WorldWideScience

Sample records for ontologies meet industry

  1. Industry Resource Meets Creative Originality

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Accompanied with the industry value chain extension,the creative originality research and promotion are becoming the major voice of textile industry.Currently,"2010 China International Fabric Design Contest & China Textile City Recommendation Meeting" convened in Beijing ceremoniously.Vice-chairman of China Textile & Apparel Council,Wang Tiankai and head of Shaoxing city government participated in the conference and gave speech on the industry market circumstance.

  2. 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 d...... classification systems and meta data taxonomies, should be based on ontologies.......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...

  3. An Ontological Solution to Support Interoperability in the Textile Industry

    Science.gov (United States)

    Duque, Arantxa; Campos, Cristina; Jiménez-Ruiz, Ernesto; Chalmeta, Ricardo

    Significant developments in information and communication technologies and challenging market conditions have forced enterprises to adapt their way of doing business. In this context, providing mechanisms to guarantee interoperability among heterogeneous organisations has become a critical issue. Even though prolific research has already been conducted in the area of enterprise interoperability, we have found that enterprises still struggle to introduce fully interoperable solutions, especially, in terms of the development and application of ontologies. Thus, the aim of this paper is to introduce basic ontology concepts in a simple manner and to explain the advantages of the use of ontologies to improve interoperability. We will also present a case study showing the implementation of an application ontology for an enterprise in the textile/clothing sector.

  4. Green meetings in the hospitality industry

    OpenAIRE

    Rieder, Julia

    2013-01-01

    The object of this research thesis is focused mostly on green meetings in the hospitality industry to be environment friendlier. It concerns what the hospitality industry and especially hotels can do within their meeting facilities to be environment friendlier and sustainable. The research will start with an introduction and a first impression of the reasons for the appearance of green meetings. Then the theoretical framework starts with the summary of green meetings and green technology....

  5. Application of the Financial Industry Business Ontology (FIBO) for development of a financial organization ontology

    Science.gov (United States)

    Petrova, G. G.; Tuzovsky, A. F.; Aksenova, N. V.

    2017-01-01

    The article considers an approach to a formalized description and meaning harmonization for financial terms and means of semantic modeling. Ontologies for the semantic models are described with the help of special languages developed for the Semantic Web. Results of FIBO application to solution of different tasks in the Russian financial sector are given.

  6. An Ontology-based Knowledge Management System for Industry Clusters

    CERN Document Server

    Sureephong, Pradorn; Ouzrout, Yacine; Bouras, Abdelaziz

    2008-01-01

    Knowledge-based economy forces companies in the nation to group together as a cluster in order to maintain their competitiveness in the world market. The cluster development relies on two key success factors which are knowledge sharing and collaboration between the actors in the cluster. Thus, our study tries to propose knowledge management system to support knowledge management activities within the cluster. To achieve the objectives of this study, ontology takes a very important role in knowledge management process in various ways; such as building reusable and faster knowledge-bases, better way for representing the knowledge explicitly. However, creating and representing ontology create difficulties to organization due to the ambiguity and unstructured of source of knowledge. Therefore, the objectives of this paper are to propose the methodology to create and represent ontology for the organization development by using knowledge engineering approach. The handicraft cluster in Thailand is used as a case stu...

  7. Industry Resource Meets Creative Originality

    Institute of Scientific and Technical Information of China (English)

    Nie Ting

    2010-01-01

    @@ As the most authoritative professional tournament in textile industry,China International Fabric Design Contest has been held eleven years since 1999,which is indicated of Chinese textile fabrics highest level and platforms of fabrics design.

  8. Ontology-based Patent Licensing and Litigation Strategic Knowledge System for the Light Emitting Diode Industry

    OpenAIRE

    Trappey, Amy J. C.; Yu-Hui Wang; Charles V. Trappey; Chun-Yi Wu; Tzu-Hsuan Lin

    2013-01-01

    This research studies the patents, intellectual properties and licensing landscape of the Light Emitting Diode (LED) industry. The ontology of LED technology is described and defined as four major sub-technology domains. The finding provides LED companies with consistent knowledge of their own and their competitors’ patents and intellectual property rights (IPR) ownership. Major LED companies often use their IPRs to gain and protect their market competitiveness, to form alliances, and to crea...

  9. A Tailored Ontology Supporting Sensor Implementation for the Maintenance of Industrial Machines.

    Science.gov (United States)

    Maleki, Elaheh; Belkadi, Farouk; Ritou, Mathieu; Bernard, Alain

    2017-09-08

    The longtime productivity of an industrial machine is improved by condition-based maintenance strategies. To do this, the integration of sensors and other cyber-physical devices is necessary in order to capture and analyze a machine's condition through its lifespan. Thus, choosing the best sensor is a critical step to ensure the efficiency of the maintenance process. Indeed, considering the variety of sensors, and their features and performance, a formal classification of a sensor's domain knowledge is crucial. This classification facilitates the search for and reuse of solutions during the design of a new maintenance service. Following a Knowledge Management methodology, the paper proposes and develops a new sensor ontology that structures the domain knowledge, covering both theoretical and experimental sensor attributes. An industrial case study is conducted to validate the proposed ontology and to demonstrate its utility as a guideline to ease the search of suitable sensors. Based on the ontology, the final solution will be implemented in a shared repository connected to legacy CAD (computer-aided design) systems. The selection of the best sensor is, firstly, obtained by the matching of application requirements and sensor specifications (that are proposed by this sensor repository). Then, it is refined from the experimentation results. The achieved solution is recorded in the sensor repository for future reuse. As a result, the time and cost of the design process of new condition-based maintenance services is reduced.

  10. A Tailored Ontology Supporting Sensor Implementation for the Maintenance of Industrial Machines

    Directory of Open Access Journals (Sweden)

    Elaheh Maleki

    2017-09-01

    Full Text Available The longtime productivity of an industrial machine is improved by condition-based maintenance strategies. To do this, the integration of sensors and other cyber-physical devices is necessary in order to capture and analyze a machine’s condition through its lifespan. Thus, choosing the best sensor is a critical step to ensure the efficiency of the maintenance process. Indeed, considering the variety of sensors, and their features and performance, a formal classification of a sensor’s domain knowledge is crucial. This classification facilitates the search for and reuse of solutions during the design of a new maintenance service. Following a Knowledge Management methodology, the paper proposes and develops a new sensor ontology that structures the domain knowledge, covering both theoretical and experimental sensor attributes. An industrial case study is conducted to validate the proposed ontology and to demonstrate its utility as a guideline to ease the search of suitable sensors. Based on the ontology, the final solution will be implemented in a shared repository connected to legacy CAD (computer-aided design systems. The selection of the best sensor is, firstly, obtained by the matching of application requirements and sensor specifications (that are proposed by this sensor repository. Then, it is refined from the experimentation results. The achieved solution is recorded in the sensor repository for future reuse. As a result, the time and cost of the design process of new condition-based maintenance services is reduced.

  11. A standards-based ontology and support for Big Data Analytics in the insurance industry

    Directory of Open Access Journals (Sweden)

    Dimitrios A. Koutsomitropoulos

    2017-06-01

    Full Text Available Standardization efforts have led to the emergence of conceptual models in the insurance industry. Simultaneously, the proliferation of digital information poses new challenges for the efficient management and analysis of available data. Based on the property and casualty data model, we propose an OWL ontology to represent insurance processes and to map large data volumes collected in traditional data stores. By the virtue of reasoning, we demonstrate a set of semantic queries using the ontology vocabulary that can simplify analytics and deduce implicit facts from these data. We compare this mapping approach to data in native RDF format, as in a triple store. As proof-of-concept, we use a large anonymized dataset for car policies from an actual insurance company.

  12. Engineering Ontologies

    OpenAIRE

    Borst, Pim; Akkermans, Hans; Top, Jan

    1997-01-01

    We analyse the construction as well as the role of ontologies in knowledge sharing and reuse for complex industrial applications. In this article, the practical use of ontologies in large-scale applications not restricted to knowledge-based systems is demonstrated, for the domain of engineering systems modelling, simulation and design. A general and formal ontology, called PHYSSYS, for dynamic physical systems is presented and its structuring principles are discussed. We show how the PHYSSYS ...

  13. Engineering Ontologies

    NARCIS (Netherlands)

    Borst, Pim; Akkermans, Hans; Top, Jan

    1997-01-01

    We analyse the construction as well as the role of ontologies in knowledge sharing and reuse for complex industrial applications. In this article, the practical use of ontologies in large-scale applications not restricted to knowledge-based systems is demonstrated, for the domain of engineering syst

  14. 75 FR 14564 - Dairy Industry Advisory Committee; Public Meeting

    Science.gov (United States)

    2010-03-26

    ... Farm Service Agency Dairy Industry Advisory Committee; Public Meeting AGENCY: Farm Service Agency, USDA..., the Farm Service Agency (FSA) announces a public meeting of the newly established Dairy Industry Advisory Committee (Dairy Committee) to review the current state of the dairy industry, discuss...

  15. Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy

    Directory of Open Access Journals (Sweden)

    Hakenberg Jörg

    2009-01-01

    Full Text Available Abstract Background Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as simple terminologies, without making use of the ontology structure or the semantic similarity between terms. Another useful source of information for disambiguation are metadata. Here, we systematically compare three approaches to word sense disambiguation, which use ontologies and metadata, respectively. Results The 'Closest Sense' method assumes that the ontology defines multiple senses of the term. It computes the shortest path of co-occurring terms in the document to one of these senses. The 'Term Cooc' method defines a log-odds ratio for co-occurring terms including co-occurrences inferred from the ontology structure. The 'MetaData' approach trains a classifier on metadata. It does not require any ontology, but requires training data, which the other methods do not. To evaluate these approaches we defined a manually curated training corpus of 2600 documents for seven ambiguous terms from the Gene Ontology and MeSH. All approaches over all conditions achieve 80% success rate on average. The 'MetaData' approach performed best with 96%, when trained on high-quality data. Its performance deteriorates as quality of the training data decreases. The 'Term Cooc' approach performs better on Gene Ontology (92% success than on MeSH (73% success as MeSH is not a strict is-a/part-of, but rather a loose is-related-to hierarchy. The 'Closest Sense' approach achieves on average 80% success rate. Conclusion Metadata is valuable for disambiguation, but requires high quality training data. Closest Sense requires no training, but a large, consistently modelled ontology, which are two opposing conditions. Term Cooc achieves greater 90

  16. 76 FR 4611 - Dairy Industry Advisory Committee; Public Meeting

    Science.gov (United States)

    2011-01-26

    ... Farm Service Agency Dairy Industry Advisory Committee; Public Meeting AGENCY: Farm Service Agency, USDA..., the Farm Service Agency (FSA) announces a public meeting of the Dairy Industry Advisory Committee (Dairy Committee) to review and approve the final recommendations to the Secretary of Agriculture....

  17. 76 FR 8998 - Dairy Industry Advisory Committee; Public Meeting

    Science.gov (United States)

    2011-02-16

    ... Farm Service Agency Dairy Industry Advisory Committee; Public Meeting AGENCY: Farm Service Agency, USDA..., the Farm Service Agency (FSA) announces a public meeting of the Dairy Industry Advisory Committee (Dairy Committee) to review and approve the final recommendations to the Secretary of Agriculture....

  18. Ontology-based Patent Licensing and Litigation Strategic Knowledge System for the Light Emitting Diode Industry

    Directory of Open Access Journals (Sweden)

    Amy J.C. Trappey

    2013-08-01

    Full Text Available This research studies the patents, intellectual properties and licensing landscape of the Light Emitting Diode (LED industry. The ontology of LED technology is described and defined as four major sub-technology domains. The finding provides LED companies with consistent knowledge of their own and their competitors’ patents and intellectual property rights (IPR ownership. Major LED companies often use their IPRs to gain and protect their market competitiveness, to form alliances, and to create patent licensing or cross-licensing strategies. Newly established LED technology companies competing with global industry leaders face many challenges unaddressed in the research literature. This research focuses on the empirical and quantitative analysis of historical IP and patent related conduct in relation to corporate strategy. Based on the heuristic rules derived from historical conduct, the research establishes a standardized analytical procedure to use in the evaluation of patent licensing and litigation. The results help researchers effectively and consistently analyze their technical capabilities, evaluate their patent licensing strategies, and review litigation in view of the LED-related IP and patent marketplace.

  19. China Mobile Phone Industry CEO Annual Meeting Opening in November

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ 2006 China Mobile Phone Industry CEO Annual Meeting (www.cmqc.org.cn) will open at Beijing State Guest Hotel On November 1. By that time, over 300 CEO will gather there to contend about the theme of this annual meeting "The World Competitiveness of China Mobile Industry Right Territory", view the unforgettable evening of "2006 Wisdom Sharing Brainstorming, 2007 Perspective Plan Hand in Hand".

  20. Industrial Health—Meeting the Challenge*

    Science.gov (United States)

    Meiklejohn, A.

    1959-01-01

    The modern industrial system had its origin in England just over 200 years ago. This period historically is referred to as the Industrial Revolution. It was marked by mechanical inventions in textile machinery, by advances in the manufacture of iron, and by the introduction of steam power. These, in turn, were the foundations of the factory system. In 1784 at a cotton mill at Radcliffe, near Manchester, an epidemic of malignant fever affected the operatives and spread to the surrounding population. The situation became serious and the local justices invited Dr. Thomas Percival, a leading local physician, to investigate the nature and circumstances of the outbreak. With his colleagues and leading citizens he formed the Manchester Board of Health. The Board, through authoritative reports, made recommendations for the control of such epidemics by the establishment of isolation hospitals. They also urged the need for the improvement of environmental conditions in mills and factories and for the diminution of working hours, especially for children and women. In pursuance of these objects the Government in 1802 passed the Health and Morals of Apprentices Act. This was the first Factory Act. Since then factory legislation has been greatly extended and is the basis of statutory supervision of factories and factory workers under the inspector of factories. The development of this supervision is traced with special reference to the work of the certifying surgeons, now the appointed factory doctors, and the medical inspectors. Concurrently, public health education and workmen's compensation were advanced through legislation. Since 1935 voluntary medical services have been developed in industry. These services have not been restricted to the observance of the minimum standards prescribed by statute and so have been able to pioneer advances directed to the promotion of safety, health, and welfare in factories and other places of employment. Radcliffe, Percival, and steam power

  1. Ontology or formal ontology

    Science.gov (United States)

    Žáček, Martin

    2017-07-01

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

  2. National Textile Industrial Cluster Meeting Held in Beijing Successfully

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    On the day of November 22nd, National Textile Industrial Cluster Meeting was held in the Great Hall of the People in Beijing,Du Yuzhou,president of China National Textile and Apparel Council attended and addressed,meanwhile, representatives from more than 170 textile

  3. Ontology based integration of heterogeneous structures in the energy industry; Ontologiebasierte Integration heterogener Standards in der Energiewirtschaft

    Energy Technology Data Exchange (ETDEWEB)

    Uslar, Mathias

    2010-07-01

    substations but now also is extended to the scope of distributed energy generation systems. Both large standards families have been developed by the same task committee at IEC by different working groups having different challenges and different viewpoints which led to both structural and semantic incompatibilities to be resolved. A basic harmonization on the level of data models and identifiers is no longer possible as many vendors have adopted the standards for their products. Therefore, the semantic gap has to be closed using other techniques. The approach to use ontologies in order to explicitly specify conceptualisations has spread wide in both science and industry. The goal of this work is to create a semantic description of individual standards in order to have a model and a formal specification of the standards. The next step in the aligning process is to create a mediator ontology which closes the semantic gap between two ontological representations of two or more standards by explicitly and formally stating the equivalent or similar concepts between two standards. This ontology can be used as an artifact in systems like enterprise application integration frameworks in order to provide rules and descriptions how to convert instances and, therefore, leads to an indirect practical harmonization of the standards mentioned before. (orig.)

  4. 76 FR 21712 - Meeting of the Ocean Research and Resources Advisory Industry Sub-Panel

    Science.gov (United States)

    2011-04-18

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF DEFENSE Department of the Navy Meeting of the Ocean Research and Resources Advisory Industry Sub-Panel AGENCY... Advisory Industry Sub-Panel will hold a meeting. The meeting will be open to the public. DATES: The...

  5. Performing ontology.

    Science.gov (United States)

    Aspers, Patrik

    2015-06-01

    Ontology, and in particular, the so-called ontological turn, is the topic of a recent themed issue of Social Studies of Science (Volume 43, Issue 3, 2013). Ontology, or metaphysics, is in philosophy concerned with what there is, how it is, and forms of being. But to what is the science and technology studies researcher turning when he or she talks of ontology? It is argued that it is unclear what is gained by arguing that ontology also refers to constructed elements. The 'ontological turn' comes with the risk of creating a pseudo-debate or pseudo-activity, in which energy is used for no end, at the expense of empirical studies. This text rebuts the idea of an ontological turn as foreshadowed in the texts of the themed issue. It argues that there is no fundamental qualitative difference between the ontological turn and what we know as constructivism.

  6. 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.

  7. Efficient use of data resources using the example of meetings and events industry management in Poland

    OpenAIRE

    Krzysztof Celuch

    2015-01-01

    The main objective is to present results, which determine the number, size of meetings and events, which are held in Poland in 2014 and present their economic value. In addition, the research presents the profile of participants, characteristics of meetings and material concerning the importance of meeting industry in shaping competitive position of world and Polish cities. The research presents the image of 18820 meetings and events of quantitative and qualitative characteristics and analysi...

  8. 78 FR 7306 - Energy Efficiency Program for Commercial and Industrial Equipment: Public Meeting and...

    Science.gov (United States)

    2013-02-01

    ... Meeting and Availability of the Framework Document for Commercial and Industrial Fans and Blowers AGENCY... considering energy conservation standards for commercial and industrial fans and blowers. To inform interested... Technologies Program, Mailstop EE-2J, Framework Document for Commercial and Industrial Fans and Blowers,...

  9. Smoke Stack Meets Ivory Tower: Collaborations with Local Industry.

    Science.gov (United States)

    Logan, Lawrence B.; Stampen, Jacob O.

    1985-01-01

    The results of a nationwide study of developing relationships between industry and leading public comprehensive universities are highlighted. Eight kinds of programs included consulting, industry-funded research, government-funded research, personnel exchange, industrial liaison, consortia, jointly owned laboratory facilities, and industrial…

  10. 76 FR 12211 - Government/Industry Aeronautical Charting Forum Meeting

    Science.gov (United States)

    2011-03-04

    ..., from 8:30 a.m. to 5 p.m. at Advanced Management Technology, Inc. (AMTI), 1515 Wilson Boulevard... meet April 27 and 28, 2011 from 8:30 a.m. to 5 p.m. ADDRESSES: The meeting will be hosted by Advanced Management Technology, Inc. (AMTI), 1515 Wilson Boulevard, Arlington, VA 22209. FOR FURTHER...

  11. Industrial Tourism: Where the Public Meets the Private

    NARCIS (Netherlands)

    A.H.J. Otgaar (Alexander)

    2010-01-01

    textabstractThis thesis is about the development of industrial tourism in urban regions. It presents a systematic analysis of the conditions under which companies and regions can take advantage of industrial tourism development. By combining insights from tourism, marketing, regional economics, urba

  12. 75 FR 56651 - ITS Joint Program Office; Trucking Industry Mobility & Technology Coalition Annual Meeting

    Science.gov (United States)

    2010-09-16

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF TRANSPORTATION ITS Joint Program Office; Trucking Industry Mobility & Technology Coalition Annual Meeting AGENCY... the 9th day of September 2010. John Augustine, Managing Director, ITS Joint Program Office....

  13. 75 FR 55846 - Public Meeting/Working Group With Industry on Volcanic Ash

    Science.gov (United States)

    2010-09-14

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF TRANSPORTATION Federal Aviation Administration Public Meeting/Working Group With Industry on Volcanic Ash AGENCY: Federal... meeting hosted by the FAA's Aviation Weather Group in coordination with the National Oceanic...

  14. Ontology Research

    OpenAIRE

    Welty, Christopher

    2003-01-01

    In this issue, I have collected a fairly broad, although by no means exhaustive, sampling of work in the field of ontology research. To define a field is often quite difficult; it is more a collection of people and ideas than it is a specific technology. To represent our field, I present six articles that cover several of the major thrusts of ontology research from the past decade.

  15. Effective Emotions The Enactment of a Work Ethic in the Swedish Meeting Industry

    Directory of Open Access Journals (Sweden)

    Erika Andersson Cederholm

    2010-09-01

    Full Text Available The meeting industry – an encompassing term for services related to various kinds of professional meetings, from mega-conventions to the ordinary work meetings – is increasingly consolidated and legitimated as a specific sector in the service in-dustry. New professions such as meeting designers, meeting facilitators and meet-ing consultants are emerging, promoting new knowledge in this field. By focuss-ing on processes and social interaction, and highlighting emotional dimensions of meetings, these professions pave the way for new modes of conceptualising and practising professional relationships. The intangible, emotional and playful di-mensions of social interactions are promoted as effective means to achieve eco-nomic goals, thus highlighting a professional ideal that is here called “effective emotions”. The aim of this article is to show how the work ethic promoted by the meeting industry encourages new intersections, and tensions, between the ideali-sation of the tangible/measurable/rational on the one hand and the intangi-ble/emotional/magical on the other hand, and between working life and intimate spheres. Through a discourse analysis of a Swedish corporate meeting magazine, it is shown how the distinction between work and leisure is dissolved in this spe-cific work culture, and by this, it is discussed how the meeting profession acts as a normative regulator by reinforcing ideal ways of being and interacting with oth-ers. Creativity, personal growth, reflexivity and flexibility are enacted as idealised personal assets as well as moral imperatives in the discourse of the meeting pro-fession and through the practices of various meeting techniques, thus reinforcing not merely a professional ethic but cultural ideals of being as a person as well. It is also suggested that this reinforcement may, under certain circumstances, turn into its opposite and undermine the promoted ideals, thus pointing at the impor-tance to pinpoint the

  16. Generating Application Ontologies from Reference Ontologies

    OpenAIRE

    Shaw, Marianne; Detwiler, Landon T.; Brinkley, James F.; Suciu, Dan

    2008-01-01

    The semantic web provides the possiblity of linking together large numbers of biomedical ontologies. Unfortunately, many of the biomedical ontologies that have been developed are domain-specific and do not share a common structure that will allow them to be easily combined. Reference ontologies provide the necessary ontological framework for linking together these smaller, specialized ontologies.

  17. Theory and Practice Meets in Industrial Process Design -Educational Perspective-

    Science.gov (United States)

    Aramo-Immonen, Heli; Toikka, Tarja

    Software engineer should see himself as a business process designer in enterprise resource planning system (ERP) re-engineering project. Software engineers and managers should have design dialogue. The objective of this paper is to discuss the motives to study the design research in connection of management education in order to envision and understand the soft human issues in the management context. Second goal is to develop means of practicing social skills between designers and managers. This article explores the affective components of design thinking in industrial management domain. In the conceptual part of this paper are discussed concepts of network and project economy, creativity, communication, use of metaphors, and design thinking. Finally is introduced empirical research plan and first empirical results from design method experiments among the multi-disciplined groups of the master-level students of industrial engineering and management and software engineering.

  18. 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...

  19. Ontology Localization

    OpenAIRE

    2009-01-01

    Nuestra meta principal en esta tesis es proponer una solución para construir una ontología multilingüe, a través de la localización automática de una ontología. La noción de localización viene del área de Desarrollo de Software que hace referencia a la adaptación de un producto de software a un ambiente no nativo. En la Ingeniería Ontológica, la localización de ontologías podría ser considerada como un subtipo de la localización de software en el cual el producto es un modelo compartido de un...

  20. Meeting the challenges related to material issues in chemical industries

    Indian Academy of Sciences (India)

    Baldev Raj; U Kamachi Mudali; T Jayakumar; K V Kasiviswanathn; K Natarajan

    2000-12-01

    Reliable performance and profitability are two important requirements for any chemical industry. In order to achieve high level of reliability and excellent performance, several issues related to design, materials selection, fabrication, quality assurance, transport, storage, inputs from condition monitoring, failure analysis etc. have to be adequately addressed and implemented. Technology related to nondestructive testing and monitoring of the plant is also essential for precise identification of defect sites and to take appropriate remedial decision regarding repair, replacement or modification of process conditions. The interdisciplinary holistic approach enhances the life of critical engineering components in chemical plants. Further, understanding the failure modes of the components through the analysis of failed components throws light on the choice of appropriate preventive measures to be taken well in advance, to have a control over the overall health of the plant. The failure analysis also leads to better design modification and condition monitoring methodologies, for the next generation components and plants. At the Indira Gandhi Centre for Atomic Research (IGCAR), Kalpakkam, a unique combination of the expertise in design, materials selection, fabrication, NDT development, condition monitoring, life prediction and failure analysis exists to obtain desired results for achieving high levels of reliability and performance assessment of critical engineering components in chemical industries. Case studies related to design, materials selection and fabrication aspects of critical components in nuclear fuel reprocessing plants, NDT development and condition monitoring of various components of nuclear power plants, and important failure investigations on critical engineering components in chemical and allied industries are discussed in this paper. Future directions are identified and planned approaches are briefly described.

  1. Proceedings of the DOE/Industry Sensor Working Group meeting, Austin, Texas

    Energy Technology Data Exchange (ETDEWEB)

    1988-11-01

    This paper report contains topics presented at a sensor workshop group meeting. The topics describe measuring instruments of use in the pulp and paper industry. Topics include: measurement of solids fraction; process instrumentation research for the pulp paper industry; real-time non-contact optical surface motion monitor; on-machine sensors to measure paper mechanical properties; hierarchical intelligent control of industrial processes -- an in-parallel lime kiln application; proposal for research on lignin concentration measurement in pulping liquors; and advanced polymeric sensor materials for industrial drying.

  2. Ontology Requirements Specification

    OpenAIRE

    Suárez-Figueroa, Mari Carmen; Gómez-Pérez, A.

    2012-01-01

    The goal of the ontology requirements specification activity is to state why the ontology is being built, what its intended uses are, who the end users are, and which requirements the ontology should fulfill. This chapter presents detailed methodological guidelines for specifying ontology requirements efficiently. These guidelines will help ontology engineers to capture ontology requirements and produce the ontology requirements specification document (ORSD). The ORSD will play a key role dur...

  3. 78 FR 19492 - Draft Guidance for Industry on Formal Meetings Between FDA and Biosimilar Biological Product...

    Science.gov (United States)

    2013-04-01

    ... and Biosimilar Biological Product Sponsors or Applicants; Availability AGENCY: Food and Drug... availability of a draft guidance for industry entitled ``Formal Meetings Between the FDA and Biosimilar... biosimilar biological products regulated by the Center for Drug Evaluation and Research (CDER) and the...

  4. China-Russia Enterprises' and Industrial Cooperation Promotion Committee Holding Meetings in CCPIT

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    @@ On November 17,China-Russia Enterprises' and Industrial Cooperation Promotion Committee,which is branch to China-Russia Commission of Friendship,Peace and Development held meeting in CCPIT,discussing issues confronting the Sino-Russian economic and trade exchanges.

