WorldWideScience

Sample records for underlying reference ontology

  1. 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.

  2. 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

  3. 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

  4. A methodology and supply chain management inspired reference ontology for modeling healthcare teams.

    Science.gov (United States)

    Kuziemsky, Craig E; Yazdi, Sara

    2011-01-01

    Numerous studies and strategic plans are advocating more team based healthcare delivery that is facilitated by information and communication technologies (ICTs). However before we can design ICTs to support teams we need a solid conceptual model of team processes and a methodology for using such a model in healthcare settings. This paper draws upon success in the supply chain management domain to develop a reference ontology of healthcare teams and a methodology for modeling teams to instantiate the ontology in specific settings. This research can help us understand how teams function and how we can design ICTs to support teams.

  5. 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

  6. 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...

  7. There is no quantum ontology without classical ontology

    Energy Technology Data Exchange (ETDEWEB)

    Fink, Helmut [Institut fuer Theoretische Physik, Univ. Erlangen-Nuernberg (Germany)

    2011-07-01

    The relation between quantum physics and classical physics is still under debate. In his recent book ''Rational Reconstructions of Modern Physics'', Peter Mittelstaedt explores a route from classical to quantum mechanics by reduction and elimination of (some of) the ontological hypotheses underlying classical mechanics. While, according to Mittelstaedt, classical mechanics describes a fictitious world that does not exist in reality, he claims to achieve a universal quantum ontology that can be improved by incorporating unsharp properties and equipped with Planck's constant without any need to refer to classical concepts. In this talk, we argue that quantum ontology in Mittelstaedt's sense is not enough. Quantum ontology can never be universal as long as the difference between potential and real properties is not represented adequately. Quantum properties are potential, not (yet) real, be they sharp or unsharp. Hence, preparation and measurement presuppose classical concepts, even in quantum theory. We end up with a classical-quantum sandwich ontology, which is still less extravagant than Bohmian or many-worlds ontologies are.

  8. GFVO: the Genomic Feature and Variation Ontology

    KAUST Repository

    Baran, Joachim; Durgahee, Bibi Sehnaaz Begum; Eilbeck, Karen; Antezana, Erick; Hoehndorf, Robert; Dumontier, Michel

    2015-01-01

    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.

  9. Toxicology ontology perspectives.

    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

    The field of predictive toxicology requires the development of open, public, computable, standardized toxicology vocabularies and ontologies to support the applications required by in silico, in vitro, and in vivo toxicology methods and related analysis and reporting activities. In this article we review ontology developments based on a set of perspectives showing how ontologies are being used in predictive toxicology initiatives and applications. Perspectives on resources and initiatives reviewed include OpenTox, eTOX, Pistoia Alliance, ToxWiz, Virtual Liver, EU-ADR, BEL, ToxML, and Bioclipse. We also review existing ontology developments in neighboring fields that can contribute to establishing an ontological framework for predictive toxicology. A significant set of resources is already available to provide a foundation for an ontological framework for 21st century mechanistic-based toxicology research. Ontologies such as ToxWiz provide a basis for application to toxicology investigations, whereas other ontologies under development in the biological, chemical, and biomedical communities could be incorporated in an extended future framework. OpenTox has provided a semantic web framework for the implementation of such ontologies into software applications and linked data resources. Bioclipse developers have shown the benefit of interoperability obtained through ontology by being able to link their workbench application with remote OpenTox web services. Although these developments are promising, an increased international coordination of efforts is greatly needed to develop a more unified, standardized, and open toxicology ontology framework.

  10. 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

  11. 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.

  12. 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.

  13. Dosimetric verification for radiotherapy quality audit under reference and non-reference conditions in Jiangsu province

    International Nuclear Information System (INIS)

    Wang Jin; Yu Ningle; Yang Chunyong; Du Xiang; Chen Wei; Luo Suming

    2014-01-01

    Objective: To verify the methodology for auditing dosimetric parameters in reference and non-reference conditions with thermoluminescent dosimeters (TLDs). Methods: Under reference and non-reference conditions, the established TLD methods were used to observe the absorbed dose variations with depth, SSD, field size and 45 wedges for 10 photon beams at 5 hospitals. Dosimetric parameters, including doses at D_m_a_x points in axis, on 5 electron beams of 9 MeV were measured. The measurement results were compared between the TLDs and plane parallel ionization chambers. Results: For 6 MV photon beams, the relative deviation of between finger ionization chamber method and TLD chips was in the range of -1.7% to 5.4% under on-axis non-reference conditions, and -6.3% to -0.6% under off-axis non-reference conditions, respectively, all within the range of ≤ ±7% as required by the IAEA. The relative deviation between plane parallel chamber and TLD method was -2.3% to 3.7%, within ±5% as required by the IAEA. Conclusions: It is convenient and feasible to use TLD method for quality audits of dosimetric parameters in radiotherapy. (authors)

  14. Ontological Planning

    Directory of Open Access Journals (Sweden)

    Ahmet Alkan

    2017-12-01

    • Is it possible to redefine ontology within the hierarchical structure of planning? We are going to seek answers to some of these questions within the limited scope of this paper and we are going to offer the rest for discussion by just asking them. In light of these assessments, drawing attention, based on ontological knowledge relying on the wholeness of universe, to the question, on macro level planning, of whether or not the ontological realities of man, energy and movements of thinking can provide macro data for planning on a universal level as important factors affecting mankind will be one of the limited objectives of the paper.

  15. 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

  16. 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...

  17. 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...

  18. 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

  19. 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

  20. Ontology and medical diagnosis.

    Science.gov (United States)

    Bertaud-Gounot, Valérie; Duvauferrier, Régis; Burgun, Anita

    2012-03-01

    Ontology and associated generic tools are appropriate for knowledge modeling and reasoning, but most of the time, disease definitions in existing description logic (DL) ontology are not sufficient to classify patient's characteristics under a particular disease because they do not formalize operational definitions of diseases (association of signs and symptoms=diagnostic criteria). The main objective of this study is to propose an ontological representation which takes into account the diagnostic criteria on which specific patient conditions may be classified under a specific disease. This method needs as a prerequisite a clear list of necessary and sufficient diagnostic criteria as defined for lots of diseases by learned societies. It does not include probability/uncertainty which Web Ontology Language (OWL 2.0) cannot handle. We illustrate it with spondyloarthritis (SpA). Ontology has been designed in Protégé 4.1 OWL-DL2.0. Several kinds of criteria were formalized: (1) mandatory criteria, (2) picking two criteria among several diagnostic criteria, (3) numeric criteria. Thirty real patient cases were successfully classified with the reasoner. This study shows that it is possible to represent operational definitions of diseases with OWL and successfully classify real patient cases. Representing diagnostic criteria as descriptive knowledge (instead of rules in Semantic Web Rule Language or Prolog) allows us to take advantage of tools already available for OWL. While we focused on Assessment of SpondyloArthritis international Society SpA criteria, we believe that many of the representation issues addressed here are relevant to using OWL-DL for operational definition of other diseases in ontology.

  1. 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

  2. Ontology evolution in physics

    OpenAIRE

    Chan, Michael

    2013-01-01

    With the advent of reasoning problems in dynamic environments, there is an increasing need for automated reasoning systems to automatically adapt to unexpected changes in representations. In particular, the automation of the evolution of their ontologies needs to be enhanced without substantially sacrificing expressivity in the underlying representation. Revision of beliefs is not enough, as adding to or removing from beliefs does not change the underlying formal language. Gene...

  3. 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...

  4. Ontology authoring with Forza

    CSIR Research Space (South Africa)

    Keet, CM

    2014-11-01

    Full Text Available Generic, reusable ontology elements, such as a foundational ontology's categories and part-whole relations, are essential for good and interoperable knowledge representation. Ontology developers, which include domain experts and novices, face...

  5. Ontological Surprises

    DEFF Research Database (Denmark)

    Leahu, Lucian

    2016-01-01

    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.......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...

  6. Gene Ontology

    Directory of Open Access Journals (Sweden)

    Gaston K. Mazandu

    2012-01-01

    Full Text Available The wide coverage and biological relevance of the Gene Ontology (GO, confirmed through its successful use in protein function prediction, have led to the growth in its popularity. In order to exploit the extent of biological knowledge that GO offers in describing genes or groups of genes, there is a need for an efficient, scalable similarity measure for GO terms and GO-annotated proteins. While several GO similarity measures exist, none adequately addresses all issues surrounding the design and usage of the ontology. We introduce a new metric for measuring the distance between two GO terms using the intrinsic topology of the GO-DAG, thus enabling the measurement of functional similarities between proteins based on their GO annotations. We assess the performance of this metric using a ROC analysis on human protein-protein interaction datasets and correlation coefficient analysis on the selected set of protein pairs from the CESSM online tool. This metric achieves good performance compared to the existing annotation-based GO measures. We used this new metric to assess functional similarity between orthologues, and show that it is effective at determining whether orthologues are annotated with similar functions and identifying cases where annotation is inconsistent between orthologues.

  7. 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

  8. Didactical Ontologies

    Directory of Open Access Journals (Sweden)

    Steffen Mencke, Reiner Dumke

    2008-03-01

    Full Text Available Ontologies are a fundamental concept of theSemantic Web envisioned by Tim Berners-Lee [1]. Togetherwith explicit representation of the semantics of data formachine-accessibility such domain theories are the basis forintelligent next generation applications for the web andother areas of interest [2]. Their application for specialaspects within the domain of e-learning is often proposed tosupport the increasing complexity ([3], [4], [5], [6]. So theycan provide a better support for course generation orlearning scenario description [7]. By the modeling ofdidactics-related expertise and their provision for thecreators of courses many improvements like reuse, rapiddevelopment and of course increased learning performancebecome possible due to the separation from other aspects ofe-learning platforms as already proposed in [8].

  9. 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

  10. Formal Ontologies and Uncertainty. In Geographical Knowledge

    Directory of Open Access Journals (Sweden)

    Matteo Caglioni

    2014-05-01

    Full Text Available Formal ontologies have proved to be a very useful tool to manage interoperability among data, systems and knowledge. In this paper we will show how formal ontologies can evolve from a crisp, deterministic framework (ontologies of hard knowledge to new probabilistic, fuzzy or possibilistic frameworks (ontologies of soft knowledge. This can considerably enlarge the application potential of formal ontologies in geographic analysis and planning, where soft knowledge is intrinsically linked to the complexity of the phenomena under study.  The paper briefly presents these new uncertainty-based formal ontologies. It then highlights how ontologies are formal tools to define both concepts and relations among concepts. An example from the domain of urban geography finally shows how the cause-to-effect relation between household preferences and urban sprawl can be encoded within a crisp, a probabilistic and a possibilistic ontology, respectively. The ontology formalism will also determine the kind of reasoning that can be developed from available knowledge. Uncertain ontologies can be seen as the preliminary phase of more complex uncertainty-based models. The advantages of moving to uncertainty-based models is evident: whether it is in the analysis of geographic space or in decision support for planning, reasoning on geographic space is almost always reasoning with uncertain knowledge of geographic phenomena.

  11. Patient dose with quality image under diagnostic reference levels

    International Nuclear Information System (INIS)

    Akula, Suresh Kumar; Singh, Gurvinder; Chougule, Arun

    2016-01-01

    Need to set Diagnostic Reference Level (DRL) for locations for all diagnostic procedures in local as compared to National. The review of DRL's should compare local with national or referenced averages and a note made of any significant variances to these averages and the justification for it. To survey and asses radiation doses to patient and reduce the redundancy in patient imaging to maintain DRLs

  12. Protein Annotation from Protein Interaction Networks and Gene Ontology

    OpenAIRE

    Nguyen, Cao D.; Gardiner, Katheleen J.; Cios, Krzysztof J.

    2011-01-01

    We introduce a novel method for annotating protein function that combines Naïve Bayes and association rules, and takes advantage of the underlying topology in protein interaction networks and the structure of graphs in the Gene Ontology. We apply our method to proteins from the Human Protein Reference Database (HPRD) and show that, in comparison with other approaches, it predicts protein functions with significantly higher recall with no loss of precision. Specifically, it achieves 51% precis...

  13. Assessment Applications of Ontologies.

    Science.gov (United States)

    Chung, Gregory K. W. K.; Niemi, David; Bewley, William L.

    This paper discusses the use of ontologies and their applications to assessment. An ontology provides a shared and common understanding of a domain that can be communicated among people and computational systems. The ontology captures one or more experts' conceptual representation of a domain expressed in terms of concepts and the relationships…

  14. 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....

  15. Geo-Ontologies Are Scale Dependent

    Science.gov (United States)

    Frank, A. U.

    2009-04-01

    Philosophers aim at a single ontology that describes "how the world is"; for information systems we aim only at ontologies that describe a conceptualization of reality (Guarino 1995; Gruber 2005). A conceptualization of the world implies a spatial and temporal scale: what are the phenomena, the objects and the speed of their change? Few articles (Reitsma et al. 2003) seem to address that an ontology is scale specific (but many articles indicate that ontologies are scale-free in another sense namely that they are scale free in the link densities between concepts). The scale in the conceptualization can be linked to the observation process. The extent of the support of the physical observation instrument and the sampling theorem indicate what level of detail we find in a dataset. These rules apply for remote sensing or sensor networks alike. An ontology of observations must include scale or level of detail, and concepts derived from observations should carry this relation forward. A simple example: in high resolution remote sensing image agricultural plots and roads between them are shown, at lower resolution, only the plots and not the roads are visible. This gives two ontologies, one with plots and roads, the other with plots only. Note that a neighborhood relation in the two different ontologies also yield different results. References Gruber, T. (2005). "TagOntology - a way to agree on the semantics of tagging data." Retrieved October 29, 2005., from http://tomgruber.org/writing/tagontology-tagcapm-talk.pdf. Guarino, N. (1995). "Formal Ontology, Conceptual Analysis and Knowledge Representation." International Journal of Human and Computer Studies. Special Issue on Formal Ontology, Conceptual Analysis and Knowledge Representation, edited by N. Guarino and R. Poli 43(5/6). Reitsma, F. and T. Bittner (2003). Process, Hierarchy, and Scale. Spatial Information Theory. Cognitive and Computational Foundations of Geographic Information ScienceInternational Conference

  16. Model Driven Engineering with Ontology Technologies

    Science.gov (United States)

    Staab, Steffen; Walter, Tobias; Gröner, Gerd; Parreiras, Fernando Silva

    Ontologies constitute formal models of some aspect of the world that may be used for drawing interesting logical conclusions even for large models. Software models capture relevant characteristics of a software artifact to be developed, yet, most often these software models have limited formal semantics, or the underlying (often graphical) software language varies from case to case in a way that makes it hard if not impossible to fix its semantics. In this contribution, we survey the use of ontology technologies for software modeling in order to carry over advantages from ontology technologies to the software modeling domain. It will turn out that ontology-based metamodels constitute a core means for exploiting expressive ontology reasoning in the software modeling domain while remaining flexible enough to accommodate varying needs of software modelers.

  17. 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.

  18. 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.

  19. 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

  20. Logic and Ontology

    Directory of Open Access Journals (Sweden)

    Newton C. A. da Costa

    2002-12-01

    Full Text Available In view of the present state of development of non classical logic, especially of paraconsistent logic, a new stand regarding the relations between logic and ontology is defended In a parody of a dictum of Quine, my stand May be summarized as follows. To be is to be the value of a variable a specific language with a given underlying logic Yet my stand differs from Quine’s, because, among other reasons, I accept some first order heterodox logics as genuine alternatives to classical logic I also discuss some questions of non classical logic to substantiate my argument, and suggest that may position complements and extends some ideas advanced by L Apostel.

  1. 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

  2. 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...

  3. 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…

  4. 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.

  5. Use artificial neural network to align biological ontologies.

    Science.gov (United States)

    Huang, Jingshan; Dang, Jiangbo; Huhns, Michael N; Zheng, W Jim

    2008-09-16

    Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics. In this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others. The promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore, our method represents a large leap forward towards automating biological ontology alignment.

  6. Towards Agile Ontology Maintenance

    Science.gov (United States)

    Luczak-Rösch, Markus

    Ontologies are an appropriate means to represent knowledge on the Web. Research on ontology engineering reached practices for an integrative lifecycle support. However, a broader success of ontologies in Web-based information systems remains unreached while the more lightweight semantic approaches are rather successful. We assume, paired with the emerging trend of services and microservices on the Web, new dynamic scenarios gain momentum in which a shared knowledge base is made available to several dynamically changing services with disparate requirements. Our work envisions a step towards such a dynamic scenario in which an ontology adapts to the requirements of the accessing services and applications as well as the user's needs in an agile way and reduces the experts' involvement in ontology maintenance processes.

  7. 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....

  8. Survey on Ontology Mapping

    Science.gov (United States)

    Zhu, Junwu

    To create a sharable semantic space in which the terms from different domain ontology or knowledge system, Ontology mapping become a hot research point in Semantic Web Community. In this paper, motivated factors of ontology mapping research are given firstly, and then 5 dominating theories and methods, such as information accessing technology, machine learning, linguistics, structure graph and similarity, are illustrated according their technology class. Before we analyses the new requirements and takes a long view, the contributions of these theories and methods are summarized in details. At last, this paper suggest to design a group of semantic connector with the ability of migration learning for OWL-2 extended with constrains and the ontology mapping theory of axiom, so as to provide a new methodology for ontology mapping.

  9. A UML profile for the OBO relation ontology

    Science.gov (United States)

    2012-01-01

    intuitive form of capturing and representing knowledge than using only text-based notations. The use of the profile requires the domain expert to reason about the underlying semantics of the concepts and relationships being modeled, which helps preventing the introduction of inconsistencies in an ontology under development and facilitates the identification and correction of errors in an already defined ontology. PMID:23095840

  10. 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 ...

  11. 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

  12. Interoperability between phenotype and anatomy ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Oellrich, Anika; Rebholz-Schuhmann, Dietrich

    2010-12-15

    Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning. We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge. http://bioonto.de/pmwiki.php/Main/PheneOntology.

  13. 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.

  14. Protein annotation from protein interaction networks and Gene Ontology.

    Science.gov (United States)

    Nguyen, Cao D; Gardiner, Katheleen J; Cios, Krzysztof J

    2011-10-01

    We introduce a novel method for annotating protein function that combines Naïve Bayes and association rules, and takes advantage of the underlying topology in protein interaction networks and the structure of graphs in the Gene Ontology. We apply our method to proteins from the Human Protein Reference Database (HPRD) and show that, in comparison with other approaches, it predicts protein functions with significantly higher recall with no loss of precision. Specifically, it achieves 51% precision and 60% recall versus 45% and 26% for Majority and 24% and 61% for χ²-statistics, respectively. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. 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,

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. OpenKnowledge Deliverable 3.3.: A methodology for ontology matching quality evaluation

    OpenAIRE

    Yatskevich, Mikalai; Giunchiglia, Fausto; McNeill, Fiona; Shvaiko, Pavel

    2007-01-01

    This document presents an evaluation methodology for the assessment of quality results produced by ontology matchers. In particular, it discusses: (i) several standard quality measures used in the ontology matching evaluation, (ii) a methodology of how to build semiautomatically an incomplete reference alignment allowing for the assessment of quality results produced by ontology matchers and (iii) a preliminary empirical evaluation of the OpenKnowledge ontology matching component.

  1. 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.

  2. 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.

  3. A Method for Evaluating and Standardizing Ontologies

    Science.gov (United States)

    Seyed, Ali Patrice

    2012-01-01

    The Open Biomedical Ontology (OBO) Foundry initiative is a collaborative effort for developing interoperable, science-based ontologies. The Basic Formal Ontology (BFO) serves as the upper ontology for the domain-level ontologies of OBO. BFO is an upper ontology of types as conceived by defenders of realism. Among the ontologies developed for OBO…

  4. 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.

  5. 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.

  6. The Electronic Notebook Ontology

    OpenAIRE

    Chalk, Stuart

    2016-01-01

    Science is rapidly being brought into the electronic realm and electronic laboratory notebooks (ELN) are a big part of this activity. The representation of the scientific process in the context of an ELN is an important component to making the data recorded in ELNs semantically integrated. This presentation will outline initial developments of an Electronic Notebook Ontology (ENO) that will help tie together the ExptML ontology, HCLS Community Profile data descriptions, and the VIVO-ISF ontol...

  7. 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

  8. Ontology Update in the Cognitive Model of Ontology Learning

    Directory of Open Access Journals (Sweden)

    Zhang De-Hai

    2016-01-01

    Full Text Available Ontology has been used in many hot-spot fields, but most ontology construction methods are semiautomatic, and the construction process of ontology is still a tedious and painstaking task. In this paper, a kind of cognitive models is presented for ontology learning which can simulate human being’s learning from world. In this model, the cognitive strategies are applied with the constrained axioms. Ontology update is a key step when the new knowledge adds into the existing ontology and conflict with old knowledge in the process of ontology learning. This proposal designs and validates the method of ontology update based on the axiomatic cognitive model, which include the ontology update postulates, axioms and operations of the learning model. It is proved that these operators subject to the established axiom system.

