and in two tissues (young shoots and roots) were generated with geNorm, NormFinder and BestKeeper programs. All programs provided similar rankings and, strikingly, in most cases identified one of the new candidates, RPN6, as the most suitable reference gene. This novel set of reliable references allows to choose either the best combination of reference genes across multiple stress/organ conditions or to select condition-specific genes that can improve the quality of qRT-PCR analysis. This work provides a solid basis for the functional characterization of A. donax, by enabling accurate quantification of the transcriptional responsiveness under a series of common stress conditions of any gene of interest in this promising biomass/bioenergy species.

  13. Food for thought ... A toxicology ontology roadmap.

    Science.gov (United States)

    Hardy, Barry; Apic, Gordana; Carthew, Philip; Clark, Dominic; Cook, David; Dix, Ian; Escher, Sylvia; Hastings, Janna; Heard, David J; Jeliazkova, Nina; Judson, Philip; Matis-Mitchell, Sherri; Mitic, Dragana; Myatt, Glenn; Shah, Imran; Spjuth, Ola; Tcheremenskaia, Olga; Toldo, Luca; Watson, David; White, Andrew; Yang, Chihae

    2012-01-01

    Foreign substances can have a dramatic and unpredictable adverse effect on human health. In the development of new therapeutic agents, it is essential that the potential adverse effects of all candidates be identified as early as possible. The field of predictive toxicology strives to profile the potential for adverse effects of novel chemical substances before they occur, both with traditional in vivo experimental approaches and increasingly through the development of in vitro and computational methods which can supplement and reduce the need for animal testing. To be maximally effective, the field needs access to the largest possible knowledge base of previous toxicology findings, and such results need to be made available in such a fashion so as to be interoperable, comparable, and compatible with standard toolkits. This necessitates the development of open, public, computable, and standardized toxicology vocabularies and ontologies so as to support the applications required by in silico, in vitro, and in vivo toxicology methods and related analysis and reporting activities. Such ontology development will support data management, model building, integrated analysis, validation and reporting, including regulatory reporting and alternative testing submission requirements as required by guidelines such as the REACH legislation, leading to new scientific advances in a mechanistically-based predictive toxicology. Numerous existing ontology and standards initiatives can contribute to the creation of a toxicology ontology supporting the needs of predictive toxicology and risk assessment. Additionally, new ontologies are needed to satisfy practical use cases and scenarios where gaps currently exist. Developing and integrating these resources will require a well-coordinated and sustained effort across numerous stakeholders engaged in a public-private partnership. In this communication, we set out a roadmap for the development of an integrated toxicology ontology

  14. Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology.

    Science.gov (United States)

    Mortensen, Jonathan M; Telis, Natalie; Hughey, Jacob J; Fan-Minogue, Hua; Van Auken, Kimberly; Dumontier, Michel; Musen, Mark A

    2016-04-01

    Biomedical ontologies contain errors. Crowdsourcing, defined as taking a job traditionally performed by a designated agent and outsourcing it to an undefined large group of people, provides scalable access to humans. Therefore, the crowd has the potential to overcome the limited accuracy and scalability found in current ontology quality assurance approaches. Crowd-based methods have identified errors in SNOMED CT, a large, clinical ontology, with an accuracy similar to that of experts, suggesting that crowdsourcing is indeed a feasible approach for identifying ontology errors. This work uses that same crowd-based methodology, as well as a panel of experts, to verify a subset of the Gene Ontology (200 relationships). Experts identified 16 errors, generally in relationships referencing acids and metals. The crowd performed poorly in identifying those errors, with an area under the receiver operating characteristic curve ranging from 0.44 to 0.73, depending on the methods configuration. However, when the crowd verified what experts considered to be easy relationships with useful definitions, they performed reasonably well. Notably, there are significantly fewer Google search results for Gene Ontology concepts than SNOMED CT concepts. This disparity may account for the difference in performance - fewer search results indicate a more difficult task for the worker. The number of Internet search results could serve as a method to assess which tasks are appropriate for the crowd. These results suggest that the crowd fits better as an expert assistant, helping experts with their verification by completing the easy tasks and allowing experts to focus on the difficult tasks, rather than an expert replacement. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. An Ontology-centered Approach for Designing an Interactive Competence Management System for IT Companies

    Directory of Open Access Journals (Sweden)

    Stefan TRAUSAN-MATU

    2009-01-01

    Full Text Available The paper presents a generic framework for an intelligent information system of competence management based on ontologies for information technology companies. In a first step it will be applied in an information technology (IT small enterprise and then its applicability will be verified for other organizations of the same type. The work presented in the paper is performed under the project "CONTO – Ontology-based Competencies Management in Information Technology" funded by the Romanian Ministry of Education and Research, involving two universities, a research institute and an IT private company. A competence management system (CMS, in our vision has to achieve three functions: (a to support the complete and systematic acquisition of knowledge about the competence of the members of an enterprise; (b to provide the knowledge about competences and their owners; (c to apply the available knowledge to serve a purpose. The core of the competence management information system is an ontology that plays the role of the declarative knowledge repository containing the basic concepts (such as: company-job, competence, domain, group, person etc. and their relationships with other concepts, instances and properties. The Protégé environment was used for the development of this ontology. The structure of the ontology is conceived so that description logics can be used to represent the concept definitions of the application domain in a structured and formally well-understood way. Knowledge acquisition is performed in our approach by enriching the ontology, according to the requirements of the IT company. An advantage of using an ontology-based system is the possibility of the identification of new relations among concepts based on inferences starting from the existing knowledge. The user can choose to query instances of one type of concept. The paper also presents some use-cases.

  16. Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology.

    Science.gov (United States)

    Bibault, Jean-Emmanuel; Zapletal, Eric; Rance, Bastien; Giraud, Philippe; Burgun, Anita

    2018-01-01

    Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources. We present the ontology we developed to address this issue. Radiation Oncology anatomical and target volumes were categorized in anatomical and treatment planning classes. International delineation guidelines specific to radiation oncology were used for lymph nodes areas and target volumes. Hierarchical classes were created to generate The Radiation Oncology Structures (ROS) Ontology. The ROS was then applied to the data from our institution. Four hundred and seventeen classes were created with a maximum of 14 children classes (average = 5). The ontology was then converted into a Web Ontology Language (.owl) format and made available online on Bioportal and GitHub under an Apache 2.0 License. We extracted all structures delineated in our department since the opening in 2001. 20,758 structures were exported from our "record-and-verify" system, demonstrating a significant heterogeneity within a single center. All structures were matched to the ROS ontology before integration into our clinical data warehouse (CDW). In this study we describe a new ontology, specific to radiation oncology, that reports all anatomical and treatment planning structures that can be delineated. This ontology will be used to integrate dosimetric data in the Assistance Publique-Hôpitaux de Paris CDW that stores data from 6.5 million patients (as of February 2017).

  17. What is nature capable of? Evidence, ontology and speculative medical humanities.

    Science.gov (United States)

    Savransky, Martin; Rosengarten, Marsha

    2016-09-01

    Expanding on the recent call for a 'critical medical humanities' to intervene in questions of the ontology of health, this article develops a what we call a 'speculative' orientation to such interventions in relation to some of the ontological commitments on which contemporary biomedical cultures rest. We argue that crucial to this task is an approach to ontology that treats it not as a question of first principles, but as a matter of the consequences of the images of nature that contemporary biomedical research practices espouse when they make claims to evidence, as well as the possible consequences of imagining different worlds in which health and disease processes partake. By attending to the implicit ontological assumptions involved in the method par excellence of biomedical research, namely the randomised controlled trial (RCT), we argue that the mechanistic ontology that tacitly informs evidence-based biomedical research simultaneously authorises a series of problematic consequences for understanding and intervening practically in the concrete realities of health. As a response, we develop an alternative ontological proposition that regards processes of health and disease as always situated achievements. We show that, without disqualifying RCT-based evidence, such a situated ontology enables one to resist the reduction of the realities of health and disease to biomedicine's current forms of explanation. In so doing, we call for medical humanities scholars to actively engage in the speculative question of what nature may be capable of. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  18. Validation of reference genes for RT-qPCR studies of gene expression in preharvest and postharvest longan fruits under different experimental conditions

    Directory of Open Access Journals (Sweden)

    Jianyang eWu

    2016-06-01

    Full Text Available Reverse transcription quantitative PCR (RT-qPCR, a sensitive technique for quantifying gene expression, relies on stable reference gene(s for data normalization. Although a few studies have been conducted on reference gene validation in fruit trees, none have been done on preharvest and postharvest longan fruits. In this study, 12 candidate reference genes, namely, CYP, RPL, GAPDH, TUA, TUB, Fe-SOD, Mn-SOD, Cu/Zn-SOD, 18SrRNA, Actin, Histone H3 and EF-1a, were selected. Expression stability of these genes in 150 longan samples was evaluated and analyzed using geNorm and NormFinder algorithms. Preharvest samples consisted of seven experimental sets, including different developmental stages, organs, hormone stimuli (NAA, 2,4-D and ethephon and abiotic stresses (bagging and girdling with defoliation. Postharvest samples consisted of different temperature treatments (4 and 22 °C and varieties. Our findings indicate that appropriate reference gene(s should be picked for each experimental condition. Our data further showed that the commonly used reference gene Actin does not exhibit stable expression across experimental conditions in longan. Expression levels of the DlACO gene, which is a key gene involved in regulating fruit abscission under girdling with defoliation treatment, was evaluated to validate our findings. In conclusion, our data provide a useful framework for choice of suitable reference genes across different experimental conditions for RT-qPCR analysis of preharvest and postharvest longan fruits.

  19. A computer network attack taxonomy and ontology

    CSIR Research Space (South Africa)

    Van Heerden, RP

    2012-01-01

    Full Text Available taxonomy and ontology RP van Heerden1,2, B Irwin2, ID Burke1, L Leenen1 1CSIR, Pretoria, South Africa 2Rhodes University, Grahamstown, South Africa Keywords/ Key Phrases: Network Attack, Network Attack Classification, Taxonomy, Ontology, Attack... Scenario rvheerden@csir.co.za b.irwin@ru.ac.za iburke@csir.co.za lleenen@csir.co.za Abstract: Computer network attacks differ in the motivation of the entity behind the attack, the execution and the end result. The diversity of attacks has a...

  20. Patient Centric Ontology for Telehealth Domain

    DEFF Research Database (Denmark)

    Jørgensen, Daniel Bjerring; Hallenborg, Kasper; Demazeau, Yves

    2015-01-01

    to the needs, habits, and personality of the patient through user modeling and context awareness. The ontology will be our foundation for user modeling of patients in the telehealth domain, and hence it is one of the initial steps toward our vision. Compared to other ontologies within the domain, ours has...... explicit focus on: 1) personality traits of the patient, which is vital for fulfillment of our vision in term of adaptability, and 2) use of international standards to describe diseases, func-tioning and physiological measurement – ICD, ICF and SNOMED respectively – to promote interoperability...

  1. Towards unsupervised ontology learning from data

    CSIR Research Space (South Africa)

    Klarman, S

    2015-07-01

    Full Text Available [Baader et al., 2003], which have risen to promi- nence as, among others, the logics underpinning different profiles of the Web Ontology Language OWL1. In this pa- per, we focus on the lightweight DL EL [Baader et al., 2005] and some of its more specific... in establishing formal foundations for the task of ontology learning from data. Some immediate problems that are left open with this work concern finite learnability of ELlhs TBoxes in an unsupervised setting, and possibly of other lightweight fragments of DLs...

  2. Feasibility of automated foundational ontology interchangeability

    CSIR Research Space (South Africa)

    Khan, ZC

    2014-11-01

    Full Text Available by the domain entities in the tO. The full algorithm can be accessed at the ROMULUS repository at the afore- mentioned URL, and it is illustrated in the next example. Example 1. The BFO-aligned Subcellular Anatomy Ontology (SAO) is linked to DOLCE by SUGOI... mapping files, for interchanging between DOLCE↔BFO, BFO↔GFO, GFO↔DOLCE, DOLCE↔GFOBasic, and GFOBasic↔BFO. The sample size was 16 source ontologies covering various subject domains, such as data mining, animals, dermatology, and spatial scenes, of which 5...

  3. Ontological metaphors for negative energy in an interdisciplinary context

    Directory of Open Access Journals (Sweden)

    Benjamin W. Dreyfus

    2014-07-01

    Full Text Available Teaching about energy in interdisciplinary settings that emphasize coherence among physics, chemistry, and biology leads to a more central role for chemical bond energy. We argue that an interdisciplinary approach to chemical energy leads to modeling chemical bonds in terms of negative energy. While recent work on ontological metaphors for energy has emphasized the affordances of the substance ontology, this ontology is problematic in the context of negative energy. Instead, we apply a dynamic ontologies perspective to argue that blending the substance and location ontologies for energy can be effective in reasoning about negative energy in the context of reasoning about chemical bonds. We present data from an introductory physics for the life sciences course in which both experts and students successfully use this blended ontology. Blending these ontologies is most successful when the substance and location ontologies are combined such that each is strategically utilized in reasoning about particular aspects of energetic processes.

  4. Ontology-based Metadata Portal for Unified Semantics

    Data.gov (United States)

    National Aeronautics and Space Administration — The Ontology-based Metadata Portal for Unified Semantics (OlyMPUS) will extend the prototype Ontology-Driven Interactive Search Environment for Earth Sciences...

  5. Prospects and Possibilities for Ontology Evaluation: The View from NCOR

    National Research Council Canada - National Science Library

    Obrst, Leo; Hughes, Todd; Ray, Steve

    2006-01-01

    ...) on ontology evaluation. NCOR's inauguration was recently held (October 2005), and at that time goals were identified and committees formed to pursue those goals, including the Ontology Evaluation Committee...

  6. One Song, Many Works: A Pluralist Ontology of Rock

    Directory of Open Access Journals (Sweden)

    Dan Burkett

    2016-01-01

    Full Text Available A number of attempts have been made to construct a plausible ontology of rock music. Each of these ontologies identifies a single type of ontological entity as the “work” in rock music. Yet, all the suggestions advanced to date fail to capture some important considerations about how we engage with music of this tradition. This prompted Lee Brown to advocate a healthy skepticism of higher-order musical ontologies. I argue here that we should instead embrace a pluralist ontology of rock, an ontology that recognizes more than one kind of entity as “the work” in rock music. I contend that this approach has a number of advantages over other ontologies of rock, including that of allowing us to make some comparisons across ontological kinds.