  5. El patrimonio cultural industrial: un lugar de encuentro = Industrial heritage: a meeting point

    Directory of Open Access Journals (Sweden)

    Antonio Muñoz Carrión

    2012-09-01

    Full Text Available Resumen Un interés renovado ha ido surgiendo desde finales del siglo XX entre los demandantes de cultura de las sociedades desarrolladas: comprender algunos de los eslabones de la cadena que nos ha conducido a los niveles de calidad de vida que hemos alcanzado, especialmente aquellos en los que están implicadas directamente las diferentes tecnologías. Cada vez existe mayor interés por aprender a reconocer cómo han surgido esas tecnologías, comprender el papel que han desempeñado en la configuración de nuestro entorno social en momentos anteriores, cuando eran más simples y recientemente descubrir el grado de dependencia que les tributamos. Palabras clave: Patrimonio industrial, espacio industrial, cultura industrial Abstract A renewed interest has been growing from the end of the XX’s century within the culture’s petitioners in the developed society: understand about some of the links of the chain that has brought us to the quality of life that we have reached, especially those who are involved directly in different technologies. There’s a higher interest to learn how those technologies have rose, to understand the role that they have played in the configuration of our social environment, time ago, when they were simpler, and lately, to find the dependence degree that we profess to them. Key words: Industrial heritage, industrial space, industrial culture.

  6. Meeting Summary Advanced Light Water Reactor Fuels Industry Meeting Washington DC October 27 - 28, 2011

    Energy Technology Data Exchange (ETDEWEB)

    Not Listed

    2011-11-01

    The Advanced LWR Fuel Working Group first met in November of 2010 with the objective of looking 20 years ahead to the role that advanced fuels could play in improving light water reactor technology, such as waste reduction and economics. When the group met again in March 2011, the Fukushima incident was still unfolding. After the March meeting, the focus of the program changed to determining what we could do in the near term to improve fuel accident tolerance. Any discussion of fuels with enhanced accident tolerance will likely need to consider an advanced light water reactor with enhanced accident tolerance, along with the fuel. The Advanced LWR Fuel Working Group met in Washington D.C. on October 72-18, 2011 to continue discussions on this important topic.

  7. Ontological backdrop

    DEFF Research Database (Denmark)

    Galle, Per

    2000-01-01

    In this report I keep track of ontological assumptions or implications of other OARs, introducing a system of categories and concepts that is compatible with them. The purpose was originally to keep terminology consistent throughout all OARs. However, the report also gives a condensed picture...... of the world view which underlies my current work on product modelling. It contains a justification of my view of concept exemplification, with lines traced back to Kant's work on epistemology....

  8. Building ontologies with basic formal ontology

    CERN Document Server

    Arp, Robert; Spear, Andrew D.

    2015-01-01

    In the era of "big data," science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now u...

  9. CODEX: exploration of semantic changes between ontology versions.

    Science.gov (United States)

    Hartung, Michael; Gross, Anika; Rahm, Erhard

    2012-03-15

    Life science ontologies substantially change over time to meet the requirements of their users and to include the newest domain knowledge. Thus, an important task is to know what has been modified between two versions of an ontology (diff). This diff should contain all performed changes as compact and understandable as possible. We present CODEX (Complex Ontology Diff Explorer), a tool that allows determining semantic changes between two versions of an ontology, which users can interactively analyze in multiple ways.

  10. 75 FR 3197 - Notice of a Public Meeting on Administration of the Business and Industry Guaranteed Loan Program

    Science.gov (United States)

    2010-01-20

    ... Rural Business-Cooperative Service Notice of a Public Meeting on Administration of the Business and Industry Guaranteed Loan Program AGENCY: Rural Business-Cooperative Service, USDA. ACTION: Notice of public... Development Mission area, will hold a public meeting entitled ``Business and Industry Guaranteed Loan...

  11. Efficient use of data resources using the example of meetings and events industry management in Poland

    Directory of Open Access Journals (Sweden)

    Krzysztof Celuch

    2015-05-01

    Full Text Available The main objective is to present results, which determine the number, size of meetings and events, which are held in Poland in 2014 and present their economic value. In addition, the research presents the profile of participants, characteristics of meetings and material concerning the importance of meeting industry in shaping competitive position of world and Polish cities. The research presents the image of 18820 meetings and events of quantitative and qualitative characteristics and analysis of cities and regions. The contribution of the meetings industry to a state economy, estimated based on the data, is 1121,1 million PLN of value added generated in the hotel base and 141,5 million PLN in gastronomy, i.e. 1262,6 million PLN in total. The contribution to creation of jobs is 15519 employees in the hotel base and 11954 in gastronomic services, characterized by much smaller productivity than jobs in the hotel base. It gives 27473 jobs nationwide in total.

  12. Ontological Surprises

    DEFF Research Database (Denmark)

    Leahu, Lucian

    2016-01-01

    This paper investigates how we might rethink design as the technological crafting of human-machine relations in the context of a machine learning technique called neural networks. It analyzes Google’s Inceptionism project, which uses neural networks for image recognition. The surprising output of...... 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....

  13. Generating application ontologies from reference ontologies.

    Science.gov (United States)

    Shaw, Marianne; Detwiler, Landon T; Brinkley, James F; Suciu, Dan

    2008-11-06

    The semantic web provides the possiblity of linking together large numbers of biomedical ontologies. Unfortunately, many of the biomedical ontologies that have been developed are domain-specific and do not share a common structure that will allow them to be easily combined. Reference ontologies provide the necessary ontological framework for linking together these smaller, specialized ontologies. We present extensions to the semantic web query language SparQL that will allow researchers to develop application ontologies that are derived from reference ontologies. We have modified the ARQ query processor to support subqueries, recursive subqueries, and Skolem functions for node creation. We demonstrate the utility of these extensions by deriving an application ontology from the Foundational Model of Anatomy.

  14. Geothermal power for communities and industry. Lecture meeting; Geothermische Energie fuer Kommunen und Industrie. Vortragsveranstaltung

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-07-01

    Geothermal energy is utilized in many ways in Germany for heating, cooling and power generation. The first industrial-scale power generation plant was commissioned in Neustadt-Glewe, Mecklenburg, in late 2003. This marks the beginning of an era of rapid development which will make geothermal power a key element of power supply in Germany. Studies show a vast geothermal potential. This proceedings volume comprises 17 papers which illustrate the many applications of geothermal power and its legal and economic boundary conditions. (orig.)

  15. 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.

  16. 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...

  17. Simple Ontology Format (SOFT)

    Energy Technology Data Exchange (ETDEWEB)

    2011-10-01

    Simple Ontology Format (SOFT) library and file format specification provides a set of simple tools for developing and maintaining ontologies. The library, implemented as a perl module, supports parsing and verification of the files in SOFt format, operations with ontologies (adding, removing, or filtering of entities), and converting of ontologies into other formats. SOFT allows users to quickly create ontologies using only a basic text editor, verify it, and portray it in a graph layout system using customized styles.

  18. 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

  19. Datamining with Ontologies.

    Science.gov (United States)

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

    2016-01-01

    The use of ontologies has increased rapidly over the past decade and they now provide a key component of most major databases in biology and biomedicine. Consequently, datamining over these databases benefits from considering the specific structure and content of ontologies, and several methods have been developed to use ontologies in datamining applications. Here, we discuss the principles of ontology structure, and datamining methods that rely on ontologies. The impact of these methods in the biological and biomedical sciences has been profound and is likely to increase as more datasets are becoming available using common, shared ontologies.

  20. A Spiral Step-by-Step Educational Method for Cultivating Competent Embedded System Engineers to Meet Industry Demands

    Science.gov (United States)

    Jing,Lei; Cheng, Zixue; Wang, Junbo; Zhou, Yinghui

    2011-01-01

    Embedded system technologies are undergoing dramatic change. Competent embedded system engineers are becoming a scarce resource in the industry. Given this, universities should revise their specialist education to meet industry demands. In this paper, a spirally tight-coupled step-by-step educational method, based on an analysis of industry…

  1. A Spiral Step-by-Step Educational Method for Cultivating Competent Embedded System Engineers to Meet Industry Demands

    Science.gov (United States)

    Jing,Lei; Cheng, Zixue; Wang, Junbo; Zhou, Yinghui

    2011-01-01

    Embedded system technologies are undergoing dramatic change. Competent embedded system engineers are becoming a scarce resource in the industry. Given this, universities should revise their specialist education to meet industry demands. In this paper, a spirally tight-coupled step-by-step educational method, based on an analysis of industry…

  2. The foundational ontology library ROMULUS

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-09-01

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

  3. 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.

  4. 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.

  5. OBML - Ontologies in Biomedicine and Life Sciences.

    Science.gov (United States)

    Herre, Heinrich; Hoehndorf, Robert; Kelso, Janet; Loebe, Frank; Schulz, Stefan

    2011-08-09

    The OBML 2010 workshop, held at the University of Mannheim on September 9-10, 2010, is the 2nd in a series of meetings organized by the Working Group "Ontologies in Biomedicine and Life Sciences" of the German Society of Computer Science (GI) and the German Society of Medical Informatics, Biometry and Epidemiology (GMDS). Integrating, processing and applying the rapidly expanding information generated in the life sciences - from public health to clinical care and molecular biology - is one of the most challenging problems that research in these fields is facing today. As the amounts of experimental data, clinical information and scientific knowledge increase, there is a growing need to promote interoperability of these resources, support formal analyses, and to pre-process knowledge for further use in problem solving and hypothesis formulation.The OBML workshop series pursues the aim of gathering scientists who research topics related to life science ontologies, to exchange ideas, discuss new results and establish relationships. The OBML group promotes the collaboration between ontologists, computer scientists, bio-informaticians and applied logicians, as well as the cooperation with physicians, biologists, biochemists and biometricians, and supports the establishment of this new discipline in research and teaching. Research topics of OBML 2010 included medical informatics, Semantic Web applications, formal ontology, bio-ontologies, knowledge representation as well as the wide range of applications of biomedical ontologies to science and medicine. A total of 14 papers were presented, and from these we selected four manuscripts for inclusion in this special issue.An interdisciplinary audience from all areas related to biomedical ontologies attended OBML 2010. In the future, OBML will continue as an annual meeting that aims to bridge the gap between theory and application of ontologies in the life sciences. The next event emphasizes the special topic of the ontology

  6. The geothermal partnership: Industry, utilities, and government meeting the challenges of the 90's

    Energy Technology Data Exchange (ETDEWEB)

    1991-01-01

    Each year the Geothermal Division of the US Department of Energy conducts an in-depth review of its entire geothermal R D program. The conference serves several purposes: a status report on current R D activities, an assessment of progress and problems, a review of management issues, and a technology transfer opportunity between DOE and the US geothermal community. This year's conference, Program Review IX, was held in San Francisco on March 19--21, 1991. The theme of this review was The Geothermal Partnership -- Industry, Utilities, and Government Meeting the Challenges of the 90's.'' The importance of this partnership has increased markedly as demands for improved technology must be balanced with available research resources. By working cooperatively, the geothermal community, including industry, utilities, DOE, and other state and federal agencies, can more effectively address common research needs. The challenge currently facing the geothermal partnership is to strengthen the bonds that ultimately will enhance opportunities for future development of geothermal resources. Program Review IX consisted of eight sessions including an opening session. The seven technical sessions included presentations by the relevant field researchers covering DOE-sponsored R D in hydrothermal, hot dry rock, and geopressured energy and the progress associated with the Long Valley Exploratory Well. Individual papers have been cataloged separately.

  7. 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.

  8. 77 FR 43416 - Notice of Meeting of the Industry Trade Advisory Committee on Small and Minority Business (ITAC-11)

    Science.gov (United States)

    2012-07-24

    .... Small Business Administration State Trade and Export Promotion (STEP) Grants by San Diego-area business... Business (ITAC-11) AGENCY: Office of the United States Trade Representative. ACTION: Notice of a partially opened meeting. SUMMARY: The Industry Trade Advisory Committee on Small and Minority Business...

  9. 76 FR 66040 - Announcement of Meeting To Explore Feasibility of Establishing a NIST/Industry Consortium on...

    Science.gov (United States)

    2011-10-25

    ... National Institute of Standards and Technology Announcement of Meeting To Explore Feasibility of Establishing a NIST/Industry Consortium on ``Concrete Rheology: Enabling Metrology (CREME)'' AGENCY: National... Institute of Standards and Technology (NIST) invites interested parties to attend a pre-consortium...

  10. Primer on Ontologies.

    Science.gov (United States)

    Hastings, Janna

    2017-01-01

    As molecular biology has increasingly become a data-intensive discipline, ontologies have emerged as an essential computational tool to assist in the organisation, description and analysis of data. Ontologies describe and classify the entities of interest in a scientific domain in a computationally accessible fashion such that algorithms and tools can be developed around them. The technology that underlies ontologies has its roots in logic-based artificial intelligence, allowing for sophisticated automated inference and error detection. This chapter presents a general introduction to modern computational ontologies as they are used in biology.

  11. Kuhn's Ontological Relativism.

    Science.gov (United States)

    Sankey, Howard

    2000-01-01

    Discusses Kuhn's model of scientific theory change. Documents Kuhn's move away from conceptual relativism and rational relativism. Provides an analysis of his present ontological form of relativism. (CCM)

  12. Meetings

    Institute of Scientific and Technical Information of China (English)

    HUGuowen; QINPeng; FENGYilun

    1994-01-01

    The International Workshop on Rice Sheath Bright Management was held in the Experimental Farm of CNRRI from Oct 10 to 15, 1993. The workshop was sponsored by IRRI and co-hosted by CNRRI. About 38 scientists from IRRI, Indonesia, South Korea, Thailand, Vietnam,Japan, Great Britain, France, Malaysia and P. R. China attended the meeting.

  13. DECHEMA annual meetings `96. Summaries. Vol. 2. Plenary papers, technical meeting on safety technology, technical meeting on computer applications in the chemical industry, technical meeting on membranes in process technology, technical meeting on dispersions, technical meeting on reaction technology, information day on sonochemistry; DECHEMA-Jahrestagungen `96. Kurzfassungen. Bd. 2. Plenarvortraege - Fachtreffen Sicherheitstechnik - Fachtreffen Computeranwendung in der Chemischen Industrie - Fachtreffen Membranen in der Prozesstechnik - Fachtreffen Dispersionen - Fachtreffen Reaktionstechnik - Informationstag Sonochemie

    Energy Technology Data Exchange (ETDEWEB)

    Kreysa, G. [ed.

    1996-08-01

    This volume comprises the programme of the annual meeting and the summaries of the lectures given. The following subjects were discussed: Safety technology, computer applications in the chemical industry, membranes in process technology, dispersions, reaction technology, sonochemistry. (SR) [Deutsch] Dieser Band enthaelt das Programm der Jahrestagung und die Kurzfassungen der Vortraege. Folgende Gebiete werden behandelt: Sicherheitstechnik, Computeranwendungen in der Chemischen Industrie, Membranen in der Prozesstechnik, Dispersionen, Reaktionstechnik, Sonochemie. (SR)

  14. 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...

  15. The Ontology of Disaster.

    Science.gov (United States)

    Thompson, Neil

    1995-01-01

    Explores some key existential or ontological concepts to show their applicability to the complex area of disaster impact as it relates to health and social welfare practice. Draws on existentialist philosophy, particularly that of John Paul Sartre, and introduces some key ontological concepts to show how they specifically apply to the experience…

  16. 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…

  17. 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…

  18. The Ontology of Disaster.

    Science.gov (United States)

    Thompson, Neil

    1995-01-01

    Explores some key existential or ontological concepts to show their applicability to the complex area of disaster impact as it relates to health and social welfare practice. Draws on existentialist philosophy, particularly that of John Paul Sartre, and introduces some key ontological concepts to show how they specifically apply to the experience…

  19. Determining Fitness-For-Use of Ontologies Through Change Management, Versioning and Publication Best Practices

    Science.gov (United States)

    West, P.; Zednik, S.; Fu, L.; Ma, X.; Fox, P. A.

    2015-12-01

    There is a large and growing number of domain ontologies available for researchers to leverage in their applications. When evaluating the use of an ontology it is important to not only consider whether the concepts and relationships defined in the ontology meet the requirements for purpose of use, but also how the change management, versioning and publication practices followed by the ontology publishers affect the maturity, stability, and long-term fitness-for-use of the ontology. In this presentation we share our experiences and a list of best practices we have developed when determining fitness for use of existing ontologies, and the process we follow when developing of our own ontologies and extensions to existing ontologies. Our experience covers domains such as solar terrestrial physics, geophysics and oceanography; and the use of general purpose ontologies such as those with representations of people, organizations, data catalogs, observations and measurements and provenance. We will cover how we determine ontology scope, manage ontology change, specify ontology version, and what best practices we follow for ontology publication and use. The implications of following these best practices is that the ontologies we use and develop are mature, stable, have a well-defined scope, and are published in accordance with linked data principles.

  20. Ayurveda research: Ontological challenges.

    Science.gov (United States)

    Nayak, Jayakrishna

    2012-01-01

    Collaborative research involving Ayurveda and the current sciences is undoubtedly an imperative and is emerging as an exciting horizon, particularly in basic sciences. Some work in this direction is already going on and outcomes are awaited with bated breath. For instance the 'ASIIA (A Science Initiative In Ayurveda)' projects of Dept of Science and Technology, Govt of India, which include studies such as Ayurvedic Prakriti and Genetics. Further intense and sustained collaborative research needs to overcome a subtle and fundamental challenge-the ontologic divide between Ayurveda and all the current sciences. Ontology, fundamentally, means existence; elaborated, ontology is a particular perspective of an object of existence and the vocabulary developed to share that perspective. The same object of existence is susceptible to several ontologies. Ayurveda and modern biomedical as well as other sciences belong to different ontologies, and as such, collaborative research cannot be carried out at required levels until a mutually acceptable vocabulary is developed.

  1. Ayurveda research: Ontological challenges

    Directory of Open Access Journals (Sweden)

    Jayakrishna Nayak

    2012-01-01

    Full Text Available Collaborative research involving Ayurveda and the current sciences is undoubtedly an imperative and is emerging as an exciting horizon, particularly in basic sciences. Some work in this direction is already going on and outcomes are awaited with bated breath. For instance the ′ASIIA (A Science Initiative In Ayurveda′ projects of Dept of Science and Technology, Govt of India, which include studies such as Ayurvedic Prakriti and Genetics. Further intense and sustained collaborative research needs to overcome a subtle and fundamental challenge-the ontologic divide between Ayurveda and all the current sciences. Ontology, fundamentally, means existence; elaborated, ontology is a particular perspective of an object of existence and the vocabulary developed to share that perspective. The same object of existence is susceptible to several ontologies. Ayurveda and modern biomedical as well as other sciences belong to different ontologies, and as such, collaborative research cannot be carried out at required levels until a mutually acceptable vocabulary is developed.

  2. The neurological disease ontology.

    Science.gov (United States)

    Jensen, Mark; Cox, Alexander P; Chaudhry, Naveed; Ng, Marcus; Sule, Donat; Duncan, William; Ray, Patrick; Weinstock-Guttman, Bianca; Smith, Barry; Ruttenberg, Alan; Szigeti, Kinga; Diehl, Alexander D

    2013-12-06

    We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer's disease, multiple sclerosis, and stroke. ND is implemented in OWL 2 and currently has more than 450 terms that refer to and describe various aspects of neurological diseases. ND directly imports the development version of OGMS, which uses BFO 2. Term development in ND has primarily extended the OGMS terms 'disease', 'diagnosis', 'disease course', and 'disorder'. We have imported and utilize over 700 classes from related ontology efforts including the Foundational Model of Anatomy, Ontology for Biomedical Investigations, and Protein Ontology. ND terms are annotated with ontology metadata such as a label (term name), term editors, textual definition, definition source, curation status, and alternative terms (synonyms). Many terms have logical definitions in addition to these annotations. Current development has focused on the establishment of the upper-level structure of the ND hierarchy, as well as on the representation of Alzheimer's disease, multiple sclerosis, and stroke. The ontology is available as a version-controlled file at http://code.google.com/p/neurological-disease-ontology along with a discussion list and an issue tracker. ND seeks to provide a formal foundation for the representation of clinical and research data

  3. 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 ...

  4. Ontologies in biological data visualization.

    Science.gov (United States)

    Carpendale, Sheelagh; Chen, Min; Evanko, Daniel; Gehlenborg, Nils; Gorg, Carsten; Hunter, Larry; Rowland, Francis; Storey, Margaret-Anne; Strobelt, Hendrik

    2014-01-01

    In computer science, an ontology is essentially a graph-based knowledge representation in which each node corresponds to a concept and each edge specifies a relation between two concepts. Ontological development in biology can serve as a focus to discuss the challenges and possible research directions for ontologies in visualization. The principle challenges are the dynamic and evolving nature of ontologies, the ever-present issue of scale, the diversity and richness of the relationships in ontologies, and the need to better understand the relationship between ontologies and the data analysis tasks scientists wish to support. Research directions include visualizing ontologies; visualizing semantically or ontologically annotated texts, documents, and corpora; automated generation of visualizations using ontologies; and visualizing ontological context to support search. Although this discussion uses issues of ontologies in biological data visualization as a springboard, these topics are of general relevance to visualization.

  5. Ontologies for software engineering and software technology

    CERN Document Server

    Calero, Coral; Piattini, Mario

    2006-01-01

    Covers two applications of ontologies in software engineering and software technology: sharing knowledge of the problem domain and using a common terminology among all stakeholders; and filtering the knowledge when defining models and metamodels. This book is of benefit to software engineering researchers in both academia and industry.

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

    NARCIS (Netherlands)

    J.W. Stoelhorst

    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 speci

  7. A rapid place name locating algorithm based on ontology qualitative retrieval, ranking and recommendation

    Science.gov (United States)

    Fan, Hong; Zhu, Anfeng; Zhang, Weixia

    2015-12-01

    In order to meet the rapid positioning of 12315 complaints, aiming at the natural language expression of telephone complaints, a semantic retrieval framework is proposed which is based on natural language parsing and geographical names ontology reasoning. Among them, a search result ranking and recommended algorithms is proposed which is regarding both geo-name conceptual similarity and spatial geometry relation similarity. The experiments show that this method can assist the operator to quickly find location of 12,315 complaints, increased industry and commerce customer satisfaction.

  8. New frontiers in oilseed biotechnology: meeting the global demand for vegetable oils for food, feed, biofuel, and industrial applications.

    Science.gov (United States)

    Lu, Chaofu; Napier, Johnathan A; Clemente, Thomas E; Cahoon, Edgar B

    2011-04-01

    Vegetable oils have historically been a valued commodity for food use and to a lesser extent for non-edible applications such as detergents and lubricants. The increasing reliance on biodiesel as a transportation fuel has contributed to rising demand and higher prices for vegetable oils. Biotechnology offers a number of solutions to meet the growing need for affordable vegetable oils and vegetable oils with improved fatty acid compositions for food and industrial uses. New insights into oilseed metabolism and its transcriptional control are enabling biotechnological enhancement of oil content and quality. Alternative crop platforms and emerging technologies for metabolic engineering also hold promise for meeting global demand for vegetable oils and for enhancing nutritional, industrial, and biofuel properties of vegetable oils. Copyright © 2010 Elsevier Ltd. All rights reserved.

  9. [ ] Toward an Ontology of Finitude

    Directory of Open Access Journals (Sweden)

    Julia Hölzl

    2011-09-01

    Full Text Available Hölzl palpates an ontology of fracture. Unlike original ontologies that are concerned with essence rather than being, the ontology proposed here does not believe in its originality. This project is concerned with becoming as such rather than with its Wesen. With the indefinite striving for remaining in itself. This ontology is a fissure, fissuring itself.

  10. 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

  11. The sexual and ontology

    Directory of Open Access Journals (Sweden)

    Zupančič Alenka

    2014-01-01

    Full Text Available This paper explores some of the crucial ontological implications of the psychoanalytic theory of sexuality in its Freudo-Lacanian orientation. As irreducible to different sexual practices and contents, the concept of sexuality obtains conceptual weight that makes it particularly relevant for philosophical ontological thinking. Starting from the hypothesis that something about sexuality is constitutively unconscious - that is to say, existing only in the form of the unconscious - the paper points at the singular short-circuit of the epistemological and ontological level which is at work in psychoanalytic theory, and which cannot be neglected in philosophical examination of the relation between knowledge and being.

  12. 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.

  13. Towards automated biomedical ontology harmonization.

    Science.gov (United States)

    Uribe, Gustavo A; Lopez, Diego M; Blobel, Bernd

    2014-01-01

    The use of biomedical ontologies is increasing, especially in the context of health systems interoperability. Ontologies are key pieces to understand the semantics of information exchanged. However, given the diversity of biomedical ontologies, it is essential to develop tools that support harmonization processes amongst them. Several algorithms and tools are proposed by computer scientist for partially supporting ontology harmonization. However, these tools face several problems, especially in the biomedical domain where ontologies are large and complex. In the harmonization process, matching is a basic task. This paper explains the different ontology harmonization processes, analyzes existing matching tools, and proposes a prototype of an ontology harmonization service. The results demonstrate that there are many open issues in the field of biomedical ontology harmonization, such as: overcoming structural discrepancies between ontologies; the lack of semantic algorithms to automate the process; the low matching efficiency of existing algorithms; and the use of domain and top level ontologies in the matching process.

  14. 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…

  15. 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…

  16. The design ontology

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  17. Ontologies for Bioinformatics

    Directory of Open Access Journals (Sweden)

    Agnieszka Leszczynski

    2008-01-01

    Full Text Available The past twenty years have witnessed an explosion of biological data in diverse database formats governed by heterogeneous infrastructures. Not only are semantics (attribute terms different in meaning across databases, but their organization varies widely. Ontologies are a concept imported from computing science to describe different conceptual frameworks that guide the collection, organization and publication of biological data. An ontology is similar to a paradigm but has very strict implications for formatting and meaning in a computational context. The use of ontologies is a means of communicating and resolving semantic and organizational differences between biological databases in order to enhance their integration. The purpose of interoperability (or sharing between divergent storage and semantic protocols is to allow scientists from around the world to share and communicate with each other. This paper describes the rapid accumulation of biological data, its various organizational structures, and the role that ontologies play in interoperability.

  18. Mechanisms in biomedical ontology

    National Research Council Canada - National Science Library

    Röhl, Johannes

    2012-01-01

    .... Taking some hints from an "ontology of devices" I suggest as a general approach for this task the introduction of functional kinds and functional parts by which the particular relations between a mechanism and its components can be captured.

  19. An Ontology of Gene

    OpenAIRE

    Masuya, Hiroshi; Mizoguchi, Riichiro

    2012-01-01

    The concept of a gene was established in the era of classical genetics and is now essential for life science for elucidating the molecular basis of the coding of genetic information necessary to realize the body of an organism and its biological functions. However, an ontology fully representing multiple aspects of a gene is still not available. In this study, we dissected the biological and ontological definitions of bearers of genetic information, including genes and alleles. Based on this ...

  20. Ontology alignment with OLA

    OpenAIRE

    Euzenat, Jérôme; Loup, David; Touzani, Mohamed; Valtchev, Petko

    2004-01-01

    euzenat2004d; International audience; Using ontologies is the standard way to achieve interoperability of heterogeneous systems within the Semantic web. However, as the ontologies underlying two systems are not necessarily compatible, they may in turn need to be aligned. Similarity-based approaches to alignment seems to be both powerful and flexible enough to match the expressive power of languages like OWL. We present an alignment tool that follows the similarity-based paradigm, called OLA. ...