  9. Automatic Tamil lyric generation based on ontological interpretation ...

    Indian Academy of Sciences (India)

    In this work, we use an ontology to determine the semantic information from ... Hence, to study the context-based lyric generation process, we referred to ...... Mann C W and Moore A J 1981 Computer Generation of Multiparagraph English text.

  10. CRAVE: a database, middleware and visualization system for phenotype ontologies.

    Science.gov (United States)

    Gkoutos, Georgios V; Green, Eain C J; Greenaway, Simon; Blake, Andrew; Mallon, Ann-Marie; Hancock, John M

    2005-04-01

    A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

  11. 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

  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. Unintended consequences of existential quantifications in biomedical ontologies

    Directory of Open Access Journals (Sweden)

    Boeker Martin

    2011-11-01

    Full Text Available Abstract Background The Open Biomedical Ontologies (OBO Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the semantic web format Web Ontology Language (OWL, which draws upon formal logic. Based on the interpretations underlying OWL description logics (OWL-DL semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors. Results We analyzed ontologies and ontology cross products available via the OBO Foundry site http://www.obofoundry.org for existential restrictions (someValuesFrom, from which we examined a random sample of 2,836 clauses. According to a rating done by four experts, 23% of all existential restrictions in OBO Foundry candidate ontologies are suspicious (Cohens' κ = 0.78. We found a smaller proportion of existential restrictions in OBO Foundry cross products are suspicious, but in this case an accurate quantitative judgment is not possible due to a low inter-rater agreement (κ = 0.07. We identified several typical modeling problems, for which satisfactory ontology design patterns based on OWL-DL were proposed. We further describe several usability issues with OBO ontologies, including the lack of ontological commitment for several common terms, and the proliferation of domain-specific relations. Conclusions The current OWL releases of OBO Foundry (and Foundry candidate ontologies contain numerous assertions which do not properly describe the underlying biological reality, or are ambiguous and difficult to interpret. The solution is a better anchoring in upper ontologies and a restriction to relatively few, well defined relation types with given domain and range constraints.

  14. 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…

  15. A tri-reference point theory of decision making under risk.

    Science.gov (United States)

    Wang, X T; Johnson, Joseph G

    2012-11-01

    The tri-reference point (TRP) theory takes into account minimum requirements (MR), the status quo (SQ), and goals (G) in decision making under risk. The 3 reference points demarcate risky outcomes and risk perception into 4 functional regions: success (expected value of x ≥ G), gain (SQ G > SQ. We present TRP assumptions and value functions and a mathematical formalization of the theory. We conducted empirical tests of crucial TRP predictions using both explicit and implicit reference points. We show that decision makers consider both G and MR and give greater weight to MR than G, indicating failure aversion (i.e., the disutility of a failure is greater than the utility of a success in the same task) in addition to loss aversion (i.e., the disutility of a loss is greater than the utility of the same amount of gain). Captured by a double-S shaped value function with 3 inflection points, risk preferences switched between risk seeking and risk aversion when the distribution of a gamble straddled a different reference point. The existence of MR (not G) significantly shifted choice preference toward risk aversion even when the outcome distribution of a gamble was well above the MR. Single reference point based models such as prospect theory cannot consistently account for these findings. The TRP theory provides simple guidelines for evaluating risky choices for individuals and organizational management. (PsycINFO Database Record (c) 2012 APA, all rights reserved).

  16. New digital reference current generation for shunt active power filter under distorted voltage conditions

    Energy Technology Data Exchange (ETDEWEB)

    Abdusalam, Mohamed; Karimi, Shahram; Saadate, Shahrokh [Groupe de Recherche en Electrotechnique et Electronique de Nancy (GREEN), CNRS UMR 7037 (France); Poure, Philippe [Laboratoire d' Instrumentation Electronique de Nancy (LIEN), EA 3440, Universite Henri Poincare - Nancy Universite, B.P. 239, 54506 Vandoeuvre les Nancy Cedex (France)

    2009-05-15

    In this paper, a new reference current computation method suitable for shunt active power filter control under distorted voltage conditions is proposed. The active power filter control is based on the use of self-tuning filters (STF) for the reference current generation and on a modulated hysteresis current controller. This active filter is intended for harmonic compensation of a diode rectifier feeding a RL load under distorted voltage conditions. The study of the active filter control is divided in two parts. The first one deals with the harmonic isolator which generates the harmonic reference currents and is experimentally implemented in a DS1104 card of a DSPACE prototyping system. The second part focuses on the generation of the switching pattern of the inverter by using a modulated hysteresis current controller, implemented in an analogue card. The use of STF instead of classical extraction filters allows extracting directly the voltage and current fundamental components in the {alpha}-{beta} axis without phase locked loop (PLL). The performances are good even under distorted voltage conditions. First, the effectiveness of the new proposed method is mathematically studied and verified by computer simulation. Then, experimental results are presented using a DSPACE system associated with the analogue current controller for a real shunt active power filter. (author)

  17. 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.

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

    Science.gov (United States)

    Cook, Daniel L; Bookstein, Fred L; Gennari, John H

    2011-01-01

    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. © 2011 Cook et al.

  19. 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.

  20. 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.

  1. 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.

  2. 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 ...

  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. 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

  5. ONTOLOGY IN PHARMACY

    Directory of Open Access Journals (Sweden)

    L. Yu. Babintseva

    2015-05-01

    Full Text Available It’s considered ontological models for formalization of knowledge in pharmacy. There is emphasized the view that the possibility of rapid exchange of information in the pharmaceutical industry, it is necessary to create a single information space. This means not only the establishment of uniform standards for the presentation of information on pharmaceutical groups pharmacotherapeutic classifications, but also the creation of a unified and standardized system for the transfer and renewal of knowledge. It is the organization of information in the ontology helps quickly in the future to build expert systems and applications to work with data.

  6. 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

  7. 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....

  8. Biomedical ontologies: toward scientific debate.

    Science.gov (United States)

    Maojo, V; Crespo, J; García-Remesal, M; de la Iglesia, D; Perez-Rey, D; Kulikowski, C

    2011-01-01

    Biomedical ontologies have been very successful in structuring knowledge for many different applications, receiving widespread praise for their utility and potential. Yet, the role of computational ontologies in scientific research, as opposed to knowledge management applications, has not been extensively discussed. We aim to stimulate further discussion on the advantages and challenges presented by biomedical ontologies from a scientific perspective. We review various aspects of biomedical ontologies going beyond their practical successes, and focus on some key scientific questions in two ways. First, we analyze and discuss current approaches to improve biomedical ontologies that are based largely on classical, Aristotelian ontological models of reality. Second, we raise various open questions about biomedical ontologies that require further research, analyzing in more detail those related to visual reasoning and spatial ontologies. We outline significant scientific issues that biomedical ontologies should consider, beyond current efforts of building practical consensus between them. For spatial ontologies, we suggest an approach for building "morphospatial" taxonomies, as an example that could stimulate research on fundamental open issues for biomedical ontologies. Analysis of a large number of problems with biomedical ontologies suggests that the field is very much open to alternative interpretations of current work, and in need of scientific debate and discussion that can lead to new ideas and research directions.

  9. Mining rare associations between biological ontologies.

    Science.gov (United States)

    Benites, Fernando; Simon, Svenja; Sapozhnikova, Elena

    2014-01-01

    The constantly increasing volume and complexity of available biological data requires new methods for their management and analysis. An important challenge is the integration of information from different sources in order to discover possible hidden relations between already known data. In this paper we introduce a data mining approach which relates biological ontologies by mining cross and intra-ontology pairwise generalized association rules. Its advantage is sensitivity to rare associations, for these are important for biologists. We propose a new class of interestingness measures designed for hierarchically organized rules. These measures allow one to select the most important rules and to take into account rare cases. They favor rules with an actual interestingness value that exceeds the expected value. The latter is calculated taking into account the parent rule. We demonstrate this approach by applying it to the analysis of data from Gene Ontology and GPCR databases. Our objective is to discover interesting relations between two different ontologies or parts of a single ontology. The association rules that are thus discovered can provide the user with new knowledge about underlying biological processes or help improve annotation consistency. The obtained results show that produced rules represent meaningful and quite reliable associations.

  10. Mining rare associations between biological ontologies.

    Directory of Open Access Journals (Sweden)

    Fernando Benites

    Full Text Available The constantly increasing volume and complexity of available biological data requires new methods for their management and analysis. An important challenge is the integration of information from different sources in order to discover possible hidden relations between already known data. In this paper we introduce a data mining approach which relates biological ontologies by mining cross and intra-ontology pairwise generalized association rules. Its advantage is sensitivity to rare associations, for these are important for biologists. We propose a new class of interestingness measures designed for hierarchically organized rules. These measures allow one to select the most important rules and to take into account rare cases. They favor rules with an actual interestingness value that exceeds the expected value. The latter is calculated taking into account the parent rule. We demonstrate this approach by applying it to the analysis of data from Gene Ontology and GPCR databases. Our objective is to discover interesting relations between two different ontologies or parts of a single ontology. The association rules that are thus discovered can provide the user with new knowledge about underlying biological processes or help improve annotation consistency. The obtained results show that produced rules represent meaningful and quite reliable associations.

  11. 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.

  12. Reference-free fatigue crack detection using nonlinear ultrasonic modulation under various temperature and loading conditions

    Science.gov (United States)

    Lim, Hyung Jin; Sohn, Hoon; DeSimio, Martin P.; Brown, Kevin

    2014-04-01

    This study presents a reference-free fatigue crack detection technique using nonlinear ultrasonic modulation. When low frequency (LF) and high frequency (HF) inputs generated by two surface-mounted lead zirconate titanate (PZT) transducers are applied to a structure, the presence of a fatigue crack can provide a mechanism for nonlinear ultrasonic modulation and create spectral sidebands around the frequency of the HF signal. The crack-induced spectral sidebands are isolated using a combination of linear response subtraction (LRS), synchronous demodulation (SD) and continuous wavelet transform (CWT) filtering. Then, a sequential outlier analysis is performed on the extracted sidebands to identify the crack presence without referring any baseline data obtained from the intact condition of the structure. Finally, the robustness of the proposed technique is demonstrated using actual test data obtained from simple aluminum plate and complex aircraft fitting-lug specimens under varying temperature and loading variations.

  13. 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 ...

  14. 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…

  15. Audit Validation Using Ontologies

    Directory of Open Access Journals (Sweden)

    Ion IVAN

    2015-01-01

    Full Text Available Requirements to increase quality audit processes in enterprises are defined. It substantiates the need for assessment and management audit processes using ontologies. Sets of rules, ways to assess the consistency of rules and behavior within the organization are defined. Using ontologies are obtained qualifications that assess the organization's audit. Elaboration of the audit reports is a perfect algorithm-based activity characterized by generality, determinism, reproducibility, accuracy and a well-established. The auditors obtain effective levels. Through ontologies obtain the audit calculated level. Because the audit report is qualitative structure of information and knowledge it is very hard to analyze and interpret by different groups of users (shareholders, managers or stakeholders. Developing ontology for audit reports validation will be a useful instrument for both auditors and report users. In this paper we propose an instrument for validation of audit reports contain a lot of keywords that calculates indicators, a lot of indicators for each key word there is an indicator, qualitative levels; interpreter who builds a table of indicators, levels of actual and calculated levels.

  16. Biomedicine: an ontological dissection.

    Science.gov (United States)

    Baronov, David

    2008-01-01

    Though ubiquitous across the medical social sciences literature, the term "biomedicine" as an analytical concept remains remarkably slippery. It is argued here that this imprecision is due in part to the fact that biomedicine is comprised of three interrelated ontological spheres, each of which frames biomedicine as a distinct subject of investigation. This suggests that, depending upon one's ontological commitment, the meaning of biomedicine will shift. From an empirical perspective, biomedicine takes on the appearance of a scientific enterprise and is defined as a derivative category of Western science more generally. From an interpretive perspective, biomedicine represents a symbolic-cultural expression whose adherence to the principles of scientific objectivity conceals an ideological agenda. From a conceptual perspective, biomedicine represents an expression of social power that reflects structures of power and privilege within capitalist society. No one perspective exists in isolation and so the image of biomedicine from any one presents an incomplete understanding. It is the mutually-conditioning interrelations between these ontological spheres that account for biomedicine's ongoing development. Thus, the ontological dissection of biomedicine that follows, with particular emphasis on the period of its formal crystallization in the latter nineteenth and early twentieth century, is intended to deepen our understanding of biomedicine as an analytical concept across the medical social sciences literature.

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

    African Journals Online (AJOL)

    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 between scientific realists and antirealists.

  18. 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

  19. 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

  20. 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.

  1. 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...

  2. 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

  3. 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

  4. Selection of relatively exact reference genes for gene expression studies in goosegrass (Eleusine indica) under herbicide stress.

    Science.gov (United States)

    Chen, Jingchao; Huang, Zhaofeng; Huang, Hongjuan; Wei, Shouhui; Liu, Yan; Jiang, Cuilan; Zhang, Jie; Zhang, Chaoxian

    2017-04-21

    Goosegrass (Eleusine indica) is one of the most serious annual grassy weeds worldwide, and its evolved herbicide-resistant populations are more difficult to control. Quantitative real-time PCR (qPCR) is a common technique for investigating the resistance mechanism; however, there is as yet no report on the systematic selection of stable reference genes for goosegrass. This study proposed to test the expression stability of 9 candidate reference genes in goosegrass in different tissues and developmental stages and under stress from three types of herbicide. The results show that for different developmental stages and organs (control), eukaryotic initiation factor 4 A (eIF-4) is the most stable reference gene. Chloroplast acetolactate synthase (ALS) is the most stable reference gene under glyphosate stress. Under glufosinate stress, eIF-4 is the best reference gene. Ubiquitin-conjugating enzyme (UCE) is the most stable reference gene under quizalofop-p-ethyl stress. The gene eIF-4 is the recommended reference gene for goosegrass under the stress of all three herbicides. Moreover, pairwise analysis showed that seven reference genes were sufficient to normalize the gene expression data under three herbicides treatment. This study provides a list of reliable reference genes for transcript normalization in goosegrass, which will facilitate resistance mechanism studies in this weed species.

  5. 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.

  6. [Towards a structuring fibrillar ontology].

    Science.gov (United States)

    Guimberteau, J-C

    2012-10-01

    Over previous decades and centuries, the difficulty encountered in the manner in which the tissue of our bodies is organised, and structured, is clearly explained by the impossibility of exploring it in detail. Since the creation of the microscope, the perception of the basic unity, which is the cell, has been essential in understanding the functioning of reproduction and of transmission, but has not been able to explain the notion of form; since the cells are not everywhere and are not distributed in an apparently balanced manner. The problems that remain are those of form and volume and also of connection. The concept of multifibrillar architecture, shaping the interfibrillar microvolumes in space, represents a solution to all these questions. The architectural structures revealed, made up of fibres, fibrils and microfibrils, from the mesoscopic to the microscopic level, provide the concept of a living form with structural rationalism that permits the association of psychochemical molecular biodynamics and quantum physics: the form can thus be described and interpreted, and a true structural ontology is elaborated from a basic functional unity, which is the microvacuole, the intra and interfibrillar volume of the fractal organisation, and the chaotic distribution. Naturally, new, less linear, less conclusive, and less specific concepts will be implied by this ontology, leading one to believe that the emergence of life takes place under submission to forces that the original form will have imposed and oriented the adaptive finality. Copyright © 2012. Published by Elsevier SAS.

  7. 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.

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

    KAUST Repository

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

    2015-01-01

    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

  9. 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

  10. Completeness, supervenience and ontology

    Energy Technology Data Exchange (ETDEWEB)

    Maudlin, Tim W E [Department of Philosophy, Rutgers University, 26 Nichol Avenue, New Brunswick, NJ 08901-1411 (United States)

    2007-03-23

    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.

  11. LOGISTICS OPTIMIZATION USING ONTOLOGIES

    OpenAIRE

    Hendi , Hayder; Ahmad , Adeel; Bouneffa , Mourad; Fonlupt , Cyril

    2014-01-01

    International audience; Logistics processes involve complex physical flows and integration of different elements. It is widely observed that the uncontrolled processes can decline the state of logistics. The optimization of logistic processes can support the desired growth and consistent continuity of logistics. In this paper, we present a software framework for logistic processes optimization. It primarily defines logistic ontologies and then optimize them. It intends to assist the design of...

  12. 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.

  13. 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.

  14. 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. PMID:23251424

  15. Verification of dosimetric methodology for auditing radiotherapy quality under non-reference condition in Hubei province

    International Nuclear Information System (INIS)

    Ma Xinxing; Luo Suming; He Zhijian; Zhou Wenshan

    2014-01-01

    Objective: To verify the reliability of TLD-based quality audit for radiotherapy dosimetry of medical electron accelerator in non-reference condition by monitoring the dose variations from electron beams with different field sizes and 45° wedge and the dose variations from photon beams with different field sizes and source-skin distance. Methods: Both TLDs and finger ionization chambers were placed at a depth of 10 cm in water to measure the absorbed dose from photon beams, and also placed at the depth of maximum dose from electron beams under non-reference condition. TLDs were then mailed to National Institute for Radiological Protection, China CDC for further measurement. Results: Among the 70 measuring points for photon beams, 58 points showed the results with a relative error less than ±7.0% (IAEA's acceptable deviation: ±7.0%) between TLDs and finger ionization chambers measurements, and the percentage of qualified point numbers was 82.8%. After corrected by Ps value, 62 points were qualified and the percentage was up to 88.6%. All of the measuring points for electron beams, with the total number of 24, presented a relative error within ±5.0% (IAEA's acceptable deviation: ±5.0%) between TLDs and finger ioization cylindrical chambers measurements. Conclusions: TLD-based quality audit is convenient for determining radiotherapy dosimetric parameters of electron beams in non-reference condition and can improve the accuracy of the measuring parameters in connection with finger chambers. For electron beams of 5 MeV < E_0 < 10 MeV, the absorbed dose parameters measured by finger ionization chambers, combined with TLD audit, can help obtain the precise and reliable results. (authors)

  16. Feasibility of automated foundational ontology interchangeability

    CSIR Research Space (South Africa)

    Khan, ZC

    2014-11-01

    Full Text Available the Source Domain Ontology (sOd), with the domain knowledge com- ponent of the source ontology, the Source Foundational Ontology (sOf ) that is the foundational ontology component of the source ontology that is to be interchanged, and any equivalence... or subsumption mappings between enti- ties in sOd and sOf . – The Target Ontology (tO) which has been interchanged, which comprises the Target Domain Ontology (tOd), with the domain knowledge component of the target ontology, and the Target Foundational Ontology...

  17. Standard Test Method for Electrical Performance of Photovoltaic Cells Using Reference Cells Under Simulated Sunlight

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2009-01-01

    1.1 This test method covers the determination of the electrical performance of a photovoltaic cell under simulated sunlight by means of a calibrated reference cell procedure. 1.2 Electrical performance measurements are reported with respect to a select set of standard reporting conditions (SRC) (see Table 1) or to user-specified conditions. 1.2.1 The SRC or user-specified conditions include the cell temperature, the total irradiance, and the reference spectral irradiance distribution. 1.3 This test method is applicable only to photovoltaic cells with a linear response over the range of interest. 1.4 The cell parameters determined by this test method apply only at the time of test, and imply no past or future performance level. 1.5 The values stated in SI units are to be regarded as standard. No other units of measurement are included in this standard. 1.6 This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this s...

  18. 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…

  19. TrhOnt: building an ontology to assist rehabilitation processes.

    Science.gov (United States)

    Berges, Idoia; Antón, David; Bermúdez, Jesús; Goñi, Alfredo; Illarramendi, Arantza

    2016-10-04

    One of the current research efforts in the area of biomedicine is the representation of knowledge in a structured way so that reasoning can be performed on it. More precisely, in the field of physiotherapy, information such as the physiotherapy record of a patient or treatment protocols for specific disorders must be adequately modeled, because they play a relevant role in the management of the evolutionary recovery process of a patient. In this scenario, we introduce TRHONT, an application ontology that can assist physiotherapists in the management of the patients' evolution via reasoning supported by semantic technology. The ontology was developed following the NeOn Methodology. It integrates knowledge from ontological (e.g. FMA ontology) and non-ontological resources (e.g. a database of movements, exercises and treatment protocols) as well as additional physiotherapy-related knowledge. We demonstrate how the ontology fulfills the purpose of providing a reference model for the representation of the physiotherapy-related information that is needed for the whole physiotherapy treatment of patients, since they step for the first time into the physiotherapist's office, until they are discharged. More specifically, we present the results for each of the intended uses of the ontology listed in the document that specifies its requirements, and show how TRHONT can answer the competency questions defined within that document. Moreover, we detail the main steps of the process followed to build the TRHONT ontology in order to facilitate its reproducibility in a similar context. Finally, we show an evaluation of the ontology from different perspectives. TRHONT has achieved the purpose of allowing for a reasoning process that changes over time according to the patient's state and performance.