  7. PSOM2—partitioning-based scalable ontology matching using ...

    Indian Academy of Sciences (India)

    B Sathiya

    2017-11-16

    -based systems to reduce the matching space. ... reduction in execution time, leading to an effective and scalable ontology matching system. Keywords. ... ontology matching results, collaborative and social ontol- ogy matching ...

  8. Annotating Evidence Based Clinical Guidelines : A Lightweight Ontology

    NARCIS (Netherlands)

    Hoekstra, R.; de Waard, A.; Vdovjak, R.; Paschke, A.; Burger, A.; Romano, P.; Marshall, M.S.; Splendiani, A.

    2012-01-01

    This paper describes a lightweight ontology for representing annotations of declarative evidence based clinical guidelines. We present the motivation and requirements for this representation, based on an analysis of several guidelines. The ontology provides the means to connect clinical questions

  9. The Ontology of Lukács and the Restoration of Ontological Criticism in Marx

    Directory of Open Access Journals (Sweden)

    Mario Duayer

    2013-06-01

    Full Text Available This article emphasizes the relevance of Lukács’ posthumous work Ontology of the Social Being for the restitution of the dimension of ontological criticism of Marxian thinking. It especially considers the chapter on labor, in which Lukács begins to delineate the social being and capture his specific categories. It is in labor, as a mediating category par excellence, that the author seeks the genesis of the categories: finality, awareness, separation of subject-object, science, alternative, value and liberty. The paper focuses on some of these categories that are not usually emphasized, including in works dedicated to Ontology.

  10. A meta-ontological framework for multi-agent systems design

    OpenAIRE

    Sokolova, Marina; Fernández Caballero, Antonio

    2007-01-01

    The paper introduces an approach to using a meta-ontology framework for complex multi-agent systems design, and illustrates it in an application related to ecological-medical issues. The described shared ontology is pooled from private sub-ontologies, which represent a problem area ontology, an agent ontology, a task ontology, an ontology of interactions, and the multi-agent system architecture ontology.

  11. Initial Implementation of a comparative Data Analysis Ontology

    Directory of Open Access Journals (Sweden)

    Francisco Prosdocimi

    2009-01-01

    Full Text Available Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: “Operational Taxonomic Units” (OTUs, representing the entities to be compared; “character-state data” representing the observations compared among OTUs; “phylogenetic tree”, representing the historical path of evolution among the entities; and “transitions”, the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL, we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO. CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc. that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research.

  12. For reflexivity as an epistemic criterion of ontological coherence and virtuous social theorizing

    Science.gov (United States)

    2017-01-01

    This article offers an approach that combines, on the one hand, the philosophical notion of reflexivity, which is related to the ideas of self-reference and paradox, and, on the other hand, the sociological discussion of epistemic reflexivity as a problem of coherence, which was mainly initiated by certain branches of ethnomethodology and social constructionism. This combinatory approach argues for reflexivity as an epistemic criterion of ontological coherence, which suggests that social ontologies should account for the possibility of self-reflective subjectivity – for otherwise they result in a paradoxical conclusion according to which a social scientist reflects on her or his ontological commitments even though these commitments deny her or him the capacity for self-reflection. This analysis presupposes that all human sciences are categorically premised on social ontologies; and it argues for an analytical distinction between self-reflection, which refers to the agential capacity for reflecting on one’s own commitments, and the epistemic criterion of reflexivity hereby proposed. These two analytically distinct though interdependent socio-theoretical concepts are frequently conflated in the literature; thus, this article also aims at a ‘clearing of the ground’ that can be of categorical use to the human sciences. PMID:29276343

  13. Regaining the Square of Opposition in Formal Ontology Development

    OpenAIRE

    Nilsson, Jørgen Fischer

    2014-01-01

    Use of formal ontologies is becoming widespread in information systems. Forerunners of formal ontologies are scientific classification systems such as the Linnaean biological ones. Unlike biological classifications modern formal ontologies are often non-hierarchical. A formal ontology in its basic form simply specifies all direct inclusion relationships between a finite repertoire of classes. Individuals may be conceived of as singleton classes. An assertion "P sub Q" states that class P is a...

  14. Text Mining to Support Gene Ontology Curation and Vice Versa.

    Science.gov (United States)

    Ruch, Patrick

    2017-01-01

    In this chapter, we explain how text mining can support the curation of molecular biology databases dealing with protein functions. We also show how curated data can play a disruptive role in the developments of text mining methods. We review a decade of efforts to improve the automatic assignment of Gene Ontology (GO) descriptors, the reference ontology for the characterization of genes and gene products. To illustrate the high potential of this approach, we compare the performances of an automatic text categorizer and show a large improvement of +225 % in both precision and recall on benchmarked data. We argue that automatic text categorization functions can ultimately be embedded into a Question-Answering (QA) system to answer questions related to protein functions. Because GO descriptors can be relatively long and specific, traditional QA systems cannot answer such questions. A new type of QA system, so-called Deep QA which uses machine learning methods trained with curated contents, is thus emerging. Finally, future advances of text mining instruments are directly dependent on the availability of high-quality annotated contents at every curation step. Databases workflows must start recording explicitly all the data they curate and ideally also some of the data they do not curate.

  15. Gene ontology based transfer learning for protein subcellular localization

    Directory of Open Access Journals (Sweden)

    Zhou Shuigeng

    2011-02-01

    Full Text Available Abstract Background Prediction of protein subcellular localization generally involves many complex factors, and using only one or two aspects of data information may not tell the true story. For this reason, some recent predictive models are deliberately designed to integrate multiple heterogeneous data sources for exploiting multi-aspect protein feature information. Gene ontology, hereinafter referred to as GO, uses a controlled vocabulary to depict biological molecules or gene products in terms of biological process, molecular function and cellular component. With the rapid expansion of annotated protein sequences, gene ontology has become a general protein feature that can be used to construct predictive models in computational biology. Existing models generally either concatenated the GO terms into a flat binary vector or applied majority-vote based ensemble learning for protein subcellular localization, both of which can not estimate the individual discriminative abilities of the three aspects of gene ontology. Results In this paper, we propose a Gene Ontology Based Transfer Learning Model (GO-TLM for large-scale protein subcellular localization. The model transfers the signature-based homologous GO terms to the target proteins, and further constructs a reliable learning system to reduce the adverse affect of the potential false GO terms that are resulted from evolutionary divergence. We derive three GO kernels from the three aspects of gene ontology to measure the GO similarity of two proteins, and derive two other spectrum kernels to measure the similarity of two protein sequences. We use simple non-parametric cross validation to explicitly weigh the discriminative abilities of the five kernels, such that the time & space computational complexities are greatly reduced when compared to the complicated semi-definite programming and semi-indefinite linear programming. The five kernels are then linearly merged into one single kernel for

  16. Towards an ontology for data quality in integrated chronic disease management: a realist review of the literature.

    Science.gov (United States)

    Liaw, S T; Rahimi, A; Ray, P; Taggart, J; Dennis, S; de Lusignan, S; Jalaludin, B; Yeo, A E T; Talaei-Khoei, A

    2013-01-01

    Effective use of routine data to support integrated chronic disease management (CDM) and population health is dependent on underlying data quality (DQ) and, for cross system use of data, semantic interoperability. An ontological approach to DQ is a potential solution but research in this area is limited and fragmented. Identify mechanisms, including ontologies, to manage DQ in integrated CDM and whether improved DQ will better measure health outcomes. A realist review of English language studies (January 2001-March 2011) which addressed data quality, used ontology-based approaches and is relevant to CDM. We screened 245 papers, excluded 26 duplicates, 135 on abstract review and 31 on full-text review; leaving 61 papers for critical appraisal. Of the 33 papers that examined ontologies in chronic disease management, 13 defined data quality and 15 used ontologies for DQ. Most saw DQ as a multidimensional construct, the most used dimensions being completeness, accuracy, correctness, consistency and timeliness. The majority of studies reported tool design and development (80%), implementation (23%), and descriptive evaluations (15%). Ontological approaches were used to address semantic interoperability, decision support, flexibility of information management and integration/linkage, and complexity of information models. DQ lacks a consensus conceptual framework and definition. DQ and ontological research is relatively immature with little rigorous evaluation studies published. Ontology-based applications could support automated processes to address DQ and semantic interoperability in repositories of routinely collected data to deliver integrated CDM. We advocate moving to ontology-based design of information systems to enable more reliable use of routine data to measure health mechanisms and impacts. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  17. Menthor Editor: An Ontology-Driven Conceptual Modeling Platform

    NARCIS (Netherlands)

    Moreira, João Luiz; Sales, Tiago Prince; Guerson, John; Braga, Bernardo F.B; Brasileiro, Freddy; Sobral, Vinicius

    2016-01-01

    The lack of well-founded constructs in ontology tools can lead to the construction of non-intended models. In this demonstration we present the Menthor Editor, an ontology-driven conceptual modelling platform which incorporates the theories of the Unified Foundational Ontology (UFO). We illustrate

  18. Towards Ontological Foundations for Agent Modeling Concepts using UFO

    NARCIS (Netherlands)

    Guizzardi, G.; Wagner, Gerd

    Foundational ontologies provide the basic concepts upon which any domain-specific ontology is built. This paper presents a new foundational ontology, UFO, and shows how it can be used as a foundation of agent concepts and for evaluating agent-oriented modeling methods. UFO is derived from a

  19. ContoExam: an ontology on context-aware examinations

    NARCIS (Netherlands)

    Brandt, P.; Basten, A.A.; Stuijk, S.

    2014-01-01

    Patient observations in health care, subjective surveys in social research or dyke sensor data in water management are all examples of measurements. Several ontologies already exist to express measurements, W3C's SSN ontology being a prominent example. However, these ontologies address quantities

  20. Developing Learning Materials Using an Ontology of Mathematical Logic

    Science.gov (United States)

    Boyatt, Russell; Joy, Mike

    2012-01-01

    Ontologies describe a body of knowledge and give formal structure to a domain by describing concepts and their relationships. The construction of an ontology provides an opportunity to develop a shared understanding and a consistent vocabulary to be used for a given activity. This paper describes the construction of an ontology for an area of…

  1. Unsupervised Ontology Generation from Unstructured Text. CRESST Report 827

    Science.gov (United States)

    Mousavi, Hamid; Kerr, Deirdre; Iseli, Markus R.

    2013-01-01

    Ontologies are a vital component of most knowledge acquisition systems, and recently there has been a huge demand for generating ontologies automatically since manual or supervised techniques are not scalable. In this paper, we introduce "OntoMiner", a rule-based, iterative method to extract and populate ontologies from unstructured or…

  2. The Relationship between User Expertise and Structural Ontology Characteristics

    Science.gov (United States)

    Waldstein, Ilya Michael

    2014-01-01

    Ontologies are commonly used to support application tasks such as natural language processing, knowledge management, learning, browsing, and search. Literature recommends considering specific context during ontology design, and highlights that a different context is responsible for problems in ontology reuse. However, there is still no clear…

  3. On the general ontological foundations of conceptual modeling

    NARCIS (Netherlands)

    Guizzardi, G.; Herre, Heinrich; Wagner, Gerd; Spaccapietra, Stefano; March, Salvatore T.; Kambayashi, Yahiko

    2002-01-01

    As pointed out in the pioneering work of [WSW99,EW01], an upper level ontology allows to evaluate the ontological correctness of a conceptual model and to develop guidelines how the constructs of a conceptual modeling language should be used. In this paper we adopt the General Ontological Language

  4. On Automatic Modeling and Use of Domain-specific Ontologies

    DEFF Research Database (Denmark)

    Andreasen, Troels; Knappe, Rasmus; Bulskov, Henrik

    2005-01-01

    In this paper, we firstly introduce an approach to the modeling of a domain-specific ontology for use in connection with a given document collection. Secondly, we present a methodology for deriving conceptual similarity from the domain-specific ontology. Adopted for ontology representation is a s...

  5. On Automatic Modeling and Use of Domain-specific Ontologies

    DEFF Research Database (Denmark)

    Andreasen, Troels; Knappe, Rasmus; Bulskov, Henrik

    2005-01-01

    collection the general ontology is restricted to a domain specific ontology encompassing concepts instantiated in the collection. The resulting domain specific ontology and similarity can be applied for surveying the collection through key concepts and conceptual relations and provides a means for topic...

  6. Process Ontology Specification for Enhancing the Process Compliance of a Measurement and Evaluation Strategy

    Directory of Open Access Journals (Sweden)

    Pablo Becker

    2015-04-01

    Full Text Available In this paper, we specify a generic ontology for the process domain considering the related state-of-the-art research literature. As a result, the recently built process ontology contributes to enrich semantically the terms for the (previously developed measurement and evaluation domain ontology by means of stereotypes. One of the underlying hypothesis in this research is that the generic ontology for process can be seen as a reusable artifact which can be used to enrich semantically not only the measurement and evaluation domain ontology but also to other domains involved in different organizational endeavors. For instance, for the measurement domain, now is explicit that the measurement term has the semantic of task, the measure term has the meaning of outcome, and the metric term has the semantic of method, from the process terminological base standpoint. The augmented conceptual framework, i.e. measurement and evaluation concepts plus process concepts, has also a positive impact on the GOCAME (Goal-Oriented Context-Aware Measurement and Evaluation strategy capabilities since ensures terminological uniformity, consistency and verifiability to its process and method specifications. In order to illustrate how the augmented conceptual framework impacts on the verifiability of GOCAME process and method specifications in addition to the consistency and comparability of results in measurement and evaluation projects, an ICT (Information and Communications Technology security and risk evaluation case study is used.