  1. Ontology Usage at ZFIN

    CERN Document Server

    Howe, Doug

    2010-01-01

    The Zebrafish Model Organism Database (ZFIN) provides a Web resource of zebrafish genomic, genetic, developmental, and phenotypic data. Four different ontologies are currently used to annotate data to the most specific term available facilitating a better comparison between inter-species data. In addition, ontologies are used to help users find and cluster data more quickly without the need of knowing the exact technical name for a term.

  2. Applications of ontology design patterns in biomedical ontologies.

    Science.gov (United States)

    Mortensen, Jonathan M; Horridge, Matthew; Musen, Mark A; Noy, Natalya F

    2012-01-01

    Ontology design patterns (ODPs) are a proposed solution to facilitate ontology development, and to help users avoid some of the most frequent modeling mistakes. ODPs originate from similar approaches in software engineering, where software design patterns have become a critical aspect of software development. There is little empirical evidence for ODP prevalence or effectiveness thus far. In this work, we determine the use and applicability of ODPs in a case study of biomedical ontologies. We encoded ontology design patterns from two ODP catalogs. We then searched for these patterns in a set of eight ontologies. We found five patterns of the 69 patterns. Two of the eight ontologies contained these patterns. While ontology design patterns provide a vehicle for capturing formally reoccurring models and best practices in ontology design, we show that today their use in a case study of widely used biomedical ontologies is limited.

  3. Applications of Ontology Design Patterns in Biomedical Ontologies

    Science.gov (United States)

    Mortensen, Jonathan M.; Horridge, Matthew; Musen, Mark A.; Noy, Natalya F.

    2012-01-01

    Ontology design patterns (ODPs) are a proposed solution to facilitate ontology development, and to help users avoid some of the most frequent modeling mistakes. ODPs originate from similar approaches in software engineering, where software design patterns have become a critical aspect of software development. There is little empirical evidence for ODP prevalence or effectiveness thus far. In this work, we determine the use and applicability of ODPs in a case study of biomedical ontologies. We encoded ontology design patterns from two ODP catalogs. We then searched for these patterns in a set of eight ontologies. We found five patterns of the 69 patterns. Two of the eight ontologies contained these patterns. While ontology design patterns provide a vehicle for capturing formally reoccurring models and best practices in ontology design, we show that today their use in a case study of widely used biomedical ontologies is limited. PMID:23304337

  4. ENRICHMENT OF OBO ONTOLOGIES

    Science.gov (United States)

    Bada, Michael; Hunter, Lawrence

    2006-01-01

    This paper describes a frame-based integration of the three GO subontologies, the Chemicals of Biological Interest ontology (ChEBI), and the Cell Type Ontology (CTO) in which relationships between elements of the ontologies are modeled in a way that better captures the relational semantics between biological concepts represented by the terms, rather than between the terms themselves, than previous frame-based efforts. We also describe a methodology for creating suggested enriching assertions of the form (subject, relationship, object) by identifying patterns in GO terms, mapping these patterns and subpatterns to relationships, matching concepts to these patterns and subpatterns, and integrating these assertions into the ontologies. Using this methodology, a large number of reliable assertions linking previously unlinked OBO terms using a wide variety of specific, hierarchically arranged relationships were created: A predicted assertion was made for 62% of GO terms that matched one of 31 patterns, and 97% of these predicted assertions were assessed to be valid; a further 429 assertions (corresponding to 6% of the matching terms) were manually created, resulting in an initial set of 4,497 assertions. Furthermore, this methodology programmatically integrates assertions into a base ontology such that each assertion is fully consistent with respect to higher (i.e., more general) relevant class and slot levels. Such an integration is absent from previous compositional efforts, and we argue its necessity for the creation of coherent biological ontologies when linking previously unlinked terms. PMID:17011833

  5. The Ontology of the Gene Ontology

    Science.gov (United States)

    Smith, Barry; Williams, Jennifer; Steffen, Schulze-Kremer

    2003-01-01

    The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. PMID:14728245

  6. Data Mining Ontology Development for High User Usability

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    This paper mainly introduces the development and implementation of the user-centered data mining service ontology on Universal Knowledge Grid (UKG). UKG is an ontology-based grid architecture model to build large-scale distributed knowledge discovery system on the grid. The data mining ontology services are the main service offering by UKG. It can meet the user requirements of knowledge discovery in different domains and different hierarchies and make the system exoteric, extensible and high usable. A data mining solution for money laundering is introduced.

  7. Commercial Nuclear Power Industry: Assessing and Meeting the Radiation Protection Workforce Needs.

    Science.gov (United States)

    Hiatt, Jerry W

    2017-02-01

    This paper will provide an overview of the process used by the commercial nuclear power industry in assessing the status of existing industry staffing and projecting future supply demand needs. The most recent Nuclear Energy Institute-developed "Pipeline Survey Results" will be reviewed with specific emphasis on the radiation protection specialty. Both radiation protection technician and health physicist specialties will be discussed. The industry-initiated Nuclear Uniform Curriculum Program will be reviewed as an example of how the industry has addressed the need for developing additional resources. Furthermore, the reality of challenges encountered in maintaining the needed number of health physicists will also be discussed.

  8. Efficiency Costs of Meeting Industry-Distributional Constraints under Environmental Permits and Taxes

    NARCIS (Netherlands)

    Bovenberg, A.L.; Goulder, L.H.; Gurney, D.J.

    2003-01-01

    Many pollution-related industries wield strong political influence and can e.ectively veto policy initiatives that would harm their profits.A politically realistic approach to environmental policy therefore seems to require the alleviation of significant profitlosses to these industries.The regulato

  9. Premier Wen Jiabao Chaired a State Council Executive Meeting to Review and Deploy the Program to Further Implement the Restructuring and Reinvigoration Plan for Key Industries

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    @@ Premier Wen Jiabao chaired a State Council executive meeting to review and deploy the program to further implement the restructuring and reinvigoration plan for key industries on February 24th,2010.

  10. Overview of Ontology Servers Research

    Directory of Open Access Journals (Sweden)

    Robert M. Colomb

    2007-06-01

    Full Text Available An ontology is increasingly becoming an essential tool for solving problems in many research areas. The ontology is a complex information object. It can contain millions of concepts in complex relationships. When we want to manage complex information objects, we generally turn to information systems technology. An information system intended to manage ontology is called an ontology server. The ontology server technology is at the time of writing quite immature. Therefore, this paper reviews and compares the main ontology servers that have been reported in the literatures. As a result, we point out several research questions related to server technology.

  11. Ontology-Based Retrieval of Spatially Related Objects for Location Based Services

    Science.gov (United States)

    Haav, Hele-Mai; Kaljuvee, Aivi; Luts, Martin; Vajakas, Toivo

    Advanced Location Based Service (LBS) applications have to integrate information stored in GIS, information about users' preferences (profile) as well as contextual information and information about application itself. Ontology engineering provides methods to semantically integrate several data sources. We propose an ontology-driven LBS development framework: the paper describes the architecture of ontologies and their usage for retrieval of spatially related objects relevant to the user. Our main contribution is to enable personalised ontology driven LBS by providing a novel approach for defining personalised semantic spatial relationships by means of ontologies. The approach is illustrated by an industrial case study.

  12. Ontology alignment architecture for semantic sensor Web integration.

    Science.gov (United States)

    Fernandez, Susel; Marsa-Maestre, Ivan; Velasco, Juan R; Alarcos, Bernardo

    2013-09-18

    Sensor networks are a concept that has become very popular in data acquisition and processing for multiple applications in different fields such as industrial, medicine, home automation, environmental detection, etc. Today, with the proliferation of small communication devices with sensors that collect environmental data, semantic Web technologies are becoming closely related with sensor networks. The linking of elements from Semantic Web technologies with sensor networks has been called Semantic Sensor Web and has among its main features the use of ontologies. One of the key challenges of using ontologies in sensor networks is to provide mechanisms to integrate and exchange knowledge from heterogeneous sources (that is, dealing with semantic heterogeneity). Ontology alignment is the process of bringing ontologies into mutual agreement by the automatic discovery of mappings between related concepts. This paper presents a system for ontology alignment in the Semantic Sensor Web which uses fuzzy logic techniques to combine similarity measures between entities of different ontologies. The proposed approach focuses on two key elements: the terminological similarity, which takes into account the linguistic and semantic information of the context of the entity's names, and the structural similarity, based on both the internal and relational structure of the concepts. This work has been validated using sensor network ontologies and the Ontology Alignment Evaluation Initiative (OAEI) tests. The results show that the proposed techniques outperform previous approaches in terms of precision and recall.

  13. Ontology Alignment Architecture for Semantic Sensor Web Integration

    Directory of Open Access Journals (Sweden)

    Bernardo Alarcos

    2013-09-01

    Full Text Available Sensor networks are a concept that has become very popular in data acquisition and processing for multiple applications in different fields such as industrial, medicine, home automation, environmental detection, etc. Today, with the proliferation of small communication devices with sensors that collect environmental data, semantic Web technologies are becoming closely related with sensor networks. The linking of elements from Semantic Web technologies with sensor networks has been called Semantic Sensor Web and has among its main features the use of ontologies. One of the key challenges of using ontologies in sensor networks is to provide mechanisms to integrate and exchange knowledge from heterogeneous sources (that is, dealing with semantic heterogeneity. Ontology alignment is the process of bringing ontologies into mutual agreement by the automatic discovery of mappings between related concepts. This paper presents a system for ontology alignment in the Semantic Sensor Web which uses fuzzy logic techniques to combine similarity measures between entities of different ontologies. The proposed approach focuses on two key elements: the terminological similarity, which takes into account the linguistic and semantic information of the context of the entity’s names, and the structural similarity, based on both the internal and relational structure of the concepts. This work has been validated using sensor network ontologies and the Ontology Alignment Evaluation Initiative (OAEI tests. The results show that the proposed techniques outperform previous approaches in terms of precision and recall.

  14. Human resources - meeting the challenge. An Organization of CANDU Industries perspective

    Energy Technology Data Exchange (ETDEWEB)

    Wash, M. [OCI, Organization of CANDU Industries, Pickering, Ontario (Canada)

    2008-07-01

    This paper discusses the topic of human resources in the nuclear industry. The primary drivers for new human resources are retirement or normal turnover of existing human resources base and sustained new or increased reliance on nuclear energy.

  15. Uncertainty in Ontologies: Dempster-Shafer Theory for Data Fusion Applications

    CERN Document Server

    Bellenger, Amandine

    2011-01-01

    Nowadays ontologies present a growing interest in Data Fusion applications. As a matter of fact, the ontologies are seen as a semantic tool for describing and reasoning about sensor data, objects, relations and general domain theories. In addition, uncertainty is perhaps one of the most important characteristics of the data and information handled by Data Fusion. However, the fundamental nature of ontologies implies that ontologies describe only asserted and veracious facts of the world. Different probabilistic, fuzzy and evidential approaches already exist to fill this gap; this paper recaps the most popular tools. However none of the tools meets exactly our purposes. Therefore, we constructed a Dempster-Shafer ontology that can be imported into any specific domain ontology and that enables us to instantiate it in an uncertain manner. We also developed a Java application that enables reasoning about these uncertain ontological instances.

  16. Ontology Based Access Control

    Directory of Open Access Journals (Sweden)

    Özgü CAN

    2010-02-01

    Full Text Available As computer technologies become pervasive, the need for access control mechanisms grow. The purpose of an access control is to limit the operations that a computer system user can perform. Thus, access control ensures to prevent an activity which can lead to a security breach. For the success of Semantic Web, that allows machines to share and reuse the information by using formal semantics for machines to communicate with other machines, access control mechanisms are needed. Access control mechanism indicates certain constraints which must be achieved by the user before performing an operation to provide a secure Semantic Web. In this work, unlike traditional access control mechanisms, an "Ontology Based Access Control" mechanism has been developed by using Semantic Web based policies. In this mechanism, ontologies are used to model the access control knowledge and domain knowledge is used to create policy ontologies.

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

    Science.gov (United States)

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

    2012-01-01

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

  18. OTO: Ontology Term Organizer.

    Science.gov (United States)

    Huang, Fengqiong; Macklin, James A; Cui, Hong; Cole, Heather A; Endara, Lorena

    2015-02-15

    The need to create controlled vocabularies such as ontologies for knowledge organization and access has been widely recognized in various domains. Despite the indispensable need of thorough domain knowledge in ontology construction, most software tools for ontology construction are designed for knowledge engineers and not for domain experts to use. The differences in the opinions of different domain experts and in the terminology usages in source literature are rarely addressed by existing software. OTO software was developed based on the Agile principles. Through iterations of software release and user feedback, new features are added and existing features modified to make the tool more intuitive and efficient to use for small and large data sets. The software is open source and built in Java. Ontology Term Organizer (OTO; http://biosemantics.arizona.edu/OTO/ ) is a user-friendly, web-based, consensus-promoting, open source application for organizing domain terms by dragging and dropping terms to appropriate locations. The application is designed for users with specific domain knowledge such as biology but not in-depth ontology construction skills. Specifically OTO can be used to establish is_a, part_of, synonym, and order relationships among terms in any domain that reflects the terminology usage in source literature and based on multiple experts' opinions. The organized terms may be fed into formal ontologies to boost their coverage. All datasets organized on OTO are publicly available. OTO has been used to organize the terms extracted from thirty volumes of Flora of North America and Flora of China combined, in addition to some smaller datasets of different taxon groups. User feedback indicates that the tool is efficient and user friendly. Being open source software, the application can be modified to fit varied term organization needs for different domains.

  19. Appreciating ontological struggles

    DEFF Research Database (Denmark)

    Danholt, Peter

    the world in the singular is taken for granted, but where each and every one of us may have different perspectives and understandings of the world. Latour following the work of Brazilian anthropologist Eduardo Viveiros de Castro suggests the concept of multinaturalism. Multinaturalism in contrast...... it in relation, not to Amerindian ontology vs. Euroamerican ontology as Viveiros de Castro does, but in relation to the clinical practice of diabetes treatment. I will argue that by conceiving of the encounter in the clinic between a person with diabetes and a diabetes nurse, not as a matter of treating...

  20. 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

  1. 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....

  2. Ontology development for Sufism domain

    Science.gov (United States)

    Iqbal, Rizwan

    2012-01-01

    Domain ontology is a descriptive representation of any particular domain which in detail describes the concepts in a domain, the relationships among those concepts and organizes them in a hierarchal manner. It is also defined as a structure of knowledge, used as a means of knowledge sharing to the community. An Important aspect of using ontologies is to make information retrieval more accurate and efficient. Thousands of domain ontologies from all around the world are available online on ontology repositories. Ontology repositories like SWOOGLE currently have over 1000 ontologies covering a wide range of domains. It was found that up to date there was no ontology available covering the domain of "Sufism". This unavailability of "Sufism" domain ontology became a motivation factor for this research. This research came up with a working "Sufism" domain ontology as well a framework, design of the proposed framework focuses on the resolution to problems which were experienced while creating the "Sufism" ontology. The development and working of the "Sufism" domain ontology are covered in detail in this research. The word "Sufism" is a term which refers to Islamic mysticism. One of the reasons to choose "Sufism" for ontology creation is its global curiosity. This research has also managed to create some individuals which inherit the concepts from the "Sufism" ontology. The creation of individuals helps to demonstrate the efficient and precise retrieval of data from the "Sufism" domain ontology. The experiment of creating the "Sufism" domain ontology was carried out on a tool called Protégé. Protégé is a tool which is used for ontology creation, editing and it is open source.

  3. Classifying orofacial pains: a new proposal of taxonomy based on ontology

    OpenAIRE

    Nixdorf, D.R.; DRANGSHOLT, M. T.; ETTLIN, D. A.; Gaul, C.; van der Leeuw, R.; Svensson, P.; Zakrzewska, J M; de Laat, A.; Ceusters, W.

    2011-01-01

    Propose a new taxonomy model based on ontological principles for disorders that manifest themselves through the symptom of persistent orofacial pain and are commonly seen in clinical practice and difficult to manage. Consensus meeting of eight experts from various geographic areas representing different perspectives (orofacial pain, headache, oral medicine and ontology) as an initial step towards improving the taxonomy. Ontological principles were introduced, reviewed and applied during the c...

  4. 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.

  5. COnto-Diff: generation of complex evolution mappings for life science ontologies.

    Science.gov (United States)

    Hartung, Michael; Groß, Anika; Rahm, Erhard

    2013-02-01

    Life science ontologies evolve frequently to meet new requirements or to better reflect the current domain knowledge. The development and adaptation of large and complex ontologies is typically performed collaboratively by several curators. To effectively manage the evolution of ontologies it is essential to identify the difference (Diff) between ontology versions. Such a Diff supports the synchronization of changes in collaborative curation, the adaptation of dependent data such as annotations, and ontology version management. We propose a novel approach COnto-Diff to determine an expressive and invertible diff evolution mapping between given versions of an ontology. Our approach first matches the ontology versions and determines an initial evolution mapping consisting of basic change operations (insert/update/delete). To semantically enrich the evolution mapping we adopt a rule-based approach to transform the basic change operations into a smaller set of more complex change operations, such as merge, split, or changes of entire subgraphs. The proposed algorithm is customizable in different ways to meet the requirements of diverse ontologies and application scenarios. We evaluate the proposed approach for large life science ontologies including the Gene Ontology and the NCI Thesaurus and compare it with PromptDiff. We further show how the Diff results can be used for version management and annotation migration in collaborative curation. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Multiple ontologies in action: composite annotations for biosimulation models.

    Science.gov (United States)

    Gennari, John H; Neal, Maxwell L; Galdzicki, Michal; Cook, Daniel L

    2011-02-01

    There now exists a rich set of ontologies that provide detailed semantics for biological entities of interest. However, there is not (nor should there be) a single source ontology that provides all the necessary semantics for describing biological phenomena. In the domain of physiological biosimulation models, researchers use annotations to convey semantics, and many of these annotations require the use of multiple reference ontologies. Therefore, we have developed the idea of composite annotations that access multiple ontologies to capture the physics-based meaning of model variables. These composite annotations provide the semantic expressivity needed to disambiguate the often-complex features of biosimulation models, and can be used to assist with model merging and interoperability. In this paper, we demonstrate the utility of composite annotations for model merging by describing their use within SemGen, our semantics-based model composition software. More broadly, if orthogonal reference ontologies are to meet their full potential, users need tools and methods to connect and link these ontologies. Our composite annotations and the SemGen tool provide one mechanism for leveraging multiple reference ontologies.

  7. 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…

  8. 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…

  9. "And Never the Twain Shall Meet": Investigating the Hospitality Industry-Education Relationship in Cyprus

    Science.gov (United States)

    Zopiatis, Anastasios; Constanti, Panikkos

    2007-01-01

    Purpose: The primary purpose is to investigate the relationship between hospitality education and the industry of Cyprus as it relates to students' internship practices. The mismatch between the educational experience delivered to hospitality students and the "real world" practice they experience is investigated.…

  10. 78 FR 17890 - Energy Efficiency Program for Commercial and Industrial Equipment: Public Meeting and...

    Science.gov (United States)

    2013-03-25

    .... Department of Energy, Office of Energy Efficiency and Renewable Energy, Building Technologies Program, EE-2J... CFR Part 431 RIN 1904-AC82 Energy Efficiency Program for Commercial and Industrial Equipment: Public... Terminal Heat Pumps AGENCY: Office of Energy Efficiency and Renewable Energy, Department of Energy....

  11. 78 FR 26544 - Energy Efficiency Program for Commercial and Industrial Equipment: Public Meeting and...

    Science.gov (United States)

    2013-05-07

    ... commercial and industrial fan and blower equipment that published on February 1, 2013, (78 FR 7306) is... amended (76 FR 37628, June 28, 2011). As part of its further consideration of this determination, DOE is... availability of the framework document to consider such standards (78 FR 7306, Feb. 1, 2013). The...

  12. Universities and Industry: Does the Lambert Code of Governance Meet the Requirements of Good Governance?

    Science.gov (United States)

    Buckland, Roger

    2004-01-01

    The Lambert Model Code of Governance proposes to institutionalise the dominance of governors from commercial and industrial organisations as core members of compact and effective boards controlling UK universities. It is the latest expression of a fashion for viewing university governance as an overly-simple example of an obsolete system, where…

  13. Building Ontology Networks: How to Obtain a Particular Ontology Network Life Cycle?

    OpenAIRE

    Suárez-Figueroa, Mari Carmen; Gómez-Pérez, A.

    2008-01-01

    To build an ontology, ontology developers should devise first a concrete plan for the ontology development, that is, they should establish the ontology life cycle. To do this, ontology developers should answer two key questions: a) which ontology life cycle model is the most appropriate for their ontology project? and b) which particular activities should be carried out in their ontology life cycle? In this paper we present a set of guidelines to help ontology developers and al...

  14. 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

  15. Ontology-based application integration

    CERN Document Server

    Paulheim, Heiko

    2011-01-01

    Ontology-based Application Integration introduces UI-level (User Interface Level) application integration and discusses current problems which can be remedied by using ontologies. It shows a novel approach for applying ontologies in system integration. While ontologies have been used for integration of IT systems on the database and on the business logic layer, integration on the user interface layer is a novel field of research. This book also discusses how end users, not only developers, can benefit from semantic technologies. Ontology-based Application Integration presents the development o

  16. 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.

  17. Benchmarking Ontologies: Bigger or Better?

    Science.gov (United States)

    Yao, Lixia; Divoli, Anna; Mayzus, Ilya; Evans, James A.; Rzhetsky, Andrey

    2011-01-01

    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. PMID:21249231

  18. Benchmarking ontologies: bigger or better?

    Science.gov (United States)

    Yao, Lixia; Divoli, Anna; Mayzus, Ilya; Evans, James A; Rzhetsky, Andrey

    2011-01-13

    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.

  19. Estonia`s oil shale industry - meeting environmental standards of the future

    Energy Technology Data Exchange (ETDEWEB)

    Tanner, T. [Jaakko Poyry International, Helsinki (Finland); Bird, G.; Wallace, D. [Alberta Research Council, Edmonton (Canada)] [and others

    1995-12-31

    Oil shale is Estonia`s greatest mineral resource. In the 1930s, it was used as a source of gasoline and fuel oil, but now it is mined primarily for thermal generation of electricity. With the loss of its primary market for electricity in the early 1990s and in the absence of another domestic source of fuel Estonia once again is considering the use of a larger proportion of its shale for oil production. However, existing retorting operations in Estonia may not attain western European environmental standards and desired conversion efficiencies. As a reference point, the Estonian authorities have documented existing environmental impacts. It is evaluating technologies to reduce the impacts and is setting a direction for the industry that will serve domestic needs. This paper provides a description of the existing oil shale industry in Estonia and options for the future.

  20. Government and industry meet to discuss environmental stewardship and economic development

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, O. Jr.

    1996-05-01

    At the New Mexico Conference on the Environment, government and industry representatives met to address environmental stewardship and economic development, particularly as these issues relate to New Mexico. The session took place March 13, 1996, from 1:30 PM to 5:00 PM, in the Cochiti/Taos room at the Albuquerque Convection Center. The first part of the session dealt with environmental stewardship. The second session discussed economic development. This paper chronicles the highlights of this unique session. It attempts to capture the essence of each speaker; therefore, rather than a strict narrative, this paper consists of a series of quotes that, when seen as a whole, provide an understanding of how government and industry view environmental stewardship and economic development. Moreover, these quotes reveal that these organizations continue to develop effective methodologies to collaborate.

  1. Sustainable Development of the Cement Industry and Blended Cements to Meet Ecological Challenges

    OpenAIRE

    Konstantin Sobolev

    2003-01-01

    The world production of cement has greatly increased in the past 10 years. This trend is the most significant factor affecting technological development and the updating of manufacturing facilities in the cement industry. Existing technology for the production of cement clinker is ecologically damaging; it consumes much energy and natural resources and also emits pollutants. A new approach to the production of blended or high-volume mineral additive (HVMA) cement helps to improve its ecologi...

  2. Sustainable Development of the Cement Industry and Blended Cements to Meet Ecological Challenges

    Directory of Open Access Journals (Sweden)

    Konstantin Sobolev

    2003-01-01

    Full Text Available The world production of cement has greatly increased in the past 10 years. This trend is the most significant factor affecting technological development and the updating of manufacturing facilities in the cement industry. Existing technology for the production of cement clinker is ecologically damaging; it consumes much energy and natural resources and also emits pollutants. A new approach to the production of blended or high-volume mineral additive (HVMA cement helps to improve its ecological compatibility. HVMA cement technology is based on the intergrinding of portland cement clinker, gypsum, mineral additives, and a special complex admixture. This new method increases the compressive strength of ordinary cement, improves durability of the cement-based materials, and - at the same time - uses inexpensive natural mineral additives or industrial by-products. This improvement leads to a reduction of energy consumption per unit of the cement produced. Higher strength, better durability, reduction of pollution at the clinker production stage, and decrease of landfill area occupied by industrial by-products, all provide ecological advantages for HVMA cement.

  3. Sustainable development of the cement industry and blended cements to meet ecological challenges.

    Science.gov (United States)

    Sobolev, Konstantin

    2003-05-05

    The world production of cement has greatly increased in the past 10 years. This trend is the most significant factor affecting technological development and the updating of manufacturing facilities in the cement industry. Existing technology for the production of cement clinker is ecologically damaging; it consumes much energy and natural resources and also emits pollutants. A new approach to the production of blended or high-volume mineral additive (HVMA) cement helps to improve its ecological compatibility. HVMA cement technology is based on the intergrinding of portland cement clinker, gypsum, mineral additives, and a special complex admixture. This new method increases the compressive strength of ordinary cement, improves durability of the cement-based materials, and--at the same time--uses inexpensive natural mineral additives or industrial by-products. This improvement leads to a reduction of energy consumption per unit of the cement produced. Higher strength, better durability, reduction of pollution at the clinker production stage, and decrease of landfill area occupied by industrial by-products, all provide ecological advantages for HVMA cement.

  4. The Application of Ontological Methods toward Coastal Restoration

    Science.gov (United States)

    Ramachandran, R.; Movva, S.; Hardin, D.

    2007-12-01

    At the fall 2006 AGU meeting the Information Technology and Systems Center at the University of Alabama in Huntsville debuted a tool for ontology based search and resource aggregation called Noesis. Since that time Noesis, with a new ontology for seagrass habitats in the Gulf of Mexico, has been utilized to support evaluations of potential seagrass restoration sites. The seagrass ontology was generated from a standard stressor conceptual model description for five species of seagrass common to the Northern Gulf of Mexico. Coupling the seagrass ontology with the existing atmospheric science ontology allowed scientists to locate and retrieve substantial information about the seagrass habitat as well as stressors that impact the habitat induced by climate change and short term atmospheric phenomena. A domain specific catalog of seagrass resources was constructed and an application ontology developed that mapped the keywords of the catalog to the combined (atmospheric and seagrass) ontologies of Noesis. Noesis uses domain ontologies to help the user scope the search queries to ensure that the search results are both accurate and complete. The domain ontologies guide the user to refine their search query and thereby reduce the user's burden of experimenting with different search strings. Semantics are captured by refining the query terms to cover synonyms, specializations, generalizations and related concepts. As a resource aggregator Noesis categorizes search results from different online resources such as education materials, publications, datasets, web search engines that might be of interest to the user. This presentation will give an overview of Noesis and describe how it has been applied to coastal restoration investigations.