  20. 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

  1. State reference design and saturated control of doubly-fed induction generators under voltage dips

    Science.gov (United States)

    Tilli, Andrea; Conficoni, Christian; Hashemi, Ahmad

    2017-04-01

    In this paper, the stator/rotor currents control problem of doubly-fed induction generator under faulty line voltage is carried out. Common grid faults cause a steep decline in the line voltage profile, commonly denoted as voltage dip. This point is critical for such kind of machines, having their stator windings directly connected to the grid. In this respect, solid methodological nonlinear control theory arguments are exploited and applied to design a novel controller, whose main goal is to improve the system behaviour during voltage dips, endowing it with low voltage ride through capability, a fundamental feature required by modern Grid Codes. The proposed solution exploits both feedforward and feedback actions. The feedforward part relies on suitable reference trajectories for the system internal dynamics, which are designed to prevent large oscillations in the rotor currents and command voltages, excited by line perturbations. The feedback part uses state measurements and is designed according to Linear Matrix Inequalities (LMI) based saturated control techniques to further reduce oscillations, while explicitly accounting for the system constraints. Numerical simulations verify the benefits of the internal dynamics trajectory planning, and the saturated state feedback action, in crucially improving the Doubly-Fed Induction Machine response under severe grid faults.

  2. 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.

  3. 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.

  4. Robust Floor Determination Algorithm for Indoor Wireless Localization Systems under Reference Node Failure

    Directory of Open Access Journals (Sweden)

    Kriangkrai Maneerat

    2016-01-01

    Full Text Available One of the challenging problems for indoor wireless multifloor positioning systems is the presence of reference node (RN failures, which cause the values of received signal strength (RSS to be missed during the online positioning phase of the location fingerprinting technique. This leads to performance degradation in terms of floor accuracy, which in turn affects other localization procedures. This paper presents a robust floor determination algorithm called Robust Mean of Sum-RSS (RMoS, which can accurately determine the floor on which mobile objects are located and can work under either the fault-free scenario or the RN-failure scenarios. The proposed fault tolerance floor algorithm is based on the mean of the summation of the strongest RSSs obtained from the IEEE 802.15.4 Wireless Sensor Networks (WSNs during the online phase. The performance of the proposed algorithm is compared with those of different floor determination algorithms in literature. The experimental results show that the proposed robust floor determination algorithm outperformed the other floor algorithms and can achieve the highest percentage of floor determination accuracy in all scenarios tested. Specifically, the proposed algorithm can achieve greater than 95% correct floor determination under the scenario in which 40% of RNs failed.

  5. 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...

  6. 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.

  7. Application of Alignment Methodologies to Spatial Ontologies in the Hydro Domain

    Science.gov (United States)

    Lieberman, J. E.; Cheatham, M.; Varanka, D.

    2015-12-01

    Ontologies are playing an increasing role in facilitating mediation and translation between datasets representing diverse schemas, vocabularies, or knowledge communities. This role is relatively straightforward when there is one ontology comprising all relevant common concepts that can be mapped to entities in each dataset. Frequently, one common ontology has not been agreed to. Either each dataset is represented by a distinct ontology, or there are multiple candidates for commonality. Either the one most appropriate (expressive, relevant, correct) ontology must be chosen, or else concepts and relationships matched across multiple ontologies through an alignment process so that they may be used in concert to carry out mediation or other semantic operations. A resulting alignment can be effective to the extent that entities in in the ontologies represent differing terminology for comparable conceptual knowledge. In cases such as spatial ontologies, though, ontological entities may also represent disparate conceptualizations of space according to the discernment methods and application domains on which they are based. One ontology's wetland concept may overlap in space with another ontology's recharge zone or wildlife range or water feature. In order to evaluate alignment with respect to spatial ontologies, alignment has been applied to a series of ontologies pertaining to surface water that are used variously in hydrography (characterization of water features), hydrology (study of water cycling), and water quality (nutrient and contaminant transport) application domains. There is frequently a need to mediate between datasets in each domain in order to develop broader understanding of surface water systems, so there is a practical as well theoretical value in the alignment. From a domain expertise standpoint, the ontologies under consideration clearly contain some concepts that are spatially as well as conceptually identical and then others with less clear

  8. An ontological analysis of the electrocardiogram - DOI: 10.3395/reciis.v3i1.242en

    Directory of Open Access Journals (Sweden)

    Bernardo Gonçalves

    2009-04-01

    Full Text Available Bioinformatics has been a fertile field for the application of the discipline of formal ontology. The principled representation of biomedical entities has increasingly supported biological research, with direct benefits ranging from the reformulation of medical terminologies to the introduction of new perspectives for enhanced models of Electronic Health Records (EHR. This paper introduces an application-independent ontological analysis of the electrocardiogram (ECG grounded in the Unified Foundational Ontology. With the objective of investigating the phenomena underlying this cardiological exam, we deal with the sub-domains of human heart electrophysiology and anatomy. We then outline an ECG Ontology built upon the OBO Relation Ontology. In addition, the domain ontology sketched here takes inspiration both in the Foundational Model of Anatomy and in the Ontology of Functions proposed under the auspices of the General Formal Ontology (GFO research program.

  9. 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.

  10. Ontology Based Model Transformation Infrastructure

    NARCIS (Netherlands)

    Göknil, Arda; Topaloglu, N.Y.

    2005-01-01

    Using MDA in ontology development has been investigated in several works recently. The mappings and transformations between the UML constructs and the OWL elements to develop ontologies are the main concern of these research projects. We propose another approach in order to achieve the collaboration

  11. 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.…

  12. The foundational ontology library ROMULUS

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-09-01

    Full Text Available . We present here a basic step in that direction with the Repository of Ontologies for MULtiple USes, ROMULUS, which is the first online library of machine-processable, modularised, aligned, and logic-based merged foundational ontologies. In addition...

  13. 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

  14. Expert2OWL: A Methodology for Pattern-Based Ontology Development.

    Science.gov (United States)

    Tahar, Kais; Xu, Jie; Herre, Heinrich

    2017-01-01

    The formalization of expert knowledge enables a broad spectrum of applications employing ontologies as underlying technology. These include eLearning, Semantic Web and expert systems. However, the manual construction of such ontologies is time-consuming and thus expensive. Moreover, experts are often unfamiliar with the syntax and semantics of formal ontology languages such as OWL and usually have no experience in developing formal ontologies. To overcome these barriers, we developed a new method and tool, called Expert2OWL that provides efficient features to support the construction of OWL ontologies using GFO (General Formal Ontology) as a top-level ontology. This method allows a close and effective collaboration between ontologists and domain experts. Essentially, this tool integrates Excel spreadsheets as part of a pattern-based ontology development and refinement process. Expert2OWL enables us to expedite the development process and modularize the resulting ontologies. We applied this method in the field of Chinese Herbal Medicine (CHM) and used Expert2OWL to automatically generate an accurate Chinese Herbology ontology (CHO). The expressivity of CHO was tested and evaluated using ontology query languages SPARQL and DL. CHO shows promising results and can generate answers to important scientific questions such as which Chinese herbal formulas contain which substances, which substances treat which diseases, and which ones are the most frequently used in CHM.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. Exogenous reference gene normalization for real-time reverse transcription-polymerase chain reaction analysis under dynamic endogenous transcription.

    Science.gov (United States)

    Johnston, Stephen; Gallaher, Zachary; Czaja, Krzysztof

    2012-05-15

    Quantitative real-time reverse transcription-polymerase chain reaction (qPCR) is widely used to investigate transcriptional changes following experimental manipulations to the nervous system. Despite the widespread utilization of qPCR, the interpretation of results is marred by the lack of a suitable reference gene due to the dynamic nature of endogenous transcription. To address this inherent deficiency, we investigated the use of an exogenous spike-in mRNA, luciferase, as an internal reference gene for the 2(-∆∆Ct) normalization method. To induce dynamic transcription, we systemically administered capsaicin, a neurotoxin selective for C-type sensory neurons expressing the TRPV-1 receptor, to adult male Sprague-Dawley rats. We later isolated nodose ganglia for qPCR analysis with the reference being either exogenous luciferase mRNA or the commonly used endogenous reference β-III tubulin. The exogenous luciferase mRNA reference clearly demonstrated the dynamic expression of the endogenous reference. Furthermore, variability of the endogenous reference would lead to misinterpretation of other genes of interest. In conclusion, traditional reference genes are often unstable under physiologically normal situations, and certainly unstable following the damage to the nervous system. The use of exogenous spike-in reference provides a consistent and easily implemented alternative for the analysis of qPCR data.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Proposed actions are no actions: re-modeling an ontology design pattern with a realist top-level ontology.

    Science.gov (United States)

    Seddig-Raufie, Djamila; Jansen, Ludger; Schober, Daniel; Boeker, Martin; Grewe, Niels; Schulz, Stefan

    2012-09-21

    Ontology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, re-usability and expansion, and to make the result of ontology engineering more predictable. In this paper, we analyze ODP repositories and investigate their relation with upper-level ontologies. In particular, we compare the BioTop upper ontology to the Action ODP from the NeOn an ODP repository. In view of the differences in the respective approaches, we investigate whether the Action ODP can be embedded into BioTop. We demonstrate that this requires re-interpreting the meaning of classes of the NeOn Action ODP in the light of the precepts of realist ontologies. As a result, the re-design required clarifying the ontological commitment of the ODP classes by assigning them to top-level categories. Thus, ambiguous definitions are avoided. Classes of real entities are clearly distinguished from classes of information artifacts. The proposed approach avoids the commitment to the existence of unclear future entities which underlies the NeOn Action ODP. Our re-design is parsimonious in the sense that existing BioTop content proved to be largely sufficient to define the different types of actions and plans. The proposed model demonstrates that an expressive upper-level ontology provides enough resources and expressivity to represent even complex ODPs, here shown with the different flavors of Action as proposed in the NeOn ODP. The advantage of ODP inclusion into a top-level ontology is the given predetermined dependency of each class, an existing backbone structure and well-defined relations. Our comparison shows that the use of some ODPs is more likely to cause problems for ontology developers, rather than to guide them. Besides the structural properties, the explanation of classification results were particularly hard to grasp for 'self-sufficient' ODPs as

  7. 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

  8. Interpretations of Ontologies for Breast Cancer

    Directory of Open Access Journals (Sweden)

    Srinandan Dasmahapatra

    2008-07-01

    ontology building as guarantors of fidelity to reality. We find that ontologies intended to support medical practice can only be understood within the context of their intended use. The declarative framework within which they are encoded generates the hope that their meaning transcends the specific application context. We show, however, that these declarative statements are to be understood as end products of chains of procedural engagements between humans, materials and communitarian norms. It is only when this scaffolding that brings this representation into existence becomes routine and consensual (within the community that exchanges information indexed against it that the concepts stand in for physiological states with independent dynamics. However, as the state of biomedical knowledge is always in a state of flux, and different institutions and practitioners may be out of sync with respect to such modifications, the concepts embedded in the ontologies are constantly subject to reinterpretation within the context of specific institutional practices. Given the fragmentation of the patient’s body when viewed through various specialised lenses, ontologies can provide placeholders for co-ordinating disparate viewpoints to provide suitable medical interventions. The extent to which such interventions reflect any underlying reality, as manifest in measures of their efficacy, is closely wrapped up in the regulatory apparatus of protocol-guided consensus making. The value of ontologies lies in their reflection of, and support for, the sense-making activities that constitute expertise, not in their transparent access to a metaphysical reality.

  9. 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.

  10. A New role of ontologies and advanced scientific visualization in big data analytics

    OpenAIRE

    Chuprina, Svetlana

    2016-01-01

    Accessing and contextual semantic searching structured, semi-structured and unstructured information resources and their ontology based analysis in a uniform way across text-free Big Data query implementation is a main feature of approach under discussion. To increase the semantic power of query results’ analysis the ontology based implementation of multiplatform adaptive tools of scientific visualization are demonstrated. The ontologies are used not for integration of heterogeneous resources...

  11. 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...

  12. development of ontological knowledge representation

    African Journals Online (AJOL)

    Preferred Customer

    ABSTRACT. This paper presents the development of an ontological knowledge organization and .... intelligence in order to facilitate knowledge sharing and reuse of acquired knowledge (15). Soon, ..... Water Chemistry, AJCE, 1(2), 50-58. 25.

  13. A Mobile Army of Ontologies

    DEFF Research Database (Denmark)

    Juul, Jesper

    2015-01-01

    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...... commercialization of games and videogames their study has shifted between approaches focused on players (ludic processes) and artifacts (ludic objects). Some attempts to analyze the relationship between the process and the object have occasionally been done in terms of ‘ontology’ (Zagal 2005; Leino 2010; Gualeni...

  14. 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.

  15. 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.

  16. A Uniform Ontology for Software Interfaces

    Science.gov (United States)

    Feyock, Stefan

    2002-01-01

    It is universally the case that computer users who are not also computer specialists prefer to deal with computers' in terms of a familiar ontology, namely that of their application domains. For example, the well-known Windows ontology assumes that the user is an office worker, and therefore should be presented with a "desktop environment" featuring entities such as (virtual) file folders, documents, appointment calendars, and the like, rather than a world of machine registers and machine language instructions, or even the DOS command level. The central theme of this research has been the proposition that the user interacting with a software system should have at his disposal both the ontology underlying the system, as well as a model of the system. This information is necessary for the understanding of the system in use, as well as for the automatic generation of assistance for the user, both in solving the problem for which the application is designed, and for providing guidance in the capabilities and use of the system.

  17. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries

    Directory of Open Access Journals (Sweden)

    Apweiler Rolf

    2006-02-01

    Full Text Available Abstract Background With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. Results The Ontology Lookup Service (OLS was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence. Conclusion The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO format. It can be accessed interactively or programmatically at http://www.ebi.ac.uk/ontology-lookup/.

  18. Building a Chemical Ontology using Methontology and the Ontology Design Environment

    OpenAIRE

    Fernández López, Mariano; Gómez-Pérez, A.; Pazos Sierra, Alejandro; Pazos Sierra, Juan

    1999-01-01

    METHONTOLOGY PROVIDES GUIDELINES FOR SPECIFYING ONTOLOGIES AT THE KNOWLEDGE LEVEL, AS A SPECIFICATION OF A CONCEPTUALIZATION. ODE ENABLES ONTOLOGY CONSTRUCTION, COVERING THE ENTIRE LIFE CYCLE AND AUTOMATICALLY IMPLEMENTING ONTOLOGIES

  19. 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.

  20. 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

  1. 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....

  2. Evolving BioAssay Ontology (BAO): modularization, integration and applications.

    Science.gov (United States)

    Abeyruwan, Saminda; Vempati, Uma D; Küçük-McGinty, Hande; Visser, Ubbo; Koleti, Amar; Mir, Ahsan; Sakurai, Kunie; Chung, Caty; Bittker, Joshua A; Clemons, Paul A; Brudz, Steve; Siripala, Anosha; Morales, Arturo J; Romacker, Martin; Twomey, David; Bureeva, Svetlana; Lemmon, Vance; Schürer, Stephan C

    2014-01-01

    The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and

  3. Evaluation of Reference Genes to Analyze Gene Expression in Silverside Odontesthes humensis Under Different Environmental Conditions

    Directory of Open Access Journals (Sweden)

    Tony L. R. Silveira

    2018-03-01

    Full Text Available Some mammalian reference genes, which are widely used to normalize the qRT-PCR, could not be used for this purpose due to its high expression variation. The normalization with false reference genes leads to misinterpretation of results. The silversides (Odontesthes spp. has been used as models for evolutionary, osmoregulatory and environmental pollution studies but, up to now, there are no studies about reference genes in any Odontesthes species. Furthermore, many studies on silversides have used reference genes without previous validations. Thus, present study aimed to was to clone and sequence potential reference genes, thereby identifying the best ones in Odontesthes humensis considering different tissues, ages and conditions. For this purpose, animals belonging to three ages (adults, juveniles, and immature were exposed to control, Roundup®, and seawater treatments for 24 h. Blood samples were subjected to flow-cytometry and other collected tissues to RNA extraction; cDNA synthesis; molecular cloning; DNA sequencing; and qRT-PCR. The candidate genes tested included 18s, actb, ef1a, eif3g, gapdh, h3a, atp1a, and tuba. Gene expression results were analyzed using five algorithms that ranked the candidate genes. The flow-cytometry data showed that the environmental challenges could trigger a systemic response in the treated fish. Even during this systemic physiological disorder, the consensus analysis of gene expression revealed h3a to be the most stable gene expression when only the treatments were considered. On the other hand, tuba was the least stable gene in the control and gapdh was the least stable in both Roundup® and seawater groups. In conclusion, the consensus analyses of different tissues, ages, and treatments groups revealed that h3a is the most stable gene whereas gapdh and tuba are the least stable genes, even being considered two constitutive genes.

  4. ``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.

  5. 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.

  6. Selection of reliable reference genes for gene expression studies in Trichoderma afroharzianum LTR-2 under oxalic acid stress.

    Science.gov (United States)

    Lyu, Yuping; Wu, Xiaoqing; Ren, He; Zhou, Fangyuan; Zhou, Hongzi; Zhang, Xinjian; Yang, Hetong

    2017-10-01

    An appropriate reference gene is required to get reliable results from gene expression analysis by quantitative real-time reverse transcription PCR (qRT-PCR). In order to identify stable and reliable reference genes in Trichoderma afroharzianum under oxalic acid (OA) stress, six commonly used housekeeping genes, i.e., elongation factor 1, ubiquitin, ubiquitin-conjugating enzyme, glyceraldehyde-3-phosphate dehydrogenase, α-tubulin, actin, from the effective biocontrol isolate T. afroharzianum strain LTR-2 were tested for their expression during growth in liquid culture amended with OA. Four in silico programs (comparative ΔCt, NormFinder, geNorm and BestKeeper) were used to evaluate the expression stabilities of six candidate reference genes. The elongation factor 1 gene EF-1 was identified as the most stably expressed reference gene, and was used as the normalizer to quantify the expression level of the oxalate decarboxylase coding gene OXDC in T. afroharzianum strain LTR-2 under OA stress. The result showed that the expression of OXDC was significantly up-regulated as expected. This study provides an effective method to quantify expression changes of target genes in T. afroharzianum under OA stress. Copyright © 2017 Elsevier B.V. All rights reserved.

  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. 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

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. Toward semantic interoperability with linked foundational ontologies in ROMULUS

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-06-01

    Full Text Available A purpose of a foundational ontology is to solve interoperability issues among ontologies. Many foundational ontologies have been developed, reintroducing the ontology interoperability problem. We address this with the new online foundational...

  14. 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)

  15. 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.

  16. 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

  17. 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.

  18. Geographic Ontologies, Gazetteers and Multilingualism

    Directory of Open Access Journals (Sweden)

    Robert Laurini

    2015-01-01

    Full Text Available Different languages imply different visions of space, so that terminologies are different in geographic ontologies. In addition to their geometric shapes, geographic features have names, sometimes different in diverse languages. In addition, the role of gazetteers, as dictionaries of place names (toponyms, is to maintain relations between place names and location. The scope of geographic information retrieval is to search for geographic information not against a database, but against the whole Internet: but the Internet stores information in different languages, and it is of paramount importance not to remain stuck to a unique language. In this paper, our first step is to clarify the links between geographic objects as computer representations of geographic features, ontologies and gazetteers designed in various languages. Then, we propose some inference rules for matching not only types, but also relations in geographic ontologies with the assistance of gazetteers.

  19. Ontology Matching with Semantic Verification.

    Science.gov (United States)

    Jean-Mary, Yves R; Shironoshita, E Patrick; Kabuka, Mansur R

    2009-09-01

    ASMOV (Automated Semantic Matching of Ontologies with Verification) is a novel algorithm that uses lexical and structural characteristics of two ontologies to iteratively calculate a similarity measure between them, derives an alignment, and then verifies it to ensure that it does not contain semantic inconsistencies. In this paper, we describe the ASMOV algorithm, and then present experimental results that measure its accuracy using the OAEI 2008 tests, and that evaluate its use with two different thesauri: WordNet, and the Unified Medical Language System (UMLS). These results show the increased accuracy obtained by combining lexical, structural and extensional matchers with semantic verification, and demonstrate the advantage of using a domain-specific thesaurus for the alignment of specialized ontologies.

  20. 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.

  1. 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.

  2. Inferring ontology graph structures using OWL reasoning

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel; Hoehndorf, Robert

    2018-01-01

    ' 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

  3. 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...