  7. MaHCO: an ontology of the major histocompatibility complex for immunoinformatic applications and text mining.

    Science.gov (United States)

    DeLuca, David S; Beisswanger, Elena; Wermter, Joachim; Horn, Peter A; Hahn, Udo; Blasczyk, Rainer

    2009-08-15

    The high level of polymorphism associated with the major histocompatibility complex (MHC) poses a challenge to organizing associated bioinformatic data, particularly in the area of hematopoietic stem cell transplantation. Thus, this area of research has great potential to profit from the ongoing development of biomedical ontologies, which offer structure and definition to MHC-data related communication and portability issues. We introduce the design considerations, methodological foundations and implementational issues underlying MaHCO, an ontology which represents the alleles and encoded molecules of the major histocompatibility complex. Importantly for human immunogenetics, it includes a detailed level of human leukocyte antigen (HLA) classification. We then present an ontology browser, search interfaces for immunogenetic fact and document retrieval, and the specification of an annotation language for semantic metadata, based on MaHCO. These use cases are intended to demonstrate the utility of ontology-driven bioinformatics in the field of immunogenetics. The MaHCO Ontology is available via the BioPortal: http://www.bioontology.org/tools/portal/bioportal.html, and at: http://purl.org/stemnet/.

  8. A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes.

    Science.gov (United States)

    Hansen, Jens; Meretzky, David; Woldesenbet, Simeneh; Stolovitzky, Gustavo; Iyengar, Ravi

    2017-12-18

    Whole cell responses arise from coordinated interactions between diverse human gene products functioning within various pathways underlying sub-cellular processes (SCP). Lower level SCPs interact to form higher level SCPs, often in a context specific manner to give rise to whole cell function. We sought to determine if capturing such relationships enables us to describe the emergence of whole cell functions from interacting SCPs. We developed the Molecular Biology of the Cell Ontology based on standard cell biology and biochemistry textbooks and review articles. Currently, our ontology contains 5,384 genes, 753 SCPs and 19,180 expertly curated gene-SCP associations. Our algorithm to populate the SCPs with genes enables extension of the ontology on demand and the adaption of the ontology to the continuously growing cell biological knowledge. Since whole cell responses most often arise from the coordinated activity of multiple SCPs, we developed a dynamic enrichment algorithm that flexibly predicts SCP-SCP relationships beyond the current taxonomy. This algorithm enables us to identify interactions between SCPs as a basis for higher order function in a context dependent manner, allowing us to provide a detailed description of how SCPs together can give rise to whole cell functions. We conclude that this ontology can, from omics data sets, enable the development of detailed SCP networks for predictive modeling of emergent whole cell functions.

  9. Identification and validation of reference genes for quantification of target gene expression with quantitative real-time PCR for tall fescue under four abiotic stresses.

    Directory of Open Access Journals (Sweden)

    Zhimin Yang

    Full Text Available Tall fescue (Festuca arundinacea Schreb. is widely utilized as a major forage and turfgrass species in the temperate regions of the world and is a valuable plant material for studying molecular mechanisms of grass stress tolerance due to its superior drought and heat tolerance among cool-season species. Selection of suitable reference genes for quantification of target gene expression is important for the discovery of molecular mechanisms underlying improved growth traits and stress tolerance. The stability of nine potential reference genes (ACT, TUB, EF1a, GAPDH, SAND, CACS, F-box, PEPKR1 and TIP41 was evaluated using four programs, GeNorm, NormFinder, BestKeeper, and RefFinder. The combinations of SAND and TUB or TIP41 and TUB were most stably expressed in salt-treated roots or leaves. The combinations of GAPDH with TIP41 or TUB were stable in roots and leaves under drought stress. TIP41 and PEPKR1 exhibited stable expression in cold-treated roots, and the combination of F-box, TIP41 and TUB was also stable in cold-treated leaves. CACS and TUB were the two most stable reference genes in heat-stressed roots. TIP41 combined with TUB and ACT was stably expressed in heat-stressed leaves. Finally, quantitative real-time polymerase chain reaction (qRT-PCR assays of the target gene FaWRKY1 using the identified most stable reference genes confirmed the reliability of selected reference genes. The selection of suitable reference genes in tall fescue will allow for more accurate identification of stress-tolerance genes and molecular mechanisms conferring stress tolerance in this stress-tolerant species.

  10. Structure-based classification and ontology in chemistry

    Directory of Open Access Journals (Sweden)

    Hastings Janna

    2012-04-01

    Full Text Available Abstract Background Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those results, become even harder problems. Computational processing is essential to filter and organise the available resources so as to better facilitate the work of scientists. Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI. ChEBI provides a classification of chemicals based on their structural features and a role or activity-based classification. An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures, while an example of a role-based class is 'analgesic', since many different chemicals can act as analgesics without sharing structural features. Structure-based classification in chemistry exploits elegant regularities and symmetries in the underlying chemical domain. As yet, there has been neither a systematic analysis of the types of structural classification in use in chemistry nor a comparison to the capabilities of available technologies. Results We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches. Conclusion Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational

  11. Towards transgressive learning through ontological politics

    NARCIS (Netherlands)

    Chaves Villegas, Martha; Macintyre, Thomas; Verschoor, Gerard; Wals, Arjen E.J.

    2017-01-01

    In line with the increasing calls for more transformative and transgressive learning in the context of sustainability studies, this article explores how encounters between different ontologies can lead to socio-ecological sustainability. With the dominant one-world universe increasingly being

  12. Implementation of Ontology Mapping for Computational Agents

    Czech Academy of Sciences Publication Activity Database

    Neruda, Roman

    2006-01-01

    Roč. 1, č. 1 (2006), s. 58-63 ISSN 1991-8755 R&D Projects: GA AV ČR 1ET100300419 Institutional research plan: CEZ:AV0Z10300504 Keywords : multi-agent systems * ontology * computational intelligence Subject RIV: IN - Informatics, Computer Science

  13. A priorean approach to time ontologies

    DEFF Research Database (Denmark)

    Øhrstrøm, Peter; Schärfe, Henrik

    2004-01-01

    Any non-trivial top-level ontology should take temporal notions into account. The details of how this should be done, however, are frequently debated. In this paper it is argued that "the four grades of tense-logical involvement" suggested by A.N. Prior form a useful framework for discussing how...

  14. A case study in ontology library construction

    NARCIS (Netherlands)

    van Heijst, G.; Falasconi, S.; Abu-Hanna, A.; Schreiber, G.; Stefanelli, M.

    1995-01-01

    The goal of our work is to facilitate the development of medical knowledge-based systems by providing a library of reusable ontologies. The availability of such a library reduces the amount of knowledge acquisition required to create knowledge bases of new applications, and makes it easier to

  15. Ontologies for commitment-based smart contracts

    NARCIS (Netherlands)

    de Kruijff, Joost; Weigand, Hans; Panetto, H; Debruyne, C.; Gaaloul, W.; Papazoglou, M.; Paschke, A.; Ardagna, C.A.; Meersman, R.

    2017-01-01

    Smart contracts gain rapid exposure since the inception of blockchain technology. Yet there is no unified ontology for smart contracts. Being categorized as coded contracts or substitutes of conventional legal contracts, there is a need to reduce the conceptual ambiguity of smart contracts. We

  16. Contributions to a Conceptual Ontology for Wittgenstein

    DEFF Research Database (Denmark)

    Addis, Mark; Brock, Steen; Pichler, Alois

    2015-01-01

    A conceptual ontology was used to semantically enrich the Wittgenstein Archives at the University of Bergen’s taxonomy for Wittgenstein Source to facilitate improved searching in the areas of the philosophies of mathematics and psychology. The classes and sub-classes of the multilingual taxonomy...

  17. Development of an Ontology for Occupational Exposure

    Science.gov (United States)

    When discussing a scientific domain, the use of a common language is required, particularly when communicating across disciplines. This common language, or ontology, is a prescribed vocabulary and a web of contextual relationships within the vocabulary that describe the given dom...

  18. Toward an Ontology of Simulated Social Interaction

    DEFF Research Database (Denmark)

    Seibt, Johanna

    2017-01-01

    The paper develops a general conceptual framework for the ontological classification of human-robot interaction. After arguing against fictionalist interpretations of human-robot interactions, I present five notions of simulation or partial realization, formally defined in terms of relationships...

  19. Africanity: A Combative Ontology | Mafeje | CODESRIA Bulletin

    African Journals Online (AJOL)

    Africanity: A Combative Ontology. Archie Mafeje. AJOL African Journals Online. HOW TO USE AJOL... for Researchers · for Librarians · for Authors · FAQ's · More about AJOL · AJOL's Partners · Terms and Conditions of Use · Contact AJOL · News. OTHER RESOURCES... for Researchers · for Journals · for Authors · for Policy ...

  20. Activity theories and the ontology of psychology

    DEFF Research Database (Denmark)

    Mammen, Jens Skaun; Mironenko, Irina

    2015-01-01

    to exceed some, mostly implicit, ontological restrictions in traditional AT and free it from an embracement of functionalism and mechanicism, rooted in Renaissance Physics. The analysis goes back to Aristotle’s understanding of the freely moving animal in its ecology and introduces some dualities...

  1. Asian Educational Discourse: Construction of Ontological Security

    Science.gov (United States)

    Khalina, Natalya V.; Kovaleva, Alla V.; Voronin, Maksim S.; Anikin, Denis V.; Valyulina, Ekaterina V.

    2018-01-01

    This article considers the problem of ontology security through Asian educational discourse, which is structurally determined by the process of moral self-improvement. Considered are trends in improving the management of educational system by developing the culture of quality, which is considered as the next stage of the Asian education systems…

  2. Ontological semantics in modified categorial grammar

    DEFF Research Database (Denmark)

    Szymczak, Bartlomiej Antoni

    2009-01-01

    Categorial Grammar is a well established tool for describing natural language semantics. In the current paper we discuss some of its drawbacks and how it could be extended to overcome them. We use the extended version for deriving ontological semantics from text. A proof-of-concept implementation...

  3. Løgstrup’s Ontological Ethics

    DEFF Research Database (Denmark)

    Rabjerg, Bjørn

    2017-01-01

    to different aspects of ontological ethics. By negative and positive I mean the two opposing possibilities of all human interaction that we can either destroy the other person’s life (to a greater or smaller degree) or cause the other person’s life to flourish. We can either be a blessing in the other person...

  4. Historical and Conceptual Foundation of Diagrammatical Ontology

    DEFF Research Database (Denmark)

    Øhrstrøm, Peter; Uckelman, Sara L.; Schärfe, Henrik

    2007-01-01

    During the Renaissance there was a growing interest for the use of diagrams within conceptual studies. This paper investigates the historical and philosophical foundation of this renewed use of diagrams in ontology as well as the modern relevance of this foundation. We discuss the historical...

  5. Rehabilitation robotics ontology on the cloud.

    Science.gov (United States)

    Dogmus, Zeynep; Papantoniou, Agis; Kilinc, Muhammed; Yildirim, Sibel A; Erdem, Esra; Patoglu, Volkan

    2013-06-01

    We introduce the first formal rehabilitation robotics ontology, called RehabRobo-Onto, to represent information about rehabilitation robots and their properties; and a software system RehabRobo-Query to facilitate access to this ontology. RehabRobo-Query is made available on the cloud, utilizing Amazon Web services, so that 1) rehabilitation robot designers around the world can add/modify information about their robots in RehabRobo-Onto, and 2) rehabilitation robot designers and physical medicine experts around the world can access the knowledge in RehabRobo-Onto by means of questions about robots, in natural language, with the guide of the intelligent userinterface of RehabRobo-Query. The ontology system consisting of RehabRobo-Onto and RehabRobo-Query is of great value to robot designers as well as physical therapists and medical doctors. On the one hand, robot designers can access various properties of the existing robots and to the related publications to further improve the state-of-the-art. On the other hand, physical therapists and medical doctors can utilize the ontology to compare rehabilitation robots and to identify the ones that serve best to cover their needs, or to evaluate the effects of various devices for targeted joint exercises on patients with specific disorders.

  6. New trends of research in ontologies and lexical resources ideas, projects, systems

    CERN Document Server

    Oltramari, Alessandro; Qin, Lu

    2011-01-01

    In order to exchange knowledge, humans need to share a common lexicon of words as well as to access the world models underlying that lexicon. What is a natural process for a human turns out to be an extremely hard task for a machine: computers can't represent knowledge as effectively as humans do, which hampers, for example, meaning disambiguation and communication. Applied ontologies and NLP have been developed to face these challenges. Integrating ontologies with (possibly multilingual) lexical resources is an essential requirement to make human language understandable by machines, and also

  7. COMe: the ontology of bioinorganic proteins

    Directory of Open Access Journals (Sweden)

    Contrino Sergio

    2004-02-01

    Full Text Available Abstract Background Many characterised proteins contain metal ions, small organic molecules or modified residues. In contrast, the huge amount of data generated by genome projects consists exclusively of sequences with almost no annotation. One of the goals of the structural genomics initiative is to provide representative three-dimensional (3-D structures for as many protein/domain folds as possible to allow successful homology modelling. However, important functional features such as metal co-ordination or a type of prosthetic group are not always conserved in homologous proteins. So far, the problem of correct annotation of bioinorganic proteins has been largely ignored by the bioinformatics community and information on bioinorganic centres obtained by methods other than crystallography or NMR is only available in literature databases. Results COMe (Co-Ordination of Metals represents the ontology for bioinorganic and other small molecule centres in complex proteins. COMe consists of three types of entities: 'bioinorganic motif' (BIM, 'molecule' (MOL, and 'complex proteins' (PRX, with each entity being assigned a unique identifier. A BIM consists of at least one centre (metal atom, inorganic cluster, organic molecule and two or more endogenous and/or exogenous ligands. BIMs are represented as one-dimensional (1-D strings and 2-D diagrams. A MOL entity represents a 'small molecule' which, when in complex with one or more polypeptides, forms a functional protein. The PRX entities refer to the functional proteins as well as to separate protein domains and subunits. The complex proteins in COMe are subdivided into three categories: (i metalloproteins, (ii organic prosthetic group proteins and (iii modified amino acid proteins. The data are currently stored in both XML format and a relational database and are available at http://www.ebi.ac.uk/come/. Conclusion COMe provides the classification of proteins according to their 'bioinorganic' features

  8. Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.