  5. How Indonesian Accounting Education Providers Meet The Demand of The Industry

    Directory of Open Access Journals (Sweden)

    Dyah Setyaningrum

    2015-04-01

    Full Text Available The purpose of this study is to evaluate performance of accounting education providers in Indonesia in producing graduates required by the industry. This study compares different perception between the employers, lecturers, junior auditors and students regarding: (1 auditors’ early employment problem; (2 university performance; and (3 university improvement. We employ quantitative methods to present descriptive analysis of different perceptions of stakeholders regarding university performance. The top early employment problem of the newly hires auditor is problems with orientation and adaptation with new working environment; technical competence and soft-skill problem. Although all respondent agree that university performed well in preparing graduates for the job market, but graduates still lacking in several factors (technical skills and soft-skills that university need to overcome. Suggestions for university improvement in order to producing graduates required by the industry are: (1 incorporate internship as compulsory subjects; (2 partnership with public accounting firm in recruitment process; (3 practical training with real audit cases via seminar/workshop; (4 student-centered learning approach; and (5 regular updates of current audit practice to lecturer.

  6. How Indonesian Accounting Education Providers Meet The Demand of The Industry (1-11

    Directory of Open Access Journals (Sweden)

    Dyah Setyaningrum

    2016-06-01

    Full Text Available The purpose of this study is to evaluate performance of accounting education providers in Indonesia in producing graduates required by the industry. This study compares different perception between the employers, lecturers, junior auditors and students regarding:  (1 auditors’ early employment problem; (2 university performance; and (3 university improvement. We employ quantitative methods to present descriptive analysis of different perceptions of stakeholders regarding university performance. The top early employment problem of the newly hires auditor is problems with orientation and adaptation with new working environment; technical competence and soft-skill problem. Although all respondent agree that university performed well in preparing graduates for the job market, but graduates still lacking in several factors (technical skills and soft-skills that university need to overcome. Suggestions for university improvement in order to producing graduates required by the industry are: (1 incorporate internship as compulsory subjects; (2 partnership with public accounting firm in recruitment process; (3 practical training with real audit cases via seminar/workshop; (4 student-centered learning approach; and (5 regular updates of current audit practice to lecturer.Keywords:early employment problem, employability, soft-skills, university performance.

  7. Ontology of the False State

    Directory of Open Access Journals (Sweden)

    Testa Italo

    2015-09-01

    Full Text Available In this paper I will argue that critical theory needs to make its socio-ontological commitments explicit, whilst on the other hand I will posit that contemporary social ontology needs to amend its formalistic approach by embodying a critical theory perspective. In the first part of my paper I will discuss how the question was posed in Horkheimer’s essays of the 1930s, which leave open two options: (1 a constructive inclusion of social ontology within social philosophy, or else (2 a program of social philosophy that excludes social ontology. Option (2 corresponds to Adorno’s position, which I argue is forced to recur to a hidden social ontology. Following option (1, I first develop a meta-critical analysis of Searle, arguing that his social ontology presupposes a notion of ‘recognition’ which it cannot account for. Furthermore, by means of a critical reading of Honneth, I argue that critical theory could incorporate a socio-ontological approach, giving value to the constitutive socio-ontological role of recognition and to the socio-ontological role of objectification. I will finish with a proposal for a socio-ontological characterization of reification which involves that the basic occurrence of recognition is to be grasped at the level of background practices.

  8. Biomedical ontologies: a functional perspective.

    Science.gov (United States)

    Rubin, Daniel L; Shah, Nigam H; Noy, Natalya F

    2008-01-01

    The information explosion in biology makes it difficult for researchers to stay abreast of current biomedical knowledge and to make sense of the massive amounts of online information. Ontologies--specifications of the entities, their attributes and relationships among the entities in a domain of discourse--are increasingly enabling biomedical researchers to accomplish these tasks. In fact, bio-ontologies are beginning to proliferate in step with accruing biological data. The myriad of ontologies being created enables researchers not only to solve some of the problems in handling the data explosion but also introduces new challenges. One of the key difficulties in realizing the full potential of ontologies in biomedical research is the isolation of various communities involved: some workers spend their career developing ontologies and ontology-related tools, while few researchers (biologists and physicians) know how ontologies can accelerate their research. The objective of this review is to give an overview of biomedical ontology in practical terms by providing a functional perspective--describing how bio-ontologies can and are being used. As biomedical scientists begin to recognize the many different ways ontologies enable biomedical research, they will drive the emergence of new computer applications that will help them exploit the wealth of research data now at their fingertips.

  9. An Ontology-Driven Dependable Water Treatment Plant CPS

    Directory of Open Access Journals (Sweden)

    SANISLAV Teodora

    2013-05-01

    Full Text Available The paper introduces an ontology-drivenCyber-Physical System with dependability features tocontrol, monitor and diagnose a water treatment plant,with emphasis on the ontology, as a new approach forthe existing industrial control systems used in thisfield. The proposed dependability ontology is based ona fault forecasting technique, a qualitative evaluationof the water treatment plant Cyber-Physical Systembehaviour - Failure Modes and Effects Analysis. Theontology has two important parts: one is the ontologyof faults including several categories of system faultsand the other is the ontology of failures includingseveral categories of system failures. The dependabilityontology plays a central role in the Cyber-PhysicalSystem architecture and drives various aspects of thissystem, especially the ones related to system diagnosis.

  10. Infrastructures as Ontological Experiments

    Directory of Open Access Journals (Sweden)

    Casper Bruun Jensen

    2015-11-01

    Full Text Available Ontology has recently gained renewed attention in science and technology studies and anthropology (e.g. Gad, Jensen and Winthereik 2015; Holbraad, Pedersen and Viveiros de Castro 2014; Woolgar and Lezaun 2013. Yet, it has a considerably longer pedigree than these recent debates might lead one to think. Experiments, of course, have long held the attention of sociologists, historians, and philosophers of science (Collins 1985; Gooding 1990; Shapin and Schaffer 1985. And infrastructures have been the focus of sustained inquiry in the sociology and history of technology (Bowker 1994; Hughes 1983. Once these terms are put into conjunction, however, each gets a somewhat different inflection. The following note briefly explores the conceptual purchase of considering infrastructures as ontological experiments.

  11. ONTOLOGY: UNREAL REALITY

    Directory of Open Access Journals (Sweden)

    Piotr Jaroszynski

    2014-12-01

    Full Text Available The article examines the difference between ontology and metaphysics. It shows that as soon as the composition of being from essence and existence is treated as purely mental or in a “reified” way (where essence and existence are independent elements, then essence as essence becomes a thing, and then simply becomes a being, or what is called reality. Both versions in which the real difference disappears or in which the road leads to “reification,” influence the treatment of essence as independent, where essence as thing fills the field of reality. However, if essence was only possibility, then (1 the reality also would be merely possible, (2 the realistic field of philosophical terminology would get curtailed, and (3 there would be no terms to maintain the difference between reality and possibility, between metaphysics and ontology.

  12. Meeting around industrial sites; Concertation autour des sites d'installations industrielles

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Th. [Centre d' etude sur l' Evaluation de la Protection dans le domaine Nucleaire (CEPN), 92 - Fontenay aux Roses (France); Sene, M. [Groupement de Scientifiques pour l' Information sur l' Energie Nucleaire, 91 - Orsay (France); Melguen, M. [Electricite de France (EDF), 75 - Paris (France); Saint-Raymond, Ph. [Direction Generale de la Surete Nucleaire et de la Radioprotection, 75 - Paris (France); Oudiz, A. [Institut de Radioprotection et de Surete Nucleaire, 92 - Fontenay-aux-Roses (France); Brie, J. [Charente Nature (France); Schmitt, P. [CLS de Fessenheim, 68 (France); Verot, Y [Atofina, 92 -Paris la Defense (France); Quintin, Ch. [DRIRE Rhone Alpes, 69 (France); Dubuis, Th. [Secretariat Permanent pour la Prevention des Pollutions Industrielles, 59 - Dunkerque (France); Adelfa, J.S.; Hocquet, M.P. [CLCV, France (France); Gheerardyn, P. [MEDEF Cote d' Opale (France); Villers, S. [EDA, France (France); Modrzejewski, F. [DRIRE Nord-Pas-de-Calais (France); Gadbois, S.; Heriard-Dubreuil, G. [MUTADIS, 75 - Paris (France); Geismar, N.; Eimer, M. [CLI de Saint-Laurent (France); Andre, S. [CEA Cadarache, 13 - Saint-Paul-lez-Durance (France); Vindimian, E. [Institut National de l' Environnement Industriel et des Risques, 60 - Verneuil en Halatte (INERIS) (France); Remond-Gouilloud, M. [Universite Paris-Sorbonne, 75 (France)

    2005-07-01

    Following the research work on the ' stakes in the social dialogue around the follow-up of the nuclear industrial installations ' engaged by the I.R.S.N. in 2000, a seminar was organized on January 21. and 22., 2003 in Ville d Avray. This seminar gathered personalities of different origins (administration, institutional experts, operators, associations, Local Commissions of Information, elected representatives) to discuss and enrich the conclusions of the research work and elaborate collectively a contribution to the current remarks in France on the public debate and the processes of dialogue. The present report establishes the acts of this seminar and redraws all the discussions between the participants. (N.C.)

  13. 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…

  14. Ontology Partitioning: Clustering Based Approach

    Directory of Open Access Journals (Sweden)

    Soraya Setti Ahmed

    2015-05-01

    Full Text Available The semantic web goal is to share and integrate data across different domains and organizations. The knowledge representations of semantic data are made possible by ontology. As the usage of semantic web increases, construction of the semantic web ontologies is also increased. Moreover, due to the monolithic nature of the ontology various semantic web operations like query answering, data sharing, data matching, data reuse and data integration become more complicated as the size of ontology increases. Partitioning the ontology is the key solution to handle this scalability issue. In this work, we propose a revision and an enhancement of K-means clustering algorithm based on a new semantic similarity measure for partitioning given ontology into high quality modules. The results show that our approach produces meaningful clusters than the traditional algorithm of K-means.

  15. Building an Ontology of Product/Service-Systems

    DEFF Research Database (Denmark)

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

    2014-01-01

    In recent years, the innovation strategy and development process entitled Product/Service-Systems (PSS), has attracted considerable attention from the research and industrial communities. The many contributions have come from various academic and professional viewpoints, which despite providing...... a rich view of PSS as a strategy, also leaves some confusion as to what actually constitutes a PSS. The definition of a PSS ontology could provide the basis for a more systematic knowledge gathering within the field and facilitate the application of integrated solutions within the industry. Ontologies...

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

    Lifescience Database Archive (English)

    Full Text Available List Contact us FANTOM5 Sample ontology, GOstat and ontology term enrichment Data detail Data name Sample on...tology, GOstat and ontology term enrichment DOI 10.18908/lsdba.nbdc01389-006.V002 Version V2 10.18908/lsdba....t Us Sample ontology, GOstat and ontology term enrichment - FANTOM5 | LSDB Archive ...

  17. A Political Review of International Literacy Meetings in Industrialized Countries, 1981-1994

    Science.gov (United States)

    Hautecoeur, Jean-Paul

    1997-03-01

    The author presents a historical survey of the official discourse on functional literacy in the industrialized countries on the basis of the reports of 20 seminars and international conferences linked to UNESCO. The article has two objectives: (1) to document and interpret globally the political evolution of the literacy movement in the north - in fact limited to western Europe and north America; (2) within the context of the Fifth International Conference on Adult Education, to pose the question: to what extent are the same issues involved throughout the world under the rubric of literacy? The author goes on to underline the broad geopolitical tendencies of the literacy movement, sketching its symbolic features and the tensions and areas of consensus within it. He traces the evolution of its dominant symbology and the ideological positions of its key figures. He concludes with a typology of the principal political tendencies of this movement, while making it clear that the real objectives of fighting poverty and exclusion are pursued outside the literacy movement and within the "minor literacies" of everyday life.

  18. The ontology of biological sequences

    Directory of Open Access Journals (Sweden)

    Kelso Janet

    2009-11-01

    Full Text Available Abstract Background Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike. Results We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving. Conclusion Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.

  19. Biomedical ontologies: a functional perspective

    National Research Council Canada - National Science Library

    Rubin, Daniel L; Shah, Nigam H; Noy, Natalya F

    .... Ontologies-specifications of the entities, their attributes and relationships among the entities in a domain of discourse-are increasingly enabling biomedical researchers to accomplish these tasks...

  20. Towards ontology based search and knowledgesharing using domain ontologies

    DEFF Research Database (Denmark)

    Zambach, Sine

    ontologies for enterprises are as background for search and knowledge sharing used for e.g. multi lingual product development. Our aim is to use linguistic methods and logic to construct consistent ontologies that can be used in both a search perspective and as knowledge sharing.This focuses on identifying...

  1. 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

  2. The Ontology for Biomedical Investigations.

    Directory of Open Access Journals (Sweden)

    Anita Bandrowski

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

  3. Towards ontology based search and knowledgesharing using domain ontologies

    DEFF Research Database (Denmark)

    Zambach, Sine

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

  4. The organization ontology

    OpenAIRE

    2014-01-01

    Este documento describe una ontología fundamental para las estructuras de organización, destinada a apoyar la publicación de datos vinculados de información de la organización a través de un número de dominios. Está diseñado para permitir a las extensiones de dominios específicos agregar clasificaciones de organizaciones y funciones, así como extensiones para mantener información relacionada como por ejemplo actividades de la organización.

  5. Applications of Genome-based Science in Shaping Citrus Industries of the World (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    Energy Technology Data Exchange (ETDEWEB)

    Gmitter Jr, Fred [University of Florida

    2012-03-21

    Fred Gmitter from the University of Florida on "Applications of Genome-based Science in Shaping the Future of the World's Citrus Industries" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  6. 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.…

  7. Ontological turns, turnoffs and roundabouts.

    Science.gov (United States)

    Sismondo, Sergio

    2015-06-01

    There has been much talk of an 'ontological turn' in Science and Technology Studies. This commentary explores some recent work on multiple and historical ontologies, especially articles published in this journal, against a background of constructivism. It can be tempting to read an ontological turn as based and promoting a version of perspectivism, but that is inadequate to the scholarly work and opens multiple ontologies to serious criticisms. Instead, we should read our ontological turn or turns as being about multiplicities of practices and the ways in which these practices shape the material world. Ontologies arise out of practices through which people engage with things; the practices are fundamental and the ontologies derivative. The purchase in this move comes from the elucidating power of the verbs that scholars use to analyze relations of practices and objects--which turn out to be specific cases of constructivist verbs. The difference between this ontological turn and constructivist work in Science and Technology Studies appears to be a matter of emphases found useful for different purposes.

  8. A Temporal Web Ontology Language

    NARCIS (Netherlands)

    V. Milea (Viorel); F. Frasincar (Flavius); U. Kaymak (Uzay)

    2009-01-01

    textabstractThe Web Ontology Language (OWL) is the most expressive standard language for modeling ontologies on the Semantic Web. In this paper, we present a temporal extension of the very expressive fragment SHIN(D) of the OWL-DL language resulting in the tOWL language. Through a layered approach w

  9. 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.…

  10. Ontology Based Model Transformation Infrastructure

    NARCIS (Netherlands)

    Göknil, A.; 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. Building Ontologies in DAML + OIL

    Science.gov (United States)

    Wroe, Chris; Bechhofer, Sean; Lord, Phillip; Rector, Alan; Goble, Carole

    2003-01-01

    In this article we describe an approach to representing and building ontologies advocated by the Bioinformatics and Medical Informatics groups at the University of Manchester. The hand-crafting of ontologies offers an easy and rapid avenue to delivering ontologies. Experience has shown that such approaches are unsustainable. Description logic approaches have been shown to offer computational support for building sound, complete and logically consistent ontologies. A new knowledge representation language, DAML + OIL, offers a new standard that is able to support many styles of ontology, from hand-crafted to full logic-based descriptions with reasoning support. We describe this language, the OilEd editing tool, reasoning support and a strategy for the language’s use. We finish with a current example, in the Gene Ontology Next Generation (GONG) project, that uses DAML + OIL as the basis for moving the Gene Ontology from its current hand-crafted, form to one that uses logical descriptions of a concept’s properties to deliver a more complete version of the ontology. PMID:18629114

  12. Ontology Supported Information Systems: A Review

    Directory of Open Access Journals (Sweden)

    Padmavathi, T.

    2014-12-01

    Full Text Available The exponential growth of information on the web far exceeds the capacity of present day information retrieval systems and search engines, making information integration on the web difficult. In order to overcome this, semantic web technologies were proposed by the World Wide Web Consortium (W3C to achieve a higher degree of automation and precision in information retrieval systems. Semantic web, with its promise to deliver machine understanding to the traditional web, has attracted a significant amount of research from academia as well as from industries. Semantic web is an extension of the current web in which data can be shared and reused across the internet. RDF and ontology are two essential components of the semantic web architecture which support a common framework for data storage and representation of data semantics, respectively. Ontologies being the backbone of semantic web applications, it is more relevant to study various approaches in their application, usage, and integration into web services. In this article, an effort has been made to review the research work being undertaken in the area of design and development of ontology supported information systems. This paper also briefly explains the emerging semantic web technologies and standards.

  13. Ontology-based Information Retrieval

    DEFF Research Database (Denmark)

    Styltsvig, Henrik Bulskov

    of concept similarity in query evaluation is discussed. A semantic expansion approach that incorporates concept similarity is introduced and a generalized fuzzy set retrieval model that applies expansion during query evaluation is presented. While not commonly used in present information retrieval systems......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...

  14. Data Migration for Ontology Evolution

    Institute of Scientific and Technical Information of China (English)

    赵彦; 张雷; 林晨曦; 张卓; 俞勇

    2004-01-01

    Ontology is the conceptual backbone that provides meaning to data on the semantic web. However, ontology is not a static resource and may evolve over time, which often leaves the meaning of data in an undefined or inconsistent state. It is thus very important to have a method to preserve the data and its meaning when ontology changes. This paper proposed a general method that solves the problem using data migration. It analyzed some of the issues in the method including separation of ontology and data, migration specification, migration result and migration algorithm. The paper also instantiates the general mothod in RDF(S) as an example. The RDF(S) example itself is a simple but complete method for migrating RDF data when RDFS ontology changes.

  15. 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

  16. Developing a semantically rich ontology for the biobank-administration domain.

    Science.gov (United States)

    Brochhausen, Mathias; Fransson, Martin N; Kanaskar, Nitin V; Eriksson, Mikael; Merino-Martinez, Roxana; Hall, Roger A; Norlin, Loreana; Kjellqvist, Sanela; Hortlund, Maria; Topaloglu, Umit; Hogan, William R; Litton, Jan-Eric

    2013-10-08

    accuracy. In addition, we began development of a mapping from the ontology to pre-existing biobank data structures commonly used in the U.S. In conclusion, we created OMIABIS, an ontology of biobank administration. We found that basing its development on pre-existing resources to meet the BBMRI use cases resulted in a biobanking ontology that is re-useable in environments other than BBMRI. Our ontology retrieved all true positives and no false positives when queried according to the competency questions we derived from the BBMRI use cases. Mapping OMIABIS to a data structure used for biospecimen collections in a medical center in Little Rock, AR showed adequate coverage of our ontology.

  17. Industry

    Energy Technology Data Exchange (ETDEWEB)

    Bernstein, Lenny; Roy, Joyashree; Delhotal, K. Casey; Harnisch, Jochen; Matsuhashi, Ryuji; Price, Lynn; Tanaka, Kanako; Worrell, Ernst; Yamba, Francis; Fengqi, Zhou; de la Rue du Can, Stephane; Gielen, Dolf; Joosen, Suzanne; Konar, Manaswita; Matysek, Anna; Miner, Reid; Okazaki, Teruo; Sanders, Johan; Sheinbaum Parado, Claudia

    2007-12-01

    This chapter addresses past, ongoing, and short (to 2010) and medium-term (to 2030) future actions that can be taken to mitigate GHG emissions from the manufacturing and process industries. Globally, and in most countries, CO{sub 2} accounts for more than 90% of CO{sub 2}-eq GHG emissions from the industrial sector (Price et al., 2006; US EPA, 2006b). These CO{sub 2} emissions arise from three sources: (1) the use of fossil fuels for energy, either directly by industry for heat and power generation or indirectly in the generation of purchased electricity and steam; (2) non-energy uses of fossil fuels in chemical processing and metal smelting; and (3) non-fossil fuel sources, for example cement and lime manufacture. Industrial processes also emit other GHGs, e.g.: (1) Nitrous oxide (N{sub 2}O) is emitted as a byproduct of adipic acid, nitric acid and caprolactam production; (2) HFC-23 is emitted as a byproduct of HCFC-22 production, a refrigerant, and also used in fluoroplastics manufacture; (3) Perfluorocarbons (PFCs) are emitted as byproducts of aluminium smelting and in semiconductor manufacture; (4) Sulphur hexafluoride (SF{sub 6}) is emitted in the manufacture, use and, decommissioning of gas insulated electrical switchgear, during the production of flat screen panels and semiconductors, from magnesium die casting and other industrial applications; (5) Methane (CH{sub 4}) is emitted as a byproduct of some chemical processes; and (6) CH{sub 4} and N{sub 2}O can be emitted by food industry waste streams. Many GHG emission mitigation options have been developed for the industrial sector. They fall into three categories: operating procedures, sector-wide technologies and process-specific technologies. A sampling of these options is discussed in Sections 7.2-7.4. The short- and medium-term potential for and cost of all classes of options are discussed in Section 7.5, barriers to the application of these options are addressed in Section 7.6 and the implication of

  18. 77 FR 31368 - Guidance on Meetings With Industry and Investigators on the Research and Development of Tobacco...

    Science.gov (United States)

    2012-05-25

    ... Collection Totals 1,876 \\1\\ There are no capital costs or operating and maintenance costs associated with... productive meeting. For the information that was previously submitted in the meeting request, the information... Meeting requests and information Number of responses per Total annual per response Total hours...

  19. 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.

  20. 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. PMID:25428369

  1. Cosmological Ontology and Epistemology

    CERN Document Server

    Page, Don N

    2014-01-01

    In cosmology, we would like to explain our observations and predict future observations from theories of the entire universe. Such cosmological theories make ontological assumptions of what entities exist and what their properties and relationships are. One must also make epistemological assumptions or metatheories of how one can test cosmological theories. Here I shall propose a Bayesian analysis in which the likelihood of a complete theory is given by the normalized measure it assigns to the observation used to test the theory. In this context, a discussion is given of the trade-off between prior probabilities and likelihoods, of the measure problem of cosmology, of the death of Born's rule, of the Boltzmann brain problem, of whether there is a better principle for prior probabilities than mathematical simplicity, and of an Optimal Argument for the Existence of God.

  2. Bridge Ontology:A Multi-Ontologies-Based Approach for Semantic Annotation

    Institute of Scientific and Technical Information of China (English)

    WANG Peng; XU Bao-wen; LU Jian-jiang; LI Yan-hui; JIANG Jian-hua

    2004-01-01

    Representing the relationships between ontologies is the key problem of semantic annotations based on multi-ontologies.Traditional approaches only had the ability of denoting the simple concept subsumption relations between ontologies.Through analyzing and classifying the relationships between ontologies, the idea of bridge ontology was proposed, which had the powerful capability of expressing the complex relationships between concepts and relationships between relations in multi-ontologies.Meanwhile, a new approach employing bridge ontology was proposed to deal with the multi-ontologies-based semantic annotation problem.The bridge ontology is a peculiar ontology, which can be created and maintained conveniently, and is effective in the multi-ontologies-based semantic annotation.The approach using bridge ontology has the advantages of low-cost, scalable, robust in the web circumstance, and avoiding the unnecessary ontology extending and integration.

  3. IDOMAL: an ontology for malaria

    Directory of Open Access Journals (Sweden)

    Topalis Pantelis

    2010-08-01

    Full Text Available Abstract Background Ontologies are rapidly becoming a necessity for the design of efficient information technology tools, especially databases, because they permit the organization of stored data using logical rules and defined terms that are understood by both humans and machines. This has as consequence both an enhanced usage and interoperability of databases and related resources. It is hoped that IDOMAL, the ontology of malaria will prove a valuable instrument when implemented in both malaria research and control measures. Methods The OBOEdit2 software was used for the construction of the ontology. IDOMAL is based on the Basic Formal Ontology (BFO and follows the rules set by the OBO Foundry consortium. Results The first version of the malaria ontology covers both clinical and epidemiological aspects of the disease, as well as disease and vector biology. IDOMAL is meant to later become the nucleation site for a much larger ontology of vector borne diseases, which will itself be an extension of a large ontology of infectious diseases (IDO. The latter is currently being developed in the frame of a large international collaborative effort. Conclusions IDOMAL, already freely available in its first version, will form part of a suite of ontologies that will be used to drive IT tools and databases specifically constructed to help control malaria and, later, other vector-borne diseases. This suite already consists of the ontology described here as well as the one on insecticide resistance that has been available for some time. Additional components are being developed and introduced into IDOMAL.

  4. OWL 2 Web Ontology Language: XML serialization

    NARCIS (Netherlands)

    Motik, B.; Patel-Schneider, P.; Bechhofer, S.; Cuenca Grau, B.; Fokoue, A.; Hoekstra, R.; Parsia, B.

    2008-01-01

    The OWL 2 Web Ontology Language, informally OWL 2, is an ontology language for the Semantic Web with formally defined meaning. OWL 2 ontologies provide classes, properties, individuals, and data values and are stored as Semantic Web documents. OWL 2 ontologies can be used along with information writ

  5. OBIB-a novel ontology for biobanking.

    Science.gov (United States)

    Brochhausen, Mathias; Zheng, Jie; Birtwell, David; Williams, Heather; Masci, Anna Maria; Ellis, Helena Judge; Stoeckert, Christian J

    2016-01-01

    Biobanking necessitates extensive integration of data to allow data analysis and specimen sharing. Ontologies have been demonstrated to be a promising approach in fostering better semantic integration of biobank-related data. Hitherto no ontology provided the coverage needed to capture a broad spectrum of biobank user scenarios. Based in the principles laid out by the Open Biological and Biomedical Ontologies Foundry two biobanking ontologies have been developed. These two ontologies were merged using a modular approach consistent with the initial development principles. The merging was facilitated by the fact that both ontologies use the same Upper Ontology and re-use classes from a similar set of pre-existing ontologies. Based on the two previous ontologies the Ontology for Biobanking (http://purl.obolibrary.org/obo/obib.owl) was created. Due to the fact that there was no overlap between the two source ontologies the coverage of the resulting ontology is significantly larger than of the two source ontologies. The ontology is successfully used in managing biobank information of the Penn Medicine BioBank. Sharing development principles and Upper Ontologies facilitates subsequent merging of ontologies to achieve a broader coverage.

  6. 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...

  7. A cognitive science perspective on legal ontologies

    NARCIS (Netherlands)

    Breuker, J.; Hoekstra, R.; Sartor, G.; Casanovas, P.; Biasiotti, M.; Fernández-Barrera, M.