  4. Addressing issues in foundational ontology mediation

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-09-01

    Full Text Available An approach in achieving semantic interoperability among heterogeneous systems is to offer infrastructure to assist with linking and integration using a foundational ontology. Due to the creation of multiple foundational ontologies, this also means...

  5. 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.

  6. 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

  7. 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

  8. 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...

  9. 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.

  10. Towards ontology based search and knowledgesharing using domain ontologies

    DEFF Research Database (Denmark)

    Zambach, Sine

    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....

  11. An Ontology for Knowledge Representation and Applications

    OpenAIRE

    Nhon Do

    2008-01-01

    Ontology is a terminology which is used in artificial intelligence with different meanings. Ontology researching has an important role in computer science and practical applications, especially distributed knowledge systems. In this paper we present an ontology which is called Computational Object Knowledge Base Ontology. It has been used in designing some knowledge base systems for solving problems such as the system that supports studying knowledge and solving analytic ...

  12. On Algebraic Spectrum of Ontology Evaluation

    OpenAIRE

    Adekoya Adebayo Felix; kinwale Adio Taofiki; Sofoluwe Adetokunbo

    2011-01-01

    Ontology evaluation remains an important open problem in the area of its application. The ontology structure evaluation framework for benchmarking the internal graph structures was proposed. The framework was used in transport and biochemical ontology. The corresponding adjacency, incidence matrices and other structural properties due to the class hierarchical structure of the transport and biochemical ontology were computed using MATLAB. The results showed that the choice of suitable choice ...

  13. An ontological approach to domain engineering

    NARCIS (Netherlands)

    Falbo, R.A.; Guizzardi, G.; Duarte, K.

    2002-01-01

    Domain engineering aims to support systematic reuse, focusing on modeling common knowledge in a problem domain. Ontologies have also been pointed as holding great promise for software reuse. In this paper, we present ODE (Ontology-based Domain Engineering), an ontological approach for domain

  14. 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

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

    International Nuclear Information System (INIS)

    MacNeil, K.

    1999-01-01

    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

  16. Alignment of ICNP? 2.0 Ontology and a proposed INCP? Brazilian Ontology1

    OpenAIRE

    Carvalho, Carina Maris Gaspar; Cubas, Marcia Regina; Malucelli, Andreia; da N?brega, Maria Miriam Lima

    2014-01-01

    OBJECTIVE: to align the International Classification for Nursing Practice (ICNP®) Version 2.0 ontology and a proposed INCP® Brazilian Ontology.METHOD: document-based, exploratory and descriptive study, the empirical basis of which was provided by the ICNP® 2.0 Ontology and the INCP® Brazilian Ontology. The ontology alignment was performed using a computer tool with algorithms to identify correspondences between concepts, which were organized and analyzed according to their presence or absence...

  17. 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

  18. Emotion Education without Ontological Commitment?

    Science.gov (United States)

    Kristjansson, Kristjan

    2010-01-01

    Emotion education is enjoying new-found popularity. This paper explores the "cosy consensus" that seems to have developed in education circles, according to which approaches to emotion education are immune from metaethical considerations such as contrasting rationalist and sentimentalist views about the moral ontology of emotions. I spell out five…

  19. 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.

  20. 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.

  1. An ontological approach to logistics

    NARCIS (Netherlands)

    Daniele, L.M.; Ferreira Pires, Luis; Zelm, M.; van Sinderen, Marten J.; Doumeingts, G.

    2013-01-01

    In today’s global market, the competitiveness of enterprises is strongly dictated by their ability to collaborate with other enterprises. Ontologies enable common understanding of concepts and have been acknowledged as a powerful means to foster collaboration, both within the boundaries of an

  2. 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…

  3. An overview of the ontological basis of African jurisprudence | Agbo ...

    African Journals Online (AJOL)

    Life for the African is encapsulated in his understanding of the concept of ontology in which 'beings' and 'forces' are hierarchically ordered. A distortion of this order affects the African's 'vital force' and consequent 'vital rank'. This understanding underlies the African conception of law and juridical restitution as regulating ...

  4. 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

    Unbalanced grid voltage dips may lead to unbalanced non-sinusoidal current injections, dc-link voltage oscillations, and active and/or reactive power oscillations with twice the grid fundamental frequency in three-phase grid-connected Photovoltaic (PV) systems. Double grid frequency oscillations...... 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...... at the dc-link of the conventional two-stage PV inverters can further deteriorate the dc-link capacitor, which is one of the most life-limiting components in the system. Proper controls of these converters may efficiently address this problem. In those solutions, Current Reference Calculation (CRC) is one...

  5. Behaviour of Molten Beryllium with ITER Reference CFC NB31 (SNECMA) Under Moisture

    International Nuclear Information System (INIS)

    Lipa, M.; Martin, G.; Linke, J.

    2006-01-01

    A dramatic exothermic reaction with aluminium, a carbide forming metal, has been observed in Tore Supra. A small rod of 30 mm 3 , acting as a temperature proof, was enclosed in a blind hole of a thermally loaded low density PAN fiber CFC 1001Z block (SGL), which reached a temperature of about 1300 o C during plasma operation. The molten aluminium had penetrated the carbon matrix through to the block's front surface. After component removal and roughly 2 months of exposure to air in the laboratory, the CFC in front of the blind hole was found to have been locally destroyed over a crater-shaped structure of 2 cm diameter. This was due to an enhanced decomposition of aluminium carbide to aluminium hydroxide. Beryllium (Be), also a carbide forming metal, is used on the ITER first wall. Carbon reinforced carbon (CFC) of type NB31 (Snecma) covers the vertical divertor targets. It is expected that beryllium material will be transported during normal and/or off normal plasma operation to the carbon based divertor targets to form beryllium carbide. During air venting or a supposed accidental in-vessel water leak event, it will react exothermically under moisture to beryllium oxide. In order to investigate to which extent the CFC structure could be modified or eventually destroyed, this reaction process has been simulated with a CFC block NB31 of size 16 x 32 x 20 mm 3 , where about 40 mm 3 of Be S65 C (Brush Wellmann) has been placed in a previously drilled blind hole of 4 mm diameter oriented parallel to the high conductivity pitch fibers. When melted, by heating the CFC block, the Be penetrated in the carbon matrix through to the block's front surface. The front surface of the CFC was then exposed to humidity (tap water) for about 2 weeks and then stored for a further 2 months in a closed vinyl bag under atmospheric pressure after which the sample was analysed. After the exposure of the CFC to humidity, reaction products have been detected at the surface of the carbon

  6. 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

  7. 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

  8. 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.

  9. History Matters: Incremental Ontology Reasoning Using Modules

    Science.gov (United States)

    Cuenca Grau, Bernardo; Halaschek-Wiener, Christian; Kazakov, Yevgeny

    The development of ontologies involves continuous but relatively small modifications. Existing ontology reasoners, however, do not take advantage of the similarities between different versions of an ontology. In this paper, we propose a technique for incremental reasoning—that is, reasoning that reuses information obtained from previous versions of an ontology—based on the notion of a module. Our technique does not depend on a particular reasoning calculus and thus can be used in combination with any reasoner. We have applied our results to incremental classification of OWL DL ontologies and found significant improvement over regular classification time on a set of real-world ontologies.

  10. 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

  11. 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.

    2014-01-01

    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

  12. 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

    synchronization method for three-phase three-wire networks, namely dual second-order generalized integrator (SOGI) frequency-locked loop. The method is based on two adaptive filters, implemented by using a SOGI on the stationary αβ reference frame, and it is able to perform an excellent estimation......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...

  13. Using Assertion Capabilities of an OWL-Based Ontology for Query Formulation

    CERN Document Server

    Munir, Kamran; Bloodsworth, Peter; McClatchey, Richard

    2008-01-01

    This paper reports on the development of a framework to assist users in formulating relational queries without requiring a complete knowledge of the information structure and access mechanisms to underlying data sources. The emphasis here is on exploiting the semantic relationships and assertion capabilities of OWL ontologies to assist clinicians in writing complex queries. This has been achieved using both a bottom-up and top-down approaches to build an ontology model to be the repository for complex end user queries. Relational database schemas are mapped into the newly generated ontology schema to reinforce the current domain ontology being developed. One of the key merits of this approach is that it does not require storing data interpretation, with the added advantage of even not storing database instances as part of the domain ontology, especially for systems with huge volume of data.

  14. 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.

  15. Alignment of ICNP® 2.0 ontology and a proposed INCP® Brazilian ontology.

    Science.gov (United States)

    Carvalho, Carina Maris Gaspar; Cubas, Marcia Regina; Malucelli, Andreia; Nóbrega, Maria Miriam Lima da

    2014-01-01

    to align the International Classification for Nursing Practice (ICNP®) Version 2.0 ontology and a proposed INCP® Brazilian Ontology. document-based, exploratory and descriptive study, the empirical basis of which was provided by the ICNP® 2.0 Ontology and the INCP® Brazilian Ontology. The ontology alignment was performed using a computer tool with algorithms to identify correspondences between concepts, which were organized and analyzed according to their presence or absence, their names, and their sibling, parent, and child classes. there were 2,682 concepts present in the ICNP® 2.0 Ontology that were missing in the Brazilian Ontology; 717 concepts present in the Brazilian Ontology were missing in the ICNP® 2.0 Ontology; and there were 215 pairs of matching concepts. it is believed that the correspondences identified in this study might contribute to the interoperability between the representations of nursing practice elements in ICNP®, thus allowing the standardization of nursing records based on this classification system.

  16. 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.

  17. 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.

  18. Spatial cyberinfrastructures, ontologies, and the humanities.

    Science.gov (United States)

    Sieber, Renee E; Wellen, Christopher C; Jin, Yuan

    2011-04-05

    We report on research into building a cyberinfrastructure for Chinese biographical and geographic data. Our cyberinfrastructure contains (i) the McGill-Harvard-Yenching Library Ming Qing Women's Writings database (MQWW), the only online database on historical Chinese women's writings, (ii) the China Biographical Database, the authority for Chinese historical people, and (iii) the China Historical Geographical Information System, one of the first historical geographic information systems. Key to this integration is that linked databases retain separate identities as bases of knowledge, while they possess sufficient semantic interoperability to allow for multidatabase concepts and to support cross-database queries on an ad hoc basis. Computational ontologies create underlying semantics for database access. This paper focuses on the spatial component in a humanities cyberinfrastructure, which includes issues of conflicting data, heterogeneous data models, disambiguation, and geographic scale. First, we describe the methodology for integrating the databases. Then we detail the system architecture, which includes a tier of ontologies and schema. We describe the user interface and applications that allow for cross-database queries. For instance, users should be able to analyze the data, examine hypotheses on spatial and temporal relationships, and generate historical maps with datasets from MQWW for research, teaching, and publication on Chinese women writers, their familial relations, publishing venues, and the literary and social communities. Last, we discuss the social side of cyberinfrastructure development, as people are considered to be as critical as the technical components for its success.

  19. Spatial cyberinfrastructures, ontologies, and the humanities

    Science.gov (United States)

    Sieber, Renee E.; Wellen, Christopher C.; Jin, Yuan

    2011-01-01

    We report on research into building a cyberinfrastructure for Chinese biographical and geographic data. Our cyberinfrastructure contains (i) the McGill-Harvard-Yenching Library Ming Qing Women's Writings database (MQWW), the only online database on historical Chinese women's writings, (ii) the China Biographical Database, the authority for Chinese historical people, and (iii) the China Historical Geographical Information System, one of the first historical geographic information systems. Key to this integration is that linked databases retain separate identities as bases of knowledge, while they possess sufficient semantic interoperability to allow for multidatabase concepts and to support cross-database queries on an ad hoc basis. Computational ontologies create underlying semantics for database access. This paper focuses on the spatial component in a humanities cyberinfrastructure, which includes issues of conflicting data, heterogeneous data models, disambiguation, and geographic scale. First, we describe the methodology for integrating the databases. Then we detail the system architecture, which includes a tier of ontologies and schema. We describe the user interface and applications that allow for cross-database queries. For instance, users should be able to analyze the data, examine hypotheses on spatial and temporal relationships, and generate historical maps with datasets from MQWW for research, teaching, and publication on Chinese women writers, their familial relations, publishing venues, and the literary and social communities. Last, we discuss the social side of cyberinfrastructure development, as people are considered to be as critical as the technical components for its success. PMID:21444819

  20. Taking Critical Ontology Seriously

    DEFF Research Database (Denmark)

    Wigger, Angela; Horn, Laura

    2017-01-01

    To be ‘critical’ has become fashionable among social scientists in various disciplines. Only a few decades ago, the prefix ‘critical’ was almost automatically associated with Western Marxism and in particular the Frankfurt School. Today, the term critical is no longer limited to a single...... theoretical approach, but pertains to a vast range of approaches, including feminist, reflexive, postcolonial, postmodern or poststructuralist studies, and studies committed to a post-positivist epistemology more generally. But what does critical social science actually mean? Which implications does critical...... a primer on a few core dimensions of critical social science and its central premises. It discusses first what critical social science is not, and clarifies key differences between what is commonly referred to as ‘mainstream’ and ‘critical’ social science perspectives. It addresses the role of normative...

  1. 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.

  2. IfcOWL: A case of transforming EXPRESS schemas into ontologies

    NARCIS (Netherlands)

    Beetz, J.; Leeuwen, van J.P.; Vries, de B.

    2009-01-01

    Ontologies have been successfully applied as a semantic enabler of communication between both users and applications in fragmented, heterogeneous multinational business environments. In this paper we discuss the underlying principles, their current implementation status, and most importantly, their

  3. 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...

  4. Using concept similarity in cross ontology for adaptive e-Learning systems

    Directory of Open Access Journals (Sweden)

    B. Saleena

    2015-01-01

    Full Text Available e-Learning is one of the most preferred media of learning by the learners. The learners search the web to gather knowledge about a particular topic from the information in the repositories. Retrieval of relevant materials from a domain can be easily implemented if the information is organized and related in some way. Ontologies are a key concept that helps us to relate information for providing the more relevant lessons to the learner. This paper proposes an adaptive e-Learning system, which generates a user specific e-Learning content by comparing the concepts with more than one system using similarity measures. A cross ontology measure is defined, which consists of fuzzy domain ontology as the primary ontology and the domain expert’s ontology as the secondary ontology, for the comparison process. A personalized document is provided to the user with a user profile, which includes the data obtained from the processing of the proposed method under a User score, which is obtained through the user evaluation. The results of the proposed e-Learning system under the designed cross ontology similarity measure show a significant increase in performance and accuracy under different conditions. The assessment of the comparative analysis, showed the difference in performance of our proposed method over other methods. Based on the assessment results it is proved that the proposed approach is effective over other methods.

  5. Knowledge Portals: Ontologies at Work

    OpenAIRE

    Staab, Steffen; Maedche, Alexander

    2001-01-01

    Knowledge portals provide views onto domain-specific information on the World Wide Web, thus helping their users find relevant, domain-specific information. The construction of intelligent access and the contribution of information to knowledge portals, however, remained an ad hoc task, requiring extensive manual editing and maintenance by the knowledge portal providers. To diminish these efforts, we use ontologies as a conceptual backbone for providing, accessing, and structuring information...

  6. The Christological Ontology of Reason

    DEFF Research Database (Denmark)

    Nissen, Ulrik Becker

    2006-01-01

    Taking the startingpoint in an assertion of an ambiguity in the Lutheran tradition’s assessment of reason, the essay argues that the Kantian unreserved confidence in reason is criticised in Bonhoeffer. Based upon a Christological understanding of reason, Bonhoeffer endorses a view of reason which...... is treated in the essay. Here it is argued that Bonhoeffer may be appropriated in attempting to outline a Christological ontology of reason holding essential implications for the sources and conditions of public discourse....

  7. Emotion Ontology for Context Awareness

    OpenAIRE

    Berthelon , Franck; Sander , Peter

    2013-01-01

    International audience; We present an emotion ontology for describing and reasoning on emotion context in order to improve emotion detection based on bodily expression. We incorporate context into the two-factor theory of emotion (bodily reaction plus cognitive input) and demonstrate the importance of context in the emotion experience. In attempting to determine emotion felt by another person, the bodily expresson of their emotion is the only evidence directly available, eg, ''John looks angr...

  8. Towards an Ontology of Software

    OpenAIRE

    Wang, Xiaowei

    2016-01-01

    Software is permeating every aspect of our personal and social life. And yet, the cluster of concepts around the notion of software, such as the notions of a software product, software requirements, software specifications, are still poorly understood with no consensus on the horizon. For many, software is just code, something intangible best defined in contrast with hardware, but it is not particularly illuminating. This erroneous notion, software is just code, presents both in the ontology ...

  9. 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.

  10. 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

  11. An ontology approach to comparative phenomics in plants

    KAUST Repository

    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

    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

  12. 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.

  13. Ontology-aided Data Fusion (Invited)

    Science.gov (United States)

    Raskin, R.

    2009-12-01

    An ontology provides semantic descriptions that are analogous to those in a dictionary, but are readable by both computers and humans. A data or service is semantically annotated when it is formally associated with elements of an ontology. The ESIP Federation Semantic Web Cluster has developed a set of ontologies to describe datatypes and data services that can be used to support automated data fusion. The service ontology includes descriptors of the service function, its inputs/outputs, and its invocation method. The datatype descriptors resemble typical metadata fields (data format, data model, data structure, originator, etc.) augmented with descriptions of the meaning of the data. These ontologies, in combination with the SWEET science ontology, enable a registered data fusion service to be chained together and implemented that is scientifically meaningful based on machine understanding of the associated data and services. This presentation describes initial results and experiences in automated data fusion.

  14. Anatomy Ontology Matching Using Markov Logic Networks

    Directory of Open Access Journals (Sweden)

    Chunhua Li

    2016-01-01

    Full Text Available The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relationships between ontologies describing different species. Ontology matching is a kind of solutions to find semantic correspondences between entities of different ontologies. Markov logic networks which unify probabilistic graphical model and first-order logic provide an excellent framework for ontology matching. We combine several different matching strategies through first-order logic formulas according to the structure of anatomy ontologies. Experiments on the adult mouse anatomy and the human anatomy have demonstrated the effectiveness of proposed approach in terms of the quality of result alignment.

  15. Expert Judgement Assessment & SCENT Ontological Analysis

    Directory of Open Access Journals (Sweden)

    NICHERSU Iulian

    2018-05-01

    Full Text Available This study aims to provide insights in the starting point of the Horizon 2020 ECfunded project SCENT (Smart Toolbox for Εngaging Citizens into a People-Centric Observation Web Citizen Observatory (CO in terms of existing infrastructure, existing monitoring systems and some discussion on the existing legal and administrative framework that relate to flood monitoring and management in the area of Danube Delta. The methodology used in this approach is based on expert judgement and ontological analysis, using the information collected from the identified end-users of the SCENT toolbox. In this type of analysis the stages of flood monitoring and management that the experts are involved in are detailed. This is done through an Expert Judgement Assessment analysis. The latter is complemented by a set of Key Performance Indicators that the stakeholders have assessed and/or proposed for the evaluation of the SCENT demonstrations, for the impact of the project and finally for SCENT toolbox performance and usefulness. The second part of the study presents an analysis that attempts to map the interactions between different organizations and components of the existing monitoring systems in the Danube Delta case study. Expert Judgement (EJ allows to gain information from specialists in a specific field through a consultation process with one or more experts that have experience in similar and complementary topics. Expert judgment, expert estimates, or expert opinion are all terms that refer to the contents of the problem; estimates, outcomes, predictions, uncertainties, and their corresponding assumptions and conditions are all examples of expert judgment. Expert Judgement is affected by the process used to gather it. On the other hand, the ontological analysis comes to complete this study, by organizing and presenting the connections behind the flood management and land use systems in the three phases of the flood event.

  16. 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.

  17. An Ontological Architecture for Orbital Debris Data

    OpenAIRE

    Rovetto, Robert J.

    2017-01-01

    The orbital debris problem presents an opportunity for inter-agency and international cooperation toward the mutually beneficial goals of debris prevention, mitigation, remediation, and improved space situational awareness (SSA). Achieving these goals requires sharing orbital debris and other SSA data. Toward this, I present an ontological architecture for the orbital debris domain, taking steps in the creation of an orbital debris ontology (ODO). The purpose of this ontological system is to ...

  18. Versioning System for Distributed Ontology Development

    Science.gov (United States)

    2016-03-15

    Framework for Grid Computing and Semantic Web Services,” Trust Management, Springer Berlin Heidelberg (2004), pp. 16−26. [TIME] W3C, “Time Ontology in...Distributed Ontology Development S.K. Damodaran 15 March 2016 This material is based on work supported by the Assistant Secretary of Defense for...Distributed Ontology Development S.K. Damodaran Formerly Group 59 15 March 2016 Massachusetts Institute of Technology Lincoln Laboratory

  19. Coupling ontology driven semantic representation with multilingual natural language generation for tuning international terminologies.