    Science.gov (United States)

    Chen, Guocai; Zhao, Jieyi; Cohen, Trevor; Tao, Cui; Sun, Jingchun; Xu, Hua; Bernstam, Elmer V; Lawson, Andrew; Zeng, Jia; Johnson, Amber M; Holla, Vijaykumar; Bailey, Ann M; Lara-Guerra, Humberto; Litzenburger, Beate; Meric-Bernstam, Funda; Jim Zheng, W

    2015-01-01

    Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names. We obtained 93.6% precision for the test gene set and 80.4% for the area under a receiver-operating characteristics curve for gene and article association. The core algorithm was implemented using a graphics processing unit-based MapReduce framework to handle big data and to improve performance. We conclude that Ontology Fingerprints can help disambiguate gene names mentioned in text and analyse the association between genes and articles. Database URL: http://www.ontologyfingerprint.org © The Author(s) 2015. Published by Oxford University Press.

  9. Ontology-Based Device Descriptions and Device Repository for Building Automation Devices

    Directory of Open Access Journals (Sweden)

    Dibowski Henrik

    2011-01-01

    Full Text Available Device descriptions play an important role in the design and commissioning of modern building automation systems and help reducing the design time and costs. However, all established device descriptions are specialized for certain purposes and suffer from several weaknesses. This hinders a further design automation, which is strongly needed for the more and more complex building automation systems. To overcome these problems, this paper presents novel Ontology-based Device Descriptions (ODDs along with a layered ontology architecture, a specific ontology view approach with virtual properties, a generic access interface, a triple store-based database backend, and a generic search mask GUI with underlying query generation algorithm. It enables a formal, unified, and extensible specification of building automation devices, ensures their comparability, and facilitates a computer-enabled retrieval, selection, and interoperability evaluation, which is essential for an automated design. The scalability of the approach to several ten thousand devices is demonstrated.

  10. Mapping between the OBO and OWL ontology languages.

    Science.gov (United States)

    Tirmizi, Syed Hamid; Aitken, Stuart; Moreira, Dilvan A; Mungall, Chris; Sequeda, Juan; Shah, Nigam H; Miranker, Daniel P

    2011-03-07

    Ontologies are commonly used in biomedicine to organize concepts to describe domains such as anatomies, environments, experiment, taxonomies etc. NCBO BioPortal currently hosts about 180 different biomedical ontologies. These ontologies have been mainly expressed in either the Open Biomedical Ontology (OBO) format or the Web Ontology Language (OWL). OBO emerged from the Gene Ontology, and supports most of the biomedical ontology content. In comparison, OWL is a Semantic Web language, and is supported by the World Wide Web consortium together with integral query languages, rule languages and distributed infrastructure for information interchange. These features are highly desirable for the OBO content as well. A convenient method for leveraging these features for OBO ontologies is by transforming OBO ontologies to OWL. We have developed a methodology for translating OBO ontologies to OWL using the organization of the Semantic Web itself to guide the work. The approach reveals that the constructs of OBO can be grouped together to form a similar layer cake. Thus we were able to decompose the problem into two parts. Most OBO constructs have easy and obvious equivalence to a construct in OWL. A small subset of OBO constructs requires deeper consideration. We have defined transformations for all constructs in an effort to foster a standard common mapping between OBO and OWL. Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness. Our Java implementation of the mapping is part of the official Gene Ontology project source. Our transformation system provides a lossless roundtrip mapping for OBO ontologies, i.e. an OBO ontology may be translated to OWL and back without loss of knowledge. In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner.

  11. Cross-Ontology Multi-level Association Rule Mining in the Gene Ontology

    Science.gov (United States)

    Manda, Prashanti; Ozkan, Seval; Wang, Hui; McCarthy, Fiona; Bridges, Susan M.

    2012-01-01

    The Gene Ontology (GO) has become the internationally accepted standard for representing function, process, and location aspects of gene products. The wealth of GO annotation data provides a valuable source of implicit knowledge of relationships among these aspects. We describe a new method for association rule mining to discover implicit co-occurrence relationships across the GO sub-ontologies at multiple levels of abstraction. Prior work on association rule mining in the GO has concentrated on mining knowledge at a single level of abstraction and/or between terms from the same sub-ontology. We have developed a bottom-up generalization procedure called Cross-Ontology Data Mining-Level by Level (COLL) that takes into account the structure and semantics of the GO, generates generalized transactions from annotation data and mines interesting multi-level cross-ontology association rules. We applied our method on publicly available chicken and mouse GO annotation datasets and mined 5368 and 3959 multi-level cross ontology rules from the two datasets respectively. We show that our approach discovers more and higher quality association rules from the GO as evaluated by biologists in comparison to previously published methods. Biologically interesting rules discovered by our method reveal unknown and surprising knowledge about co-occurring GO terms. PMID:23071802

  12. Decision making under risk : a study of models and measurement procedures with special reference to the farmer's marketing behavior

    NARCIS (Netherlands)

    Smidts, A.

    1990-01-01

    The objectives of the study were: a) to review, discuss and test a number of theories on individual decision making under risk; much attention is specifically given to the definition and empirical testing of the concept of relative risk attitude, b) to investigate in a large scale survey

  13. A Stationary Reference Frame Grid Synchronization System for Three-Phase Grid-Connected Power Converters Under Adverse Grid Conditions

    DEFF Research Database (Denmark)

    Rodríguez, P.; Luna, A.; Muñoz-Aguilar, R. S.

    2012-01-01

    Grid synchronization algorithms are of great importance in the control of grid-connected power converters, as fast and accurate detection of the grid voltage parameters is crucial in order to implement stable control strategies under generic grid conditions. This paper presents a new grid synchro...

  14. Decision making under risk. A study of models and measurement procedures with special reference to the farmers' marketing behavior

    NARCIS (Netherlands)

    A. Smidts (Ale)

    1990-01-01

    textabstractThe objectives of the study were: a) to review, discuss and test a number of theories on individual decision making under risk; much attention is specifically given to the definition and empirical testing of the concept of relative risk attitude, b) to investigate in a large scale survey

  15. Selection and Validation of Housekeeping Genes as Reference for Gene Expression Studies in Pigeonpea (Cajanus cajan) under Heat and Salt Stress Conditions.

    Science.gov (United States)

    Sinha, Pallavi; Saxena, Rachit K; Singh, Vikas K; Krishnamurthy, L; Varshney, Rajeev K

    2015-01-01

    To identify stable housekeeping genes as a reference for expression analysis under heat and salt stress conditions in pigeonpea, the relative expression variation for 10 commonly used housekeeping genes (EF1α, UBQ10, GAPDH, 18Sr RNA, 25Sr RNA, TUB6, ACT1, IF4α, UBC, and HSP90) was studied in root, stem, and leaves tissues of Asha (ICPL 87119), a leading pigeonpea variety. Three statistical algorithms geNorm, NormFinder, and BestKeeper were used to define the stability of candidate genes. Under heat stress, UBC, HSP90, and GAPDH were found to be the most stable reference genes. In the case of salinity stress, GAPDH followed by UBC and HSP90 were identified to be the most stable reference genes. Subsequently, the above identified genes were validated using qRT-PCR based gene expression analysis of two universal stress-resposive genes namely uspA and uspB. The relative quantification of these two genes varied according to the internal controls (most stable, least stable, and combination of most stable and least stable housekeeping genes) and thus confirmed the choice as well as validation of internal controls in such experiments. The identified and validated housekeeping genes will facilitate gene expression studies under heat and salt stress conditions in pigeonpea.

  16. A histological ontology of the human cardiovascular system.

    Science.gov (United States)

    Mazo, Claudia; Salazar, Liliana; Corcho, Oscar; Trujillo, Maria; Alegre, Enrique

    2017-10-02

    In this paper, we describe a histological ontology of the human cardiovascular system developed in collaboration among histology experts and computer scientists. The histological ontology is developed following an existing methodology using Conceptual Models (CMs) and validated using OOPS!, expert evaluation with CMs, and how accurately the ontology can answer the Competency Questions (CQ). It is publicly available at http://bioportal.bioontology.org/ontologies/HO and https://w3id.org/def/System . The histological ontology is developed to support complex tasks, such as supporting teaching activities, medical practices, and bio-medical research or having natural language interactions.

  17. Logical Characterisation of Ontology Construction using Fuzzy Description Logics

    DEFF Research Database (Denmark)

    Badie, Farshad; Götzsche, Hans

    Ontologies based on Description Logics (DLs) have proved to be effective in formally sharing knowledge across semantic technologies, e.g. Semantic Web, Natural Language Processing, Text Analytics, Business intelligence. Our main goal is analysing ontology construction considering vagueness. We have...... had the extension of ontologies with Fuzzy Logic capabilities which plan to make proper backgrounds for ontology driven reasoning and argumentation on vague and imprecise domains. This presentation conceptualises learning from fuzzy classes using the Inductive Logic Programming framework. Then......, employs Description Logics in characterising and analysing fuzzy statements. And finally, provides a conceptual framework describing fuzzy concept learning in ontologies using the Inductive Logic Programming....

  18. Scenario testing using formal ontologies

    CSIR Research Space (South Africa)

    Harmse, HF

    2014-09-01

    Full Text Available project that has been done for a South African hotel group where scenario testing has been employed to detect and rectify errors during the requirements phase of the SDLC. In the hospitality industry the business requirements around calculating the rate.... Firstly a flat rate can be charged across all rooms in the hotel. Secondly the rate can be charged based on the number of guests who form part of the booking. In the hospitality industry this is often referred to as PAX. Lastly the rate can be determined...

  19. An Organizational Knowledge Ontology for Automotive Supply Chains

    Science.gov (United States)

    Hellingrath, Bernd; Witthaut, Markus; Böhle, Carsten; Brügger, Stephan

    The currently completed ILIPT (Intelligent Logistics for Innovative Product Technologies) project was concerned with the concept of the “5 day car” (a customized car that is delivered within five days after its ordering) and encompassed extensive research on the required production and logistics network structures and processes. As car manufacturers in the automotive industry (commonly referred to as OEMs) rely heavily on their suppliers, the major challenge lies in the organization of inter-enterprise cooperation supported by information systems (IS) in an efficient manner. A common understanding of supply chain concepts is indispensable for this. Ontologies as formal representations of concepts can be used as a semantic basis for cooperation. Relevant results from ILIPT are presented followed by a concept as well as a prototype of how to transfer the theoretical findings to a practical implementation, in this case a multi-agent system.

  20. Ontology for assessment studies of human-computer-interaction in surgery.

    Science.gov (United States)

    Machno, Andrej; Jannin, Pierre; Dameron, Olivier; Korb, Werner; Scheuermann, Gerik; Meixensberger, Jürgen

    2015-02-01

    New technologies improve modern medicine, but may result in unwanted consequences. Some occur due to inadequate human-computer-interactions (HCI). To assess these consequences, an investigation model was developed to facilitate the planning, implementation and documentation of studies for HCI in surgery. The investigation model was formalized in Unified Modeling Language and implemented as an ontology. Four different top-level ontologies were compared: Object-Centered High-level Reference, Basic Formal Ontology, General Formal Ontology (GFO) and Descriptive Ontology for Linguistic and Cognitive Engineering, according to the three major requirements of the investigation model: the domain-specific view, the experimental scenario and the representation of fundamental relations. Furthermore, this article emphasizes the distinction of "information model" and "model of meaning" and shows the advantages of implementing the model in an ontology rather than in a database. The results of the comparison show that GFO fits the defined requirements adequately: the domain-specific view and the fundamental relations can be implemented directly, only the representation of the experimental scenario requires minor extensions. The other candidates require wide-ranging extensions, concerning at least one of the major implementation requirements. Therefore, the GFO was selected to realize an appropriate implementation of the developed investigation model. The ensuing development considered the concrete implementation of further model aspects and entities: sub-domains, space and time, processes, properties, relations and functions. The investigation model and its ontological implementation provide a modular guideline for study planning, implementation and documentation within the area of HCI research in surgery. This guideline helps to navigate through the whole study process in the form of a kind of standard or good clinical practice, based on the involved foundational frameworks

  1. Improving ontologies by automatic reasoning and evaluation of logical definitions

    Directory of Open Access Journals (Sweden)

    Köhler Sebastian

    2011-10-01

    Full Text Available Abstract Background Ontologies are widely used to represent knowledge in biomedicine. Systematic approaches for detecting errors and disagreements are needed for large ontologies with hundreds or thousands of terms and semantic relationships. A recent approach of defining terms using logical definitions is now increasingly being adopted as a method for quality control as well as for facilitating interoperability and data integration. Results We show how automated reasoning over logical definitions of ontology terms can be used to improve ontology structure. We provide the Java software package GULO (Getting an Understanding of LOgical definitions, which allows fast and easy evaluation for any kind of logically decomposed ontology by generating a composite OWL ontology from appropriate subsets of the referenced ontologies and comparing the inferred relationships with the relationships asserted in the target ontology. As a case study we show how to use GULO to evaluate the logical definitions that have been developed for the Mammalian Phenotype Ontology (MPO. Conclusions Logical definitions of terms from biomedical ontologies represent an important resource for error and disagreement detection. GULO gives ontology curators a fast and simple tool for validation of their work.

  2. Negative findings in electronic health records and biomedical ontologies: a realist approach.

    Science.gov (United States)

    Ceusters, Werner; Elkin, Peter; Smith, Barry

    2007-12-01

    A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in "absence of pulse" or "surgical procedure not performed"). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. The purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. We introduced a new family of 'lacks' relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal u when p has no instance of u as part. Since p and u both exist, assertions involving 'lacks_part' and its cognates meet the requirements of positivity. By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied.

  3. Research on the complex network of the UNSPSC ontology

    Science.gov (United States)

    Xu, Yingying; Zou, Shengrong; Gu, Aihua; Wei, Li; Zhou, Ta

    The UNSPSC ontology mainly applies to the classification system of the e-business and governments buying the worldwide products and services, and supports the logic structure of classification of the products and services. In this paper, the related technologies of the complex network were applied to analyzing the structure of the ontology. The concept of the ontology was corresponding to the node of the complex network, and the relationship of the ontology concept was corresponding to the edge of the complex network. With existing methods of analysis and performance indicators in the complex network, analyzing the degree distribution and community of the ontology, and the research will help evaluate the concept of the ontology, classify the concept of the ontology and improve the efficiency of semantic matching.