    2011-01-01

    We can trace five origins of ontology engineering, and all five still play a major role in ontology engineering. Each of these roots gives a different perspective on content and use of ontologies. Philosophical ontology is concerned with "reality"; Information science with systematic terminology;

  8. Ontology-Oriented Programming for Biomedical Informatics.

    Science.gov (United States)

    Lamy, Jean-Baptiste

    2016-01-01

    Ontologies are now widely used in the biomedical domain. However, it is difficult to manipulate ontologies in a computer program and, consequently, it is not easy to integrate ontologies with databases or websites. Two main approaches have been proposed for accessing ontologies in a computer program: traditional API (Application Programming Interface) and ontology-oriented programming, either static or dynamic. In this paper, we will review these approaches and discuss their appropriateness for biomedical ontologies. We will also present an experience feedback about the integration of an ontology in a computer software during the VIIIP research project. Finally, we will present OwlReady, the solution we developed.

  9. Industrialization

    African Journals Online (AJOL)

    Lucy

    Second World era international system (1945-1990) may not have done any good to ... wedge between the capitalist and socialist blocs, not only blurred Third World .... Politics and the Stages of Economic Growth, Cambridge: Cambridge ... complex industries producing mainly for export, but also producing for local.

  10. 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.

  11. Local Knitting Cluster: Concentrated for New Growth Model---Zaozhuang Held the First China Knitting Industry Cluster Annual Meeting%Local Knitting Cluster: Concentrated for New Growth Model---Zaozhuang Held the First China Knitting Industry Cluster Annual Meeting

    Institute of Scientific and Technical Information of China (English)

    Chen Xiangli

    2012-01-01

    Industry cluster is an economic phenomenon; that sees regionalized concentration of production here and there in the country. Currently, there are 14 pilot units of knitting industry clusters of which the production output exceeded 100 billion yuan in 2011. The industry cluster is divided into two categories;

  12. Introducing defeasibility into OWL ontologies

    CSIR Research Space (South Africa)

    Casini, G

    2015-10-01

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

  13. Concept Approximation between Fuzzy Ontologies

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Fuzzy ontologies are efficient tools to handle fuzzy and uncertain knowledge on the semantic web; but there are heterogeneity problems when gaining interoperability among different fuzzy ontologies. This paper uses concept approximation between fuzzy ontologies based on instances to solve the heterogeneity problems. It firstly proposes an instance selection technology based on instance clustering and weighting to unify the fuzzy interpretation of different ontologies and reduce the number of instances to increase the efficiency. Then the paper resolves the problem of computing the approximations of concepts into the problem of computing the least upper approximations of atom concepts. It optimizes the search strategies by extending atom concept sets and defining the least upper bounds of concepts to reduce the searching space of the problem. An efficient algorithm for searching the least upper bounds of concept is given.

  14. Social ontologi og metodologisk individualisme

    DEFF Research Database (Denmark)

    Baldursson, Einar Baldvin

    2013-01-01

    spørgsmålet om hvorvidt metode fordrer en bestemt ontologi, gives eksempler på social metodologi. Dermed etableres et afsæt for en konkret vurdering af, om der er - og i givet fald hvilken - sammenhæng mellem ontologi og metodologi (Red.).for at modellering og simulation åbner muligheden for at afprøvning og...

  15. How the gene ontology evolves.

    Science.gov (United States)

    Leonelli, Sabina; Diehl, Alexander D; Christie, Karen R; Harris, Midori A; Lomax, Jane

    2011-08-05

    Maintaining a bio-ontology in the long term requires improving and updating its contents so that it adequately captures what is known about biological phenomena. This paper illustrates how these processes are carried out, by studying the ways in which curators at the Gene Ontology have hitherto incorporated new knowledge into their resource. Five types of circumstances are singled out as warranting changes in the ontology: (1) the emergence of anomalies within GO; (2) the extension of the scope of GO; (3) divergence in how terminology is used across user communities; (4) new discoveries that change the meaning of the terms used and their relations to each other; and (5) the extension of the range of relations used to link entities or processes described by GO terms. This study illustrates the difficulties involved in applying general standards to the development of a specific ontology. Ontology curation aims to produce a faithful representation of knowledge domains as they keep developing, which requires the translation of general guidelines into specific representations of reality and an understanding of how scientific knowledge is produced and constantly updated. In this context, it is important that trained curators with technical expertise in the scientific field(s) in question are involved in supervising ontology shifts and identifying inaccuracies.

  16. Musical Ontology: Critical, not Metaphysical

    Directory of Open Access Journals (Sweden)

    Jonathan A. Neufeld

    2014-01-01

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

  17. 76 FR 20633 - Announcement of Meeting to Explore Feasibility of Establishing a NIST/Industry Consortium on...

    Science.gov (United States)

    2011-04-13

    ... Establishing a NIST/Industry Consortium on Neutron Measurements for Soft Materials Manufacturing AGENCY... National Institute of Standards and Technology (NIST) invites interested parties to attend a pre-consortium... industry interest in creating a NIST/industry consortium focused on advanced neutron-based probes for...

  18. ``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.

  19. 77 FR 23673 - Notice of Stakeholder Meeting: Industry Roundtable-DON/USDA/DOE/DOT-FAA Advanced Drop-In Biofuels...

    Science.gov (United States)

    2012-04-20

    ... Drop-In Biofuels Initiative AGENCY: Department of the Navy, DoD. ACTION: Notice of public meeting... biofuels supply chain. The purpose of the roundtable meeting is for the federal government to present... Biofuels Production Project. Questions related to the Special Notices or the pending Broad Agency...

  20. PERANCANGAN DAN IMPLEMENTASI APLIKASI INTERNET RADIO MENGGUNAKAN MULTIMEDIA DATABASE MELALUI PENERAPAN ONTOLOGY DAN METADATA

    Directory of Open Access Journals (Sweden)

    M. Rudy Erwansyah

    2012-05-01

    scheduling, reporting, user and ontology. In the implementation of internet application of this radio, the audio data management uses multimedia database by applying metadata and ontology, so that the process of indexing and retrieval can be reused quickly on the broadcast. This application can also be used in carrying out the radio broadcast automatically during specified hours. This internet radio application has been able to meet the needs of radio Heartline.

  1. Efficient Management of Biomedical Ontology Versions

    Science.gov (United States)

    Kirsten, Toralf; Hartung, Michael; Groß, Anika; Rahm, Erhard

    Ontologies have become very popular in life sciences and other domains. They mostly undergo continuous changes and new ontology versions are frequently released. However, current analysis studies do not consider the ontology changes reflected in different versions but typically limit themselves to a specific ontology version which may quickly become obsolete. To allow applications easy access to different ontology versions we propose a central and uniform management of the versions of different biomedical ontologies. The proposed database approach takes concept and structural changes of succeeding ontology versions into account thereby supporting different kinds of change analysis. Furthermore, it is very space-efficient by avoiding redundant storage of ontology components which remain unchanged in different versions. We evaluate the storage requirements and query performance of the proposed approach for the Gene Ontology.

  2. FYPO: the fission yeast phenotype ontology.

    Science.gov (United States)

    Harris, Midori A; Lock, Antonia; Bähler, Jürg; Oliver, Stephen G; Wood, Valerie

    2013-07-01

    To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast. The fission yeast phenotype ontology (FYPO) is a modular ontology that uses several existing ontologies from the open biological and biomedical ontologies (OBO) collection as building blocks, including the phenotypic quality ontology PATO, the Gene Ontology and Chemical Entities of Biological Interest. Modular ontology development facilitates partially automated effective organization of detailed phenotype descriptions with complex relationships to each other and to underlying biological phenomena. As a result, FYPO supports sophisticated querying, computational analysis and comparison between different experiments and even between species. FYPO releases are available from the Subversion repository at the PomBase SourceForge project page (https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/). The current version of FYPO is also available on the OBO Foundry Web site (http://obofoundry.org/).

  3. Critical Theory and Processual Social Ontology

    Directory of Open Access Journals (Sweden)

    Renault Emmanuel

    2016-03-01

    Full Text Available The purpose of this article is to bridge the gap between critical theory as understood in the Frankfurt school tradition on the one hand, and social ontology understood as a reflection on the ontological presuppositions of social sciences and social theories on the other. What is at stake is the type of social ontology that critical theory needs if it wants to tackle its main social ontological issue: that of social transformation. This paper’s claim is that what is required is neither a substantial social ontology, nor a relational social ontology, but a processual one. The first part of this article elaborates the distinction between substantial, relational and processual social ontologies. The second part analyzes the various ways in which this distinction can be used in social ontological discussions. Finally, the third part focuses on the various possible social ontological approaches to the issue of social transformation.

  4. An Ontology for the Discovery of Time-series Data

    Science.gov (United States)

    Hooper, R. P.; Choi, Y.; Piasecki, M.; Zaslavsky, I.; Valentine, D. W.; Whitenack, T.

    2010-12-01

    An ontology was developed to enable a single-dimensional keyword search of time-series data collected at fixed points, such as stream gage records, water quality observations, or repeated biological measurements collected at fixed stations. The hierarchical levels were developed to allow navigation from general concepts to more specific ones, terminating in a leaf concept, which is the specific property measured. For example, the concept “nutrient” has child concepts of “nitrogen”, “phosphorus”, and “carbon”; each of these children concepts are then broken into the actual constituent measured (e.g., “total kjeldahl nitrogen” or “nitrate + nitrite”). In this way, a non-expert user can find all nutrients containing nitrogen without knowing all the species measured, but an expert user can go immediately to the compound of interest. In addition, a property, such as dissolved silica, can appear as a leaf concept under nutrients or weathering products. This flexibility allows users from various disciplines to find properties of interest. The ontology can be viewed at http://water.sdsc.edu/hiscentral/startree.aspx. Properties measured by various data publishers (e.g., universities and government agencies) are tagged with leaf concepts from this ontology. A discovery client, HydroDesktop, creates a search request by defining the spatial and temporal extent of interest and a keyword taken from the discovery ontology. Metadata returned from the catalog describes the time series which meet the specified search criteria. This ontology is considered to be an initial description of physical, chemical and biological properties measured in water and suspended sediment. Future plans call for creating a moderated forum for the scientific community to add to and to modify this ontology. Further information for the Hydrologic Information Systems project, of which this is a part, is available at http://his.cuahsi.org.

  5. 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 philosophical background for Jacob Lorhard’s invention of the word ‘ontology’ as well as the scientific status of ontology in the 16th and 17th century. We also consider the use of Ramean style diagrams and diagrammatic ontology in general. A modern implementation of Lorhard’s ontology is discussed...... and this classical ontology is compared to some modern ontologies....

  6. 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 philosophical background for Jacob Lorhard’s invention of the word ‘ontology’ as well as the scientific status of ontology in the 16th and 17th century. We also consider the use of Ramean style diagrams and diagrammatic ontology in general. A modern implementation of Lorhard’s ontology is discussed...... and this classical ontology is compared to some modern ontologies....

  7. Role of Ontology in Information Retrieval

    Institute of Scientific and Technical Information of China (English)

    WU Dan; WANG Hui-lin

    2006-01-01

    Based on the comparison between ontology and thesaurus, and the analysis of an ontology-based Information Retrieval (IR) model, the potential advantages that ontology may contribute to IR are analyzed. Then a general architecture of ontology-based Information Retrieval System (IRS) and the approach of constructing it are presented. Based on the researches, the role of ontology in IR is summarized from four aspects and a typical system called Textpresso is analyzed. Finally, a conclusion is drawn that utilizing ontology is the trend of IR and can really improve the IRS.

  8. Cohesion Metrics for Ontology Design and Application

    Directory of Open Access Journals (Sweden)

    Haining Yao

    2005-01-01

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

  9. Ontology Mapping for a New Database Integration Model Using an Ontology-driven Mediated Warehousing Approach

    Directory of Open Access Journals (Sweden)

    Ali Ahmed

    2014-04-01

    Full Text Available Ontology mapping is a technique that has become very useful for matching semantics between ontologies or schemas that were designed independently of each other. The main goal of the ontology mapping is to enable interoperability between applications in distributed information systems based on heterogeneous ontologies. To achieve this goal it is necessary to formally define mapping rules between local data sources and ontologies and the notion of a mapping between ontologies. In this study, the authors proposed a new mapping approach, so that the ontologies have to be linked to actual information sources in order to support the integration process. In this approach, first, for each incorporated information source, a local ontology is generated to describe its semantics as well as the resulting mappings between the source and the local ontology, then the local ontologies are mapped to a global ontology using the mapping rule.

  10. Ontology Based Qos Driven Web Service Discovery

    Directory of Open Access Journals (Sweden)

    R Suganyakala

    2011-07-01

    Full Text Available In today's scenario web services have become a grand vision to implement the business process functionalities. With increase in number of similar web services, one of the essential challenges is to discover relevant web service with regard to user specification. Relevancy of web service discovery can be improved by augmenting semantics through expressive formats like OWL. QoS based service selection will play a significant role in meeting the non-functional user requirements. Hence QoS and semantics has been used as finer search constraints to discover the most relevant service. In this paper, we describe a QoS framework for ontology based web service discovery. The QoS factors taken into consideration are execution time, response time, throughput, scalability, reputation, accessibility and availability. The behavior of each web service at various instances is observed over a period of time and their QoS based performance is analyzed.

  11. Tutorial on Protein Ontology Resources.

    Science.gov (United States)

    Arighi, Cecilia N; Drabkin, Harold; Christie, Karen R; Ross, Karen E; Natale, Darren A

    2017-01-01

    The Protein Ontology (PRO) is the reference ontology for proteins in the Open Biomedical Ontologies (OBO) foundry and consists of three sub-ontologies representing protein classes of homologous genes, proteoforms (e.g., splice isoforms, sequence variants, and post-translationally modified forms), and protein complexes. PRO defines classes of proteins and protein complexes, both species-specific and species nonspecific, and indicates their relationships in a hierarchical framework, supporting accurate protein annotation at the appropriate level of granularity, analyses of protein conservation across species, and semantic reasoning. In the first section of this chapter, we describe the PRO framework including categories of PRO terms and the relationship of PRO to other ontologies and protein resources. Next, we provide a tutorial about the PRO website ( proconsortium.org ) where users can browse and search the PRO hierarchy, view reports on individual PRO terms, and visualize relationships among PRO terms in a hierarchical table view, a multiple sequence alignment view, and a Cytoscape network view. Finally, we describe several examples illustrating the unique and rich information available in PRO.

  12. 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...

  13. Inconsistencies Between Physician-Reported Disclosures at the AAOS Annual Meeting and Industry-Reported Financial Disclosures in the Open Payments Database.

    Science.gov (United States)

    Hannon, Charles P; Chalmers, Peter N; Carpiniello, Matthew F; Cvetanovich, Gregory L; Cole, Brian J; Bach, Bernard R

    2016-10-19

    The purpose of this study was to determine the rate and type of inconsistencies between disclosures self-reported by physicians at a major academic meeting in the United States and industry-reported disclosures in the Open Payments database for a concordant time period. Disclosures for every first and last author from the United States with a medical degree of a podium or poster presentation at the 2014 American Academy of Orthopaedic Surgeons (AAOS) Annual Meeting were collected and were compared with the disclosures reported in the Open Payments database to determine if any inconsistencies were present and, if so, within which category. In total, 1,925 total AAOS presenters were identified, and 1,113 met the inclusion criteria. Based on AAOS disclosures, 432 (39%) should have been listed within the Open Payments database. There were 125 presenters (11%) who reported an AAOS disclosure and thus should have been included in the Open Payments database, but were not included. An additional 259 presenters (23%) had ≥1 AAOS disclosures that were not reported or were improperly categorized in the Open Payments database. Inconsistencies were more common for authors who had significantly more poster presentations (p database (p financial relationships for presenters at the AAOS Annual Meeting and industry-reported relationships published in the Open Payments database. Copyright © 2016 by The Journal of Bone and Joint Surgery, Incorporated.

  14. 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.

  15. On the ontology of spacetime

    CERN Document Server

    Romero, Gustavo E

    2015-01-01

    I present a discussion of some issues in the ontology of spacetime. After a characterisation of the controversies among relationists, substantivalists, eternalists, and presentists, I offer a new argument for rejecting presentism, the doctrine that only present objects exist. Then, I outline and defend a form of spacetime realism that I call event substantivalism. I propose an ontological theory for the emergence of spacetime from more basic entities (timeless and spaceless `events'). Finally, I argue that a relational theory of pre-geometric entities can give rise to substantival spacetime in such a way that relationism and substantivalism are not necessarily opposed positions, but rather complementary. In an appendix I give axiomatic formulations of my ontological views.

  16. An ontology for sensor networks

    Science.gov (United States)

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

    2010-05-01

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

  17. Meeting Competence Needs in the Hotel and Catering Industry Now and in the Future. Research Report 1992.

    Science.gov (United States)

    Walker, Anne, Ed.; Hayter, Roy, Ed.

    The hotel and catering industry in the United Kingdom is estimated to have employed 2,392,000 people in 1990--about 9 percent of the total work force in employment in the country. These figures came from a major study into the skills needs of the hotel and catering industry in relation to the current provision of vocational education. Data are…

  18. Meeting Competence Needs in the Hotel and Catering Industry Now and in the Future. Research Report 1992.

    Science.gov (United States)

    Walker, Anne, Ed.; Hayter, Roy, Ed.

    The hotel and catering industry in the United Kingdom is estimated to have employed 2,392,000 people in 1990--about 9 percent of the total work force in employment in the country. These figures came from a major study into the skills needs of the hotel and catering industry in relation to the current provision of vocational education. Data are…

  19. 75 FR 34802 - Meeting To Learn of U.S. Information and Communications Technologies (ICT) Industry Efforts To...

    Science.gov (United States)

    2010-06-18

    ... To Learn of U.S. Information and Communications Technologies (ICT) Industry Efforts To Assist Haitian... access to information and communication technologies (ICT), improved efficiency in the worldwide ICT and... experiences of U.S. information and communications technologies (ICT) industry infrastructure...

  20. A Statistical Amalgamation Approach for Ontologies

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2012-02-01

    Full Text Available As ontology is subjective and varies in different domains, the amount of ontologies turns out to be huge but with poor compatibility. Mainstream method for ontology integration is mostly achieved by establishing mappings between ontologies. In this essay, the author put forward another way of ontology merging. After statistic machine learning on concept relations, the frequency of different ontologies appeared in concept relations reveals certainty factor and help to build a large-scale concept relations network including the statistic information and domain categories, so that the conceptions conveyed by different ontologies can be fused together and the merging concept space turns to be relatively objective. And the experiments results also help to demonstrate the feasibility of the ontology merging.

  1. Research on Forging Die Design Ontology

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wenlei; FAN Yushun

    2006-01-01

    Forging die design is heavily dependent on engineers' experiences. But traditional AI technologies can barely provide a standard knowledge representation style for knowledge transferring. This paper introduces ontology into forging die design. 3-layer forging die design ontology is built, which includes Meta-ontology, Domain-ontology and Bottom ontology. Further, by conceptualization, the concepts and their relations are formally addressed by primitives such as Term, Relation and Function etc, which are explicitly expressed by concept tree. Bottom ontology uses Knowledge Item and Prototype to represent and capture general knowledge for knowledge reuse and share. Forging die design ontology building approach is discussed for standard knowledge representation, knowledge mine and knowledge driven CAD design etc. And OWL language is employed for integration among different domain ontologies integration. Finally a locomotive forging die KBE system is presented to demonstrate this approach.

  2. 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...

  3. Markov Chain Ontology Analysis (MCOA)

    Science.gov (United States)

    2012-01-01

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

  4. Making Meetings Work Better.

    Science.gov (United States)

    Standke, Linda

    1978-01-01

    Focusing on the increased use by trainers of off-site facilities for employee training meetings, this article looks at some improvements and the expanding market in the meeting site industry. It also highlights emerging trends in the industry and covers the growth of meeting planning into a profession. (EM)

  5. A proposal for a Bohmian ontology of quantum gravity

    CERN Document Server

    Vassallo, Antonio

    2013-01-01

    The paper shows how the Bohmian approach to quantum physics can be applied to develop a clear and coherent ontology of non-perturbative quantum gravity. We suggest retaining discrete objects as the primitive ontology also when it comes to a quantum theory of space-time and therefore focus on loop quantum gravity. We conceive atoms of space, represented in terms of nodes linked by edges in a graph, as the primitive ontology of the theory and show how a non-local law in which a universal and stationary wave-function figures can provide an order of configurations of such atoms of space such that the classical space-time of general relativity is approximated. Although there is as yet no fully worked out physical theory of quantum gravity, we regard the Bohmian approach as setting up a standard that proposals for a serious ontology in this field should meet and as opening up a route for fruitful physical and mathematical investigations.

  6. A Proposal for a Bohmian Ontology of Quantum Gravity

    Science.gov (United States)

    Vassallo, Antonio; Esfeld, Michael

    2014-01-01

    The paper shows how the Bohmian approach to quantum physics can be applied to develop a clear and coherent ontology of non-perturbative quantum gravity. We suggest retaining discrete objects as the primitive ontology also when it comes to a quantum theory of space-time and therefore focus on loop quantum gravity. We conceive atoms of space, represented in terms of nodes linked by edges in a graph, as the primitive ontology of the theory and show how a non-local law in which a universal and stationary wave-function figures can provide an order of configurations of such atoms of space such that the classical space-time of general relativity is approximated. Although there is as yet no fully worked out physical theory of quantum gravity, we regard the Bohmian approach as setting up a standard that proposals for a serious ontology in this field should meet and as opening up a route for fruitful physical and mathematical investigations.

  7. The representation of protein complexes in the Protein Ontology (PRO

    Directory of Open Access Journals (Sweden)

    Smith Barry

    2011-09-01

    Full Text Available Abstract Background Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. Description We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. Conclusion PRO is a unique database resource for species-specific protein complexes. PRO facilitates robust annotation of variations in composition and function contexts for protein complexes within and between species.

  8. The Usability-Error Ontology

    DEFF Research Database (Denmark)

    2013-01-01

    ability to do systematic reviews and meta-analyses. In an effort to support improved and more interoperable data capture regarding Usability Errors, we have created the Usability Error Ontology (UEO) as a classification method for representing knowledge regarding Usability Errors. We expect the UEO...... will grow over time to support an increasing number of HIT system types. In this manuscript, we present this Ontology of Usability Error Types and specifically address Computerized Physician Order Entry (CPOE), Electronic Health Records (EHR) and Revenue Cycle HIT systems....

  9. Building an ontology for cyberterrorism

    CSIR Research Space (South Africa)

    Veerasamy, N

    2012-07-01

    Full Text Available packages such as GraphWiz that allows the asserted and inferred classification hierarchies to be visualised (Horridge et al. 2004). The visualisations help provide succinct images of the deductions drawn from the inserted data and specifications, see... Figures 1 to 4. The next step is the evaluation of the built ontology.The reasoning capabilities within Prot?g? are used to infer new information from the asserted ontology as part of the evaluation process. Prot?g? has a number of built-in reasoners...

  10. 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

  11. 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...

  12. 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

  13. Domain-Specific Ontology of Botany

    Institute of Scientific and Technical Information of China (English)

    Fang Gu; Cun-Gen Cao; Yue-Fei Sui; Wen Tian

    2004-01-01

    Domain-specific ontologies are greatly useful in knowledge acquisition, sharing and analysis. In this paper, botany-specific ontology for acquiring and analyzing botanical knowledge is presented. The ontology is represented in a set of well-defined categories, and each concept is viewed as an instance of certain category. The authors also introduce botany-specific axioms, an integral part of the ontology, for checking and reasoning with the acquired knowledge. Consistency, completeness and redundancy of the axioms are discussed.

  14. Ontology-driven health information systems architectures.

    Science.gov (United States)

    Blobel, Bernd; Oemig, Frank

    2009-01-01

    Following an architecture vision such as the Generic Component Model (GCM) architecture framework, health information systems for supporting personalized care have to be based on a component-oriented architecture. Representing concepts and their interrelations, the GCM perspectives system architecture, domains, and development process can be described by the domains' ontologies. The paper introduces ontology principles, ontology references to the GCM as well as some practical aspects of ontology-driven approaches to semantically interoperable and sustainable health information systems.

  15. The Distributed Ontology Language (DOL): Ontology Integration and Interoperability Applied to Mathematical Formalization

    CERN Document Server

    Lange, Christoph; Mossakowski, Till; Grüninger, Michael

    2012-01-01

    The Distributed Ontology Language (DOL) is currently being standardized within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3. It aims at providing a unified framework for (1) ontologies formalized in heterogeneous logics, (2) modular ontologies, (3) links between ontologies, and (4) annotation of ontologies. This paper focuses on an application of DOL's meta-theoretical features in mathematical formalization: validating relationships between ontological formalizations of mathematical concepts in COLORE (Common Logic Repository), which provide the foundation for formalizing real-world notions such as spatial and temporal relations.

  16. Industry 4.0 meets with China iron and steel industry%“工业4.0”与中国钢铁工业

    Institute of Scientific and Technical Information of China (English)

    李新创; 施灿涛; 赵峰

    2015-01-01

    介绍了“工业4.0”的产生背景,并对其内涵、作用和影响进行剖析,总结了“工业4.0”在全球各国的发展状况。对中国钢铁工业两化融合现状进行了总结,并剖析了存在的问题。从个性化服务、智能化制造、大数据管理、供应链集成等方面讨论了“工业4.0”对中国钢铁工业转型升级带来的积极作用。阐述了“钢铁4.0”的层次化战略实施要点,并提出了系统化的实施建议。%Industry 4.0 is systematically discussed about its emergence background,connotation,advantages and poten-tial effects,as well as the development in some typical countries. The current situation of integration of informatization and industrialization in China iron and steel industry is analyzed while the defects are summarized. The positive influence of Industry 4.0 on China iron and steel industry is presented in respects of customized service,intelligent manufacture,big data management,and supply chain integration. The strategic key points of Steel 4.0 are described hierarchically,and some advice is proposed systematically.

  17. Sample evaluation of ontology-matching systems

    NARCIS (Netherlands)

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

    2007-01-01

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

  18. 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 techniq

  19. Sample evaluation of ontology-matching systems

    NARCIS (Netherlands)

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

    2007-01-01

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

  20. 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

  1. 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 ontolo...

  2. Towards Ontological Foundations for UML Conceptual Models

    NARCIS (Netherlands)

    Guizzardi, Giancarlo; Herre, Heinrich; Wagner, Gerd; Meerman, Robert; Tari, Zahir

    2002-01-01

    UML class diagrams can be used as a language for expressing a conceptual model of a domain. We use the General Ontological Language (GOL) and its underlying upper level ontology, proposed in [1], to evaluate the ontological correctness of a conceptual UML class model and to develop guidelines for

  3. Definition of an Ontology Matching Algorithm for Context Integration in Smart Cities.

    Science.gov (United States)

    Otero-Cerdeira, Lorena; Rodríguez-Martínez, Francisco J; Gómez-Rodríguez, Alma

    2014-12-08

    In this paper we describe a novel proposal in the field of smart cities: using an ontology matching algorithm to guarantee the automatic information exchange between the agents and the smart city. A smart city is composed by different types of agents that behave as producers and/or consumers of the information in the smart city. In our proposal, the data from the context is obtained by sensor and device agents while users interact with the smart city by means of user or system agents. The knowledge of each agent, as well as the smart city's knowledge, is semantically represented using different ontologies. To have an open city, that is fully accessible to any agent and therefore to provide enhanced services to the users, there is the need to ensure a seamless communication between agents and the city, regardless of their inner knowledge representations, i.e., ontologies. To meet this goal we use ontology matching techniques, specifically we have defined a new ontology matching algorithm called OntoPhil to be deployed within a smart city, which has never been done before. OntoPhil was tested on the benchmarks provided by the well known evaluation initiative, Ontology Alignment Evaluation Initiative, and also compared to other matching algorithms, although these algorithms were not specifically designed for smart cities. Additionally, specific tests involving a smart city's ontology and different types of agents were conducted to validate the usefulness of OntoPhil in the smart city environment.