    Science.gov (United States)

    Rassinoux, Anne-Marie; Baud, Robert H; Rodrigues, Jean-Marie; Lovis, Christian; Geissbühler, Antoine

    2007-01-01

    The importance of clinical communication between providers, consumers and others, as well as the requisite for computer interoperability, strengthens the need for sharing common accepted terminologies. Under the directives of the World Health Organization (WHO), an approach is currently being conducted in Australia to adopt a standardized terminology for medical procedures that is intended to become an international reference. In order to achieve such a standard, a collaborative approach is adopted, in line with the successful experiment conducted for the development of the new French coding system CCAM. Different coding centres are involved in setting up a semantic representation of each term using a formal ontological structure expressed through a logic-based representation language. From this language-independent representation, multilingual natural language generation (NLG) is performed to produce noun phrases in various languages that are further compared for consistency with the original terms. Outcomes are presented for the assessment of the International Classification of Health Interventions (ICHI) and its translation into Portuguese. The initial results clearly emphasize the feasibility and cost-effectiveness of the proposed method for handling both a different classification and an additional language. NLG tools, based on ontology driven semantic representation, facilitate the discovery of ambiguous and inconsistent terms, and, as such, should be promoted for establishing coherent international terminologies.

  20. 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

  1. 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....

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

    OpenAIRE

    Beauheim, Catherine C; Wymore, Farrell; Nitzberg, Michael; Zachariah, Zachariah K; Jin, Heng; Skene, JH Pate; Ball, Catherine A; Sherlock, Gavin

    2007-01-01

    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 r...

  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. 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...

  5. 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...

  6. Scientific Digital Libraries, Interoperability, and Ontologies

    Science.gov (United States)

    Hughes, J. Steven; Crichton, Daniel J.; Mattmann, Chris A.

    2009-01-01

    Scientific digital libraries serve complex and evolving research communities. Justifications for the development of scientific digital libraries include the desire to preserve science data and the promises of information interconnectedness, correlative science, and system interoperability. Shared ontologies are fundamental to fulfilling these promises. We present a tool framework, some informal principles, and several case studies where shared ontologies are used to guide the implementation of scientific digital libraries. The tool framework, based on an ontology modeling tool, was configured to develop, manage, and keep shared ontologies relevant within changing domains and to promote the interoperability, interconnectedness, and correlation desired by scientists.

  7. 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....... One method uses a discrete location model to create an initial solution and we propose heuristic methods to further improve the visual result. We evaluate the visual results according to our success criteria and the feedback from users. Running times of the heuristic indicate that an improved version...

  8. 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....... One method uses a discrete location model to create an initial solution and we propose heuristic methods to further improve the visual result. We evaluate the visual results according to our success criteria and the feedback from users. Running times of the heuristic indicate that an improved version...

  9. 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...

  10. DEPONTO: A Reusable Dependability Domain Ontology

    Directory of Open Access Journals (Sweden)

    Teodora Sanislav

    2015-08-01

    Full Text Available This paper proposes a dependability reusable ontology for knowledge representation. The fundamental knowledge related to dependability follows its taxonomy. Thus, this paper gives an analysis of what is the dependability domain ontology andof its components.The dependability domain ontology plays an important role in ensuring the dependability of information systems by providing support for their diagnosis in case of faults, errors and failures.The proposed ontology is used as a dependability framework in two case study Cyber-Physical Systemswhich demonstrate its reusability within this category of systems.

  11. Learning Resources Organization Using Ontological Framework

    Science.gov (United States)

    Gavrilova, Tatiana; Gorovoy, Vladimir; Petrashen, Elena

    The paper describes the ontological approach to the knowledge structuring for the e-learning portal design as it turns out to be efficient and relevant to current domain conditions. It is primarily based on the visual ontology-based description of the content of the learning materials and this helps to provide productive and personalized access to these materials. The experience of ontology developing for Knowledge Engineering coursetersburg State University is discussed and “OntolingeWiki” tool for creating ontology-based e-learning portals is described.

  12. Ontological Engineering for the Cadastral Domain

    DEFF Research Database (Denmark)

    Stubkjær, Erik; Stuckenschmidt, Heiner

    2000-01-01

    conceptualization of the world is that much information remains implicit. Ontologies have set out to overcome the problem of implicit and hidden knowledge by making the conceptualization of a domain (e.g. mathematics) explicit. Ontological engineering is thus an approach to achieve a conceptual rigor...... 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...

  13. 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.

  14. A methodology to migrate the gene ontology to a description logic environment using DAML+OIL.

    Science.gov (United States)

    Wroe, C J; Stevens, R; Goble, C A; Ashburner, M

    2003-01-01

    The Gene Ontology Next Generation Project (GONG) is developing a staged methodology to evolve the current representation of the Gene Ontology into DAML+OIL in order to take advantage of the richer formal expressiveness and the reasoning capabilities of the underlying description logic. Each stage provides a step level increase in formal explicit semantic content with a view to supporting validation, extension and multiple classification of the Gene Ontology. The paper introduces DAML+OIL and demonstrates the activity within each stage of the methodology and the functionality gained.

  15. Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

    Science.gov (United States)

    Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

    2017-01-01

    Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. PMID:27733503

  16. Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

    Science.gov (United States)

    Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

    2017-01-04

    Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. 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.

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

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us FANTOM....biosciencedbc.jp/archive/fantom5/datafiles/LATEST/extra/Ontology/ File size: 1.8 MB Simple search URL - Dat...t Us Sample ontology, GOstat and ontology term enrichment - FANTOM5 | LSDB Archive ...

  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.

    2013-01-01

    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

  20. 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

  1. 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…

  2. 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…

  3. 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

  4. A commitment-based reference ontology for services

    NARCIS (Netherlands)

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

    2015-01-01

    The concept of “service” has been characterized in 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

  5. Towards a commitment-based reference ontology for services

    NARCIS (Netherlands)

    Nardi, Julio Cesar; de Almeida Falbo, Ricardo; Andrade Almeida, João; Guizzardi, Giancarlo; Ferreira Pires, Luis; van Sinderen, Marten J.; Guarino, Nicola; Gašević, Dragan; Hatala, Marek; Motahari Nezhad, Hamid R.; Reichert, Manfred

    The concept of “service” has been characterized by different disciplines and authors from various points of view. The variety of characterizations reveals that this notion, although an intuitive one, is far from trivial. Given the importance of services in enterprise computing and Service Science in

  6. 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

  7. Ontology-based indirect interaction of mobile robots for joint task solving: a scenario for obstacle overcoming

    Directory of Open Access Journals (Sweden)

    Petrov Mikhail

    2017-01-01

    Full Text Available This paper describes an ontology-based approach to interaction of users and mobile robots for joint task solving. The use of ontologies allows supporting semantic interoperability between robots. The ontologies store knowledge about the tasks to be performed, knowledge about the functionality of robots and the current situation factors like a robot location or busyness. Ontologies are published in a smart space which allows indirect interaction between participants. On the basis of the knowledge, a robot can define a task that is to be performed and get the current status of other robots. The paper presents a reference model of the approach to indirect interaction between mobile robots for joint task solving, an ontology model for the knowledge organization, and application of the presented approach for the scenario for obstacle overcoming.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

    to developing the ontology engineering design integrated taxonomies (EDIT) with a theoretical approach in which concepts and relations are elicited from engineering design theories ontology (DO) The limitations and advantages of each approach are discussed. The research methodology adopted is to map......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...

  14. 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.

  15. An ontological case base engineering methodology for diabetes management.

    Science.gov (United States)

    El-Sappagh, Shaker H; El-Masri, Samir; Elmogy, Mohammed; Riad, A M; Saddik, Basema

    2014-08-01

    Ontology engineering covers issues related to ontology development and use. In Case Based Reasoning (CBR) system, ontology plays two main roles; the first as case base and the second as domain ontology. However, the ontology engineering literature does not provide adequate guidance on how to build, evaluate, and maintain ontologies. This paper proposes an ontology engineering methodology to generate case bases in the medical domain. It mainly focuses on the research of case representation in the form of ontology to support the case semantic retrieval and enhance all knowledge intensive CBR processes. A case study on diabetes diagnosis case base will be provided to evaluate the proposed methodology.

  16. 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).

  17. 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

  18. Introduction to Semantic Web Ontology Languages

    NARCIS (Netherlands)

    Antoniou, Grigoris; Franconi, Enrico; Van Harmelen, Frank

    2005-01-01

    The aim of this chapter is to give a general introduction to some of the ontology languages that play a prominent role on the Semantic Web, and to discuss the formal foundations of these languages. Web ontology languages will be the main carriers of the information that we will want to share and

  19. 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.

  20. 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.

  1. Fuzzy knowledge bases integration based on ontology

    OpenAIRE

    Ternovoy, Maksym; Shtogrina, Olena

    2012-01-01

    the paper describes the approach for fuzzy knowledge bases integration with the usage of ontology. This approach is based on metadata-base usage for integration of different knowledge bases with common ontology. The design process of metadata-base is described.

  2. C2 Domain Ontology within Our Lifetime

    Science.gov (United States)

    2009-06-01

    25] Masolo, C., et al: The WonderWeb Library of Foundational Ontologies Prelimary Report, WonderWeb Deliverable D17, ISTC -CNR, May 2003. [26...www.ifomis.org/bfo/BFO  [25] Masolo, C., et al: The WonderWeb Library of Foundational Ontologies Prelimary Report, WonderWeb Deliverable D17, ISTC -CNR

  3. 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...

  4. 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,…

  5. 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

  6. 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

  7. Collaborative ontology development for the geosciences

    NARCIS (Netherlands)

    Kalbasi Khoramdashti, R.; Janowicz, K.; Reitsma, F.; Boerboom, L.G.J.; Alasheikh, A.

    2014-01-01

    Ontology-based information publishing, retrieval, reuse, and integration have become popular research topics to address the challenges involved in exchanging data between heterogeneous sources. However, in most cases ontologies are still developed in a centralized top-down manner by a few knowledge

  8. An ontology roadmap for crowdsourcing innovation intermediaries

    OpenAIRE

    Silva, Cândida; Ramos, Isabel

    2014-01-01

    Ontologies have proliferated in the last years, essentially justified by the need of achieving a consensus in the multiple representations of reality inside computers, and therefore the accomplishment of interoperability between machines and systems. Ontologies provide an explicit conceptualization that describes the semantics of the data. Crowdsourcing innovation intermediaries are organizations that mediate the communication and relationship between companies that aspire to solv...

  9. Ontology Assisted Formal Specification Extraction from Text

    Directory of Open Access Journals (Sweden)

    Andreea Mihis

    2010-12-01

    Full Text Available In the field of knowledge processing, the ontologies are the most important mean. They make possible for the computer to understand better the natural language and to make judgments. In this paper, a method which use ontologies in the semi-automatic extraction of formal specifications from a natural language text is proposed.

  10. VuWiki: An Ontology-Based Semantic Wiki for Vulnerability Assessments

    Science.gov (United States)

    Khazai, Bijan; Kunz-Plapp, Tina; Büscher, Christian; Wegner, Antje

    2014-05-01

    The concept of vulnerability, as well as its implementation in vulnerability assessments, is used in various disciplines and contexts ranging from disaster management and reduction to ecology, public health or climate change and adaptation, and a corresponding multitude of ideas about how to conceptualize and measure vulnerability exists. Three decades of research in vulnerability have generated a complex and growing body of knowledge that challenges newcomers, practitioners and even experienced researchers. To provide a structured representation of the knowledge field "vulnerability assessment", we have set up an ontology-based semantic wiki for reviewing and representing vulnerability assessments: VuWiki, www.vuwiki.org. Based on a survey of 55 vulnerability assessment studies, we first developed an ontology as an explicit reference system for describing vulnerability assessments. We developed the ontology in a theoretically controlled manner based on general systems theory and guided by principles for ontology development in the field of earth and environment (Raskin and Pan 2005). Four key questions form the first level "branches" or categories of the developed ontology: (1) Vulnerability of what? (2) Vulnerability to what? (3) What reference framework was used in the vulnerability assessment?, and (4) What methodological approach was used in the vulnerability assessment? These questions correspond to the basic, abstract structure of the knowledge domain of vulnerability assessments and have been deduced from theories and concepts of various disciplines. The ontology was then implemented in a semantic wiki which allows for the classification and annotation of vulnerability assessments. As a semantic wiki, VuWiki does not aim at "synthesizing" a holistic and overarching model of vulnerability. Instead, it provides both scientists and practitioners with a uniform ontology as a reference system and offers easy and structured access to the knowledge field of

  11. 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.

  12. 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...

  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...... various temporal notions are related in a top-level ontology. Furthermore, a number of modern ontologies are analysed with respect to their incorporation of temporal notions. It is argued that all of them correspond to Prior's first and second grade, and that none of them reflect the views which Prior......'s third and fourth grade represent. Finally, the paper deals with Prior's ideas on a tensed ontology and it is argued that a logic based on the third grade and will be useful in the further development of tensed ontology....

  14. Building an ontology of pulmonary diseases with natural language processing tools using textual corpora.

    Science.gov (United States)

    Baneyx, Audrey; Charlet, Jean; Jaulent, Marie-Christine

    2007-01-01

    Pathologies and acts are classified in thesauri to help physicians to code their activity. In practice, the use of thesauri is not sufficient to reduce variability in coding and thesauri are not suitable for computer processing. We think the automation of the coding task requires a conceptual modeling of medical items: an ontology. Our task is to help lung specialists code acts and diagnoses with software that represents medical knowledge of this concerned specialty by an ontology. The objective of the reported work was to build an ontology of pulmonary diseases dedicated to the coding process. To carry out this objective, we develop a precise methodological process for the knowledge engineer in order to build various types of medical ontologies. This process is based on the need to express precisely in natural language the meaning of each concept using differential semantics principles. A differential ontology is a hierarchy of concepts and relationships organized according to their similarities and differences. Our main research hypothesis is to apply natural language processing tools to corpora to develop the resources needed to build the ontology. We consider two corpora, one composed of patient discharge summaries and the other being a teaching book. We propose to combine two approaches to enrich the ontology building: (i) a method which consists of building terminological resources through distributional analysis and (ii) a method based on the observation of corpus sequences in order to reveal semantic relationships. Our ontology currently includes 1550 concepts and the software implementing the coding process is still under development. Results show that the proposed approach is operational and indicates that the combination of these methods and the comparison of the resulting terminological structures give interesting clues to a knowledge engineer for the building of an ontology.

  15. 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.

  16. Extrametodical truth and ontology of the praxis: The mediator rationality of the phronesis

    Directory of Open Access Journals (Sweden)

    Gaetano Chiurazzi

    2016-05-01

    Full Text Available Gadamer’s vindication of the extra-methodical feature of truth in the human sciences put forward in Truth and Method does not mean a mere refusal of method: rather, it arises from the awareness that there are truths which are not reducible to the conditions of repeatability and commensurability set up by methodical thinking. In fact, the truths of the human sciences refer to the ontological dimension of the contingent and the accidental, i.e. to the dimension of the historical. In this essay I aim at highlighting this ontological dimension, which for Aristotle is eminently that of the praxis and of human action. I will show that such an ontology is a consequence of the logical and ontological discussions which crisscrossed Greek thought after the discovery of the incommensurable magnitudes. The ontology of praxis is an ontology which takes into account the “irrationality” represented by the contingent, the accidental, to which a new form of rationality corresponds: that of phrónesis. Phrónesis is in fact not a commensurative but a mediative rationality

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. SPONGY (SPam ONtoloGY: Email Classification Using Two-Level Dynamic Ontology

    Directory of Open Access Journals (Sweden)

    Seongwook Youn

    2014-01-01

    Full Text Available Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user’s background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1 to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2 to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance.

  6. SPONGY (SPam ONtoloGY): email classification using two-level dynamic ontology.

    Science.gov (United States)

    Youn, Seongwook

    2014-01-01

    Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user's background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1) to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2) to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance.

  7. SPONGY (SPam ONtoloGY): Email Classification Using Two-Level Dynamic Ontology

    Science.gov (United States)

    2014-01-01

    Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user's background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1) to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2) to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance. PMID:25254240

  8. Asian educational discourse: construction of ontological security

    Directory of Open Access Journals (Sweden)

    Natalya V. Khalina

    2018-03-01

    Full Text Available 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 development after the “quality of education” stage. We suggest an approach for assessing the vitality of educational process and its product based on monitoring trainees’ aptitudes system and school capabilities in developing and maintaining this system. In this study we refer to the concept of vitality and viability when describing the general theory of viability in connection with the core principles of Asian educational discourse. We outline main trends in the development of modern educational system in Asian university given the process of globalization and its impact on educational reforms in the Asia-Pacific region. Thus, the category of education quality in Asian system of higher education and narrative monitoring of Chinese students’ cognitive structures viability at Altai State University are introduced.

  9. Specifying Geographic Information - Ontology, Knowledge Representation, and Formal Constraints

    DEFF Research Database (Denmark)

    Christensen, Jesper Vinther

    2007-01-01

    as in the private sector. The theoretical background is the establishment of a representational system, which ontologically comprises a representation of notions in the "real world" and notions which include the representation of these. Thus, the thesis leans towards a traditional division between modeling...... of domains and conceptualization of these. The thesis contributes a formalization of what is understood by domain models and conceptual models, when the focus is on geographic information. Moreover, it is shown how specifications for geographic information are related to this representational system...... of requirements and rules, building on terms from the domain and concept ontologies. In combination with the theoretical basis the analysis is used for developing an underlying model of notions, which defines the individual elements in a specification and the relations between them. In the chapters of the thesis...

  10. 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.

  11. Initial implementation of a comparative data analysis ontology.

    Science.gov (United States)

    Prosdocimi, Francisco; Chisham, Brandon; Pontelli, Enrico; Thompson, Julie D; Stoltzfus, Arlin

    2009-07-03

    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. 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. Ontology Versioning and Change Detection on the Web

    NARCIS (Netherlands)

    Klein, Michel; Fensel, Dieter; Kiryakov, Atanas; Ognyanov, Damyan

    2002-01-01

    To effectively use ontologies on the Web, it is essential that changes in ontologies are managed well. This paper analyzes the topic of ontology versioning in the context of the Web by looking at the characteristics of the version relation between ontologies and at the identification of online

  14. 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,…

  15. 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.

  16. 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.

  17. A Hydrological Sensor Web Ontology Based on the SSN Ontology: A Case Study for a Flood

    Directory of Open Access Journals (Sweden)

    Chao Wang

    2017-12-01

    Full Text Available Accompanying the continuous development of sensor network technology, sensors worldwide are constantly producing observation data. However, the sensors and their data from different observation platforms are sometimes difficult to use collaboratively in response to natural disasters such as floods for the lack of semantics. In this paper, a hydrological sensor web ontology based on SSN ontology is proposed to describe the heterogeneous hydrological sensor web resources by importing the time and space ontology, instantiating the hydrological classes, and establishing reasoning rules. This work has been validated by semantic querying and knowledge acquiring experiments. The results demonstrate the feasibility and effectiveness of the proposed ontology and its potential to grow into a more comprehensive ontology for hydrological monitoring collaboratively. In addition, this method of ontology modeling is generally applicable to other applications and domains.

  18. 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.

  19. The ontology-based answers (OBA) service: a connector for embedded usage of ontologies in applications.

    Science.gov (United States)

    Dönitz, Jürgen; Wingender, Edgar

    2012-01-01

    The semantic web depends on the use of ontologies to let electronic systems interpret contextual information. Optimally, the handling and access of ontologies should be completely transparent to the user. As a means to this end, we have developed a service that attempts to bridge the gap between experts in a certain knowledge domain, ontologists, and application developers. The ontology-based answers (OBA) service introduced here can be embedded into custom applications to grant access to the classes of ontologies and their relations as most important structural features as well as to information encoded in the relations between ontology classes. Thus computational biologists can benefit from ontologies without detailed knowledge about the respective ontology. The content of ontologies is mapped to a graph of connected objects which is compatible to the object-oriented programming style in Java. Semantic functions implement knowledge about the complex semantics of an ontology beyond the class hierarchy and "partOf" relations. By using these OBA functions an application can, for example, provide a semantic search function, or (in the examples outlined) map an anatomical structure to the organs it belongs to. The semantic functions relieve the application developer from the necessity of acquiring in-depth knowledge about the semantics and curation guidelines of the used ontologies by implementing the required knowledge. The architecture of the OBA service encapsulates the logic to process ontologies in order to achieve a separation from the application logic. A public server with the current plugins is available and can be used with the provided connector in a custom application in scenarios analogous to the presented use cases. The server and the client are freely available if a project requires the use of custom plugins or non-public ontologies. The OBA service and further documentation is available at http://www.bioinf.med.uni-goettingen.de/projects/oba.