  4. Child cancer follow-up ontology and information system

    DEFF Research Database (Denmark)

    El-Subaihi, J.A.; Anton, François; Mioc, Darka

    2013-01-01

    brings the methodology for child cancer treatment plan that produces an ontology to create a conceptual model and a database model. To construct the ontology, the "methontology" method is used as a structured approach for the ontology process. The method guides the ontology developer from scratch...... to building a complete model. The ontology is developed in two phases. In the first phase, research from other countries and process models are reviewed and the generic model is built from this research. The generic model is adapted to the ontology for the Danish hospitals including the NOPHO-ALL 2008...... protocol. To develop the ontology, a data dictionary is first proposed. Then, the relationships between concepts are identified and verified: the oriented graph, where nodes are concepts and oriented edges are dependence relationships, where the definition of the concept at the origin of the edge depends...

  5. Crowdsourcing the verification of relationships in biomedical ontologies.

    Science.gov (United States)

    Mortensen, Jonathan M; Musen, Mark A; Noy, Natalya F

    2013-01-01

    Biomedical ontologies are often large and complex, making ontology development and maintenance a challenge. To address this challenge, scientists use automated techniques to alleviate the difficulty of ontology development. However, for many ontology-engineering tasks, human judgment is still necessary. Microtask crowdsourcing, wherein human workers receive remuneration to complete simple, short tasks, is one method to obtain contributions by humans at a large scale. Previously, we developed and refined an effective method to verify ontology hierarchy using microtask crowdsourcing. In this work, we report on applying this method to find errors in the SNOMED CT CORE subset. By using crowdsourcing via Amazon Mechanical Turk with a Bayesian inference model, we correctly verified 86% of the relations from the CORE subset of SNOMED CT in which Rector and colleagues previously identified errors via manual inspection. Our results demonstrate that an ontology developer could deploy this method in order to audit large-scale ontologies quickly and relatively cheaply.

  6. The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions.

    Science.gov (United States)

    Wirkner, Christian S; Göpel, Torben; Runge, Jens; Keiler, Jonas; Klussmann-Fricke, Bastian-Jesper; Huckstorf, Katarina; Scholz, Stephan; Mikó, István; J Yoder, Matthew; Richter, Stefan

    2017-09-01

    Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the "linguistic problem of morphology", concerns the usage of terminology and also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use of phenotypic data in systematics and evolutionary biology. We therefore argue, that for morphological descriptions, the basis of all systematic and evolutionary interpretations, ontologies need to be utilized which are based exclusively on structural qualities/properties and which in no case include statements about homology and/or function. Statements about homology and function constitute interpretations on a different or higher level. Based on these "anatomy ontologies", further ontological dimensions (e.g., referring to functional properties or homology) may be exerted for a broad use in evolutionary phenomics. To this end we present the first organ-based ontology for the most species-rich animal group, the Arthropoda. Our Ontology of Arthropod Circulatory Systems (OArCS) contains a comprehensive collection of 383 terms (i.e., labels) tied to 296 concepts (i.e., definitions) collected from the literature on phenotypic aspects of circulatory organ features in arthropods. All of the concepts used in OArCS are based exclusively on structural features, and in the context of the ontology are independent of homology and functional assumptions. We cannot rule out that in some cases, terms are used which in traditional usage and previous accounts might have implied homology and/or function (e.g. heart, sternal artery). Concepts are composed of descriptive elements that are used to classify observed instances into the organizational framework of the

  7. Automated compound classification using a chemical ontology

    Directory of Open Access Journals (Sweden)

    Bobach Claudia

    2012-12-01

    Full Text Available Abstract Background Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound databases. MeSH and recently ChEBI are examples of chemical ontologies that provide a hierarchical classification of compounds into general compound classes of biological interest based on their structural as well as property or use features. In these ontologies, compounds have been assigned manually to their respective classes. However, with the ever increasing possibilities to extract new compounds from text documents using name-to-structure tools and considering the large number of compounds deposited in databases, automated and comprehensive chemical classification methods are needed to avoid the error prone and time consuming manual classification of compounds. Results In the present work we implement principles and methods to construct a chemical ontology of classes that shall support the automated, high-quality compound classification in chemical databases or text documents. While SMARTS expressions have already been used to define chemical structure class concepts, in the present work we have extended the expressive power of such class definitions by expanding their structure-based reasoning logic. Thus, to achieve the required precision and granularity of chemical class definitions, sets of SMARTS class definitions are connected by OR and NOT logical operators. In addition, AND logic has been implemented to allow the concomitant use of flexible atom lists and stereochemistry definitions. The resulting chemical ontology is a multi-hierarchical taxonomy of concept nodes connected by directed, transitive relationships. Conclusions A proposal for a rule based definition of chemical classes has been made that allows to define chemical compound classes more precisely than before. The proposed structure-based reasoning

  8. Automated compound classification using a chemical ontology.

    Science.gov (United States)

    Bobach, Claudia; Böhme, Timo; Laube, Ulf; Püschel, Anett; Weber, Lutz

    2012-12-29

    Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound databases. MeSH and recently ChEBI are examples of chemical ontologies that provide a hierarchical classification of compounds into general compound classes of biological interest based on their structural as well as property or use features. In these ontologies, compounds have been assigned manually to their respective classes. However, with the ever increasing possibilities to extract new compounds from text documents using name-to-structure tools and considering the large number of compounds deposited in databases, automated and comprehensive chemical classification methods are needed to avoid the error prone and time consuming manual classification of compounds. In the present work we implement principles and methods to construct a chemical ontology of classes that shall support the automated, high-quality compound classification in chemical databases or text documents. While SMARTS expressions have already been used to define chemical structure class concepts, in the present work we have extended the expressive power of such class definitions by expanding their structure-based reasoning logic. Thus, to achieve the required precision and granularity of chemical class definitions, sets of SMARTS class definitions are connected by OR and NOT logical operators. In addition, AND logic has been implemented to allow the concomitant use of flexible atom lists and stereochemistry definitions. The resulting chemical ontology is a multi-hierarchical taxonomy of concept nodes connected by directed, transitive relationships. A proposal for a rule based definition of chemical classes has been made that allows to define chemical compound classes more precisely than before. The proposed structure-based reasoning logic allows to translate chemistry expert knowledge into a

  9. PAV ontology: provenance, authoring and versioning.

    Science.gov (United States)

    Ciccarese, Paolo; Soiland-Reyes, Stian; Belhajjame, Khalid; Gray, Alasdair Jg; Goble, Carole; Clark, Tim

    2013-11-22

    Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple scientific claim with supportive evidence. Existing vocabularies such as Dublin Core Terms (DC Terms) and the W3C Provenance Ontology (PROV-O) are domain-independent and general-purpose and they allow and encourage for extensions to cover more specific needs. In particular, to track authoring and versioning information of web resources, PROV-O provides a basic methodology but not any specific classes and properties for identifying or distinguishing between the various roles assumed by agents manipulating digital artifacts, such as author, contributor and curator. We present the Provenance, Authoring and Versioning ontology (PAV, namespace http://purl.org/pav/): a lightweight ontology for capturing "just enough" descriptions essential for tracking the provenance, authoring and versioning of web resources. We argue that such descriptions are essential for digital scientific content. PAV distinguishes between contributors, authors and curators of content and creators of representations in addition to the provenance of originating resources that have been accessed, transformed and consumed. We explore five projects (and communities) that have adopted PAV illustrating their usage through concrete examples. Moreover, we present mappings that show how PAV extends the W3C PROV-O ontology to support broader interoperability. The initial design of the PAV ontology was driven by requirements from the AlzSWAN project with further requirements incorporated later from other projects detailed in this paper. The authors strived to keep PAV lightweight and compact by including only those terms that have demonstrated to be pragmatically useful in existing applications, and by recommending terms from existing ontologies when plausible. We analyze and compare PAV with related

  10. An Epidemiological Study on the Incidence of Accidents Among under 5 Years of Age Referred to Emergency Hospital Units in Hamadan Province

    Directory of Open Access Journals (Sweden)

    Salman Khazaei

    2016-09-01

    Full Text Available Background and objectives : Accidents and injuries are the leading causes of avoidable illness and death in most of the countries in the world. For health policymakers, it is essential to have knowledge about the occurrence of accidents. The aim of this study was to evaluate the incidence of accidents in children under 5 years of age referring to emergency departments in Hamadan province. Material and Methods: This is a retrospective study that all under 5 years of age patients referred to hospitals in Hamadan province were enrolled in the study during 2009 to 2014. Data were extracted from injury register software and by using descriptive and analytic statistics, data were analyzed with STATA software version 12 at the level of error less        than 5%. Results: A total of 7409 under 5 years of age patients were registered during this period. 70.4% were male and 38.97% of them were under 1 year old. Home accidents included 45.07% of the accidents. Car accidents (27.89%, hit (22.16% and fall (16.79% were the most occurred accidents in both sexes. Conclusion: Due to the high incidence of accidents at home and roads, necessary precautions should be taken in this regard

  11. Reference interaction site model investigation of homonuclear hard dumbbells under simple fluid theory closures: comparison with Monte Carlo simulations.

    Science.gov (United States)

    Munaò, G; Costa, D; Caccamo, C

    2009-04-14

    We revisit the thermodynamic and structural properties of fluids of homonuclear hard dumbbells in the framework provided by the reference interaction site model (RISM) theory of molecular fluids. Besides the previously investigated Percus-Yevick (PY) approximation, we test the accuracy of other closures to the RISM equations, imported from the theory of simple fluids; specifically, we study the hypernetted chain (HNC), the modified HNC (MHNC) and, less extensively, the Verlet approximations. We implement our approach for models characterized by several different elongations, up to the case of tangent diatomics, and investigate the whole fluid density range. The theoretical predictions are assessed against Monte Carlo simulations, either available from literature or newly generated by us. The HNC and PY equations of state, calculated via different routes, share on the whole the same level of accuracy. The MHNC is applied by enforcing an internal thermodynamic consistency constraint, leading to good predictions for the equation of state as the elongation of the dumbbell increases. As for the radial distribution function, the MHNC appears superior to other theories, especially for tangent diatomics in the high density limit; the PY approximation is better than the HNC and Verlet closures in the high density or elongation regime. Our structural analysis is supplemented by an accurate inversion procedure to reconstruct from Monte Carlo data and RISM the "exact" direct correlation function. In agreement with such calculations and consistent with the forecast of rigorous diagrammatic analysis, all theories predict the occurrence in the direct correlation function of a first cusp inside the dumbbell core and (with the obvious exception of the PY) of a second cusp outside; the cusps' heights are also qualitatively well reproduced by the theories, except at high densities.

  12. Crosswalking near-Earth and space physics ontologies in SPASE and ESPAS

    Science.gov (United States)

    Galkin, I. A.; Fung, S. F.; Benson, R. F.; Heynderickx, D.; Ritschel, B.; King, T. A.; Roberts, D. A.; Hapgood, M. A.; Belehaki, A.

    2015-12-01

    In order to support scientific discoveries in Heliophysics (HP), with modern data systems, the HP Data Centers actively pursue harmonization of available metadata that allows crossing boundaries between existing data models, conventions, and resource interfaces. The discoverability of HP observations is improved when associated metadata describes their physical content in agreed terms as a part of the resource registration. One of the great challenges of enabling such content-targeted data search capability is the harmonization of domain ontology across data providers. Ontologies are the cornerstones of the content-aware data systems: they define an agreed vocabulary of keywords that capture the essence of domain-specific concepts and their relationships. With the introduction of the Virtual Wave Observatory (VWO), as part of NASA's Virtual System Observatory in 2008, the task of formulating the HP ontology became yet more complicated. Definitions of the wave domain concepts required several layers of specifications that described the generation, propagation, and interaction of the waves with the underlying medium in addition to the observation itself. Simple keyword lists could not provide a sufficiently information-rich description, given the complexity of the wave domain, and the development of a more powerful schema was required. The ontology research at the VWO eventually resulted in a suitable multi-hierarchical design that found its first implementation in 2015 at one of the European space physics data repositories, the near-Earth Space Data Infrastructure for e-Science (ESPAS). Similar to many other European geoscience projects, ESPAS is based on the ISO 19156 Observation and Measurements standard. In cooperation with the NASA VWO, the ESPAS project has deployed a space physics ontology design for all data registration purposes. The VWO science team is now uniquely positioned to establish a crosswalk between the ESPAS ontology based on ISO 19156 and the VWO

  13. THE CIDOC CRM GAME: A Serious Game Approach to Ontology Learning

    Science.gov (United States)

    Guillem, A.; Bruseker, G.

    2017-08-01

    Formal ontologies such as CIDOC CRM (Conceptual Reference Model) form part of the central strategy for the medium and longterm integration of cultural heritage data to allow for its greater valorization and dissemination. Despite this, uptake of CIDOC CRM at the ground level of Cultural Heriage (CH) practice is limited. Part of the reason behind this lack of uptake lies in the fact that ontologies are considered too complicated and abstract for application in real life scenarios. This paper presents the rationale behind and the design of a CIDOC CRM game, the intent of which is to provide a learning mechanism to allow learners of wide backgrounds and interests to approach CIDOC CRM in a hands-on and interactive fashion. The CIDOC CRM game consist of decks of cards and game boards that allow players to engage with the concepts of a formal ontology in relation to real data in an entertaining and informative way. It is argued that the CIDOC CRM Game can form an important part of introducing the basic elements of formal ontology and this standard to a wider audience in order to aid wider understanding and adoption of the same.

  14. Evaluating the significance of protein functional similarity based on gene ontology.

    Science.gov (United States)

    Konopka, Bogumil M; Golda, Tomasz; Kotulska, Malgorzata

    2014-11-01

    Gene ontology is among the most successful ontologies in the biomedical domain. It is used to describe, unambiguously, protein molecular functions, cellular localizations, and processes in which proteins participate. The hierarchical structure of gene ontology allows quantifying protein functional similarity by application of algorithms that calculate semantic similarities. The scores, however, are meaningless without a given context. Here, we propose how to evaluate the significance of protein function semantic similarity scores by comparing them to reference distributions calculated for randomly chosen proteins. In the study, thresholds for significant functional semantic similarity, in four representative annotation corpuses, were estimated. We also show that the score significance is influenced by the number and specificity of gene ontology terms that are annotated to compared proteins. While proteins with a greater number of terms tend to yield higher similarity scores, proteins with more specific terms produce lower scores. The estimated significance thresholds were validated using protein sequence-function and structure-function relationships. Taking into account the term number and term specificity improves the distinction between significant and insignificant semantic similarity comparisons.