  4. Definition of an Ontology Matching Algorithm for Context Integration in Smart Cities

    Science.gov (United States)

    Otero-Cerdeira, Lorena; Rodríguez-Martínez, Francisco J.; Gómez-Rodríguez, Alma

    2014-01-01

    In this paper we describe a novel proposal in the field of smart cities: using an ontology matching algorithm to guarantee the automatic information exchange between the agents and the smart city. A smart city is composed by different types of agents that behave as producers and/or consumers of the information in the smart city. In our proposal, the data from the context is obtained by sensor and device agents while users interact with the smart city by means of user or system agents. The knowledge of each agent, as well as the smart city's knowledge, is semantically represented using different ontologies. To have an open city, that is fully accessible to any agent and therefore to provide enhanced services to the users, there is the need to ensure a seamless communication between agents and the city, regardless of their inner knowledge representations, i.e., ontologies. To meet this goal we use ontology matching techniques, specifically we have defined a new ontology matching algorithm called OntoPhil to be deployed within a smart city, which has never been done before. OntoPhil was tested on the benchmarks provided by the well known evaluation initiative, Ontology Alignment Evaluation Initiative, and also compared to other matching algorithms, although these algorithms were not specifically designed for smart cities. Additionally, specific tests involving a smart city's ontology and different types of agents were conducted to validate the usefulness of OntoPhil in the smart city environment. PMID:25494353

  5. Definition of an Ontology Matching Algorithm for Context Integration in Smart Cities

    Directory of Open Access Journals (Sweden)

    Lorena Otero-Cerdeira

    2014-12-01

    Full Text Available In this paper we describe a novel proposal in the field of smart cities: using an ontology matching algorithm to guarantee the automatic information exchange between the agents and the smart city. A smart city is composed by different types of agents that behave as producers and/or consumers of the information in the smart city. In our proposal, the data from the context is obtained by sensor and device agents while users interact with the smart city by means of user or system agents. The knowledge of each agent, as well as the smart city’s knowledge, is semantically represented using different ontologies. To have an open city, that is fully accessible to any agent and therefore to provide enhanced services to the users, there is the need to ensure a seamless communication between agents and the city, regardless of their inner knowledge representations, i.e., ontologies. To meet this goal we use ontology matching techniques, specifically we have defined a new ontology matching algorithm called OntoPhil to be deployed within a smart city, which has never been done before. OntoPhil was tested on the benchmarks provided by the well known evaluation initiative, Ontology Alignment Evaluation Initiative, and also compared to other matching algorithms, although these algorithms were not specifically designed for smart cities. Additionally, specific tests involving a smart city’s ontology and different types of agents were conducted to validate the usefulness of OntoPhil in the smart city environment.

  6. An ontology for microbial phenotypes.

    Science.gov (United States)

    Chibucos, Marcus C; Zweifel, Adrienne E; Herrera, Jonathan C; Meza, William; Eslamfam, Shabnam; Uetz, Peter; Siegele, Deborah A; Hu, James C; Giglio, Michelle G

    2014-11-30

    Phenotypic data are routinely used to elucidate gene function in organisms amenable to genetic manipulation. However, previous to this work, there was no generalizable system in place for the structured storage and retrieval of phenotypic information for bacteria. The Ontology of Microbial Phenotypes (OMP) has been created to standardize the capture of such phenotypic information from microbes. OMP has been built on the foundations of the Basic Formal Ontology and the Phenotype and Trait Ontology. Terms have logical definitions that can facilitate computational searching of phenotypes and their associated genes. OMP can be accessed via a wiki page as well as downloaded from SourceForge. Initial annotations with OMP are being made for Escherichia coli using a wiki-based annotation capture system. New OMP terms are being concurrently developed as annotation proceeds. We anticipate that diverse groups studying microbial genetics and associated phenotypes will employ OMP for standardizing microbial phenotype annotation, much as the Gene Ontology has standardized gene product annotation. The resulting OMP resource and associated annotations will facilitate prediction of phenotypes for unknown genes and result in new experimental characterization of phenotypes and functions.

  7. Gene Ontology annotations and resources.

    Science.gov (United States)

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

    2013-01-01

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

  8. 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…

  9. A Mobile Army of Ontologies

    DEFF Research Database (Denmark)

    Juul, Jesper

    2015-01-01

    their cultural position(s). The following scholars have agreed to participate the event: Pawel Grabarczyk (“Games Within Games: How to Properly Individuate Game Modes?”), Stefano Gualeni (“Augmented Ontologies and Games”), Jesper Juul: (“A Mobile Army of Ontologies”), Veli-Matti Karhulahti (“Videogame...

  10. 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.

  11. 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

  12. 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

  13. Ontology for vector surveillance and management.

    Science.gov (United States)

    Lozano-Fuentes, Saul; Bandyopadhyay, Aritra; Cowell, Lindsay G; Goldfain, Albert; Eisen, Lars

    2013-01-01

    Ontologies, which are made up by standardized and defined controlled vocabulary terms and their interrelationships, are comprehensive and readily searchable repositories for knowledge in a given domain. The Open Biomedical Ontologies (OBO) Foundry was initiated in 2001 with the aims of becoming an "umbrella" for life-science ontologies and promoting the use of ontology development best practices. A software application (OBO-Edit; *.obo file format) was developed to facilitate ontology development and editing. The OBO Foundry now comprises over 100 ontologies and candidate ontologies, including the NCBI organismal classification ontology (NCBITaxon), the Mosquito Insecticide Resistance Ontology (MIRO), the Infectious Disease Ontology (IDO), the IDOMAL malaria ontology, and ontologies for mosquito gross anatomy and tick gross anatomy. We previously developed a disease data management system for dengue and malaria control programs, which incorporated a set of information trees built upon ontological principles, including a "term tree" to promote the use of standardized terms. In the course of doing so, we realized that there were substantial gaps in existing ontologies with regards to concepts, processes, and, especially, physical entities (e.g., vector species, pathogen species, and vector surveillance and management equipment) in the domain of surveillance and management of vectors and vector-borne pathogens. We therefore produced an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems. The Vector Surveillance and Management Ontology (VSMO) includes >2,200 unique terms, of which the vast majority (>80%) were newly generated during the development of this ontology. One core feature of the VSMO is the linkage, through

  14. 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

  15. Data Mining Applications Using Ontologies in Biomedicine

    CERN Document Server

    Popescu, Mihail

    2009-01-01

    Presently, a growing number of ontologies are being built and used for annotating data in biomedical research. Thanks to the tremendous amount of data being generated, ontologies are now being used in numerous ways, including connecting different databases, refining search capabilities, interpreting experimental/clinical data, and inferring knowledge. This cutting-edge resource introduces you to latest developments in bio-ontologies. The book provides you with the theoretical foundations and examples of ontologies, as well as applications of ontologies in biomedicine, from molecular levels to

  16. Towards quantitative measures in applied ontology

    CERN Document Server

    Hoehndorf, Robert; Gkoutos, Georgios V

    2012-01-01

    Applied ontology is a relatively new field which aims to apply theories and methods from diverse disciplines such as philosophy, cognitive science, linguistics and formal logics to perform or improve domain-specific tasks. To support the development of effective research methodologies for applied ontology, we critically discuss the question how its research results should be evaluated. We propose that results in applied ontology must be evaluated within their domain of application, based on some ontology-based task within the domain, and discuss quantitative measures which would facilitate the objective evaluation and comparison of research results in applied ontology.

  17. 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.

  18. Ontological simulation for educational process organisation in a higher educational institution

    Science.gov (United States)

    Berestneva, O. G.; Marukhina, O. V.; Bahvalov, S. V.; Fisochenko, O. N.; Berestneva, E. V.

    2017-01-01

    Following the new-generation standards is needed to form a task list connected with planning and organizing of an academic process, structure and content formation of degree programmes. Even when planning the structure and content of an academic process, one meets some problems concerning the necessity to assess the correlation between degree programmes and demands of educational and professional standards and to consider today’s job-market and students demands. The paper presents examples of ontological simulations for solutions of organizing educational process problems in a higher educational institution and gives descriptions of model development. The article presents two examples: ontological simulation when planning an educational process in a higher educational institution and ontological simulation for describing competences of an IT-specialist. The paper sets a conclusion about ontology application perceptiveness for formalization of educational process organization in a higher educational institution.

  19. Using ontologies to improve semantic interoperability in health data.

    Science.gov (United States)

    Liyanage, Harshana; Krause, Paul; De Lusignan, Simon

    2015-07-10

    The present-day health data ecosystem comprises a wide array of complex heterogeneous data sources. A wide range of clinical, health care, social and other clinically relevant information are stored in these data sources. These data exist either as structured data or as free-text. These data are generally individual person-based records, but social care data are generally case based and less formal data sources may be shared by groups. The structured data may be organised in a proprietary way or be coded using one-of-many coding, classification or terminologies that have often evolved in isolation and designed to meet the needs of the context that they have been developed. This has resulted in a wide range of semantic interoperability issues that make the integration of data held on these different systems changing. We present semantic interoperability challenges and describe a classification of these. We propose a four-step process and a toolkit for those wishing to work more ontologically, progressing from the identification and specification of concepts to validating a final ontology. The four steps are: (1) the identification and specification of data sources; (2) the conceptualisation of semantic meaning; (3) defining to what extent routine data can be used as a measure of the process or outcome of care required in a particular study or audit and (4) the formalisation and validation of the final ontology. The toolkit is an extension of a previous schema created to formalise the development of ontologies related to chronic disease management. The extensions are focused on facilitating rapid building of ontologies for time-critical research studies.

  20. Using ontologies to improve semantic interoperability in health data

    Directory of Open Access Journals (Sweden)

    Harshana Liyanage

    2015-07-01

    Full Text Available The present–day health data ecosystem comprises a wide array of complex heterogeneous data sources. A wide range of clinical, health care, social and other clinically relevant information are stored in these data sources. These data exist either as structured data or as free-text. These data are generally individual personbased records, but social care data are generally case based and less formal data sources may be shared by groups. The structured data may be organised in a proprietary way or be coded using one-of-many coding, classification or terminologies that have often evolved in isolation and designed to meet the needs of the context that they have been developed. This has resulted in a wide range of semantic interoperability issues that make the integration of data held on these different systems changing. We present semantic interoperability challenges and describe a classification of these. We propose a four-step process and a toolkit for those wishing to work more ontologically, progressing from the identification and specification of concepts to validating a final ontology. The four steps are: (1 the identification and specification of data sources; (2 the conceptualisation of semantic meaning; (3 defining to what extent routine data can be used as a measure of the process or outcome of care required in a particular study or audit and (4 the formalisation and validation of the final ontology. The toolkit is an extension of a previous schema created to formalise the development of ontologies related to chronic disease management. The extensions are focused on facilitating rapid building of ontologies for time-critical research studies. 

  1. Ontology-Based Semantic Cache in AOKB

    Institute of Scientific and Technical Information of China (English)

    郑红; 陆汝钤; 金芝; 胡思康

    2002-01-01

    When querying on a large-scale knowledge base, a major technique of im-proving performance is to preload knowledge to minimize the number of roundtrips to theknowledge base. In this paper, an ontology-based semantic cache is proposed for an agentand ontology-oriented knowledge base (AOKB). In AOKB, an ontology is the collection of re-lationships between a group of knowledge units (agents and/or other sub-ontologies). Whenloading some agent A, its relationships with other knowledge units are examined, and thosewho have a tight semantic tie with A will be preloaded at the same time, including agents andsub-ontologies in the same ontology where A is. The preloaded agents and ontologies are savedat a semantic cache located in the memory. Test results show that up to 50% reduction inrunning time is achieved.

  2. Impact of ontology evolution on functional analyses.

    Science.gov (United States)

    Groß, Anika; Hartung, Michael; Prüfer, Kay; Kelso, Janet; Rahm, Erhard

    2012-10-15

    Ontologies are used in the annotation and analysis of biological data. As knowledge accumulates, ontologies and annotation undergo constant modifications to reflect this new knowledge. These modifications may influence the results of statistical applications such as functional enrichment analyses that describe experimental data in terms of ontological groupings. Here, we investigate to what degree modifications of the Gene Ontology (GO) impact these statistical analyses for both experimental and simulated data. The analysis is based on new measures for the stability of result sets and considers different ontology and annotation changes. Our results show that past changes in the GO are non-uniformly distributed over different branches of the ontology. Considering the semantic relatedness of significant categories in analysis results allows a more realistic stability assessment for functional enrichment studies. We observe that the results of term-enrichment analyses tend to be surprisingly stable despite changes in ontology and annotation.

  3. FOREWORD: Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12 14 June 2007)

    Science.gov (United States)

    Hafner, Jürgen

    2008-02-01

    The development of modern materials science has led to a growing need to understand the phenomena determining the properties of materials on an atomistic level. As the behavior of atoms and electrons is governed by the laws of quantum mechanics, accurate and efficient techniques for solving the basic quantum-mechanical equations for very complex many-atom, many-electron systems are required. The development of density-functional theory (DFT) represents a decisive step forwards in our efforts to develop tools for ab initio atomistic simulations of complex materials, preparing the way towards computational materials design. The development of these ab initio simulation methods, whose aim is to model processes in materials by solving the coupled Newtonian equations of motion of the atoms and the Schrödinger equation for the electrons from first principles without any other input than the atomic numbers of the constituents, is part of fundamental research. Hence, for a long time the development and application of DFT methods has been a domain of academic research. Only during the past decade, based on the development of increasingly sophisticated codes and better computer performance, has the impact of DFT-based simulation methods has spread from academia to industry. New opportunities are opening for innovative materials research across physics, chemistry, surface science and nanotechnology extending even to earth sciences and molecular biology. In 1998 we organized, at the Vienna University of Technology, a first workshop entitled 'Electronic Structure Calculations for Industry and Basic Sciences' (short title 'Theory meets Industry') to celebrate the start of the European Science Foundation (ESF) research program 'Electronic Structure Calculations for Elucidating the Complex Atomistic Behavior of Solids and Surfaces', known as the Ψk-network. At this workshop, researchers from academia presented recent results in the development of ab initio simulation methods and

  4. Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007).

    Science.gov (United States)

    Hafner, Jürgen

    2008-02-13

    The development of modern materials science has led to a growing need to understand the phenomena determining the properties of materials on an atomistic level. As the behavior of atoms and electrons is governed by the laws of quantum mechanics, accurate and efficient techniques for solving the basic quantum-mechanical equations for very complex many-atom, many-electron systems are required. The development of density-functional theory (DFT) represents a decisive step forwards in our efforts to develop tools for ab initio atomistic simulations of complex materials, preparing the way towards computational materials design. The development of these ab initio simulation methods, whose aim is to model processes in materials by solving the coupled Newtonian equations of motion of the atoms and the Schrödinger equation for the electrons from first principles without any other input than the atomic numbers of the constituents, is part of fundamental research. Hence, for a long time the development and application of DFT methods has been a domain of academic research. Only during the past decade, based on the development of increasingly sophisticated codes and better computer performance, has the impact of DFT-based simulation methods has spread from academia to industry. New opportunities are opening for innovative materials research across physics, chemistry, surface science and nanotechnology extending even to earth sciences and molecular biology. In 1998 we organized, at the Vienna University of Technology, a first workshop entitled 'Electronic Structure Calculations for Industry and Basic Sciences' (short title 'Theory meets Industry') to celebrate the start of the European Science Foundation (ESF) research program 'Electronic Structure Calculations for Elucidating the Complex Atomistic Behavior of Solids and Surfaces', known as the Ψ(k)-network. At this workshop, researchers from academia presented recent results in the development of ab initio simulation methods

  5. Building a biomedical ontology recommender web service.

    Science.gov (United States)

    Jonquet, Clement; Musen, Mark A; Shah, Nigam H

    2010-06-22

    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. 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. 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.

  6. 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.

  7. Meeting the Expectation of Industry: An Integrated Approach for the Teaching of Mechanics and Electronics to Design Students

    Science.gov (United States)

    Bingham, Guy A.; Southee, Darren J.; Page, Tom

    2015-01-01

    This paper examines the traditional engineering-based provision delivered to Product Design and Technology (B.Sc.) undergraduates at the Loughborough Design School and questions its relevancy against the increasing expectations of industry. The paper reviews final-year design projects to understand the level of transference of engineering-based…

  8. An Educational Needs Assessment of Pennsylvania Workforce: Opportunities to Redefine Secondary Career and Technical Education to Meet Food Industry Needs

    Science.gov (United States)

    Napoleon, Larry; Freedman, Debra; Seetharaman, Koushik; Sharma, Priya

    2006-01-01

    This article describes the outcomes of a needs assessment concerning current training needs and performance targets for non-degreed employees in the food industry. Focus groups were used to gather data from 5 food-processing companies: a fresh vegetable company, a canned vegetable company, 2 snack food companies, and a meat company. Focus group…

  9. CNTAC Hosted the Most Successful ITMF's Annual Meeting Shanghai,Focus the Attention of Global Textile Industry

    Institute of Scientific and Technical Information of China (English)

    Wang Ting

    2009-01-01

    @@ This October,besides the usual China International Trade Fair for Apparel Fabrics and Accessories held in the city of Shanghai,another important event was set to take place in Shanghai the 2009 Annual Conference of the International Textile Manufacturers Federation (ITMF),making Shanghai the place focusing all the attention of the global textile industries markedly.

  10. An Educational Needs Assessment of Pennsylvania Workforce: Opportunities to Redefine Secondary Career and Technical Education to Meet Food Industry Needs

    Science.gov (United States)

    Napoleon, Larry; Freedman, Debra; Seetharaman, Koushik; Sharma, Priya

    2006-01-01

    This article describes the outcomes of a needs assessment concerning current training needs and performance targets for non-degreed employees in the food industry. Focus groups were used to gather data from 5 food-processing companies: a fresh vegetable company, a canned vegetable company, 2 snack food companies, and a meat company. Focus group…

  11. WEB MINING BASED FRAMEWORK FOR ONTOLOGY LEARNING

    Directory of Open Access Journals (Sweden)

    C.Ramesh

    2015-07-01

    Full Text Available Today, the notion of Semantic Web has emerged as a prominent solution to the problem of organizing the immense information provided by World Wide Web, and its focus on supporting a better co-operation between humans and machines is noteworthy. Ontology forms the major component of Semantic Web in its realization. However, manual method of ontology construction is time-consuming, costly, error-prone and inflexible to change and in addition, it requires a complete participation of knowledge engineer or domain expert. To address this issue, researchers hoped that a semi-automatic or automatic process would result in faster and better ontology construction and enrichment. Ontology learning has become recently a major area of research, whose goal is to facilitate construction of ontologies, which reduces the effort in developing ontology for a new domain. However, there are few research studies that attempt to construct ontology from semi-structured Web pages. In this paper, we present a complete framework for ontology learning that facilitates the semi-automation of constructing and enriching web site ontology from semi structured Web pages. The proposed framework employs Web Content Mining and Web Usage mining in extracting conceptual relationship from Web. The main idea behind this concept was to incorporate the web author's ideas as well as web users’ intentions in the ontology development and its evolution.

  12. Evaluation of research in biomedical ontologies

    Science.gov (United States)

    Dumontier, Michel; Gkoutos, Georgios V.

    2013-01-01

    Ontologies are now pervasive in biomedicine, where they serve as a means to standardize terminology, to enable access to domain knowledge, to verify data consistency and to facilitate integrative analyses over heterogeneous biomedical data. For this purpose, research on biomedical ontologies applies theories and methods from diverse disciplines such as information management, knowledge representation, cognitive science, linguistics and philosophy. Depending on the desired applications in which ontologies are being applied, the evaluation of research in biomedical ontologies must follow different strategies. Here, we provide a classification of research problems in which ontologies are being applied, focusing on the use of ontologies in basic and translational research, and we demonstrate how research results in biomedical ontologies can be evaluated. The evaluation strategies depend on the desired application and measure the success of using an ontology for a particular biomedical problem. For many applications, the success can be quantified, thereby facilitating the objective evaluation and comparison of research in biomedical ontology. The objective, quantifiable comparison of research results based on scientific applications opens up the possibility for systematically improving the utility of ontologies in biomedical research. PMID:22962340

  13. The Orthology Ontology: development and applications.

    Science.gov (United States)

    Fernández-Breis, Jesualdo Tomás; Chiba, Hirokazu; Legaz-García, María Del Carmen; Uchiyama, Ikuo

    2016-06-04

    Computational comparative analysis of multiple genomes provides valuable opportunities to biomedical research. In particular, orthology analysis can play a central role in comparative genomics; it guides establishing evolutionary relations among genes of organisms and allows functional inference of gene products. However, the wide variations in current orthology databases necessitate the research toward the shareability of the content that is generated by different tools and stored in different structures. Exchanging the content with other research communities requires making the meaning of the content explicit. The need for a common ontology has led to the creation of the Orthology Ontology (ORTH) following the best practices in ontology construction. Here, we describe our model and major entities of the ontology that is implemented in the Web Ontology Language (OWL), followed by the assessment of the quality of the ontology and the application of the ORTH to existing orthology datasets. This shareable ontology enables the possibility to develop Linked Orthology Datasets and a meta-predictor of orthology through standardization for the representation of orthology databases. The ORTH is freely available in OWL format to all users at http://purl.org/net/orth . The Orthology Ontology can serve as a framework for the semantic standardization of orthology content and it will contribute to a better exploitation of orthology resources in biomedical research. The results demonstrate the feasibility of developing shareable datasets using this ontology. Further applications will maximize the usefulness of this ontology.

  14. Evaluation of research in biomedical ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Gkoutos, Georgios V

    2013-11-01

    Ontologies are now pervasive in biomedicine, where they serve as a means to standardize terminology, to enable access to domain knowledge, to verify data consistency and to facilitate integrative analyses over heterogeneous biomedical data. For this purpose, research on biomedical ontologies applies theories and methods from diverse disciplines such as information management, knowledge representation, cognitive science, linguistics and philosophy. Depending on the desired applications in which ontologies are being applied, the evaluation of research in biomedical ontologies must follow different strategies. Here, we provide a classification of research problems in which ontologies are being applied, focusing on the use of ontologies in basic and translational research, and we demonstrate how research results in biomedical ontologies can be evaluated. The evaluation strategies depend on the desired application and measure the success of using an ontology for a particular biomedical problem. For many applications, the success can be quantified, thereby facilitating the objective evaluation and comparison of research in biomedical ontology. The objective, quantifiable comparison of research results based on scientific applications opens up the possibility for systematically improving the utility of ontologies in biomedical research.

  15. Mapping of Core Components Based e-Business Standards into Ontology

    Science.gov (United States)

    Magdalenić, Ivan; Vrdoljak, Boris; Schatten, Markus

    A mapping of Core Components specification based e-business standards to an ontology is presented. The Web Ontology Language (OWL) is used for ontology development. In order to preserve the existing hierarchy of the standards, an emphasis is put on the mapping of Core Components elements to specific constructs in OWL. The main purpose of developing an e-business standards' ontology is to create a foundation for an automated mapping system that would be able to convert concepts from various standards in an independent fashion. The practical applicability and verification of the presented mappings is tested on the mapping of Universal Business Language version 2.0 and Cross Industry Invoice version 2.0 to OWL.

  16. The Usability-Error Ontology

    DEFF Research Database (Denmark)

    2013-01-01

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

  17. Jacob's Ladder and Scientific Ontologies

    CERN Document Server

    Stern, Julio Michael

    2013-01-01

    The main goal of this article is to use the epistemological framework of a specific version of Cognitive Constructivism to address Piaget's central problem of knowledge construction, namely, the re-equilibration of cognitive structures. The distinctive objective character of this constructivist framework is based on Heinz von Foerster's fundamental metaphor of - objects as tokens for eigen-solutions, and is also supported by formal inference methods of Bayesian statistics. This epistemological perspective is illustrated using some episodes in the history of chemistry concerning the definition or identification of chemical elements. Some of von Foerster's epistemological imperatives provide general guidelines of development and argumentation. Keywords: Chemical elements; Cognitive constructivism; Development of cognitive structures; Eigen-solutions; External symbol grounding; Objective knowledge; Ontology alignments; Scientific ontologies.

  18. Revealing ontological commitments by magic.

    Science.gov (United States)

    Griffiths, Thomas L

    2015-03-01

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

  19. Ontologies and tag-statistics

    CERN Document Server

    Tibely, Gergely; Vicsek, Tamas; 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 topic with great actuality 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 organisation 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 type of tagged networks available for research, where the tags are already organised 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 r...

  20. Ventilation and health in non-industrial indoor environments: report from a European Multidisciplinary Scientific Consensus Meeting (EUROVEN)

    DEFF Research Database (Denmark)

    Wargocki, Pawel; Sundell, Jan; Bischof, W.

    2002-01-01

    leave), and that an association between ventilation and productivity (performance of office work) is indicated. The group also concluded that increasing outdoor air supply rates in non-industrial environments improves perceived air quality; that outdoor air supply rates below 25 l/s per person increase...... the risk of SBS symptoms, increase short-term sick leave, and decrease productivity among occupants of office buildings; and that ventilation rates above 0.5 air changes per hour (h-1) in homes reduce infestation of house dust mites in Nordic countries. The group concluded additionally that the literature......Scientific literature on the effects of ventilation on health, comfort, and productivity in non-industrial indoor environments (offices, schools, homes, etc.) has been reviewed by a multidisciplinary group of European scientists, called EUROVEN, with expertise in medicine, epidemiology, toxicology...

  1. Ventilation and health in non-industrial indoor environments: report from a European Multidisciplinary Scientific Consensus Meeting (EUROVEN)

    DEFF Research Database (Denmark)

    Wargocki, Pawel; Sundell, Jan; Bischof, W.

    2002-01-01

    Scientific literature on the effects of ventilation on health, comfort, and productivity in non-industrial indoor environments (offices, schools, homes, etc.) has been reviewed by a multidisciplinary group of European scientists, called EUROVEN, with expertise in medicine, epidemiology, toxicology......, and engineering. The group reviewed 105 papers published in peer-reviewed scientific journals and judged 30 as conclusive, providing sufficient information on ventilation, health effects, data processing, and reporting, 14 as providing relevant background information on the issue, 43 as relevant but non...... leave), and that an association between ventilation and productivity (performance of office work) is indicated. The group also concluded that increasing outdoor air supply rates in non-industrial environments improves perceived air quality; that outdoor air supply rates below 25 l/s per person increase...

  2. 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....

  3. Social Ontology and Social Cognition

    OpenAIRE

    Lo Presti, Patrizio

    2013-01-01

    The aim of this paper is to show that there is a reciprocal dependency relationship between social cognition and social ontology. It is argued that, on the one hand, the existence conditions of socially meaningful objects and of social groups are about subjects’ social cognitive processes and interactive patterns and, on the other hand, social cognitive processes and interactive patterns are modulated by socially meaningful objects and social groups. I proceed from a historically informed dis...