  20. OntoMaven: Maven-based Ontology Development and Management of Distributed Ontology Repositories

    OpenAIRE

    Paschke, Adrian

    2013-01-01

    In collaborative agile ontology development projects support for modular reuse of ontologies from large existing remote repositories, ontology project life cycle management, and transitive dependency management are important needs. The Apache Maven approach has proven its success in distributed collaborative Software Engineering by its widespread adoption. The contribution of this paper is a new design artifact called OntoMaven. OntoMaven adopts the Maven-based development methodology and ada...

  1. 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.

  2. 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…

  3. 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

  4. Ontology-based multi-agent systems

    Energy Technology Data Exchange (ETDEWEB)

    Hadzic, Maja; Wongthongtham, Pornpit; Dillon, Tharam; Chang, Elizabeth [Digital Ecosystems and Business Intelligence Institute, Perth, WA (Australia)

    2009-07-01

    The Semantic web has given a great deal of impetus to the development of ontologies and multi-agent systems. Several books have appeared which discuss the development of ontologies or of multi-agent systems separately on their own. The growing interaction between agents and ontologies has highlighted the need for integrated development of these. This book is unique in being the first to provide an integrated treatment of the modeling, design and implementation of such combined ontology/multi-agent systems. It provides clear exposition of this integrated modeling and design methodology. It further illustrates this with two detailed case studies in (a) the biomedical area and (b) the software engineering area. The book is, therefore, of interest to researchers, graduate students and practitioners in the semantic web and web science area. (orig.)

  5. 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.

  6. Randomised controlled trials in educational research: Ontological ...

    African Journals Online (AJOL)

    based practice in medical and clinical settings because they are associated with a particular ontological and epistemological perspective that is situated within a positivist world view. It assumes that environments and variables can be controlled ...

  7. 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...

  8. Ontology Enabled Generation of Embedded Web Services

    DEFF Research Database (Denmark)

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

    2008-01-01

    Web services are increasingly adopted as a service provision mechanism in pervasive computing environments. Implementing web services on networked, embedded devices raises a number of challenges, for example efficiency of web services, handling of variability and dependencies of hardware...... 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...

  9. Metadata and Ontologies in Learning Resources Design

    Science.gov (United States)

    Vidal C., Christian; Segura Navarrete, Alejandra; Menéndez D., Víctor; Zapata Gonzalez, Alfredo; Prieto M., Manuel

    Resource design and development requires knowledge about educational goals, instructional context and information about learner's characteristics among other. An important information source about this knowledge are metadata. However, metadata by themselves do not foresee all necessary information related to resource design. Here we argue the need to use different data and knowledge models to improve understanding the complex processes related to e-learning resources and their management. This paper presents the use of semantic web technologies, as ontologies, supporting the search and selection of resources used in design. Classification is done, based on instructional criteria derived from a knowledge acquisition process, using information provided by IEEE-LOM metadata standard. The knowledge obtained is represented in an ontology using OWL and SWRL. In this work we give evidence of the implementation of a Learning Object Classifier based on ontology. We demonstrate that the use of ontologies can support the design activities in e-learning.

  10. 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...

  11. Language and embodied consciousness: A Peircean ontological ...

    African Journals Online (AJOL)

    An ontology of language: its source and place in First Language ... knowledge they supposedly gain in school with their immediate environment and their lived .... looking stick in space looks bent at the point it enters the medium of water.

  12. The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.

    Science.gov (United States)

    Malone, James; Brown, Andy; Lister, Allyson L; Ison, Jon; Hull, Duncan; Parkinson, Helen; Stevens, Robert

    2014-01-01

    Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and reproducibility. The Software Ontology (SWO) is a description of software used to store, manage and analyze data. Input to the SWO has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the SWO and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the SWO has incorporated EDAM, a vocabulary for describing data and related concepts in bioinformatics. The SWO is currently being used to describe software used in multiple biomedical applications. The SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The SWO thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user's needs. The Software Ontology is available under an Apache 2.0 license at http://theswo.sourceforge.net/; the Software Ontology blog can be read at http://softwareontology.wordpress.com.

  13. 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.

  14. Identification of reference genes for quantitative expression analysis of microRNAs and mRNAs in barley under various stress conditions.

    Directory of Open Access Journals (Sweden)

    Jannatul Ferdous

    Full Text Available For accurate and reliable gene expression analysis using quantitative real-time reverse transcription PCR (qPCR, the selection of appropriate reference genes as an internal control for normalization is crucial. We hypothesized that non-coding, small nucleolar RNAs (snoRNAswould be stably expressed in different barley varieties and under different experimental treatments,in different tissues and at different developmental stages of plant growth and therefore might prove to be suitable reference genes for expression analysis of both microRNAs (miRNAsand mRNAs. In this study, we examined the expression stability of ten candidate reference genes in six barley genotypes under five experimental stresses, drought, fungal infection,boron toxicity, nutrient deficiency and salinity. We compared four commonly used housekeeping genes; Actin (ACT, alpha-Tubulin (α-TUB, Glycolytic glyceraldehyde-3-phosphate dehydrogenase(GAPDH, ADP-ribosylation factor 1-like protein (ADP, four snoRNAs; (U18,U61, snoR14 and snoR23 and two microRNAs (miR168, miR159 as candidate reference genes. We found that ADP, snoR14 and snoR23 were ranked as the best of these candidates across diverse samples. Additionally, we found that miR168 was a suitable reference gene for expression analysis in barley. Finally, we validated the performance of our stable and unstable candidate reference genes for both mRNA and miRNA qPCR data normalization under different stress conditions and demonstrated the superiority of the stable candidates. Our data demonstrate the suitability of barley snoRNAs and miRNAs as potential reference genes form iRNA and mRNA qPCR data normalization under different stress treatments [corrected].

  15. 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....

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

    Directory of Open Access Journals (Sweden)

    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. 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.

  18. 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.

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. Theory of the Whole and the Part – Ontological Perspective (E. Husserl, R. Ingarden

    Directory of Open Access Journals (Sweden)

    Barska Katarzyna

    2015-02-01

    Full Text Available The purpose of the paper is demonstrate the thesis that Ingarden's ontological system allows a better understanding of the “part-whole” problem then previous theories. Especially, if we take into account the existential ontology of Ingarden, which refers to Husserl “part-whole” theory, we can see that development of terms made by Ingarden sheds new light on old problems. In this context, particularly important is to distinguish between two existential moments: contingancy/inseparatness, because thanks to them we can talk about many different types of relationships and hence many types of objects.

  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. Identifying optimal reference genes for the normalization of microRNA expression in cucumber under viral stress

    Science.gov (United States)

    Liang, Chaoqiong; Hao, Jianjun; Meng, Yan; Luo, Laixin; Li, Jianqiang

    2018-01-01

    Cucumber green mottle mosaic virus (CGMMV) is an economically important pathogen and causes significant reduction of both yield and quality of cucumber (Cucumis sativus). Currently, there were no satisfied strategies for controlling the disease. A better understanding of microRNA (miRNA) expression related to the regulation of plant-virus interactions and virus resistance would be of great assistance when developing control strategies for CGMMV. However, accurate expression analysis is highly dependent on robust and reliable reference gene used as an internal control for normalization of miRNA expression. Most commonly used reference genes involved in CGMMV-infected cucumber are not universally expressed depending on tissue types and stages of plant development. It is therefore crucial to identify suitable reference genes in investigating the role of miRNA expression. In this study, seven reference genes, including Actin, Tubulin, EF-1α, 18S rRNA, Ubiquitin, GAPDH and Cyclophilin, were evaluated for the most accurate results in analyses using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Gene expression was assayed on cucumber leaves, stems and roots that were collected at different days post inoculation with CGMMV. The expression data were analyzed using algorithms including delta-Ct, geNorm, NormFinder, and BestKeeper as well as the comparative tool RefFinder. The reference genes were subsequently validated using miR159. The results showed that EF-1α and GAPDH were the most reliable reference genes for normalizing miRNA expression in leaf, root and stem samples, while Ubiquitin and EF-1α were the most suitable combination overall. PMID:29543906

  4. 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...... network to a standard SRF-PLL in order to effectively separate the positive- and negative-sequence voltage components in a fast and accurate way. Experimental evaluation of the proposed grid synchronization method and simulations regarding its application to ride through transient faults verify...

  5. The MGED Ontology: a resource for semantics-based description of microarray experiments.

    Science.gov (United States)

    Whetzel, Patricia L; Parkinson, Helen; Causton, Helen C; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Game, Laurence; Heiskanen, Mervi; Morrison, Norman; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Taylor, Chris; White, Joseph; Stoeckert, Christian J

    2006-04-01

    The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). Stoeckrt@pcbi.upenn.edu Supplementary data are available at Bioinformatics online.

  6. Using Ontologies in Cybersecurity Field

    Directory of Open Access Journals (Sweden)

    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.

  7. Exploring autophagy with Gene Ontology

    Science.gov (United States)

    2018-01-01

    ABSTRACT Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular stresses and ridding cells of foreign material. Perturbations in autophagy have been implicated in a number of pathological conditions such as neurodegeneration, cardiac disease and cancer. The growing knowledge about autophagic mechanisms needs to be collected in a computable and shareable format to allow its use in data representation and interpretation. The Gene Ontology (GO) is a freely available resource that describes how and where gene products function in biological systems. It consists of 3 interrelated structured vocabularies that outline what gene products do at the biochemical level, where they act in a cell and the overall biological objectives to which their actions contribute. It also consists of ‘annotations’ that associate gene products with the terms. Here we describe how we represent autophagy in GO, how we create and define terms relevant to autophagy researchers and how we interrelate those terms to generate a coherent view of the process, therefore allowing an interoperable description of its biological aspects. We also describe how annotation of gene products with GO terms improves data analysis and interpretation, hence bringing a significant benefit to this field of study. PMID:29455577

  8. 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...

  9. 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

  10. New concepts for building vocabulary for cell image ontologies

    Directory of Open Access Journals (Sweden)

    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

  11. 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

  12. Computer support for physiological cell modelling using an ontology on cell physiology.

    Science.gov (United States)

    Takao, Shimayoshi; Kazuhiro, Komurasaki; Akira, Amano; Takeshi, Iwashita; Masanori, Kanazawa; Tetsuya, Matsuda

    2006-01-01

    The development of electrophysiological whole cell models to support the understanding of biological mechanisms is increasing rapidly. Due to the complexity of biological systems, comprehensive cell models, which are composed of many imported sub-models of functional elements, can get quite complicated as well, making computer modification difficult. Here, we propose a computer support to enhance structural changes of cell models, employing the markup languages CellML and our original PMSML (physiological model structure markup language), in addition to a new ontology for cell physiological modelling. In particular, a method to make references from CellML files to the ontology and a method to assist manipulation of model structures using markup languages together with the ontology are reported. Using these methods three software utilities, including a graphical model editor, are implemented. Experimental results proved that these methods are effective for the modification of electrophysiological models.

  13. 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...... analysis is primarily to identify paraphrases, thereby achieving a search functionality beyond mere keyword search with synsets. We further envisage use of the generative ontology as a phrase-based rather than word-based browser into text corpora....

  14. 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…

  15. 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

  16. 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

  17. Application of Ontologies for Big Earth Data

    Science.gov (United States)

    Huang, T.; Chang, G.; Armstrong, E. M.; Boening, C.

    2014-12-01

    Connected data is smarter data! Earth Science research infrastructure must do more than just being able to support temporal, geospatial discovery of satellite data. As the Earth Science data archives continue to expand across NASA data centers, the research communities are demanding smarter data services. A successful research infrastructure must be able to present researchers the complete picture, that is, datasets with linked citations, related interdisciplinary data, imageries, current events, social media discussions, and scientific data tools that are relevant to the particular dataset. The popular Semantic Web for Earth and Environmental Terminology (SWEET) ontologies is a collection of ontologies and concepts designed to improve discovery and application of Earth Science data. The SWEET ontologies collection was initially developed to capture the relationships between keywords in the NASA Global Change Master Directory (GCMD). Over the years this popular ontologies collection has expanded to cover over 200 ontologies and 6000 concepts to enable scalable classification of Earth system science concepts and Space science. This presentation discusses the semantic web technologies as the enabling technology for data-intensive science. We will discuss the application of the SWEET ontologies as a critical component in knowledge-driven research infrastructure for some of the recent projects, which include the DARPA Ontological System for Context Artifact and Resources (OSCAR), 2013 NASA ACCESS Virtual Quality Screening Service (VQSS), and the 2013 NASA Sea Level Change Portal (SLCP) projects. The presentation will also discuss the benefits in using semantic web technologies in developing research infrastructure for Big Earth Science Data in an attempt to "accommodate all domains and provide the necessary glue for information to be cross-linked, correlated, and discovered in a semantically rich manner." [1] [1] Savas Parastatidis: A platform for all that we know

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

    Science.gov (United States)

    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. Selection and Validation of Reference Genes for Quantitative Real-Time PCR Normalization Under Ethanol Stress Conditions in Oenococcus oeni SD-2a

    Directory of Open Access Journals (Sweden)

    Shuai Peng

    2018-05-01

    Full Text Available The powerful Quantitative real-time PCR (RT-qPCR was widely used to assess gene expression levels, which requires the optimal reference genes used for normalization. Oenococcus oeni (O. oeni, as the one of most important microorganisms in wine industry and the most resistant lactic acid bacteria (LAB species to ethanol, has not been investigated regarding the selection of stable reference genes for RT-qPCR normalization under ethanol stress conditions. In this study, nine candidate reference genes (proC, dnaG, rpoA, ldhD, ddlA, rrs, gyrA, gyrB, and dpoIII were analyzed to determine the most stable reference genes for RT-qPCR in O. oeni SD-2a under different ethanol stress conditions (8, 12, and 16% (v/v ethanol. The transcript stabilities of these genes were evaluated using the algorithms geNorm, NormFinder, and BestKeeper. The results showed that dnaG and dpoIII were selected as the best reference genes across all experimental ethanol conditions. Considering single stress experimental modes, dpoIII and dnaG would be suitable to normalize expression level for 8% ethanol shock treatment, while the combination of gyrA, gyrB, and rrs would be suitable for 12% ethanol shock treatment. proC and gyrB revealed the most stable expression in 16% ethanol shock treatment. This study selected and validated for the first time the reference genes for RT-qPCR normalization in O. oeni SD-2a under ethanol stress conditions.

  20. 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.

  1. 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 reuse...... will lead to the initial implementation of the meta-onotologies using design by reuse and with the objective of design for reuse. After that step new ontologies could be generated by reusing these meta-ontologies. We demonstrate our approach with a Semantic Web Service application to show how to build...

  2. 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...... ontologies for their particular purpose and a thesaurus for the terms within the ontology....

  3. Selection and evaluation of reference genes for expression studies with quantitative PCR in the model fungus Neurospora crassa under different environmental conditions in continuous culture.

    Directory of Open Access Journals (Sweden)

    Kathleen D Cusick

    Full Text Available Neurospora crassa has served as a model organism for studying circadian pathways and more recently has gained attention in the biofuel industry due to its enhanced capacity for cellulase production. However, in order to optimize N. crassa for biotechnological applications, metabolic pathways during growth under different environmental conditions must be addressed. Reverse-transcription quantitative PCR (RT-qPCR is a technique that provides a high-throughput platform from which to measure the expression of a large set of genes over time. The selection of a suitable reference gene is critical for gene expression studies using relative quantification, as this strategy is based on normalization of target gene expression to a reference gene whose expression is stable under the experimental conditions. This study evaluated twelve candidate reference genes for use with N. crassa when grown in continuous culture bioreactors under different light and temperature conditions. Based on combined stability values from NormFinder and Best Keeper software packages, the following are the most appropriate reference genes under conditions of: (1 light/dark cycling: btl, asl, and vma1; (2 all-dark growth: btl, tbp, vma1, and vma2; (3 temperature flux: btl, vma1, act, and asl; (4 all conditions combined: vma1, vma2, tbp, and btl. Since N. crassa exists as different cell types (uni- or multi-nucleated, expression changes in a subset of the candidate genes was further assessed using absolute quantification. A strong negative correlation was found to exist between ratio and threshold cycle (CT values, demonstrating that CT changes serve as a reliable reflection of transcript, and not gene copy number, fluctuations. The results of this study identified genes that are appropriate for use as reference genes in RT-qPCR studies with N. crassa and demonstrated that even with the presence of different cell types, relative quantification is an acceptable method for measuring

  4. Selection and evaluation of reference genes for expression studies with quantitative PCR in the model fungus Neurospora crassa under different environmental conditions in continuous culture.

    Science.gov (United States)

    Cusick, Kathleen D; Fitzgerald, Lisa A; Pirlo, Russell K; Cockrell, Allison L; Petersen, Emily R; Biffinger, Justin C

    2014-01-01

    Neurospora crassa has served as a model organism for studying circadian pathways and more recently has gained attention in the biofuel industry due to its enhanced capacity for cellulase production. However, in order to optimize N. crassa for biotechnological applications, metabolic pathways during growth under different environmental conditions must be addressed. Reverse-transcription quantitative PCR (RT-qPCR) is a technique that provides a high-throughput platform from which to measure the expression of a large set of genes over time. The selection of a suitable reference gene is critical for gene expression studies using relative quantification, as this strategy is based on normalization of target gene expression to a reference gene whose expression is stable under the experimental conditions. This study evaluated twelve candidate reference genes for use with N. crassa when grown in continuous culture bioreactors under different light and temperature conditions. Based on combined stability values from NormFinder and Best Keeper software packages, the following are the most appropriate reference genes under conditions of: (1) light/dark cycling: btl, asl, and vma1; (2) all-dark growth: btl, tbp, vma1, and vma2; (3) temperature flux: btl, vma1, act, and asl; (4) all conditions combined: vma1, vma2, tbp, and btl. Since N. crassa exists as different cell types (uni- or multi-nucleated), expression changes in a subset of the candidate genes was further assessed using absolute quantification. A strong negative correlation was found to exist between ratio and threshold cycle (CT) values, demonstrating that CT changes serve as a reliable reflection of transcript, and not gene copy number, fluctuations. The results of this study identified genes that are appropriate for use as reference genes in RT-qPCR studies with N. crassa and demonstrated that even with the presence of different cell types, relative quantification is an acceptable method for measuring gene

  5. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

    2011-08-11

    Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

  6. 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.

  7. 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

  8. Impact of a Reference Center on Leprosy Control under a Decentralized Public Health Care Policy in Brazil.

    Science.gov (United States)

    Barbieri, Raquel Rodrigues; Sales, Anna Maria; Hacker, Mariana Andrea; Nery, José Augusto da Costa; Duppre, Nádia Cristina; Machado, Alice de Miranda; Moraes, Milton Ozório; Sarno, Euzenir Nunes

    2016-10-01

    We evaluated the profile of patients referred to the Fiocruz Outpatient Clinic, a reference center for the diagnosis and treatment of leprosy in Rio de Janeiro, RJ, and analyzed the origins and outcomes of these referrals. This is an observational retrospective study based on information collected from the Leprosy Laboratory database at Fiocruz, Rio de Janeiro, RJ, Brazil. A total of 1,845 suspected leprosy cases examined at the reference center between 2010 and 2014 were included. The originating health service referrals and diagnostic outcomes were analyzed as well as the clinical and epidemiological data of patients diagnosed with leprosy. Our data show that the profile of the patients treated at the Clinic has changed in recent years. There was an increase in both the proportion of patients with other skin diseases and those who had visited only one health service prior to our Clinic. Among the total 1,845 cases analyzed, the outcomes of 1,380 were linked to other diseases and, in 74% of these cases, a biopsy was not necessary to reach a diagnostic conclusion. A decrease in new leprosy case detection among our patients was also observed. Yet, among the leprosy patients, 40% had some degree of disability at diagnosis. The results of the present study demonstrated the importance of referral centers in support of basic health services within the decentralization strategy. But, the success of the program depends on the advent of new developmental tools to augment diagnostic accuracy for leprosy. However, it should be emphasized that for new diagnostic methods to be developed, a greater commitment on the part of the health care system regarding research is urgently needed.

  9. 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.

  10. 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.

  11. 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.

  12. Reference values for acetyl and butyrylcholinesterases in cattle under actual management conditions, hepatic and renal function by application of chlorpyrifos.