  15. Integrating reasoning and clinical archetypes using OWL ontologies and SWRL rules.

    Science.gov (United States)

    Lezcano, Leonardo; Sicilia, Miguel-Angel; Rodríguez-Solano, Carlos

    2011-04-01

    Semantic interoperability is essential to facilitate the computerized support for alerts, workflow management and evidence-based healthcare across heterogeneous electronic health record (EHR) systems. Clinical archetypes, which are formal definitions of specific clinical concepts defined as specializations of a generic reference (information) model, provide a mechanism to express data structures in a shared and interoperable way. However, currently available archetype languages do not provide direct support for mapping to formal ontologies and then exploiting reasoning on clinical knowledge, which are key ingredients of full semantic interoperability, as stated in the SemanticHEALTH report [1]. This paper reports on an approach to translate definitions expressed in the openEHR Archetype Definition Language (ADL) to a formal representation expressed using the Ontology Web Language (OWL). The formal representations are then integrated with rules expressed with Semantic Web Rule Language (SWRL) expressions, providing an approach to apply the SWRL rules to concrete instances of clinical data. Sharing the knowledge expressed in the form of rules is consistent with the philosophy of open sharing, encouraged by archetypes. Our approach also allows the reuse of formal knowledge, expressed through ontologies, and extends reuse to propositions of declarative knowledge, such as those encoded in clinical guidelines. This paper describes the ADL-to-OWL translation approach, describes the techniques to map archetypes to formal ontologies, and demonstrates how rules can be applied to the resulting representation. We provide examples taken from a patient safety alerting system to illustrate our approach. Copyright © 2010 Elsevier Inc. All rights reserved.

  16. Application of An Ontology for Characterizing Data Quality For a Secondary Use of EHR Data.

    Science.gov (United States)

    Johnson, Steven G; Speedie, Stuart; Simon, Gyorgy; Kumar, Vipin; Westra, Bonnie L

    2016-01-01

    The goal of this study is to apply an ontology based assessment process to electronic health record (EHR) data and determine its usefulness in characterizing data quality for calculating an example eMeasure (CMS178). The process uses a data quality ontology that references separate data quality, domain and task ontologies to compute measures based on proportions of constraints that are satisfied. These quantities indicate how well the data conforms to the domain and how well it fits the task. The process was performed on a de-identified 200,000 encounter sample from a hospital EHR. CodingConsistency was poor (44%) but DomainConsistency (97%) and TaskRelevance (95%) were very good. Improvements in the data quality Measures correlated with improvements in the eMeasure. This approach can encourage the development of new detailed Domain ontologies that can be reused for data quality purposes across different organizations' EHR data. Automating the data quality assessment process using this method can enable sharing of data quality metrics that may aid in making research results that use EHR data more transparent and reproducible.

  17. Stable Internal Reference Genes for Normalizing Real-Time Quantitative PCR in Baphicacanthus cusia under Hormonal Stimuli and UV Irradiation, and in Different Plant Organs

    Directory of Open Access Journals (Sweden)

    Yuxiang Huang

    2017-05-01

    Full Text Available Baphicacanthus cusia (Nees Bremek, the plant source for many kinds of drugs in traditional Chinese medicine, is widely distributed in South China, especially in Fujian. Recent studies about B. cusia mainly focus on its chemical composition and pharmacological effects, but further analysis of the plant's gene functions and expression is required to better understand the synthesis of its effective compounds. Real-time quantitative polymerase chain reaction (RT-qPCR is a powerful method for gene expression analysis. It is necessary to select a suitable reference gene for expression normalization to ensure the accuracy of RT-qPCR results. Ten candidate reference genes were selected from the transcriptome datasets of B. cusia in this study, and the expression stability was assessed across 60 samples representing different tissues and organs under various conditions, including ultraviolet (UV irradiation, hormonal stimuli (jasmonic acid methyl ester and abscisic acid, and in different plant organs. By employing different algorithms, such as geNorm, NormFinder, and BestKeeper, which are complementary approaches based on different statistical procedures, 18S rRNA was found to be the most stable gene under UV irradiation and hormonal stimuli, whereas ubiquitin-conjugating enzyme E2 was the best suitable gene for different plant organs. This novel study aimed to screen for suitable reference genes and corresponding primer pairs specifically designed for gene expression studies in B. cusia, in particular for RT-qPCR analyses.

  18. Freedom and the psychoanalytic ontology of quantum physics.

    Science.gov (United States)

    Gullatz, Stefan; Gildersleeve, Matthew

    2018-02-01

    Jung's paper 'Synchronicity - an acausal connecting principle', defining the phenomenon as a 'meaningful' coincidence depending on archetypal activation, was published in 1952, together with a conceptually related piece by physicist and Nobel Laureate Wolfgang Pauli entitled, 'The influence of archetypal ideas on the scientific theories of Kepler'. Slavoj Žižek, in The Indivisible Remainder: On Schelling and Related Matters, suggests that, in contrast to any notion of a 'pre-modern Jungian harmony', the main lesson of quantum physics was that not only was the psychoanalytic, empty subject of the signifier constitutively out-of-joint with respect to the world, but that the Real in itself was already incomplete, out-of-joint, 'not-all'. Yet while Žižek frequently tries to separate Jung from his own ontology, this paper shows that his ontology is not as different as he suggests. Consistent with our earlier publications on Jung and Zizek, a closer investigation reveals an underlying congruence of both of their approaches. In this paper we show that this affinity lies in the rejection by both Jung and Žižek of the ideology of reductive materialism, a rejection that demonstrably draws on quantum physics in similar ways. While Jung posits an inherently meaningful universe, Žižek attempts to salvage the freedom of human subjectivity by opposing his Lacanian 'dialectical materialism' to reductive materialism. © 2018, The Society of Analytical Psychology.

  19. Ontological Realism for the Research Domain Criteria for Mental Disorders.

    Science.gov (United States)

    Ceusters, Werner; Jensen, Mark; Diehl, Alexander D

    2017-01-01

    At the heart of the Research Domain Criteria for Mental Disorders is a matrix in which functional aspects of behavior are related to genotypic and (endo-)phenotypic research findings, and the various techniques through which they can been observed. The matrix is work in progress. As such it currently suffers from several shortcomings, the resolution of which, we contend, are essential to success of NIMH's goal of fostering translational science on mental disorders. Using well-established criteria for assessing the terminological and ontological quality of biomedical representations we identified the major problems to be (1) the abundant presence of terms that lack face value, (2) the absence of what the exact nature of the represented relationships are, and (3) referential imprecision with respect to the intended granularity of what the terms denote. We propose to eliminate these shortcomings by resorting to definitions and formal representations under the umbrella of Ontological Realism as they already have been developed in the areas of mental health, anatomy and biological functions.

  20. Study on nutritional status of children under 5 years in palpa district, nepal: speacial reference to baal vita

    Directory of Open Access Journals (Sweden)

    Deelip Kumar Karki

    2013-12-01

    Full Text Available Background: Malnutrition is a pathological state resulting from a relative or absolute deficiency or excess of one or more essential nutrients. Malnutrition is a major underlying cause of the child morbidity and mortality in Nepal. Adequate nutrition is a fundamental right for every human being. Malnourished child is depriving from physical and mental development. Objectives: To assess the nutritional status of children under 5 years and to find out the knowledge and practice regarding micronutrient powder “Baal vita” Materials and Methods: Descriptive cross sectional community based study was conducted in Palpa district, total of 390 respondents at the age of 6-59 months were selected with the help of multistage sampling. Through anthropometry, prevalence of underweight, stunting and wasting was determined. Results: Prevalence of underweight, stunting and wasting was 25.9%, 27.2% and 7.3% respectively. The association between age of the mother at the birth of the children and nutritional status of children is not statistically significant. Majority of the children (80.5% used to take junk foods sometimes, followed by 16.7% very often, 2.8% children never used to take. Majority of the children (52.6% were taken the micronutrient powder (first course but the coverage of second course of micronutrient powder was 29.5% and followed by third course coverage was only 18.9%. Conclusion: The nutritional status of children in this study were found to be satisfactory because compared to the Millennium Development Goals (MDGs target but the coverage of micronutrient powder is low.

  1. Verbalizing Ontologies in Controlled Baltic Languages

    OpenAIRE

    Grūzītis, Normunds; Nešpore, Gunta; Saulīte, Baiba

    2012-01-01

    Controlled natural languages (mostly English-based) recently have emerged as seemingly informal supplementary means for OWL ontology authoring, if compared to the formal notations that are used by professional knowledge engineers. In this paper we present by examples controlled Latvian language that has been designed to be compliant with the state of the art Attempto Controlled English. We also discuss relation with controlled Lithuanian language that is being designed in parallel.

  2. Towards a posthuman collective: ontology, epistemology, ethics.

    Directory of Open Access Journals (Sweden)

    Marietta Radomska

    2010-01-01

    Full Text Available This paper is aimed at reconstruction of the basic ontological, epistemological and ethical premises of the posthumanist project (called also the posthumanist theory or the posthumanist tool, while analysing the theoretical propositions of Karen Barad, Gilles Deleuze and Felix Guattari as well as Donna Haraway. It is only by such meticulous definition of theoretical tool that one may be able to pose the question of the posthuman collective and posthumanist politics.

  3. BiOSS: A system for biomedical ontology selection.

    Science.gov (United States)

    Martínez-Romero, Marcos; Vázquez-Naya, José M; Pereira, Javier; Pazos, Alejandro

    2014-04-01

    In biomedical informatics, ontologies are considered a key technology for annotating, retrieving and sharing the huge volume of publicly available data. Due to the increasing amount, complexity and variety of existing biomedical ontologies, choosing the ones to be used in a semantic annotation problem or to design a specific application is a difficult task. As a consequence, the design of approaches and tools addressed to facilitate the selection of biomedical ontologies is becoming a priority. In this paper we present BiOSS, a novel system for the selection of biomedical ontologies. BiOSS evaluates the adequacy of an ontology to a given domain according to three different criteria: (1) the extent to which the ontology covers the domain; (2) the semantic richness of the ontology in the domain; (3) the popularity of the ontology in the biomedical community. BiOSS has been applied to 5 representative problems of ontology selection. It also has been compared to existing methods and tools. Results are promising and show the usefulness of BiOSS to solve real-world ontology selection problems. BiOSS is openly available both as a web tool and a web service. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  4. Cyber Forensics Ontology for Cyber Criminal Investigation

    Science.gov (United States)

    Park, Heum; Cho, Sunho; Kwon, Hyuk-Chul

    We developed Cyber Forensics Ontology for the criminal investigation in cyber space. Cyber crime is classified into cyber terror and general cyber crime, and those two classes are connected with each other. The investigation of cyber terror requires high technology, system environment and experts, and general cyber crime is connected with general crime by evidence from digital data and cyber space. Accordingly, it is difficult to determine relational crime types and collect evidence. Therefore, we considered the classifications of cyber crime, the collection of evidence in cyber space and the application of laws to cyber crime. In order to efficiently investigate cyber crime, it is necessary to integrate those concepts for each cyber crime-case. Thus, we constructed a cyber forensics domain ontology for criminal investigation in cyber space, according to the categories of cyber crime, laws, evidence and information of criminals. This ontology can be used in the process of investigating of cyber crime-cases, and for data mining of cyber crime; classification, clustering, association and detection of crime types, crime cases, evidences and criminals.

  5. Phenex: ontological annotation of phenotypic diversity.

    Directory of Open Access Journals (Sweden)

    James P Balhoff

    2010-05-01

    Full Text Available Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

  6. The Human Phenotype Ontology in 2017

    International Nuclear Information System (INIS)

    Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark; Foster, Erin; McMurry, Julie

    2016-01-01

    Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human PhenotypeOntology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

  7. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

    Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

    2018-03-01

    The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

  8. A fuzzy ontological knowledge document clustering methodology.

    Science.gov (United States)

    Trappey, Amy J C; Trappey, Charles V; Hsu, Fu-Chiang; Hsiao, David W

    2009-06-01

    This correspondence presents a novel hierarchical clustering approach for knowledge document self-organization, particularly for patent analysis. Current keyword-based methodologies for document content management tend to be inconsistent and ineffective when partial meanings of the technical content are used for cluster analysis. Thus, a new methodology to automatically interpret and cluster knowledge documents using an ontology schema is presented. Moreover, a fuzzy logic control approach is used to match suitable document cluster(s) for given patents based on their derived ontological semantic webs. Finally, three case studies are used to test the approach. The first test case analyzed and clustered 100 patents for chemical and mechanical polishing retrieved from the World Intellectual Property Organization (WIPO). The second test case analyzed and clustered 100 patent news articles retrieved from online Web sites. The third case analyzed and clustered 100 patents for radio-frequency identification retrieved from WIPO. The results show that the fuzzy ontology-based document clustering approach outperforms the K-means approach in precision, recall, F-measure, and Shannon's entropy.

  9. Ontology Supported Information Systems: A Review

    Directory of Open Access Journals (Sweden)

    Padmavathi, T.

    2014-12-01

    Full Text Available The exponential growth of information on the web far exceeds the capacity of present day information retrieval systems and search engines, making information integration on the web difficult. In order to overcome this, semantic web technologies were proposed by the World Wide Web Consortium (W3C to achieve a higher degree of automation and precision in information retrieval systems. Semantic web, with its promise to deliver machine understanding to the traditional web, has attracted a significant amount of research from academia as well as from industries. Semantic web is an extension of the current web in which data can be shared and reused across the internet. RDF and ontology are two essential components of the semantic web architecture which support a common framework for data storage and representation of data semantics, respectively. Ontologies being the backbone of semantic web applications, it is more relevant to study various approaches in their application, usage, and integration into web services. In this article, an effort has been made to review the research work being undertaken in the area of design and development of ontology supported information systems. This paper also briefly explains the emerging semantic web technologies and standards.