  4. Constraints in meeting food safety and quality requirements in the Turkish dairy industry: a case study of Izmir province.

    Science.gov (United States)

    Demirbaş, Nevin; Karagözlü, Cem

    2008-02-01

    Recent global developments concerning food quality and food safety have influenced and stimulated food legislation in Turkey in accordance with internal and international trade and agreements. In this study, the way in which the dairy industry conforms to this legislation was analyzed through a case study of Izmir province, which generally has all the structural characteristics of the dairy sector in Turkey. A survey in which dairy plant managers responded to a special questionnaire was used to collect data from 86 dairy plants chosen on the basis of proportional sampling. According to the results of this study, (i) there are many dairy processors in the region, (ii) most managers have a limited education concerning their positions, (iii) most firms handle small volumes of milk and have little control over the raw milk supply, (iv) resources are too limited in these firms, limiting their ability to adopt most regulations, and (v) few processors apply the regulatory practices imposed by governmental agencies. Thus, food legislation is not enough to ensure food safety in the dairy industry in Turkey. Technical and educational support should be given to farmers and the staff of dairy firms by the Ministry of Agriculture to form an appropriate food safety infrastructure in Turkey for the milk and processed dairy products industry.

  5. Improvements to cardiovascular gene ontology.

    Science.gov (United States)

    Lovering, Ruth C; Dimmer, Emily C; Talmud, Philippa J

    2009-07-01

    Gene Ontology (GO) provides a controlled vocabulary to describe the attributes of genes and gene products in any organism. Although one might initially wonder what relevance a 'controlled vocabulary' might have for cardiovascular science, such a resource is proving highly useful for researchers investigating complex cardiovascular disease phenotypes as well as those interpreting results from high-throughput methodologies. GO enables the current functional knowledge of individual genes to be used to annotate genomic or proteomic datasets. In this way, the GO data provides a very effective way of linking biological knowledge with the analysis of the large datasets of post-genomics research. Consequently, users of high-throughput methodologies such as expression arrays or proteomics will be the main beneficiaries of such annotation sets. However, as GO annotations increase in quality and quantity, groups using small-scale approaches will gradually begin to benefit too. For example, genome wide association scans for coronary heart disease are identifying novel genes, with previously unknown connections to cardiovascular processes, and the comprehensive annotation of these novel genes might provide clues to their cardiovascular link. At least 4000 genes, to date, have been implicated in cardiovascular processes and an initiative is underway to focus on annotating these genes for the benefit of the cardiovascular community. In this article we review the current uses of Gene Ontology annotation to highlight why Gene Ontology should be of interest to all those involved in cardiovascular research.

  6. The relevance of ontological commitments

    CERN Document Server

    Echenique-Robba, Pablo

    2014-01-01

    In this introductory note, I describe my particular view of the notion of ontological commitments as honest and pragmatic working hypotheses that assume the existence (out there) of certain entities represented by the symbols in our theory. I argue that this is not naive, in the sense that it does not entail the belief that the hypotheses could ever be proved to be true (or false), but it is nevertheless justified by the success and predictive power of the theory that contains the concepts assumed to exist. I also claim that the ontological commitments one holds (even if tacitly so) have a great influence on what kind of science is produced, how it is used, and how it is understood. Not only I justify this claim, but I also propose a sketch of a possible falsification of it. As a natural conclusion, I defend the importance of identifying, clarifying and making explicit one's ontological commitments if fruitful scientific discussions are to be had. Finally, I compare my point of view with that of some philosop...

  7. 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.

  8. 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.

  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. Context Ontology Implementation for Smart Home

    CERN Document Server

    Van Nguyen, Tam; Nguyen, Huy; Choi, Deokjai; Lee, Chilwoo

    2010-01-01

    Context awareness is one of the important fields in ubiquitous computing. Smart Home, a specific instance of ubiquitous computing, provides every family with opportunities to enjoy the power of hi-tech home living. Discovering that relationship among user, activity and context data in home environment is semantic, therefore, we apply ontology to model these relationships and then reason them as the semantic information. In this paper, we present the realization of smart home's context-aware system based on ontology. We discuss the current challenges in realizing the ontology context base. These challenges can be listed as collecting context information from heterogeneous sources, such as devices, agents, sensors into ontology, ontology management, ontology querying, and the issue related to environment database explosion.

  11. Ontological Queries: Rewriting and Optimization (Extended Version)

    CERN Document Server

    Gottlob, Georg; Pieris, Andreas

    2011-01-01

    Ontological queries are evaluated against an ontology rather than directly on a database. The evaluation and optimization of such queries is an intriguing new problem for database research. In this paper we discuss two important aspects of this problem: query rewriting and query optimization. Query rewriting consists of the compilation of an ontological query into an equivalent query against the underlying relational database. The focus here is on soundness and completeness. We review previous results and present a new rewriting algorithm for rather general types of ontological constraints. In particular, we show how a conjunctive query against an ontology can be compiled into a union of conjunctive queries against the underlying database. Ontological query optimization, in this context, attempts to improve this process so to produce possibly small and cost-effective UCQ rewritings for an input query. We review existing optimization methods, and propose an effective new method that works for linear Datalog+/-...

  12. 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.

  13. 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......The term 'ontology' has been used in many ways and across different communities. In th following we will introduce ontologies as an explication of some shared vocabulary or conceptualization of a specific subject matter. The main problem with the use of a shared vocabulary according to a specific...... 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...

  14. Combining Ontology Development Methodologies and Semantic Web Platforms for E-government Domain Ontology Development

    CERN Document Server

    Dombeu, Jean Vincent Fonou; 10.5121/ijwest.2011.2202

    2011-01-01

    One of the key challenges in electronic government (e-government) is the development of systems that can be easily integrated and interoperated to provide seamless services delivery to citizens. In recent years, Semantic Web technologies based on ontology have emerged as promising solutions to the above engineering problems. However, current research practicing semantic development in e-government does not focus on the application of available methodologies and platforms for developing government domain ontologies. Furthermore, only a few of these researches provide detailed guidelines for developing semantic ontology models from a government service domain. This research presents a case study combining an ontology building methodology and two state-of-the-art Semantic Web platforms namely Protege and Java Jena ontology API for semantic ontology development in e-government. Firstly, a framework adopted from the Uschold and King ontology building methodology is employed to build a domain ontology describing th...

  15. C2 Domain Ontology within Our Lifetime

    Science.gov (United States)

    2009-06-01

    process or an event). [21] Figure 1, adopted from [16], depicts the concept of ontological levels for a post office application based on the Husserl ...University, NJ, 2008. [23] Husserl , E., Id Macmillan. 1931. [24] Basic Formal Ontology (multiple references and artifacts): http://www.ifomis.org/bfo/BFO...Applied Ontology An Introduction, pp 39-56, Transaction Books, Rutgers University, NJ, 2008.  [23] Husserl , E., Ideas: General Introduction to Pure

  16. Ontology-Based Classification System Development Methodology

    OpenAIRE

    2015-01-01

    The aim of the article is to analyse and develop an ontology-based classification system methodology that uses decision tree learning with statement propositionalized attributes. Classical decision tree learning algorithms, as well as decision tree learning with taxonomy and propositionalized attributes have been observed. Thus, domain ontology can be extracted from the data sets and can be used for data classification with the help of a decision tree. The use of ontology methods in decision ...

  17. Towards Scalable Instance Retrieval over Ontologies

    Science.gov (United States)

    Kaplunova, Alissa; Möller, Ralf; Wandelt, Sebastian; Wessel, Michael

    In this paper, we consider the problem of query answering over large multimedia ontologies. Traditional reasoning systems may have problems to deal with large amounts of expressive ontological data (terminological as well as assertional data) that usually must be kept in main memory. We propose to overcome this problem with a new so-called filter and refine paradigm for ontology-based query answering.

  18. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

    Science.gov (United States)

    Bastian, Frederic B; Chibucos, Marcus C; Gaudet, Pascale; Giglio, Michelle; Holliday, Gemma L; Huang, Hong; Lewis, Suzanna E; Niknejad, Anne; Orchard, Sandra; Poux, Sylvain; Skunca, Nives; Robinson-Rechavi, Marc

    2015-01-01

    Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations has considerably grown in recent years. However, the reliability of these annotations varies; it has thus become necessary to be able to assess the confidence in annotations. Although several resources already provide confidence information about the annotations that they produce, a standard way of providing such information has yet to be defined. This lack of standardization undermines the propagation of knowledge across resources, as well as the credibility of results from high-throughput analyses. Seeded at a workshop during the Biocuration 2012 conference, a working group has been created to address this problem. We present here the elements that were identified as essential for assessing confidence in annotations, as well as a draft ontology--the Confidence Information Ontology--to illustrate how the problems identified could be addressed. We hope that this effort will provide a home for discussing this major issue among the biocuration community. Tracker URL: https://github.com/BgeeDB/confidence-information-ontology Ontology URL: https://raw.githubusercontent.com/BgeeDB/confidence-information-ontology/master/src/ontology/cio-simple.obo

  19. eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.

    Science.gov (United States)

    Hastings, Janna; Jeliazkova, Nina; Owen, Gareth; Tsiliki, Georgia; Munteanu, Cristian R; Steinbeck, Christoph; Willighagen, Egon

    2015-01-01

    Engineered nanomaterials (ENMs) are being developed to meet specific application needs in diverse domains across the engineering and biomedical sciences (e.g. drug delivery). However, accompanying the exciting proliferation of novel nanomaterials is a challenging race to understand and predict their possibly detrimental effects on human health and the environment. The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. Here, we describe the development of the eNanoMapper ontology based on adopting and extending existing ontologies of relevance for the nanosafety domain. The resulting eNanoMapper ontology is available at http://purl.enanomapper.net/onto/enanomapper.owl. We aim to make the re-use of external ontology content seamless and thus we have developed a library to automate the extraction of subsets of ontology content and the assembly of the subsets into an integrated whole. The library is available (open source) at http://github.com/enanomapper/slimmer/. Finally, we give a comprehensive survey of the domain content and identify gap areas. ENM safety is at the boundary between engineering and the life sciences, and at the boundary between molecular granularity and bulk granularity. This creates challenges for the definition of key entities in the domain, which we also discuss.

  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. Toward cognitivist ontologies : on the role of selective attention for upper ontologies.

    Science.gov (United States)

    Carstensen, Kai-Uwe

    2011-11-01

    Ontologies play a key role in modern information society although there are still many fundamental questions regarding their structure to be answered. In this paper, some of these are presented, and it is argued that they require a shift from realist to cognitivist ontologies, with ontology design crucially depending on taking both cognitive and linguistic aspects into consideration. A detailed discussion of central parts of a proposed cognitivist upper ontology based on qualitative representations of selective attention is presented.

  2. Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base

    OpenAIRE

    2010-01-01

    Abstract Background The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). Results We define the Saliva Ontology (SALO; http://www.skb...

  3. NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation

    OpenAIRE

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

    2016-01-01

    Background. 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 Biome...

  4. NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation

    OpenAIRE

    Mart?nez-Romero, Marcos; Jonquet, Clement; O'Connor, Martin J.; Graybeal, John; Pazos, Alejandro; Musen, Mark A.

    2016-01-01

    Background 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 Biomed...

  5. A Marketplace for Ontologies and Ontology-Based Tools and Applications in the Life Sciences

    Energy Technology Data Exchange (ETDEWEB)

    McEntire, R; Goble, C; Stevens, R; Neumann, E; Matuszek, P; Critchlow, T; Tarczy-Hornoch, P

    2005-06-30

    This paper describes a strategy for the development of ontologies in the life sciences, tools to support the creation and use of those ontologies, and a framework whereby these ontologies can support the development of commercial applications within the field. At the core of these efforts is the need for an organization that will provide a focus for ontology work that will engage researchers as well as drive forward the commercial aspects of this effort.

  6. Recycling of modules: the industry meets the demand; Recyclage des modules: la filiere s'organise

    Energy Technology Data Exchange (ETDEWEB)

    Houot, G.

    2011-04-15

    In a few years the number of photovoltaic plants to be decommissioned will begin to grow dramatically which will generate a huge need for the collect and recycling of old solar panels. A European association PV-Cycle proposes to set up a dedicated waste processing industry that will be able to recycle up to 85% of the wastes from old solar panels. 23 spots for recovering solar panels have been installed throughout Europe, the recovery of about 1000 to 1500 tons of equipment is expected for 2011. The German Sunicon enterprise has set up an automated process that combines thermal, mechanical and chemical processes in order to allow an almost complete recycling of glass and silicon into the solar panel industry. In a near future the capacity of Sunicon will pass from 800 tons to 20.000 tons a year. The American company First Solar organizes itself the recovery and recycling of the CdTe solar panels it manufactured. (A.C.)

  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. 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 supple......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...

  9. 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...

  10. 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.

  11. The current landscape of pitfalls in Ontologies

    CSIR Research Space (South Africa)

    Keet, CM

    2013-09-01

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

  12. Logical Development of the Cell Ontology

    Directory of Open Access Journals (Sweden)

    Blake Judith A

    2011-01-01

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

  13. Agile development of ontologies through conversation

    Science.gov (United States)

    Braines, Dave; Bhattal, Amardeep; Preece, Alun D.; de Mel, Geeth

    2016-05-01

    Ontologies and semantic systems are necessarily complex but offer great potential in terms of their ability to fuse information from multiple sources in support of situation awareness. Current approaches do not place the ontologies directly into the hands of the end user in the field but instead hide them away behind traditional applications. We have been experimenting with human-friendly ontologies and conversational interactions to enable non-technical business users to interact with and extend these dynamically. In this paper we outline our approach via a worked example, covering: OWL ontologies, ITA Controlled English, Sensor/mission matching and conversational interactions between human and machine agents.

  14. Contributions to an animal trait ontology.

    Science.gov (United States)

    Hulsegge, B; Smits, M A; te Pas, M F W; Woelders, H

    2012-06-01

    Improved understanding of the biology of traits of livestock species necessitates the use and combination of information that is stored in a variety of different sources such as databases and literature. The ability to effectively combine information from different sources, however, depends on a high level of standardization within and between various resources, at least with respect to the used terminology. Ontologies represent a set of concepts that facilitate standardization of terminology within specific domains of interest. The biological mechanisms underlying quantitative traits of farm animal species related to reproduction and host pathogen interactions are complex and not well understood. This knowledge could be improved through the availability of domain-specific ontologies that provide enhanced possibilities for data annotation, data retrieval, data integration, data exchange, data analysis, and ontology-based searches. Here we describe a framework for domain-specific ontologies and the development of 2 first-generation ontologies: Reproductive Trait and Phenotype Ontology (REPO) and Host Pathogen Interactions Ontology . In these first-generation ontologies, we focused on "female fertility in cattle" and "interactions between pigs and Salmonella". Through this, we contribute to the global initiative toward the development of an Animal Trait Ontology for livestock species. To demonstrate its usefulness, we show how REPO can be used to select candidate genes for fertility.

  15. The National Center for Biomedical Ontology.

    Science.gov (United States)

    Musen, Mark A; Noy, Natalya F; Shah, Nigam H; Whetzel, Patricia L; Chute, Christopher G; Story, Margaret-Anne; Smith, Barry

    2012-01-01

    The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data.

  16. 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.

  17. Building Ontologies to Understand Spoken Tunisian Dialect

    CERN Document Server

    Graja, Marwa; Belguith, Lamia Hadrich

    2011-01-01

    This paper presents a method to understand spoken Tunisian dialect based on lexical semantic. This method takes into account the specificity of the Tunisian dialect which has no linguistic processing tools. This method is ontology-based which allows exploiting the ontological concepts for semantic annotation and ontological relations for speech interpretation. This combination increases the rate of comprehension and limits the dependence on linguistic resources. This paper also details the process of building the ontology used for annotation and interpretation of Tunisian dialect in the context of speech understanding in dialogue systems for restricted domain.

  18. Analysis of the OWL ontologies: A survey

    OpenAIRE

    García-Peñalvo, Francisco José; García, Juan; Therón-Sánchez, Roberto

    2011-01-01

    [ES] Web Ontology Language (OWL) es una de las últimas recomendaciones de la World Wide Web Consortium (W3C) para desarrollar ontologías. El uso de ontologías OWL debe implicar la posibilidad de la evaluación de la calidad y exactitud. Se han propuesto una gran diversidad de herramientas y métricas para alcanzar este objetivo. OntoQA ONTOMETRIC, representa las herramientas más importantes para evaluar ontologías que suelen apoyarse en mediciones. Este trabajo analiza todas estas herramientas ...

  19. The National Center for Biomedical Ontology

    Science.gov (United States)

    Noy, Natalya F; Shah, Nigam H; Whetzel, Patricia L; Chute, Christopher G; Story, Margaret-Anne; Smith, Barry

    2011-01-01

    The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. PMID:22081220

  20. 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…

  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. 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.

  3. 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

  4. 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…

  5. 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…

  6. 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.

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

    Science.gov (United States)

    d'Aquin, Mathieu; Noy, Natalya F

    2012-03-01

    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.

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

    DEFF Research Database (Denmark)

    Ahmed, Saeema; Storga, M

    2009-01-01

    This paper presents a comparison of two previous and separate efforts to develop an ontology in the engineering design domain, together with an ontology proposal from which ontologies for a specific application may be derived. The research contrasts an empirical, user-centered approach to develop...

  9. The ontology of quantum field theory: Structural realism vindicated?

    Science.gov (United States)

    Glick, David

    2016-10-01

    In this paper I elicit a prediction from structural realism and compare it, not to a historical case, but to a contemporary scientific theory. If structural realism is correct, then we should expect physics to develop theories that fail to provide an ontology of the sort sought by traditional realists. If structure alone is responsible for instrumental success, we should expect surplus ontology to be eliminated. Quantum field theory (QFT) provides the framework for some of the best confirmed theories in science, but debates over its ontology are vexed. Rather than taking a stand on these matters, the structural realist can embrace QFT as an example of just the kind of theory SR should lead us to expect. Yet, it is not clear that QFT meets the structuralist's positive expectation by providing a structure for the world. In particular, the problem of unitarily inequivalent representations threatens to undermine the possibility of QFT providing a unique structure for the world. In response to this problem, I suggest that the structuralist should endorse pluralism about structure.

  10. 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.

  11. dcGOR: an R package for analysing ontologies and protein domain annotations.

    Directory of Open Access Journals (Sweden)

    Hai Fang

    2014-10-01

    Full Text Available I introduce an open-source R package 'dcGOR' to provide the bioinformatics community with the ease to analyse ontologies and protein domain annotations, particularly those in the dcGO database. The dcGO is a comprehensive resource for protein domain annotations using a panel of ontologies including Gene Ontology. Although increasing in popularity, this database needs statistical and graphical support to meet its full potential. Moreover, there are no bioinformatics tools specifically designed for domain ontology analysis. As an add-on package built in the R software environment, dcGOR offers a basic infrastructure with great flexibility and functionality. It implements new data structure to represent domains, ontologies, annotations, and all analytical outputs as well. For each ontology, it provides various mining facilities, including: (i domain-based enrichment analysis and visualisation; (ii construction of a domain (semantic similarity network according to ontology annotations; and (iii significance analysis for estimating a contact (statistical significance network. To reduce runtime, most analyses support high-performance parallel computing. Taking as inputs a list of protein domains of interest, the package is able to easily carry out in-depth analyses in terms of functional, phenotypic and diseased relevance, and network-level understanding. More importantly, dcGOR is designed to allow users to import and analyse their own ontologies and annotations on domains (taken from SCOP, Pfam and InterPro and RNAs (from Rfam as well. The package is freely available at CRAN for easy installation, and also at GitHub for version control. The dedicated website with reproducible demos can be found at http://supfam.org/dcGOR.

  12. dcGOR: an R package for analysing ontologies and protein domain annotations.

    Science.gov (United States)

    Fang, Hai

    2014-10-01

    I introduce an open-source R package 'dcGOR' to provide the bioinformatics community with the ease to analyse ontologies and protein domain annotations, particularly those in the dcGO database. The dcGO is a comprehensive resource for protein domain annotations using a panel of ontologies including Gene Ontology. Although increasing in popularity, this database needs statistical and graphical support to meet its full potential. Moreover, there are no bioinformatics tools specifically designed for domain ontology analysis. As an add-on package built in the R software environment, dcGOR offers a basic infrastructure with great flexibility and functionality. It implements new data structure to represent domains, ontologies, annotations, and all analytical outputs as well. For each ontology, it provides various mining facilities, including: (i) domain-based enrichment analysis and visualisation; (ii) construction of a domain (semantic similarity) network according to ontology annotations; and (iii) significance analysis for estimating a contact (statistical significance) network. To reduce runtime, most analyses support high-performance parallel computing. Taking as inputs a list of protein domains of interest, the package is able to easily carry out in-depth analyses in terms of functional, phenotypic and diseased relevance, and network-level understanding. More importantly, dcGOR is designed to allow users to import and analyse their own ontologies and annotations on domains (taken from SCOP, Pfam and InterPro) and RNAs (from Rfam) as well. The package is freely available at CRAN for easy installation, and also at GitHub for version control. The dedicated website with reproducible demos can be found at http://supfam.org/dcGOR.

  13. A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012

    Directory of Open Access Journals (Sweden)

    He Yongqun

    2012-12-01

    Full Text Available Abstract Vaccines and drugs have contributed to dramatic improvements in public health worldwide. Over the last decade, there have been efforts in developing biomedical ontologies that represent various areas associated with vaccines and drugs. These ontologies combined with existing health and clinical terminology systems (e.g., SNOMED, RxNorm, NDF-RT, MedDRA, VO, OAE, and AERO could play significant roles on clinical and translational research. The first “Vaccine and Drug Ontology in the Study of Mechanism and Effect” workshop (VDOSME 2012 provided a platform for discussing problems and solutions in the development and application of biomedical ontologies in representing and analyzing vaccines/drugs, vaccine/drug administrations, vaccine/drug-induced immune responses (including positive host responses and adverse events, and similar topics. The workshop covered two main areas: (i ontologies of vaccines, of drugs, and of studies thereof; and (ii analysis of administration, mechanism and effect in terms of representations based on such ontologies. Six full-length papers included in this thematic issue focus on ontology representation and time analysis of vaccine/drug administration and host responses (including positive immune responses and adverse events, vaccine and drug adverse event text mining, and ontology-based Semantic Web applications. The workshop, together with the follow-up activities and personal meetings, provided a wonderful platform for the researchers and scientists in the vaccine and drug communities to demonstrate research progresses, share ideas, address questions, and promote collaborations for better representation and analysis of vaccine and drug-related terminologies and clinical and research data.

  14. 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

  15. Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.

    Science.gov (United States)

    Jupp, Simon; Stevens, Robert; Hoehndorf, Robert

    2012-04-24

    Ontologies such as the Gene Ontology (GO) and their use in annotations make cross species comparisons of genes possible, along with a wide range of other analytical activities. The bio-ontologies community, in particular the Open Biomedical Ontologies (OBO) community, have provided many other ontologies and an increasingly large volume of annotations of gene products that can be exploited in query and analysis. As many annotations with different ontologies centre upon gene products, there is a possibility to explore gene products through multiple ontological perspectives at the same time. Questions could be asked that link a gene product's function, process, cellular location, phenotype and disease. Current tools, such as AmiGO, allow exploration of genes based on their GO annotations, but not through multiple ontological perspectives. In addition, the semantics of these ontology's representations should be able to, through automated reasoning, afford richer query opportunities of the gene product annotations than is currently possible. To do this multi-perspective, richer querying of gene product annotations, we have created the Logical Gene Ontology, or GOAL ontology, in OWL that combines the Gene Ontology, Human Disease Ontology and the Mammalian Phenotype Ontology, together with classes that represent the annotations with these ontologies for mouse gene products. Each mouse gene product is represented as a class, with the appropriate relationships to the GO aspects, phenotype and disease with which it has been annotated. We then use defined classes to query these protein classes through automated reasoning, and to build a complex hierarchy of gene products. We have presented this through a Web interface that allows arbitrary queries to be constructed and the results displayed. This standard use of OWL affords a rich interaction with Gene Ontology, Human Disease Ontology and Mammalian Phenotype Ontology annotations for the mouse, to give a fine partitioning of

  16. Ontodog: a web-based ontology community view generation tool.

    Science.gov (United States)

    Zheng, Jie; Xiang, Zuoshuang; Stoeckert, Christian J; He, Yongqun

    2014-05-01

    Biomedical ontologies are often very large and complex. Only a subset of the ontology may be needed for a specified application or community. For ontology end users, it is desirable to have community-based labels rather than the labels generated by ontology developers. Ontodog is a web-based system that can generate an ontology subset based on Excel input, and support generation of an ontology community view, which is defined as the whole or a subset of the source ontology with user-specified annotations including user-preferred labels. Ontodog allows users to easily generate community views with minimal ontology knowledge and no programming skills or installation required. Currently >100 ontologies including all OBO Foundry ontologies are available to generate the views based on user needs. We demonstrate the application of Ontodog for the generation of community views using the Ontology for Biomedical Investigations as the source ontology.

  17. 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.

  18. A gross anatomy ontology for hymenoptera.

    Directory of Open Access Journals (Sweden)

    Matthew J Yoder

    Full Text Available Hymenoptera is an extraordinarily diverse lineage, both in terms of species numbers and morphotypes, that includes sawflies, bees, wasps, and ants. These organisms serve critical roles as herbivores, predators, parasitoids, and pollinators, with several species functioning as models for agricultural, behavioral, and genomic research. The collective anatomical knowledge of these insects, however, has been described or referred to by labels derived from numerous, partially overlapping lexicons. The resulting corpus of information--millions of statements about hymenopteran phenotypes--remains inaccessible due to language discrepancies. The Hymenoptera Anatomy Ontology (HAO was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy. The HAO was built using newly developed interfaces within mx, a Web-based, open source software package, that enables collaborators to simultaneously contribute to an ontology. Over twenty people contributed to the development of this ontology by adding terms, genus differentia, references, images, relationships, and annotations. The database interface returns an Open Biomedical Ontology (OBO formatted version of the ontology and includes mechanisms for extracting candidate data and for publishing a searchable ontology to the Web. The application tools are subject-agnostic and may be used by others initiating and developing ontologies. The present core HAO data constitute 2,111 concepts, 6,977 terms (labels for concepts, 3,152 relations, 4,361 sensus (links between terms, concepts, and references and over 6,000 text and graphical annotations. The HAO is rooted with the Common Anatomy Reference Ontology (CARO, in order to facilitate interoperability with and future alignment to other anatomy ontologies, and is available through the OBO Foundry ontology repository and BioPortal. The HAO provides a foundation through which connections between genomic, evolutionary developmental

  19. A gross anatomy ontology for hymenoptera.

    Science.gov (United States)

    Yoder, Matthew J; Mikó, István; Seltmann, Katja C; Bertone, Matthew A; Deans, Andrew R

    2010-12-29

    Hymenoptera is an extraordinarily diverse lineage, both in terms of species numbers and morphotypes, that includes sawflies, bees, wasps, and ants. These organisms serve critical roles as herbivores, predators, parasitoids, and pollinators, with several species functioning as models for agricultural, behavioral, and genomic research. The collective anatomical knowledge of these insects, however, has been described or referred to by labels derived from numerous, partially overlapping lexicons. The resulting corpus of information--millions of statements about hymenopteran phenotypes--remains inaccessible due to language discrepancies. The Hymenoptera Anatomy Ontology (HAO) was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy. The HAO was built using newly developed interfaces within mx, a Web-based, open source software package, that enables collaborators to simultaneously contribute to an ontology. Over twenty people contributed to the development of this ontology by adding terms, genus differentia, references, images, relationships, and annotations. The database interface returns an Open Biomedical Ontology (OBO) formatted version of the ontology and includes mechanisms for extracting candidate data and for publishing a searchable ontology to the Web. The application tools are subject-agnostic and may be used by others initiating and developing ontologies. The present core HAO data constitute 2,111 concepts, 6,977 terms (labels for concepts), 3,152 relations, 4,361 sensus (links between terms, concepts, and references) and over 6,000 text and graphical annotations. The HAO is rooted with the Common Anatomy Reference Ontology (CARO), in order to facilitate interoperability with and future alignment to other anatomy ontologies, and is available through the OBO Foundry ontology repository and BioPortal. The HAO provides a foundation through which connections between genomic, evolutionary developmental biology

  20. 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

  1. 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.