    Science.gov (United States)

    Ferré, Daniela M; Lentini, Valeria R; Romano, R Raquel; Ludueña, Hector R; Jotallán, Paola J; Gorla, Nora B M

    2018-03-04

    Chlorpyrifos is an anticholinesterase organophosphate insecticide widely used in Argentina in the production of food derived from animal, fruit and horticultural origin and is reported as a residue within these products. Local reference values for acetyl and butyrylcholinesterase were determined in Aberdeen Angus bovine and cross bred cattle (n = 25), a requirement to be able to evaluate toxicity of commercial organophosphate and carbamate formulations. The activity of cholinesterase enzymes presented an overall mean of 2,183.00 ± 485.6 IU L -1 for erythrocyte acetylcholinesterase and 203.1 ± 42.06 IU L -1 for plasma butyrylcholinesterase, which are used as reference values for meat steers within a system of intensive production in a semi-arid region. The toxic potential of chlorpyrifos in steers of the same breeds (n = 12) was assessed applying chlorpyrifos 15.00% Tipertox® in a single therapeutic dose of 7.50 mg kg -1 by topical route. Prior to application and then on day 1 and day 21 post-application, both blood cholinesterases, serum chlorpyrifos concentration by ultra-high resolution liquid chromatography with mass detector, analysis of blood counts, total proteins, liver enzymes, urea and creatinine were evaluated. The mean plasma concentration of chlorpyrifos was 27.90 ug L -1 at 24 h. The findings indicate that the therapeutic treatment of castrated male bovines treated with chlorpyrifos, applied by pour-on according to the manufacturer's instructions, does not cause changes in the variables evaluated.

  13. 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/

  14. 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).

  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. 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.

  17. 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.

  18. 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.

  19. A Formal Theory for Modular ERDF Ontologies

    Science.gov (United States)

    Analyti, Anastasia; Antoniou, Grigoris; Damásio, Carlos Viegas

    The success of the Semantic Web is impossible without any form of modularity, encapsulation, and access control. In an earlier paper, we extended RDF graphs with weak and strong negation, as well as derivation rules. The ERDF #n-stable model semantics of the extended RDF framework (ERDF) is defined, extending RDF(S) semantics. In this paper, we propose a framework for modular ERDF ontologies, called modular ERDF framework, which enables collaborative reasoning over a set of ERDF ontologies, while support for hidden knowledge is also provided. In particular, the modular ERDF stable model semantics of modular ERDF ontologies is defined, extending the ERDF #n-stable model semantics. Our proposed framework supports local semantics and different points of view, local closed-world and open-world assumptions, and scoped negation-as-failure. Several complexity results are provided.

  20. 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...... fundamentally reconstructed during intervention. I find that the anxiety arising from a future scenario of an already weak post-Soviet ‘Russian Self’ gradually being engulfed by a confident ‘Western Self’ played a significant role in Russia’s decision to occupy Slatina airbase. My analysis paradoxically shows...

  1. Løgstrup’s Ontological Ethics

    DEFF Research Database (Denmark)

    Rabjerg, Bjørn

    2017-01-01

    aim is to provide a coherent exposition of Løgstrup’s ethics. However, the result is not a normative ethics upon which we may act, but rather a descriptive diagnosis of interdependence as the basic ontological condition of human social life, where the sovereign expressions of life may enable us to act.......The article explores K. E. Løgstrup’s ontological ethics, understood as an ethics rooted in interdependence. Interdependence, the fact that human beings always hold power over each other, has two very different aspects, which I will call negative and positive, each of them in turn leading...... 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’s...

  2. Designing Network-based Business Model Ontology

    DEFF Research Database (Denmark)

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

    2015-01-01

    Survival on dynamic environment is not achieved without a map. Scanning and monitoring of the market show business models as a fruitful tool. But scholars believe that old-fashioned business models are dead; as they are not included the effect of internet and network in themselves. This paper...... 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....

  3. Player-Specific Conflict Handling Ontology

    Directory of Open Access Journals (Sweden)

    Charline Hondrou

    2014-09-01

    Full Text Available This paper presents an ontology that leads the player of a serious game - regarding conflict handling - to the educative experience from which they will benefit the most. It provides a clearly defined tree of axioms that maps the player’s visually manifested affective cues and emotional stimuli from the serious game to conflict handling styles and proposes interventions. The importance of this ontology lies in the fact that it promotes natural interaction (non-invasive methods and at the same time makes the game as player-specific as it can be for its educational goal. It is an ontology that can be adapted to different educational theories and serve various educational purposes.

  4. Using ontology network structure in text mining.

    Science.gov (United States)

    Berndt, Donald J; McCart, James A; Luther, Stephen L

    2010-11-13

    Statistical text mining treats documents as bags of words, with a focus on term frequencies within documents and across document collections. Unlike natural language processing (NLP) techniques that rely on an engineered vocabulary or a full-featured ontology, statistical approaches do not make use of domain-specific knowledge. The freedom from biases can be an advantage, but at the cost of ignoring potentially valuable knowledge. The approach proposed here investigates a hybrid strategy based on computing graph measures of term importance over an entire ontology and injecting the measures into the statistical text mining process. As a starting point, we adapt existing search engine algorithms such as PageRank and HITS to determine term importance within an ontology graph. The graph-theoretic approach is evaluated using a smoking data set from the i2b2 National Center for Biomedical Computing, cast as a simple binary classification task for categorizing smoking-related documents, demonstrating consistent improvements in accuracy.

  5. 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.

  6. 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.

  7. OAE: The Ontology of Adverse Events.

    Science.gov (United States)

    He, Yongqun; Sarntivijai, Sirarat; Lin, Yu; Xiang, Zuoshuang; Guo, Abra; Zhang, Shelley; Jagannathan, Desikan; Toldo, Luca; Tao, Cui; Smith, Barry

    2014-01-01

    A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term 'adverse event' denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. For example, using the data extracted from the Vaccine Adverse Event Reporting System (VAERS), OAE was used to analyse vaccine adverse events associated with the administrations of different types of influenza vaccines. OAE has also been used to represent and classify the vaccine adverse events cited in package inserts of FDA-licensed human vaccines in the USA. OAE is a biomedical ontology that logically defines and classifies various adverse events occurring after medical interventions. OAE has successfully been applied in several adverse event studies. The OAE ontological framework provides a platform for systematic representation and analysis of adverse events and of the factors (e

  8. 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...

  9. 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.

  10. 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...

  11. 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

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

    Science.gov (United States)

    Bouzanis, Christoforos

    2017-12-01

    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.

  13. Ontological Model of Business Process Management Systems

    Science.gov (United States)

    Manoilov, G.; Deliiska, B.

    2008-10-01

    The activities which constitute business process management (BPM) can be grouped into five categories: design, modeling, execution, monitoring and optimization. Dedicated software packets for business process management system (BPMS) are available on the market. But the efficiency of its exploitation depends on used ontological model in the development time and run time of the system. In the article an ontological model of BPMS in area of software industry is investigated. The model building is preceded by conceptualization of the domain and taxonomy of BPMS development. On the base of the taxonomy an simple online thesaurus is created.

  14. Methodology of decreasing software complexity using ontology

    Science.gov (United States)

    DÄ browska-Kubik, Katarzyna

    2015-09-01

    In this paper a model of web application`s source code, based on the OSD ontology (Ontology for Software Development), is proposed. This model is applied to implementation and maintenance phase of software development process through the DevOntoCreator tool [5]. The aim of this solution is decreasing software complexity of that source code, using many different maintenance techniques, like creation of documentation, elimination dead code, cloned code or bugs, which were known before [1][2]. Due to this approach saving on software maintenance costs of web applications will be possible.

  15. Ontology-Based Model Of Firm Competitiveness

    Science.gov (United States)

    Deliyska, Boryana; Stoenchev, Nikolay

    2010-10-01

    Competitiveness is important characteristics of each business organization (firm, company, corporation etc). It is of great significance for the organization existence and defines evaluation criteria of business success at microeconomical level. Each criterium comprises set of indicators with specific weight coefficients. In the work an ontology-based model of firm competitiveness is presented as a set of several mutually connected ontologies. It would be useful for knowledge structuring, standardization and sharing among experts and software engineers who develop application in the domain. Then the assessment of the competitiveness of various business organizations could be generated more effectively.

  16. 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.

  17. Initial Implementation of a Comparative Data Analysis Ontology

    Directory of Open Access Journals (Sweden)

    Francisco Prosdocimi

    2009-07-01

    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.

  18. 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

  19. 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

  20. Applications of the ACGT Master Ontology on Cancer

    OpenAIRE

    Brochhausen, Mathias; Weiler, Gabriele; Martín Martín, Luis; Cocos, Cristian; Stenzhorn, Holger; Graf, Norbert; Dörr, Martin; Tsiknakis, Manolis; Smith, Barry

    2008-01-01

    In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the...

  1. Self-adaptation of Ontologies to Folksonomies in Semantic Web

    OpenAIRE

    Francisco Echarte; José Javier Astrain; Alberto Córdoba; Jesús Villadangos

    2008-01-01

    Ontologies and tagging systems are two different ways to organize the knowledge present in the current Web. In this paper we propose a simple method to model folksonomies, as tagging systems, with ontologies. We show the scalability of the method using real data sets. The modeling method is composed of a generic ontology that represents any folksonomy and an algorithm to transform the information contained in folksonomies to the generic ontology. The method allows representing folksonomies at...

  2. A collaborative recommendation framework for ontology evaluation and reuse

    OpenAIRE

    Cantador, Iván; Fernández Sánchez, Miriam; Castells, Pablo

    2006-01-01

    This is an electronic version of the paper presented at the International Workshop on Recommender Systems, held in Riva del Garda on 2006 Ontology evaluation can be defined as assessing the quality and the adequacy of an ontology for being used in a spe-cific context, for a specific goal. Although ontology reuse is being extensively addressed by the Semantic Web community, the lack of appropriate support tools and automatic techniques for the evaluation of certain ontology features are oft...

  3. 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.

  4. 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.

  5. 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

  6. Conflict Resolution in Partially Ordered OWL DL Ontologies

    NARCIS (Netherlands)

    Ji, Q.; Gao, Z.; Huang, Z.

    2014-01-01

    Inconsistency handling in OWL DL ontologies is an important problem because an ontology can easily be inconsistent when it is generated or modified. Current approaches to dealing with inconsistent ontologies often assume that there exists a total order over axioms and use such an order to select

  7. Methodology for Automatic Ontology Generation Using Database Schema Information

    Directory of Open Access Journals (Sweden)

    JungHyen An

    2018-01-01

    Full Text Available An ontology is a model language that supports the functions to integrate conceptually distributed domain knowledge and infer relationships among the concepts. Ontologies are developed based on the target domain knowledge. As a result, methodologies to automatically generate an ontology from metadata that characterize the domain knowledge are becoming important. However, existing methodologies to automatically generate an ontology using metadata are required to generate the domain metadata in a predetermined template, and it is difficult to manage data that are increased on the ontology itself when the domain OWL (Ontology Web Language individuals are continuously increased. The database schema has a feature of domain knowledge and provides structural functions to efficiently process the knowledge-based data. In this paper, we propose a methodology to automatically generate ontologies and manage the OWL individual through an interaction of the database and the ontology. We describe the automatic ontology generation process with example schema and demonstrate the effectiveness of the automatically generated ontology by comparing it with existing ontologies using the ontology quality score.

  8. Construction of Engineering Ontologies for Knowledge Sharing and Reuse

    NARCIS (Netherlands)

    Borst, Willem Nico; Borst, W.N.

    1997-01-01

    This thesis describes an investigation into the practical use of ontologies for the development of information systems. Ontologies are formal descriptions of shared knowledge in a domain. An ontology can be used as a specification of an information system because it specifies the knowledge that is

  9. Six scenarios of exploiting an ontology based, mobilized learning environment

    NARCIS (Netherlands)

    Kismihók, G.; Szabó, I.; Vas, R.

    2012-01-01

    In this article, six different exploitation possibilities of an educational ontology based, mobilized learning management system are presented. The focal point of this system is the educational ontology model. The first version of this educational ontology model serves as a foundation for curriculum

  10. 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...

  11. 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

  12. 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

  13. 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

  14. 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…

  15. 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…

  16. 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…

  17. Ontology-based intelligent fuzzy agent for diabetes application

    NARCIS (Netherlands)

    Acampora, G.; Lee, C.-S.; Wang, M.-H.; Hsu, C.-Y.; Loia, V.

    2009-01-01

    It is widely pointed out that classical ontologies are not sufficient to deal with imprecise and vague knowledge for some real world applications, but the fuzzy ontology can effectively solve data and knowledge with uncertainty. In this paper, an ontology-based intelligent fuzzy agent (OIFA),

  18. MultiFarm: A Benchmark for Multilingual Ontology Matching

    NARCIS (Netherlands)

    Meilicke, C.; García-Castro, R.; Freitas, F.; van Hage, W.R.; Montiel-Ponsoda, E.; Ribeiro de Azevedo, R.; Stuckenschmidt, H.; Svab-Zamazal, O.; Svatek, V.; Tamalin, A.; Wang, S.

    2012-01-01

    In this paper we present the MultiFarm dataset, which has been designed as a benchmark for multilingual ontology matching. The MultiFarm dataset is composed of a set of ontologies translated in different languages and the corresponding alignments between these ontologies. It is based on the OntoFarm

  19. Length bias correction in gene ontology enrichment analysis using logistic regression.

    Science.gov (United States)

    Mi, Gu; Di, Yanming; Emerson, Sarah; Cumbie, Jason S; Chang, Jeff H

    2012-01-01

    When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called "length bias", will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology categories that include longer genes are more likely to be identified as enriched. These categories, however, are not necessarily biologically more relevant. We show that one can effectively adjust for length bias in Gene Ontology analysis by including transcript length as a covariate in a logistic regression model. The logistic regression model makes the statistical issue underlying length bias more transparent: transcript length becomes a confounding factor when it correlates with both the Gene Ontology membership and the significance of the differential expression test. The inclusion of the transcript length as a covariate allows one to investigate the direct correlation between the Gene Ontology membership and the significance of testing differential expression, conditional on the transcript length. We present both real and simulated data examples to show that the logistic regression approach is simple, effective, and flexible.

  20. Determination of uncertainty of automated emission measuring systems under field conditions using a second method as a reference

    Energy Technology Data Exchange (ETDEWEB)

    Puustinen, H.; Aunela-Tapola, L.; Tolvanen, M.; Vahlman, T. [VTT Chemical Technology, Espoo (Finland). Environmental Technology; Kovanen, K. [VTT Building Technology, Espoo (Finland). Building Physics, Building Services and Fire Technology

    1999-09-01

    This report presents a procedure to determine the uncertainty of an automated emission measuring system (AMS) by comparing the results with a second method (REF). The procedure determines the uncertainty of AMS by comparing the final concentration and emission results of AMS and REF. In this way, the data processing of the plant is included in the result evaluation. This procedure assumes that the uncertainty of REF is known and determined in due form. The uncertainty determination has been divided into two cases; varying and nearly constant concentration. The suggested procedure calculates the uncertainty of AMS at the 95 % confidence level by a tabulated t-value. A minimum of three data pairs is required. However, a higher amount of data pairs is desirable, since a low amount of data pairs results in a higher uncertainty of AMS. The uncertainty of AMS is valid only within the range of concentrations at which the tests were carried out. Statistical data processing shows that the uncertainty of the reference method has a significant effect on the uncertainty of AMS, which always becomes larger than the uncertainty of REF. This should be taken into account when testing whether AMS fulfils the given uncertainty limits. Practical details, concerning parallel measurements at the plant, and the costs of the measurement campaign, have been taken into account when suggesting alternative ways for implementing the comparative measurements. (orig.) 6 refs.

  1. Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies.

    Science.gov (United States)

    Ochs, Christopher; He, Zhe; Zheng, Ling; Geller, James; Perl, Yehoshua; Hripcsak, George; Musen, Mark A

    2016-06-01

    An Abstraction Network is a compact summary of an ontology's structure and content. In previous research, we showed that Abstraction Networks support quality assurance (QA) of biomedical ontologies. The development of an Abstraction Network and its associated QA methodologies, however, is a labor-intensive process that previously was applicable only to one ontology at a time. To improve the efficiency of the Abstraction-Network-based QA methodology, we introduced a QA framework that uses uniform Abstraction Network derivation techniques and QA methodologies that are applicable to whole families of structurally similar ontologies. For the family-based framework to be successful, it is necessary to develop a method for classifying ontologies into structurally similar families. We now describe a structural meta-ontology that classifies ontologies according to certain structural features that are commonly used in the modeling of ontologies (e.g., object properties) and that are important for Abstraction Network derivation. Each class of the structural meta-ontology represents a family of ontologies with identical structural features, indicating which types of Abstraction Networks and QA methodologies are potentially applicable to all of the ontologies in the family. We derive a collection of 81 families, corresponding to classes of the structural meta-ontology, that enable a flexible, streamlined family-based QA methodology, offering multiple choices for classifying an ontology. The structure of 373 ontologies from the NCBO BioPortal is analyzed and each ontology is classified into multiple families modeled by the structural meta-ontology. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Students' flexible use of ontologies and the value of tentative reasoning: Examples of conceptual understanding in three canonical topics of quantum mechanics

    Science.gov (United States)

    Hoehn, Jessica R.; Finkelstein, Noah D.

    2018-06-01

    As part of a research study on student reasoning in quantum mechanics, we examine students' use of ontologies, or the way students' categorically organize entities they are reasoning about. In analyzing three episodes of focus group discussions with modern physics students, we present evidence of the dynamic nature of ontologies, and refine prior theoretical frameworks for thinking about dynamic ontologies. We find that in a given reasoning episode ontologies can be dynamic in construction (referring to when the reasoner constructs the ontologies) or application (referring to which ontologies are applied in a given reasoning episode). In our data, we see instances of students flexibly switching back and forth between parallel stable structures as well as constructing and negotiating new ontologies in the moment. Methodologically, we use a collective conceptual blending framework as an analytic tool for capturing student reasoning in groups. In this research, we value the messiness of student reasoning and argue that reasoning in a tentative manner can be productive for students learning quantum mechanics. As such, we shift away from a binary view of student learning which sees students as either having the correct answer or not.

  3. 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.

  4. 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

  5. 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...

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

    African Journals Online (AJOL)

    The paper begins from the claim that ontological holism is given prima facie plausibility by the apparently ineliminable role of groups in some descriptions and explanations of the social domain. If the individualist accepts the link between indispensabilty and realism, then individualism must show that groups cannot play the ...

  7. 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 ...

  8. The location problem in social ontology

    NARCIS (Netherlands)

    Hindriks, Frank

    Mental, mathematical, and moral facts are difficult to accommodate within an overall worldview due to the peculiar kinds of properties inherent to them. In this paper I argue that a significant class of social entities also presents us with an ontological puzzle that has thus far not been addressed

  9. 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

  10. Patient Centric Ontology for Telehealth Domain

    DEFF Research Database (Denmark)

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

    2015-01-01

    This paper presents an ontology for the telehealth domain, a domain that concerns the use of telecommunication to support and deliver health related services e.g. patient monitoring and rehabilitative training. Our vision for the future of telehealth solutions is that they adapt their behavior to...

  11. Ontological support for web courseware authoring

    NARCIS (Netherlands)

    Aroyo, L.M.; Dicheva, D.; Cristea, A.I.; Cerri, S.A.; Gouardères, G.; Paraguaçu, F.

    2002-01-01

    In this paper we present an ontology- oriented authoring support system for Web-based courseware. This is an elaboration of our approach to knowledge classification and indexing in the previously developed system AIMS (Agent-based Information Management System) aimed at supporting students while

  12. Ontology matching evaluation : A statistical perspective

    NARCIS (Netherlands)

    Mohammadi, M.; Hofman, W.J.; Tan, Y.H.

    2016-01-01

    This paper proposes statistical approaches to test if the difference between two ontology matchers is real. Specifically, the performances of the matchers over multiple data sets are obtained and based on their performances, the conclusion can be drawn whether one method is better than one another

  13. Ontology matching evaluation : A statistical perspective

    NARCIS (Netherlands)

    Mohammadi, M.; Hofman, Wout; Tan, Y.

    2016-01-01

    This paper proposes statistical approaches to test if the difference between two ontology matchers is real. Specifically, the performances of the matchers over multiple data sets are obtained and based on their performances, the conclusion can be drawn whether one method is better than one

  14. 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...

  15. 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 and ...

  16. 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…

  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. In Defense of Chi's Ontological Incompatibility Hypothesis

    Science.gov (United States)

    Slotta, James D.

    2011-01-01

    This article responds to an article by A. Gupta, D. Hammer, and E. F. Redish (2010) that asserts that M. T. H. Chi's (1992, 2005) hypothesis of an "ontological commitment" in conceptual development is fundamentally flawed. In this article, I argue that Chi's theoretical perspective is still very much intact and that the critique offered by Gupta…

  19. Adaptive e-learning system using ontology

    OpenAIRE

    Yarandi, Maryam; Tawil, Abdel-Rahman; Jahankhani, Hossein

    2011-01-01

    This paper proposes an innovative ontological approach to design a personalised e-learning system which creates a tailored workflow for individual learner. Moreover, the learning content and sequencing logic is separated into content model and pedagogical model to increase the reusability and flexibility of the system.