  10. Annotating the human genome with Disease Ontology

    Science.gov (United States)

    Osborne, John D; Flatow, Jared; Holko, Michelle; Lin, Simon M; Kibbe, Warren A; Zhu, Lihua (Julie); Danila, Maria I; Feng, Gang; Chisholm, Rex L

    2009-01-01

    Background The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases. Results We used the Unified Medical Language System (UMLS) MetaMap Transfer tool (MMTx) to discover gene-disease relationships from the GeneRIF database. We utilized a comprehensive subset of UMLS, which is disease-focused and structured as a directed acyclic graph (the Disease Ontology), to filter and interpret results from MMTx. The results were validated against the Homayouni gene collection using recall and precision measurements. We compared our results with the widely used Online Mendelian Inheritance in Man (OMIM) annotations. Conclusion The validation data set suggests a 91% recall rate and 97% precision rate of disease annotation using GeneRIF, in contrast with a 22% recall and 98% precision using OMIM. Our thesaurus-based approach allows for comparisons to be made between disease containing databases and allows for increased accuracy in disease identification through synonym matching. The much higher recall rate of our approach demonstrates that annotating human genome with Disease Ontology and GeneRIF for diseases dramatically increases the coverage of the disease annotation of human genome. PMID:19594883

  11. Ontological modeling of electronic health information exchange.

    Science.gov (United States)

    McMurray, J; Zhu, L; McKillop, I; Chen, H

    2015-08-01

    Investments of resources to purposively improve the movement of information between health system providers are currently made with imperfect information. No inventories of system-level electronic health information flows currently exist, nor do measures of inter-organizational electronic information exchange. Using Protégé 4, an open-source OWL Web ontology language editor and knowledge-based framework, we formalized a model that decomposes inter-organizational electronic health information flow into derivative concepts such as diversity, breadth, volume, structure, standardization and connectivity. The ontology was populated with data from a regional health system and the flows were measured. Individual instance's properties were inferred from their class associations as determined by their data and object property rules. It was also possible to visualize interoperability activity for regional analysis and planning purposes. A property called Impact was created from the total number of patients or clients that a health entity in the region served in a year, and the total number of health service providers or organizations with whom it exchanged information in support of clinical decision-making, diagnosis or treatment. Identifying providers with a high Impact but low Interoperability score could assist planners and policy-makers to optimize technology investments intended to electronically share patient information across the continuum of care. Finally, we demonstrated how linked ontologies were used to identify logical inconsistencies in self-reported data for the study. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Ontological models with epistemic constraints: Local reconstruction of a dual-rail qubit

    Science.gov (United States)

    Blasiak, Pawel

    2017-10-01

    Restrictions on gaining information may significantly affect perception of the system under study. In this paper we are concerned with mechanisms introducing epistemic constraints in the framework of ontological models and discuss a scheme leading to the minimal operational account which does not rely on the knowledge of the underlying ontology. As a case in point, we construct local ontological model which simulates behaviour of a single quantum particle in dual-rail interferometric circuits. We show that for agents analysing conceivable experimental circuits predictions of the model are indistinguishable from their quantum mechanical counterparts, that is operational account of the model is equivalent to a qubit. Note that it contrasts with the usual understanding the collapse of the wave function as non-local phenomenon, namely the model is local from the construction with any form of 'non-locality' being explained as an epistemic effect due to incomplete information about the system. This illustrates flexibility of the ontological model framework, and in particular the possibility of different interpretations behind the same operational account.

  13. Study on distributed generation algorithm of variable precision concept lattice based on ontology heterogeneous database

    Science.gov (United States)

    WANG, Qingrong; ZHU, Changfeng

    2017-06-01

    Integration of distributed heterogeneous data sources is the key issues under the big data applications. In this paper the strategy of variable precision is introduced to the concept lattice, and the one-to-one mapping mode of variable precision concept lattice and ontology concept lattice is constructed to produce the local ontology by constructing the variable precision concept lattice for each subsystem, and the distributed generation algorithm of variable precision concept lattice based on ontology heterogeneous database is proposed to draw support from the special relationship between concept lattice and ontology construction. Finally, based on the standard of main concept lattice of the existing heterogeneous database generated, a case study has been carried out in order to testify the feasibility and validity of this algorithm, and the differences between the main concept lattice and the standard concept lattice are compared. Analysis results show that this algorithm above-mentioned can automatically process the construction process of distributed concept lattice under the heterogeneous data sources.

  14. SU-E-T-516: Measurement of the Absorbed Dose Rate in Water Under Reference Conditions in a CyberKnife Unit

    Energy Technology Data Exchange (ETDEWEB)

    Aragon-Martinez, N; Hernandez-Guzman, A [Instituto de Fisica, Universidad Nacional Autonoma de Mexico, Mexico City, DF (Mexico); Gomez-Munoz, A [Centro Medico Nacional Siglo XXI, Mexico City, DF (Mexico); Massillon-JL, G

    2014-06-01

    Purpose: This paper aims to measure the absorbed-dose-rate in a CyberKnife unit reference-field (6cm diameter) using three ionization chambers (IC) following the new IAEA/AAPM formalism and Gafchromic film (MD-V3-55 and EBT3) protocol according to our work reported previously. Methods: The absorbed-dose-rates were measured at 90cm and 70cm SSD in a 10cmx10cm field and at 70cm SSD in a 5.4cmx5.4cm equivalent to 6cm diameter field using a linac Varian iX. All measurements were performed at 10cm depth in water. The correction factors that account for the difference between the IC response on the reference field and the CyberKnife reference field, k-(Q-msr,Q)^(f-msr,f-ref), were evaluated and Gafchromic film were calibrated using the results obtained above. Under the CyberKnife reference conditions, the factors were used to measure the absorbed-dose-rate with IC according to the new formalism and the calibrated film was irradiated in water. The film calibration curve was used to evaluate the absorbed-dose-rate in the CyberKnife unit. Results: Difference up to 2.56% is observed between dose-rate measured with IC in the reference 10cmx10cm field, depending where the chamber was calibrated, which was not reflected in the correction factor k-(Q-msr,Q)^(f-msr,f-ref ) where variations of ~0.15%-0.5% were obtained. Within measurements uncertainties, maximum difference of 1.8% on the absorbed-dose-rate in the CyberKnife reference field is observed between all IC and the films Conclusion: Absorbed-dose-rate to water was measured in a CyberKnife reference field with acceptable accuracy (combined uncertainties ~1.32%-1.73%, k=1) using three IC and films. The MD-V3-55 film as well as the new IAEA/AAPM formalism can be considered as a suitable dosimetric method to measure absorbed-dose-rate to water in small and non-standard CyberKnife fields used in clinical treatments However, the EBT3 film is not appropriated due to the high uncertainty provided (combined uncertainty ~9%, k=1

  15. Development and Evaluation of an Adolescents' Depression Ontology for Analyzing Social Data.

    Science.gov (United States)

    Jung, Hyesil; Park, Hyeoun-Ae; Song, Tae-Min

    2016-01-01

    This study aims to develop and evaluate an ontology for adolescents' depression to be used for collecting and analyzing social data. The ontology was developed according to the 'ontology development 101' methodology. Concepts were extracted from clinical practice guidelines and related literatures. The ontology is composed of five sub-ontologies which represent risk factors, sign and symptoms, measurement, diagnostic result and management care. The ontology was evaluated in four different ways: First, we examined the frequency of ontology concept appeared in social data; Second, the content coverage of ontology was evaluated by comparing ontology concepts with concepts extracted from the youth depression counseling records; Third, the structural and representational layer of the ontology were evaluated by 5 ontology and psychiatric nursing experts; Fourth, the scope of the ontology was examined by answering 59 competency questions. The ontology was improved by adding new concepts and synonyms and revising the level of structure.

  16. The missions and means framework as an ontology

    Science.gov (United States)

    Deitz, Paul H.; Bray, Britt E.; Michaelis, James R.

    2016-05-01

    The analysis of warfare frequently suffers from an absence of logical structure for a] specifying explicitly the military mission and b] quantitatively evaluating the mission utility of alternative products and services. In 2003, the Missions and Means Framework (MMF) was developed to redress these shortcomings. The MMF supports multiple combatants, levels of war and, in fact, is a formal embodiment of the Military Decision-Making Process (MDMP). A major effect of incomplete analytic discipline in military systems analyses is that they frequently fall into the category of ill-posed problems in which they are under-specified, under-determined, or under-constrained. Critical context is often missing. This is frequently the result of incomplete materiel requirements analyses which have unclear linkages to higher levels of warfare, system-of-systems linkages, tactics, techniques and procedures, and the effect of opposition forces. In many instances the capabilities of materiel are assumed to be immutable. This is a result of not assessing how platform components morph over time due to damage, logistics, or repair. Though ill-posed issues can be found many places in military analysis, probably the greatest challenge comes in the disciplines of C4ISR supported by ontologies in which formal naming and definition of the types, properties, and interrelationships of the entities are fundamental to characterizing mission success. Though the MMF was not conceived as an ontology, over the past decade some workers, particularly in the field of communication, have labelled the MMF as such. This connection will be described and discussed.

  17. Towards exergaming commons: composing the exergame ontology for publishing open game data.

    Science.gov (United States)

    Bamparopoulos, Giorgos; Konstantinidis, Evdokimos; Bratsas, Charalampos; Bamidis, Panagiotis D

    2016-01-01

    It has been shown that exergames have multiple benefits for physical, mental and cognitive health. Only recently, however, researchers have started considering them as health monitoring tools, through collection and analysis of game metrics data. In light of this and initiatives like the Quantified Self, there is an emerging need to open the data produced by health games and their associated metrics in order for them to be evaluated by the research community in an attempt to quantify their potential health, cognitive and physiological benefits. We have developed an ontology that describes exergames using the Web Ontology Language (OWL); it is available at http://purl.org/net/exergame/ns#. After an investigation of key components of exergames, relevant ontologies were incorporated, while necessary classes and properties were defined to model these components. A JavaScript framework was also developed in order to apply the ontology to online exergames. Finally, a SPARQL Endpoint is provided to enable open data access to potential clients through the web. Exergame components include details for players, game sessions, as well as, data produced during these game-playing sessions. The description of the game includes elements such as goals, game controllers and presentation hardware used; what is more, concepts from already existing ontologies are reused/repurposed. Game sessions include information related to the player, the date and venue where the game was played, as well as, the results/scores that were produced/achieved. These games are subsequently played by 14 users in multiple game sessions and the results derived from these sessions are published in a triplestore as open data. We model concepts related to exergames by providing a standardized structure for reference and comparison. This is the first work that publishes data from actual exergame sessions on the web, facilitating the integration and analysis of the data, while allowing open data access through

  18. Regaining the Square of Opposition in Formal Ontology Development

    DEFF Research Database (Denmark)

    Nilsson, Jørgen Fischer

    2014-01-01

    Use of formal ontologies is becoming widespread in information systems. Forerunners of formal ontologies are scientific classification systems such as the Linnaean biological ones. Unlike biological classifications modern formal ontologies are often non-hierarchical. A formal ontology in its basic...... relationship induces a partial order relation corresponding to the relationship "all P are Q" in the square of opposition. Accordingly, so far, formal ontologies provide only assertions of the form "all P are Q". However, it is our contention that the three other assertion forms in the square of opposition...... be held simply in the case that "all P are Q" does not hold. These default rules are routinely adopted in ontology development without mentioning. Appealing to these conventions, the 4 sentence forms in the square are effectively made at disposal. We discuss a first order metalogical formalization...

  19. Nuclear component design ontology building based on ASME codes

    International Nuclear Information System (INIS)

    Bao Shiyi; Zhou Yu; He Shuyan

    2005-01-01

    The adoption of ontology analysis in the study of concept knowledge acquisition and representation for the nuclear component design process based on computer-supported cooperative work (CSCW) makes it possible to share and reuse numerous concept knowledge of multi-disciplinary domains. A practical ontology building method is accordingly proposed based on Protege knowledge model in combination with both top-down and bottom-up approaches together with Formal Concept Analysis (FCA). FCA exhibits its advantages in the way it helps establish and improve taxonomic hierarchy of concepts and resolve concept conflict occurred in modeling multi-disciplinary domains. With Protege-3.0 as the ontology building tool, a nuclear component design ontology based ASME codes is developed by utilizing the ontology building method. The ontology serves as the basis to realize concept knowledge sharing and reusing of nuclear component design. (authors)

  20. Exact Score Distribution Computation for Similarity Searches in Ontologies

    Science.gov (United States)

    Schulz, Marcel H.; Köhler, Sebastian; Bauer, Sebastian; Vingron, Martin; Robinson, Peter N.

    Semantic similarity searches in ontologies are an important component of many bioinformatic algorithms, e.g., protein function prediction with the Gene Ontology. In this paper we consider the exact computation of score distributions for similarity searches in ontologies, and introduce a simple null hypothesis which can be used to compute a P-value for the statistical significance of similarity scores. We concentrate on measures based on Resnik’s definition of ontological similarity. A new algorithm is proposed that collapses subgraphs of the ontology graph and thereby allows fast score distribution computation. The new algorithm is several orders of magnitude faster than the naive approach, as we demonstrate by computing score distributions for similarity searches in the Human Phenotype Ontology.

  1. Biomedical imaging ontologies: A survey and proposal for future work

    Directory of Open Access Journals (Sweden)

    Barry Smith

    2015-01-01

    Full Text Available Background: Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as "cell" or "image" or "tissue" or "microscope" that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. Results and Conclusions: The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data.

  2. Ontology matters: a commentary on contribution to cultural historical activity

    Science.gov (United States)

    Martin, Jenny

    2017-10-01

    This commentary promotes discussion on the imaginary provided by Sanaz Farhangi in her article entitled, Contribution to activity: a lens for understanding students' potential and agency in physics education. The commentary is concerned with aligning ontological assumptions in research accounts of learning and development with transformative aims. A broad definition of ontology as the theory of existence is preferred. Sociocultural approaches share relational ontology as a common foundation. I agree with scholars elaborating Vygotsky's Transformative Activist Stance that a relational ontology does not imply activism. However, I argue that relational ontology provides a necessary and sufficient theoretical grounding for intentional transformation. I draw upon positioning theory to elaborate the moral aspects of language use and to illustrate that a theory of being as relational already eliminates the transcendental position. I draw on Farhangi's article to further the discussion on the necessity and sufficiency of relational ontology and associated grammars in accounting for activism.