  20. Ontology for cell-based geographic information

    Science.gov (United States)

    Zheng, Bin; Huang, Lina; Lu, Xinhai

    2009-10-01

    Inter-operability is a key notion in geographic information science (GIS) for the sharing of geographic information (GI). That requires a seamless translation among different information sources. Ontology is enrolled in GI discovery to settle the semantic conflicts for its natural language appearance and logical hierarchy structure, which are considered to be able to provide better context for both human understanding and machine cognition in describing the location and relationships in the geographic world. However, for the current, most studies on field ontology are deduced from philosophical theme and not applicable for the raster expression in GIS-which is a kind of field-like phenomenon but does not physically coincide to the general concept of philosophical field (mostly comes from the physics concepts). That's why we specifically discuss the cell-based GI ontology in this paper. The discussion starts at the investigation of the physical characteristics of cell-based raster GI. Then, a unified cell-based GI ontology framework for the recognition of the raster objects is introduced, from which a conceptual interface for the connection of the human epistemology and the computer world so called "endurant-occurrant window" is developed for the better raster GI discovery and sharing.

  1. 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

  2. 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

  3. 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.

  4. A Framework for Ontological Policy Reconstruction : Academic Knowledge Transfer in the Netherlands as a Case Study

    NARCIS (Netherlands)

    Pauly, Marc

    2016-01-01

    This paper provides a framework for analyzing the ontology underlying a given public policy, i.e. the categories and concepts used by the policy. It pro- vides a set of questions concerning the language, logic and deontology of a policy and their development over time. The framework is applied to a

  5. Comparison of reasoners for large ontologies in the OWL 2 EL profile

    NARCIS (Netherlands)

    Dentler, K.; Cornet, R.; ten Teije, A.C.M.; de Keizer, N.F.

    2011-01-01

    This paper provides a survey to and a comparison of state-of-the-art Semantic Web reasoners that succeed in classifying large ontologies expressed in the tractable OWL 2 EL profile. Reasoners are characterized along several dimensions: The first dimension comprises underlying reasoning

  6. Visual syntax of UML class and package diagram constructs as an ontology

    CSIR Research Space (South Africa)

    Thomas, A

    2015-11-01

    Full Text Available and package diagrams are two diagrams of UML. The motivation for this work is twofold; UML lacks a formal visual syntax specification and ontologies are under-explored for visual syntax specifications. The work in this paper, therefore, explores using...

  7. 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.

  8. 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.

  9. Methodology to build medical ontology from textual resources.

    Science.gov (United States)

    Baneyx, Audrey; Charlet, Jean; Jaulent, Marie-Christine

    2006-01-01

    In the medical field, it is now established that the maintenance of unambiguous thesauri goes through ontologies. Our research task is to help pneumologists code acts and diagnoses with a software that represents medical knowledge through a domain ontology. In this paper, we describe our general methodology aimed at knowledge engineers in order to build various types of medical ontologies based on terminology extraction from texts. The hypothesis is to apply natural language processing tools to textual patient discharge summaries to develop the resources needed to build an ontology in pneumology. Results indicate that the joint use of distributional analysis and lexico-syntactic patterns performed satisfactorily for building such ontologies.

  10. 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

  11. Comparing Relational and Ontological Triple Stores in Healthcare Domain

    Directory of Open Access Journals (Sweden)

    Ozgu Can

    2017-01-01

    Full Text Available Today’s technological improvements have made ubiquitous healthcare systems that converge into smart healthcare applications in order to solve patients’ problems, to communicate effectively with patients, and to improve healthcare service quality. The first step of building a smart healthcare information system is representing the healthcare data as connected, reachable, and sharable. In order to achieve this representation, ontologies are used to describe the healthcare data. Combining ontological healthcare data with the used and obtained data can be maintained by storing the entire health domain data inside big data stores that support both relational and graph-based ontological data. There are several big data stores and different types of big data sets in the healthcare domain. The goal of this paper is to determine the most applicable ontology data store for storing the big healthcare data. For this purpose, AllegroGraph and Oracle 12c data stores are compared based on their infrastructural capacity, loading time, and query response times. Hence, healthcare ontologies (GENE Ontology, Gene Expression Ontology (GEXO, Regulation of Transcription Ontology (RETO, Regulation of Gene Expression Ontology (REXO are used to measure the ontology loading time. Thereafter, various queries are constructed and executed for GENE ontology in order to measure the capacity and query response times for the performance comparison between AllegroGraph and Oracle 12c triple stores.

  12. The technology of under-sodium inspection in LMFBR's with particular reference to experimental measurements of the PFR core

    International Nuclear Information System (INIS)

    McKnight, J.A.; Barrett, L.M.; Burton, E.J.; Fothergill, J.R.; Gould, R.F.; Parker, J.A.; Willis, P.; Fenemore, P.

    1985-05-01

    For future Nuclear Fast Reactor systems an expected requirement will be the ability to examine components immersed in the sodium coolant. The potential of ultrasonic technology for this purpose is well illustrated by the successful experiment in the Prototype Fast Reactor at Dounreay in the UK made during the Spring of 1982 by a team from the UKAEA Risley Nuclear Power Development Laboratories. A device was loaded through the top shield of the reactor, and this was used to obtain recognisable images of the tops of reactor core components. Small on-line computers were used to store, assemble and display the images. They were also used for a subsequent analysis which measured the distortion and growth of the components due to irradiation. The experiment enables an assessment to be made of the performance to be expected from future under-sodium instruments. The need for an access manipulator with robotic functions is clear. So too are required improvements in imaging technology to enable targets to be seen whatever their orientation. thus a substantial development programme is envisaged. (author)

  13. 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.

  14. 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

  15. Parental views on delivering preventive advice to children referred for treatment of dental caries under general anaesthesia: a qualitative investigation.

    Science.gov (United States)

    Aljafari, A K; Scambler, S; Gallagher, J E; Hosey, M T

    2014-06-01

    To: 1, Explore opinions of parents of children undergoing caries treatment under general anaesthesia (GA) regarding delivery of oral health advice; 2, Discover current oral health practices and beliefs; 3, Inform further research and action. Qualitative study using semi-structured interviews and thematic data analysis, sampling parents of children aged 3-10 years undergoing GA tooth extraction due to dental caries. Twenty nine parents were interviewed (mean age 38.9 years, range 28-50, sd 6.4). The mean age of their children was seven years (range 3-10, sd 2.1). All children required deciduous tooth extractions (5.1 teeth on average). Those that also required permanent tooth extractions had on average 2.1 permanent teeth extracted. Many parents knew the importance of oral hygiene and sugar limitation, describing it as 'general knowledge' and 'common sense'. However, few understood that fruit juice is potentially cariogenic. Parenting challenges seemed to restrict their ability to control the child's diet and establish oral hygiene. Many reported not previously receiving oral health advice and reported never having fluoride varnish applied. There were requests for more caries prevention information and advice via the internet, schools or video games. Parental oral health knowledge, parenting skills, and previous advice received seem to all be issues related to the oral health of those children. Providing advice, especially in respect to fruit juice cariogenicity and the benefits of fluoride application through a child-friendly website, including a video game, as well as the use of school programmes might be an acceptable approach.

  16. Informatics in radiology: radiology gamuts ontology: differential diagnosis for the Semantic Web.

    Science.gov (United States)

    Budovec, Joseph J; Lam, Cesar A; Kahn, Charles E

    2014-01-01

    The Semantic Web is an effort to add semantics, or "meaning," to empower automated searching and processing of Web-based information. The overarching goal of the Semantic Web is to enable users to more easily find, share, and combine information. Critical to this vision are knowledge models called ontologies, which define a set of concepts and formalize the relations between them. Ontologies have been developed to manage and exploit the large and rapidly growing volume of information in biomedical domains. In diagnostic radiology, lists of differential diagnoses of imaging observations, called gamuts, provide an important source of knowledge. The Radiology Gamuts Ontology (RGO) is a formal knowledge model of differential diagnoses in radiology that includes 1674 differential diagnoses, 19,017 terms, and 52,976 links between terms. Its knowledge is used to provide an interactive, freely available online reference of radiology gamuts ( www.gamuts.net ). A Web service allows its content to be discovered and consumed by other information systems. The RGO integrates radiologic knowledge with other biomedical ontologies as part of the Semantic Web. © RSNA, 2014.

  17. 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.

  18. 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.

  19. 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

  20. Developing an Ontology for Ocean Biogeochemistry Data

    Science.gov (United States)

    Chandler, C. L.; Allison, M. D.; Groman, R. C.; West, P.; Zednik, S.; Maffei, A. R.

    2010-12-01

    Semantic Web technologies offer great promise for enabling new and better scientific research. However, significant challenges must be met before the promise of the Semantic Web can be realized for a discipline as diverse as oceanography. Evolving expectations for open access to research data combined with the complexity of global ecosystem science research themes present a significant challenge, and one that is best met through an informatics approach. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the National Science Foundation Division of Ocean Sciences to work with ocean biogeochemistry researchers to improve access to data resulting from their respective programs. In an effort to improve data access, BCO-DMO staff members are collaborating with researchers from the Tetherless World Constellation (Rensselaer Polytechnic Institute) to develop an ontology that formally describes the concepts and relationships in the data managed by the BCO-DMO. The project required transforming a legacy system of human-readable, flat files of metadata to well-ordered controlled vocabularies to a fully developed ontology. To improve semantic interoperability, terms from the BCO-DMO controlled vocabularies are being mapped to controlled vocabulary terms adopted by other oceanographic data management organizations. While the entire process has proven to be difficult, time-consuming and labor-intensive, the work has been rewarding and is a necessary prerequisite for the eventual incorporation of Semantic Web tools. From the beginning of the project, development of the ontology has been guided by a use case based approach. The use cases were derived from data access related requests received from members of the research community served by the BCO-DMO. The resultant ontology satisfies the requirements of the use cases and reflects the information stored in the metadata database. The BCO-DMO metadata database currently contains information that

  1. 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

  2. Integrating Ontology Debugging and Matching into the eXtreme Design Methodology

    OpenAIRE

    Dragisic, Zlatan; Lambrix, Patrick; Blomqvist, Eva

    2015-01-01

    Ontology design patterns (ODPs) and related ontology development methodologies were designed as ways of sharing and reusing best practices in ontology engineering. However, while the use of these reduces the number of issues in the resulting ontologies defects can still be introduced into the ontology due to improper use or misinterpretation of the patterns. Thus, the quality of the developed ontologies is still a major concern. In this paper we address this issue by describing how ontology d...

  3. 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.

  4. An ontological system for interoperable spatial generalisation in biodiversity monitoring

    Science.gov (United States)

    Nieland, Simon; Moran, Niklas; Kleinschmit, Birgit; Förster, Michael

    2015-11-01

    Semantic heterogeneity remains a barrier to data comparability and standardisation of results in different fields of spatial research. Because of its thematic complexity, differing acquisition methods and national nomenclatures, interoperability of biodiversity monitoring information is especially difficult. Since data collection methods and interpretation manuals broadly vary there is a need for automatised, objective methodologies for the generation of comparable data-sets. Ontology-based applications offer vast opportunities in data management and standardisation. This study examines two data-sets of protected heathlands in Germany and Belgium which are based on remote sensing image classification and semantically formalised in an OWL2 ontology. The proposed methodology uses semantic relations of the two data-sets, which are (semi-)automatically derived from remote sensing imagery, to generate objective and comparable information about the status of protected areas by utilising kernel-based spatial reclassification. This automatised method suggests a generalisation approach, which is able to generate delineation of Special Areas of Conservation (SAC) of the European biodiversity Natura 2000 network. Furthermore, it is able to transfer generalisation rules between areas surveyed with varying acquisition methods in different countries by taking into account automated inference of the underlying semantics. The generalisation results were compared with the manual delineation of terrestrial monitoring. For the different habitats in the two sites an accuracy of above 70% was detected. However, it has to be highlighted that the delineation of the ground-truth data inherits a high degree of uncertainty, which is discussed in this study.

  5. 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.

  6. 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......Power systems worldwide are complex and challenging environments. The increasing necessity for an adequate integration of renewable energy sources is resulting in a rising complexity in power systems operation. Multi-agent based simulation platforms have proven to be a good option to study...

  7. Ontological and Epistemological Foundations of Qualitative Research

    Directory of Open Access Journals (Sweden)

    Irene Vasilachis de Gialdino

    2009-05-01

    Full Text Available The purpose of this paper is to describe the most relevant features of qualitative research in order to show how, from the Epistemology of the Known Subject perspective I propose, it is necessary to review first the ontological and then the epistemological grounds of this type of inquiry. I begin by following the path that leads from the Epistemology of the Knowing Subject to the Epistemology of the Known Subject, proposed as a new and non exclusive way of knowing. I pass on to describe the primary and secondary characteristics of qualitative research, expressing the need for an ontological rupture. Finally, cognitive interaction and cooperative knowledge construction are considered as two fundamental features in the process of qualitative research grounded on the Epistemology of the Known Subject. URN: urn:nbn:de:0114-fqs0902307

  8. A Cognitive Support Framework for Ontology Mapping

    Science.gov (United States)

    Falconer, Sean M.; Storey, Margaret-Anne

    Ontology mapping is the key to data interoperability in the semantic web. This problem has received a lot of research attention, however, the research emphasis has been mostly devoted to automating the mapping process, even though the creation of mappings often involve the user. As industry interest in semantic web technologies grows and the number of widely adopted semantic web applications increases, we must begin to support the user. In this paper, we combine data gathered from background literature, theories of cognitive support and decision making, and an observational case study to propose a theoretical framework for cognitive support in ontology mapping tools. We also describe a tool called CogZ that is based on this framework.

  9. Discovering Diabetes Complications: an Ontology Based Model.

    Science.gov (United States)

    Daghistani, Tahani; Shammari, Riyad Al; Razzak, Muhammad Imran

    2015-12-01

    Diabetes is a serious disease that spread in the world dramatically. The diabetes patient has an average of risk to experience complications. Take advantage of recorded information to build ontology as information technology solution will help to predict patients who have average of risk level with certain complication. It is helpful to search and present patient's history regarding different risk factors. Discovering diabetes complications could be useful to prevent or delay the complications. We designed ontology based model, using adult diabetes patients' data, to discover the rules of diabetes with its complications in disease to disease relationship. Various rules between different risk factors of diabetes Patients and certain complications generated. Furthermore, new complications (diseases) might be discovered as new finding of this study, discovering diabetes complications could be useful to prevent or delay the complications. The system can identify the patients who are suffering from certain risk factors such as high body mass index (obesity) and starting controlling and maintaining plan.

  10. 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.

  11. Quality control for terms and definitions in ontologies and taxonomies

    Directory of Open Access Journals (Sweden)

    Rüegg Alexander

    2006-04-01

    Full Text Available Abstract Background Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO, the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation.

  12. Construction of ontology augmented networks for protein complex prediction.

    Science.gov (United States)

    Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian

    2013-01-01

    Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational methods for protein complex prediction. Most existing methods focus mainly on the topological structure of protein-protein interaction networks, and largely ignore the gene ontology annotation information. In this article, we constructed ontology augmented networks with protein-protein interaction data and gene ontology, which effectively unified the topological structure of protein-protein interaction networks and the similarity of gene ontology annotations into unified distance measures. After constructing ontology augmented networks, a novel method (clustering based on ontology augmented networks) was proposed to predict protein complexes, which was capable of taking into account the topological structure of the protein-protein interaction network, as well as the similarity of gene ontology annotations. Our method was applied to two different yeast protein-protein interaction datasets and predicted many well-known complexes. The experimental results showed that (i) ontology augmented networks and the unified distance measure can effectively combine the structure closeness and gene ontology annotation similarity; (ii) our method is valuable in predicting protein complexes and has higher F1 and accuracy compared to other competing methods.

  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. The Ontology of Knowledge Based Optimization

    OpenAIRE

    Nasution, Mahyuddin K. M.

    2012-01-01

    Optimization has been becoming a central of studies in mathematic and has many areas with different applications. However, many themes of optimization came from different area have not ties closing to origin concepts. This paper is to address some variants of optimization problems using ontology in order to building basic of knowledge about optimization, and then using it to enhance strategy to achieve knowledge based optimization.

  15. Business Ontology for Evaluating Corporate Social Responsibility

    OpenAIRE

    Ion Smeureanu; Andreea Dioşteanu; Camelia Delcea; Liviu Cotfas

    2011-01-01

    This paper presents a software solution that is developed to automatically classify companies by taking into account their level of social responsibility. The application is based on ontologies and on intelligent agents. In order to obtain the data needed to evaluate companies, we developed a web crawling module that analyzes the company’s website and the documents that are available online such as social responsibility report, mission statement, employment structure, etc. Based on a predefin...

  16. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

    Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

    2018-06-01

    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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Phenex: ontological annotation of phenotypic diversity.

    Science.gov (United States)

    Balhoff, James P; Dahdul, Wasila M; Kothari, Cartik R; Lapp, Hilmar; Lundberg, John G; Mabee, Paula; Midford, Peter E; Westerfield, Monte; Vision, Todd J

    2010-05-05

    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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. ComTrustO: Composite Trust-Based Ontology Framework for Information and Decision Fusion

    Science.gov (United States)

    2015-07-06

    11] presents a methodological approach for ontology management allowing development of extensible ontologies and the mapping from ontologies to...ComTrustO: Composite Trust-based Ontology Framework for Information and Decision Fusion Alessandro Oltramari Carnegie Mellon University Pittsburgh... ontology -based framework for information fusion, as a support system for human decision makers. In particular, we build upon the concept of composite

  7. 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)

  8. An Ontology for Modeling Complex Inter-relational Organizations

    Science.gov (United States)

    Wautelet, Yves; Neysen, Nicolas; Kolp, Manuel

    This paper presents an ontology for organizational modeling through multiple complementary aspects. The primary goal of the ontology is to dispose of an adequate set of related concepts for studying complex organizations involved in a lot of relationships at the same time. In this paper, we define complex organizations as networked organizations involved in a market eco-system that are playing several roles simultaneously. In such a context, traditional approaches focus on the macro analytic level of transactions; this is supplemented here with a micro analytic study of the actors' rationale. At first, the paper overviews enterprise ontologies literature to position our proposal and exposes its contributions and limitations. The ontology is then brought to an advanced level of formalization: a meta-model in the form of a UML class diagram allows to overview the ontology concepts and their relationships which are formally defined. Finally, the paper presents the case study on which the ontology has been validated.

  9. 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.

  10. 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.

  11. Logical Characterisation of Ontology Construction using Fuzzy Description Logics

    DEFF Research Database (Denmark)

    Badie, Farshad; Götzsche, Hans

    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....

  12. AN ONTOLOGY-BASED COMPETENCE MANAGEMENT SYSTEM FOR IT COMPANIES

    OpenAIRE

    Cristina NICULESCU; Stefan TRAUSAN-MATU

    2009-01-01

    The paper presents a generic framework of an intelligent information system for competence management based on ontologies for information technology companies. The 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 inferences may be performed in our approach by a reasoning engine, using classifiers in the Descriptions Logics tab associated with the Protégé ontology e...

  13. 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.

  14. Building an Ontology of Tablewares using 'Legacy Data'

    Directory of Open Access Journals (Sweden)

    Daniël van Helden

    2018-05-01

    Full Text Available This article aims to demonstrate how an ontology can be constructed to encompass many of the criteria needed for more consumption-orientated approaches to Roman tablewares. For this it demonstrates how a dataset in a relational database can be organised for the format and capabilities of an ontology, and then how these data are input into the ontology model. Finally it includes some sample analyses to show the effectiveness of such an ontology for types of analyses that are relevant to this network.

  15. Matching biomedical ontologies based on formal concept analysis.

    Science.gov (United States)

    Zhao, Mengyi; Zhang, Songmao; Li, Weizhuo; Chen, Guowei

    2018-03-19

    The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analyzing individuals and structuring concepts, Formal Concept Analysis (FCA) has been applied to ontology matching (OM) tasks since the beginning of OM research, whereas ontological knowledge exploited in FCA-based methods is limited. This motivates the study in this paper, i.e., to empower FCA with as much as ontological knowledge as possible for identifying mappings across ontologies. We propose a method based on Formal Concept Analysis to identify and validate mappings across ontologies, including one-to-one mappings, complex mappings and correspondences between object properties. Our method, called FCA-Map, incrementally generates a total of five types of formal contexts and extracts mappings from the lattices derived. First, the token-based formal context describes how class names, labels and synonyms share lexical tokens, leading to lexical mappings (anchors) across ontologies. Second, the relation-based formal context describes how classes are in taxonomic, partonomic and disjoint relationships with the anchors, leading to positive and negative structural evidence for validating the lexical matching. Third, the positive relation-based context can be used to discover structural mappings. Afterwards, the property-based formal context describes how object properties are used in axioms to connect anchor classes across ontologies, leading to property mappings. Last, the restriction-based formal context describes co-occurrence of classes across ontologies in anonymous ancestors of anchors, from which extended structural mappings and complex mappings can be identified. Evaluation on the Anatomy, the Large Biomedical Ontologies, and the Disease and Phenotype track of the 2016 Ontology Alignment Evaluation Initiative campaign

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.