  3. An improved synchronous reference frame current control strategy for a photovoltaic grid-connected inverter under unbalanced and nonlinear load conditions

    DEFF Research Database (Denmark)

    Naderipour, Amirreza; Asuhaimi Mohd Zin, Abdullah; Bin Habibuddin, Mohd Hafiz

    2017-01-01

    . It is challenging to suppress the harmonic content in the output current below a pre-set value in the GCI. It is also difficult to compensate for unbalanced loads even when the grid is under disruption due to total harmonic distortion (THD) and unbalanced loads. The primary advantage and objective of this method......In recent years, renewable energy sources have been considered the most encouraging resources for grid and off-grid power generation. This paper presents an improved current control strategy for a three-phase photovoltaic grid-connected inverter (GCI) under unbalanced and nonlinear load conditions...... to control the active and reactive power and harmonic current compensation, and it also corrects the system unbalance. The proposed control method features the synchronous reference frame (SRF) method. Simulation results are presented to demonstrate the effective performance of the proposed method....

  4. Psychological Science within a Three-Dimensional Ontology.

    Science.gov (United States)

    Lundh, Lars-Gunnar

    2018-03-01

    The present paper outlines the nature of a three-dimensional ontology and the place of psychological science within this ontology, in a way that is partly similar to and partly different from that of Pérez-Álvarez. The first dimension is the material realities, and involves different levels (physical, chemical, biological, psychological, etc.), where each level builds on a lower level but also involves the development of new emergent properties, in accordance with Bunge's emergent materialism. Each level involves systems, with components, structures and mechanisms, and an environment. This dimension can be studied with natural scientific methods. The second dimension is the subjective-experiential realities, and refers to our subjective perspective on the world. In accordance with Husserl's phenomenology, it is argued that this subjectivity does not exist in the world (i.e., should not be reified as an object among other objects), but represents a perspective on the world that we enter in our capacity as conscious human beings. Essential characteristics of this subjectivity (such as intentionality, temporality, embodiment, and intersubjectivity) can be explored by phenomenological methods. The third dimension is the social-constructional realities, and includes social institutions, norms, categories, theories, and techniques. It is argued that psychological science spans over all three dimensions. Although almost all psychological research by necessity starts from a problem formulation where the subjective-experiential dimension plays an essential role (either explicitly or implicitly), most of present-day psychological research clearly emphasizes the material dimension. It is argued that a mature psychological science needs to integrate all three dimensions.

  5. Logical Characterisation of Ontology Construction using Fuzzy Description Logics

    DEFF Research Database (Denmark)

    Badie, Farshad; Götzsche, Hans

    Ontologies based on Description Logics (DLs) have proved to be effective in formally sharing knowledge across semantic technologies, e.g. Semantic Web, Natural Language Processing, Text Analytics, Business intelligence. Our main goal is analysing ontology construction considering vagueness. We have......, employs Description Logics in characterising and analysing fuzzy statements. And finally, provides a conceptual framework describing fuzzy concept learning in ontologies using the Inductive Logic Programming....

  6. Self-Supervised Chinese Ontology Learning from Online Encyclopedias

    OpenAIRE

    Hu, Fanghuai; Shao, Zhiqing; Ruan, Tong

    2014-01-01

    Constructing ontology manually is a time-consuming, error-prone, and tedious task. We present SSCO, a self-supervised learning based chinese ontology, which contains about 255 thousand concepts, 5 million entities, and 40 million facts. We explore the three largest online Chinese encyclopedias for ontology learning and describe how to transfer the structured knowledge in encyclopedias, including article titles, category labels, redirection pages, taxonomy systems, and InfoBox modules, into on...

  7. Knowledge Representation in Patient Safety Reporting: An Ontological Approach

    Directory of Open Access Journals (Sweden)

    Liang Chen

    2016-10-01

    Full Text Available Purpose: The current development of patient safety reporting systems is criticized for loss of information and low data quality due to the lack of a uniformed domain knowledge base and text processing functionality. To improve patient safety reporting, the present paper suggests an ontological representation of patient safety knowledge. Design/methodology/approach: We propose a framework for constructing an ontological knowledge base of patient safety. The present paper describes our design, implementation, and evaluation of the ontology at its initial stage. Findings: We describe the design and initial outcomes of the ontology implementation. The evaluation results demonstrate the clinical validity of the ontology by a self-developed survey measurement. Research limitations: The proposed ontology was developed and evaluated using a small number of information sources. Presently, US data are used, but they are not essential for the ultimate structure of the ontology. Practical implications: The goal of improving patient safety can be aided through investigating patient safety reports and providing actionable knowledge to clinical practitioners. As such, constructing a domain specific ontology for patient safety reports serves as a cornerstone in information collection and text mining methods. Originality/value: The use of ontologies provides abstracted representation of semantic information and enables a wealth of applications in a reporting system. Therefore, constructing such a knowledge base is recognized as a high priority in health care.

  8. Toward a general ontology for digital forensic disciplines.

    Science.gov (United States)

    Karie, Nickson M; Venter, Hein S

    2014-09-01

    Ontologies are widely used in different disciplines as a technique for representing and reasoning about domain knowledge. However, despite the widespread ontology-related research activities and applications in different disciplines, the development of ontologies and ontology research activities is still wanting in digital forensics. This paper therefore presents the case for establishing an ontology for digital forensic disciplines. Such an ontology would enable better categorization of the digital forensic disciplines, as well as assist in the development of methodologies and specifications that can offer direction in different areas of digital forensics. This includes such areas as professional specialization, certifications, development of digital forensic tools, curricula, and educational materials. In addition, the ontology presented in this paper can be used, for example, to better organize the digital forensic domain knowledge and explicitly describe the discipline's semantics in a common way. Finally, this paper is meant to spark discussions and further research on an internationally agreed ontological distinction of the digital forensic disciplines. Digital forensic disciplines ontology is a novel approach toward organizing the digital forensic domain knowledge and constitutes the main contribution of this paper. © 2014 American Academy of Forensic Sciences.

  9. Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

    Directory of Open Access Journals (Sweden)

    Emanuel Santos

    Full Text Available Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

  10. Ontology Building Using Classification Rules and Discovered Concepts

    Directory of Open Access Journals (Sweden)

    Gorskis Henrihs

    2015-12-01

    Full Text Available Building an ontology is a difficult and time-consuming task. In order to make this task easier and faster, some automatic methods can be employed. This paper examines the feasibility of using rules and concepts discovered during the classification tree building process in the C4.5 algorithm, in a completely automated way, for the purposes of building an ontology from data. By building the ontology directly from continuous data, concepts and relations can be discovered without specific knowledge about the domain. This paper also examines how this method reproduces the classification capabilities of the classification three within an ontology using concepts and class expression axioms.

  11. Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

    Science.gov (United States)

    Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M

    2015-01-01

    Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

  12. FOCIH: Form-Based Ontology Creation and Information Harvesting

    Science.gov (United States)

    Tao, Cui; Embley, David W.; Liddle, Stephen W.

    Creating an ontology and populating it with data are both labor-intensive tasks requiring a high degree of expertise. Thus, scaling ontology creation and population to the size of the web in an effort to create a web of data—which some see as Web 3.0—is prohibitive. Can we find ways to streamline these tasks and lower the barrier enough to enable Web 3.0? Toward this end we offer a form-based approach to ontology creation that provides a way to create Web 3.0 ontologies without the need for specialized training. And we offer a way to semi-automatically harvest data from the current web of pages for a Web 3.0 ontology. In addition to harvesting information with respect to an ontology, the approach also annotates web pages and links facts in web pages to ontological concepts, resulting in a web of data superimposed over the web of pages. Experience with our prototype system shows that mappings between conceptual-model-based ontologies and forms are sufficient for creating the kind of ontologies needed for Web 3.0, and experiments with our prototype system show that automatic harvesting, automatic annotation, and automatic superimposition of a web of data over a web of pages work well.

  13. A fuzzy ontology and its application to news summarization.

    Science.gov (United States)

    Lee, Chang-Shing; Jian, Zhi-Wei; Huang, Lin-Kai

    2005-10-01

    In this paper, a fuzzy ontology and its application to news summarization are presented. The fuzzy ontology with fuzzy concepts is an extension of the domain ontology with crisp concepts. It is more suitable to describe the domain knowledge than domain ontology for solving the uncertainty reasoning problems. First, the domain ontology with various events of news is predefined by domain experts. The document preprocessing mechanism will generate the meaningful terms based on the news corpus and the Chinese news dictionary defined by the domain expert. Then, the meaningful terms will be classified according to the events of the news by the term classifier. The fuzzy inference mechanism will generate the membership degrees for each fuzzy concept of the fuzzy ontology. Every fuzzy concept has a set of membership degrees associated with various events of the domain ontology. In addition, a news agent based on the fuzzy ontology is also developed for news summarization. The news agent contains five modules, including a retrieval agent, a document preprocessing mechanism, a sentence path extractor, a sentence generator, and a sentence filter to perform news summarization. Furthermore, we construct an experimental website to test the proposed approach. The experimental results show that the news agent based on the fuzzy ontology can effectively operate for news summarization.

  14. A methodology for creating ontologies for engineering design

    DEFF Research Database (Denmark)

    Ahmed, Saeema; Kim, Sanghee; Wallace, Ken

    2005-01-01

    This paper describes a methodology for developing ontologies for engineering design. The methodology combines a number of methods from social science and computer science, together with taxonomies developed in the field of engineering design. A case study is used throughout the paper focusing upon...... the use of an ontology for searching, indexing and retrieving of engineering knowledge. An ontology for indexing design knowledge can assist the users to formulate their queries when searching for engineering design knowledge. The root concepts of the ontology were elicited from engineering designers...

  15. Learning a Large Scale of Ontology from Japanese Wikipedia

    Science.gov (United States)

    Tamagawa, Susumu; Sakurai, Shinya; Tejima, Takuya; Morita, Takeshi; Izumi, Noriaki; Yamaguchi, Takahira

    Here is discussed how to learn a large scale of ontology from Japanese Wikipedia. The learned ontology includes the following properties: rdfs:subClassOf (IS-A relationship), rdf:type (class-instance relationship), owl:Object/DatatypeProperty (Infobox triple), rdfs:domain (property domain), and skos:altLabel (synonym). Experimental case studies show us that the learned Japanese Wikipedia Ontology goes better than already existing general linguistic ontologies, such as EDR and Japanese WordNet, from the points of building costs and structure information richness.

  16. Development of an Adolescent Depression Ontology for Analyzing Social Data.

    Science.gov (United States)

    Jung, Hyesil; Park, Hyeoun-Ae; Song, Tae-Min; Jeon, Eunjoo; Kim, Ae Ran; Lee, Joo Yun

    2015-01-01

    Depression in adolescence is associated with significant suicidality. Therefore, it is important to detect the risk for depression and provide timely care to adolescents. This study aims to develop an ontology for collecting and analyzing social media data about adolescent depression. This ontology was developed using the 'ontology development 101'. The important terms were extracted from several clinical practice guidelines and postings on Social Network Service. We extracted 777 terms, which were categorized into 'risk factors', 'sign and symptoms', 'screening', 'diagnosis', 'treatment', and 'prevention'. An ontology developed in this study can be used as a framework to understand adolescent depression using unstructured data from social media.

  17. A methodology for creating ontologies for engineering design

    DEFF Research Database (Denmark)

    Ahmed, Saeema; Kim, S.; Wallace, K.M.

    2007-01-01

    This paper describes a six-stage methodology for developing ontologies for engineering design, together with the research methods and evaluation of each stage. The methodology focuses upon understanding a user's domain models through empirical research. A case study of an ontology for searching......, indexing, and retrieving engineering knowledge is described. The root concepts of the ontology were elicited from engineering designers. Relationships between concepts are extracted as the ontology is populated. The contribution of this research is a methodology to allow researchers. and industry to create...

  18. BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology

    Directory of Open Access Journals (Sweden)

    Gregorio Sergio E

    2009-05-01

    Full Text Available Abstract Motivation Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. Results We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. Availability The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

  19. Individual Building Extraction from TerraSAR-X Images Based on Ontological Semantic Analysis

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    Rong Gui

    2016-08-01

    Full Text Available Accurate building information plays a crucial role for urban planning, human settlements and environmental management. Synthetic aperture radar (SAR images, which deliver images with metric resolution, allow for analyzing and extracting detailed information on urban areas. In this paper, we consider the problem of extracting individual buildings from SAR images based on domain ontology. By analyzing a building scattering model with different orientations and structures, the building ontology model is set up to express multiple characteristics of individual buildings. Under this semantic expression framework, an object-based SAR image segmentation method is adopted to provide homogeneous image objects, and three categories of image object features are extracted. Semantic rules are implemented by organizing image object features, and the individual building objects expression based on an ontological semantic description is formed. Finally, the building primitives are used to detect buildings among the available image objects. Experiments on TerraSAR-X images of Foshan city, China, with a spatial resolution of 1.25 m × 1.25 m, have shown the total extraction rates are above 84%. The results indicate the ontological semantic method can exactly extract flat-roof and gable-roof buildings larger than 250 pixels with different orientations.

  20. STRATEGY AS PRACTICE IN THE STRUCTURATIONIST PERSPECTIVE: AN ESSAY ON ONTOLOGY OF STRATEGIC PRACTICE IN ORGANIZATIONS

    Directory of Open Access Journals (Sweden)

    MARCIO LUIZ MARIETTO

    2013-12-01

    Full Text Available The Strategy-as-Practice discipline appropriates other theories with converging ontological and epistemological assumptions to build its analytical body, thus this theoretical study offers a discussion on the appropriation of Structurationism Ontology that serves as one of the analytical theoretical structures of Strategy-as-Practice. The analytical procedure is guided by the central goal of discussing the ontological assumptions of Structurationism that support this perspective under the aegis of Strategy-as-Practice in the field of Organizational Strategy. For this purpose, the specific objectives are: a to conduct a theoretical (albeit not exhaustive review of Strategy-as-Practice; and b to conduct a review of Giddens’ Theory of Structuration, followed by c to offer a discussion on the theoretical/analytical specifics that Structurationism shown in studies of Strategy-as-Practice. The conclusion of the discussion shows adequate ontological agreement with the Structurationist assumptions adopted by the Strategy-as-Practice discipline in the investigation of strategic practice in organizations.