  2. Institutional profile. The International Society for Cellular Therapy: evolving to meet the demands of the regenerative medicine industry.

    Science.gov (United States)

    Maziarz, Richard T; Arthurs, Jane; Horwitz, Edwin

    2011-03-01

    The International Society for Cellular Therapy is a global association driving the translation of scientific research to deliver innovative cellular therapies to patients. Established in 1992, its membership and leadership comprises world-class scientists, clinicians, technologists, biotech/pharma and regulatory professionals from 40 countries focused on preclinical and translational aspects of developing cell therapy products. The International Society for Cellular Therapy has evolved in alignment with the maturation of the field of cell therapy and regenerative medicine to create forums for discussion of shared concerns for commercialization of cell therapies and of development of consensus standards, recognizing that true commercialization depends upon the translational scientific community, the regional regulatory and policy institutions, and the technology support and capital investment from industry. It exists to facilitate the international work of many, to spawn new initiatives, and to synergize with other stakeholders to create the best outcome for the many patients across the world depending on the answers and improved health that cellular therapeutics will provide them.

  3. Towards a Formalized Ontology-Based Requirements Model

    Institute of Scientific and Technical Information of China (English)

    JIANG Dan-dong; ZHANG Shen-sheng; WANG Ying-lin

    2005-01-01

    The goal of this paper is to take a further step towards an ontological approach for representing requirements information. The motivation for ontologies was discussed. The definitions of ontology and requirements ontology were given. Then, it presented a collection of informal terms, including four subject areas. It also discussed the formalization process of ontology. The underlying meta-ontology was determined, and the formalized requirements ontology was analyzed. This formal ontology is built to serve as a basis for requirements model. Finally, the implementation of software system was given.

  4. SELECTION OF ONTOLOGY FOR WEB SERVICE DESCRIPTION LANGUAGE TO ONTOLOGY WEB LANGUAGE CONVERSION

    Directory of Open Access Journals (Sweden)

    J. Mannar Mannan

    2014-01-01

    Full Text Available Semantic web is to extend the current human readable web to encoding some of the semantic of resources in a machine processing form. As a Semantic web component, Semantic Web Services (SWS uses a mark-up that makes the data into detailed and sophisticated machine readable way. One such language is Ontology Web Language (OWL. Existing conventional web service annotation can be changed to semantic web service by mapping Web Service Description Language (WSDL with the semantic annotation of OWL-S. In this conversion of WSDL to OWL process, the ontology plays a vital role. Ontology can be stored and retrieved from local repository and selecting the appropriate ontology is a complicated process and this can be achieved by Ontology Searching and Property Matching (OSPM engine. Ontology is stored in the local repository as ontology document and exact matching of ontology for the requested query can be searched using semantic similarity ranking method. High ranked classes of ontology will undergo property matching; here requested concept will be matched with the resulting property. OSPM engine act as the backbone for selecting an exact ontology and reduce the conflict that occurs while selecting the ontology for annotation purpose.

  5. 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.

  6. 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.

  7. 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.

  8. Ontology Design Patterns as Interfaces (invited)

    Science.gov (United States)

    Janowicz, K.

    2015-12-01

    In recent years ontology design patterns (ODP) have gained popularity among knowledge engineers. ODPs are modular but self-contained building blocks that are reusable and extendible. They minimize the amount of ontological commitments and thereby are easier to integrate than large monolithic ontologies. Typically, patterns are not directly used to annotate data or to model certain domain problems but are combined and extended to form data and purpose-driven local ontologies that serve the needs of specific applications or communities. By relying on a common set of patterns these local ontologies can be aligned to improve interoperability and enable federated queries without enforcing a top-down model of the domain. In previous work, we introduced ontological views as layer on top of ontology design patterns to ease the reuse, combination, and integration of patterns. While the literature distinguishes multiple types of patterns, e.g., content patterns or logical patterns, we propose to use them as interfaces here to guide the development of ontology-driven systems.

  9. An Ontology For Mobile Situation Aware Systems

    Directory of Open Access Journals (Sweden)

    Paul F O'Brien

    2008-05-01

    Full Text Available This paper introduces a novel design artefact, namely a generic situation management ontology based on situation theory. This ontology contributes to the foundation knowledge base of mobile service delivery systems for future research and systems design. It demonstrates the applicability, and feasibility of using situation theory in the design of reactive information systems. The support within the ontology for context based filtering for situation detection also contributes to the efficiency of implementation and operation of situation driven reactive information systems. Highly mobile people (HMPs require flexible, reactive service delivery due to their regularly changing location and activities and the lack of a wired network connection. A mobile service delivery system should be able to detect relevant events that occur such as change of location, availability of new last-minute specials, sales opportunities and safety issues and then reactively take action in response to these events. This paper describes a generic situation management ontology that was developed in OWL using the ontology development tool, Protégé. The ontology is combined with domain specific classes in the travel domain to create a travel situation management ontology that can be used as the basis for a ubiquitous mobile travel service application. Using a typical independent traveller scenario, the travel situation management ontology is instantiated to demonstrate its effectiveness.

  10. 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

  11. 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...

  12. Model driven engineering and ontology development

    CERN Document Server

    Gasevic, Dragan; Devedzic, Vladan; Bézivin, Jean; Selic, Bran

    2009-01-01

    Describes technologies, tools, and standards like XML, RDF, OWL, MDA, and UML. This book describes OMG's ODM (Ontology Definition Metamodel) initiative, a specification which is in the form of an OMG language like UML. It also covers applications and practical aspects of developing ontologies using MDA-based languages.

  13. Taking a view on bio-ontologies

    NARCIS (Netherlands)

    S. Jupp; A. Gibson; J. Malone; H. Parkinson; R. Stevens

    2012-01-01

    We present a technique for separating knowledge representation from application specific views that are currently often conflated within bio-ontologies. Many ontologies contain information for two tasks; one to represent the knowledge of some field of interest and another to support an application t

  14. FROG - Fingerprinting Genomic Variation Ontology.

    Directory of Open Access Journals (Sweden)

    E Abinaya

    Full Text Available Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: "FingeRprinting Ontology of Genomic variations" is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies. FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog.

  15. [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.

  16. SEMANTIC TERM BASED INFORMATION RETRIEVAL USING ONTOLOGY

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    J. Mannar Mannan

    2014-01-01

    Full Text Available Information Searching and retrieval is a challenging task in the traditional keyword based textual information retrieval system. In the growing information age, adding huge data every day the searching problem also augmented. Keyword based retrieval system returns bulk of junk document irrelevant to query. To address the limitations, this paper proposed query terms along with semantic terms for information retrieval using multiple ontology reference. User query sometimes reflects multiple domain of interest that persist us to collect semantically related ontologies. If no related ontology exists then WordNet ontology used to retrieve semantic terms related to query term. In this approach, classes on the ontology derived as semantic related text keywords, these keywords considered for rank the documents.

  17. Applying ontological realism to medically unexplained syndromes.

    Science.gov (United States)

    Doing-Harris, Kristina; Meystre, Stephane M; Samore, Matthew; Ceusters, Werner

    2013-01-01

    The past decade has witnessed an increased interest in what are called "medically unexplained syndromes" (MUS). We address the question of whether structuring the domain knowledge for MUS can be achieved by applying the principles of Ontological Realism in light of criticisms about their usefulness in areas where science has not yet led to insights univocally endorsed by the relevant communities. We analyzed whether the different perspectives held by MUS researchers can be represented without taking any particular stance and whether existing ontologies based on Ontological Realism can be further built upon. We did not find refutation of the applicability of the principles. We found the Ontology of General Medical Science and Information Artifact Ontology to provide useful frameworks for analyzing certain MUS controversies, although leaving other questions open.

  18. Ontology for Genome Comparison and Genomic Rearrangements

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    Anil Wipat

    2006-04-01

    Full Text Available We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.

  19. PERKEMBANGAN ONTOLOGI DALAM FILSAFAT ISLAM

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    Fathul Mufid

    2013-09-01

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

  20. 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

  1. Temporal Ontologies for Geoscience: Alignment Challenges

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    Cox, S. J. D.

    2014-12-01

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

  2. The Development Process of the Semantic Web and Web Ontology

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    K.Vanitha

    2011-08-01

    Full Text Available This paper deals with the semantic web and web ontology. The existing ontology development processes are not catered towards casual web ontology development, a notion analogous to standard web page development. Ontologies have become common on the World-Wide Web[2]. Key features of this process include easy and rapid creation of ontological skeletons, searching and linking to existing ontologies and a natural language-based technique to improve presentation of ontologies[6]. Ontologies, however, vary greatly in size, scope and semantics. They can range from generic upper-level ontologies to domain-specific schemas. The success of the Semantic Web is based on the existance of numerous distributed ontologies, using which users can annotate their data, thereby enabling shared machine readable content. This paper elaborates the stages in a casual ontology development process.

  3. Semantic Query Optimisation with Ontology Simulation

    CERN Document Server

    Gupta, Siddharth

    2010-01-01

    Semantic Web is, without a doubt, gaining momentum in both industry and academia. The word "Semantic" refers to "meaning" - a semantic web is a web of meaning. In this fast changing and result oriented practical world, gone are the days where an individual had to struggle for finding information on the Internet where knowledge management was the major issue. The semantic web has a vision of linking, integrating and analysing data from various data sources and forming a new information stream, hence a web of databases connected with each other and machines interacting with other machines to yield results which are user oriented and accurate. With the emergence of Semantic Web framework the na\\"ive approach of searching information on the syntactic web is clich\\'e. This paper proposes an optimised semantic searching of keywords exemplified by simulation an ontology of Indian universities with a proposed algorithm which ramifies the effective semantic retrieval of information which is easy to access and time sav...

  4. Semantic Query Optimisation with Ontology Simulation

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    Siddharth Gupta

    2010-11-01

    Full Text Available Semantic Web is, without a doubt, gaining momentum in both industry and academia. The word“Semantic” refers to “meaning” – a semantic web is a web of meaning. In this fast changing and resultoriented practical world, gone are the days where an individual had to struggle for finding informationon the Internet where knowledge management was the major issue. The semantic web has a vision oflinking, integrating and analysing data from various data sources and forming a new information stream,hence a web of databases connected with each other and machines interacting with other machines toyield results which are user oriented and accurate. With the emergence of Semantic Web framework thenaïve approach of searching information on the syntactic web is cliché. This paper proposes an optimisedsemantic searching of keywords exemplified by simulation an ontology of Indian universities with aproposed algorithm which ramifies the effective semantic retrieval of information which is easy to accessand time saving.

  5. An Ontological Informatics Framework for Pharmaceutical Product Development: Milling as a Case Study

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    Akkisetty, Venkata Sai Pavan Kumar

    2009-01-01

    Pharmaceutical product development is an expensive, time consuming and information intensive process. Providing the right information at the right time is of great importance in pharmaceutical industry. To achieve this, knowledge management is the approach to deal with the humongous quantity of information. Ontological approach proposed in Venkat…

  6. An Ontological Informatics Framework for Pharmaceutical Product Development: Milling as a Case Study

    Science.gov (United States)

    Akkisetty, Venkata Sai Pavan Kumar

    2009-01-01

    Pharmaceutical product development is an expensive, time consuming and information intensive process. Providing the right information at the right time is of great importance in pharmaceutical industry. To achieve this, knowledge management is the approach to deal with the humongous quantity of information. Ontological approach proposed in Venkat…

  7. International and National Organizations, Proceedings: International Federation for Documentation Study Committee "Information for Industry" - FID/II. Meeting Held in the Framework of the ISLIC International Conference on Information Science, Tel Aviv, Sept. 3, 1971.

    Science.gov (United States)

    Israel Society of Special Libraries and Information Centres, Tel Aviv.

    The material published here was presented at an open meeting of the International Federation for Documentation study committee, Information for Industry (FID/II) during the ISLCI International Conference on Information Science on September 3, 1971. (The full proceedings in two volumes are available as ED 065139 and ED 065140.) Contained herein are…

  8. The MMI Device Ontology: Enabling Sensor Integration

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    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

  9. 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

  10. Anthropological Component of Descartes’ Ontology

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    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

  11. 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.

  12. Evaluation of need for ontologies to manage domain content for the Reportable Conditions Knowledge Management System.

    Science.gov (United States)

    Eilbeck, Karen L; Lipstein, Julie; McGarvey, Sunanda; Staes, Catherine J

    2014-01-01

    The Reportable Condition Knowledge Management System (RCKMS) is envisioned to be a single, comprehensive, authoritative, real-time portal to author, view and access computable information about reportable conditions. The system is designed for use by hospitals, laboratories, health information exchanges, and providers to meet public health reporting requirements. The RCKMS Knowledge Representation Workgroup was tasked to explore the need for ontologies to support RCKMS functionality. The workgroup reviewed relevant projects and defined criteria to evaluate candidate knowledge domain areas for ontology development. The use of ontologies is justified for this project to unify the semantics used to describe similar reportable events and concepts between different jurisdictions and over time, to aid data integration, and to manage large, unwieldy datasets that evolve, and are sometimes externally managed.

  13. RESEARCH ON EXTENSION OF SPARQL ONTOLOGY QUERY LANGUAGE CONSIDERING THE COMPUTATION OF INDOOR SPATIAL RELATIONS

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    C. Li

    2015-05-01

    Full Text Available A method suitable for indoor complex semantic query considering the computation of indoor spatial relations is provided According to the characteristics of indoor space. This paper designs ontology model describing the space related information of humans, events and Indoor space objects (e.g. Storey and Room as well as their relations to meet the indoor semantic query. The ontology concepts are used in IndoorSPARQL query language which extends SPARQL syntax for representing and querying indoor space. And four types specific primitives for indoor query, "Adjacent", "Opposite", "Vertical" and "Contain", are defined as query functions in IndoorSPARQL used to support quantitative spatial computations. Also a method is proposed to analysis the query language. Finally this paper adopts this method to realize indoor semantic query on the study area through constructing the ontology model for the study building. The experimental results show that the method proposed in this paper can effectively support complex indoor space semantic query.

  14. Research on Extension of Sparql Ontology Query Language Considering the Computation of Indoor Spatial Relations

    Science.gov (United States)

    Li, C.; Zhu, X.; Guo, W.; Liu, Y.; Huang, H.

    2015-05-01

    A method suitable for indoor complex semantic query considering the computation of indoor spatial relations is provided According to the characteristics of indoor space. This paper designs ontology model describing the space related information of humans, events and Indoor space objects (e.g. Storey and Room) as well as their relations to meet the indoor semantic query. The ontology concepts are used in IndoorSPARQL query language which extends SPARQL syntax for representing and querying indoor space. And four types specific primitives for indoor query, "Adjacent", "Opposite", "Vertical" and "Contain", are defined as query functions in IndoorSPARQL used to support quantitative spatial computations. Also a method is proposed to analysis the query language. Finally this paper adopts this method to realize indoor semantic query on the study area through constructing the ontology model for the study building. The experimental results show that the method proposed in this paper can effectively support complex indoor space semantic query.

  15. Statistical mechanics of ontology based annotations

    CERN Document Server

    Hoyle, David C

    2016-01-01

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

  16. VATTIMO AND THE POSSIBILITIES OF NIHILISTIC ONTOLOGY

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    Myroslav Feodosijevic Hryschko

    2010-01-01

    Full Text Available La "ontología nihilista" de Gianni Vattimo se distingue inmediatamente por su antimetafísica acérrima. Así, en lugar de los que Vattimo considera los tropos definitivos de la metafísica, i. e. la permanencia temporal, la necesidad, el fundacionalismo, etc., la posibilidad de la ontología nihilista debe mantener una exigencia crítica respecto de estos tropos. De acuerdo con este imperativo, Vattimo busca equiparar la ontología nihilista con una ontología hermenéutica. Este texto examina esta equiparación e intenta separar la continuidad entre nihilismo y hermenéutica, de acuerdo con el compromiso de la segunda con una variación del antropocentrismo evidenciado en conceptos tales como la efectividad del contenido particular de una historia que, a su vez, contradice el nihilismo que ha propuesto a la historia y al hombre como contingentes. En lugar de ello, lo que está en juego en la ontología nihilista, siguiendo la lectura de Vattimo, es una ontología mínima radical dedicada a la contingencia del Ser mismo, que remueve el estatus ontológico privilegiado del hombre, característico de la ontología hermenéutica; un privilegiado análogo a la misma metafísica fundacionalista que el nihilismo ha de evitar.

  17. Towards an Ontology of Data Mining Investigations

    Science.gov (United States)

    Panov, Panče; Soldatova, Larisa N.; Džeroski, Sašo

    Motivated by the need for unification of the domain of data mining and the demand for formalized representation of outcomes of data mining investigations, we address the task of constructing an ontology of data mining. In this paper we present an updated version of the OntoDM ontology, that is based on a recent proposal of a general framework for data mining and it is aligned with the ontology of biomedical investigations (OBI) . The ontology aims at describing and formalizing entities from the domain of data mining and knowledge discovery. It includes definitions of basic data mining entities (e.g., datatype, dataset, data mining task, data mining algorithm etc.) and allows extensions with more complex data mining entities (e.g. constraints, data mining scenarios and data mining experiments). Unlike most existing approaches to constructing ontologies of data mining, OntoDM is compliant to best practices in engineering ontologies that describe scientific investigations (e.g., OBI ) and is a step towards an ontology of data mining investigations. OntoDM is available at: http://kt.ijs.si/panovp/OntoDM/ .

  18. A Method for Recommending Ontology Alignment Strategies

    Science.gov (United States)

    Tan, He; Lambrix, Patrick

    In different areas ontologies have been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there already exist a number of different alignment strategies. However, it is usually difficult for a user that needs to align two ontologies to decide which of the different available strategies are the most suitable. In this paper we propose a method that provides recommendations on alignment strategies for a given alignment problem. The method is based on the evaluation of the different available alignment strategies on several small selected pieces from the ontologies, and uses the evaluation results to provide recommendations. In the paper we give the basic steps of the method, and then illustrate and discuss the method in the setting of an alignment problem with two well-known biomedical ontologies. We also experiment with different implementations of the steps in the method.

  19. SEMANTIC INTEGRATION FOR AUTOMATIC ONTOLOGY MAPPING

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    Siham AMROUCH

    2013-11-01

    Full Text Available In the last decade, ontologies have played a key technology role for information sharing and agents interoperability in different application domains. In semantic web domain, ontologies are efficiently used to face the great challenge of representing the semantics of data, in order to bring the actual web to its full power and hence, achieve its objective. However, using ontologies as common and shared vocabularies requires a certain degree of interoperability between them. To confront this requirement, mapping ontologies is a solution that is not to be avoided. In deed, ontology mapping build a meta layer that allows different applications and information systems to access and share their informations, of course, after resolving the different forms of syntactic, semantic and lexical mismatches. In the contribution presented in this paper, we have integrated the semantic aspect based on an external lexical resource, wordNet, to design a new algorithm for fully automatic ontology mapping. This fully automatic character features the main difference of our contribution with regards to the most of the existing semi-automatic algorithms of ontology mapping, such as Chimaera, Prompt, Onion, Glue, etc. To better enhance the performances of our algorithm, the mapping discovery stage is based on the combination of two sub-modules. The former analysis the concept’s names and the later analysis their properties. Each one of these two sub-modules is it self based on the combination of lexical and semantic similarity measures.

  20. 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

  1. 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.

  2. 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,…

  3. 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,…

  4. Query Through Heterogeneous Ontologies Using Association Matrix

    Institute of Scientific and Technical Information of China (English)

    KANG Da-zhou; XU Bao-wen; LU Jian-jiang; WANG Peng; LI Yan-hui

    2004-01-01

    This paper introduces the definition and calculation of the association matrix between ontologies.It uses the association matrix to describe the relations between concepts in different ontologies and uses concept vectors to represent queries; then computes the vectors with the association matrix in order to rewrite queries.This paper proposes a simple method of querying through heterogeneous Ontology using association matrix.This method is based on the correctness of approximate information filtering theory; and it is simple to be implemented and expected to run quite fast.

  5. Ontology-Based Classification System Development Methodology

    Directory of Open Access Journals (Sweden)

    Grabusts Peter

    2015-12-01

    Full Text Available The aim of the article is to analyse and develop an ontology-based classification system methodology that uses decision tree learning with statement propositionalized attributes. Classical decision tree learning algorithms, as well as decision tree learning with taxonomy and propositionalized attributes have been observed. Thus, domain ontology can be extracted from the data sets and can be used for data classification with the help of a decision tree. The use of ontology methods in decision tree-based classification systems has been researched. Using such methodologies, the classification accuracy in some cases can be improved.

  6. 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.

  7. Oceanographic ontology-based spatial knowledge query

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The construction of oceanographic ontologies is fundamental to the "digital ocean". Therefore, on the basis of introduction of new concept of oceanographic ontology, an oceanographic ontology-based spatial knowledge query (OOBSKQ) method was proposed and developed. Because the method uses a natural language to describe query conditions and the query result is highly integrated knowledge,it can provide users with direct answers while hiding the complicated computation and reasoning processes, and achieves intelligent,automatic oceanographic spatial information query on the level of knowledge and semantics. A case study of resource and environmental application in bay has shown the implementation process of the method and its feasibility and usefulness.

  8. Hierarchical Analysis of the Omega Ontology

    Energy Technology Data Exchange (ETDEWEB)

    Joslyn, Cliff A.; Paulson, Patrick R.

    2009-12-01

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

  9. Using Ontologies for the E-learning System in Healthcare Human Resources Management

    Directory of Open Access Journals (Sweden)

    Lidia BAJENARU

    2015-01-01

    Full Text Available This paper provides a model for the use of ontology in e-learning systems for structuring educational content in the domain of healthcare human resources management (HHRM in Romania. In this respect we propose an effective method to improve the learning system by providing personalized learning paths created using ontology and advanced educational strategies to provide a personalized learning content for the medical staff. Personalization of e-learning process for the chosen target group will be achieved by setting up learning path for each user according to his profile. This will become possible using: domain ontology, learning objects, modeling student knowledge. Developing an ontology-based system for competence management allows complex interactions, providing intelligent interfacing. This is a new approach for the healthcare system managers in permanent training based on e-learning technologies and specific ontologies in a complex area that needs urgent modernization and efficiency to meet the public health economic, social and political context of Romania.

  10. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment.

    Science.gov (United States)

    Bertone, Matthew A; Mikó, István; Yoder, Matthew J; Seltmann, Katja C; Balhoff, James P; Deans, Andrew R

    2013-01-01

    Matching is an important step for increasing interoperability between heterogeneous ontologies. Here, we present alignments we produced as domain experts, using a manual mapping process, between the Hymenoptera Anatomy Ontology and other existing arthropod anatomy ontologies (representing spiders, ticks, mosquitoes and Drosophila melanogaster). The resulting alignments contain from 43 to 368 mappings (correspondences), all derived from domain-expert input. Despite the many pairwise correspondences, only 11 correspondences were found in common between all ontologies, suggesting either major intrinsic differences between each ontology or gaps in representing each group's anatomy. Furthermore, we compare our findings with putative correspondences from Bioportal (derived from LOOM software) and summarize the results in a total evidence alignment. We briefly discuss characteristics of the ontologies and issues with the matching process.

  11. Construct Primary Education Semantic Ontology Library Based Mind Mapping

    Directory of Open Access Journals (Sweden)

    Hu Dong-Hong

    2016-01-01

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

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    Akram Fathian Dastgerdi

    2012-03-01

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

  14. PREFACE: Selected contributions from the 3rd Theory Meets Industry International Workshop, TMI2009 (Nagoya, Japan, 11-13 November 2009) Selected contributions from the 3rd Theory Meets Industry International Workshop, TMI2009 (Nagoya, Japan, 11-13 November 2009)

    Science.gov (United States)

    Tanaka, Isao; Hafner, Jürgen; Wimmer, Erich; Asahi, Ryoji

    2010-09-01

    The structures, physicochemical and thermodynamic properties of materials are becoming increasingly amenable to treatment by first-principles (ab initio) quantum mechanical simulations. Calculations containing a few hundred atoms are now routine, thanks to improvements in computer technology and computational techniques. Schemes to determine electronic structures more accurately and to treat more complex systems continue to be developed. A growing number of scientists and engineers are becoming aware of the power of these approaches. By applying these new computational tools, materials science and technology is expected to enter a new era of accelerated progress and efficiency. In 1998 the first workshop entitled 'Theory Meets Industry' (TMI) was held at the Vienna University of Technology. The aim of the workshop was to direct the potential of the ab initio simulation codes developed in academia towards the necessities arising from industrial research. Over the next decade, significant advances in ab initio methodology and its application to academic and industrial research were achieved. It was thus considered timely to hold a second TMI workshop in 2007, again in Vienna. The contributions from academia concentrated on a wide range of new developments in ab initio simulations, as well as on applications at the forefront of materials research. Speakers from the industrial sector also emphasized the progress made in successfully applying ab initiotechniques to key areas of modern technology. The proceedings were published in Journal of Physics: Condensed Matter as a special issue (volume 20, number 6, 2008), which was included in the 'Top papers 2008 showcase' of that journal. Following the notable success of the first two workshops, it was decided that the third TMI workshop would be held outside Europe. Holding the workshop in Japan was intended to increase awareness of theoretical materials science and foster further international collaboration in this field

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

    Directory of Open Access Journals (Sweden)

    Irena ATANASOVA

    2011-01-01

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

  16. 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.

  17. 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.

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

    DEFF Research Database (Denmark)

    Andreasen, Troels; Knappe, Rasmus; Bulskov, Henrik

    2005-01-01

    is a specific lattice-based concept algebraic language by which ontologies are inherently generative. The modeling of a domain specific ontology is based on a general ontology built upon common knowledge resources as dictionaries and thesauri. Based on analysis of concept occurrences in the object document......-based navigation. Finally, a measure of concept similarity is derived from the domain specific ontology based on occurrences, commonalities, and distances in the ontology....

  19. Ontology and Its Application in Supply Chain Information Management

    OpenAIRE

    2009-01-01

    5.1 Conclusions In this chapter, aiming at the problems in traditional knowledge retrieval, ontology is introduced. An approach is put forward to supply chain knowledge management construction, which consists of construction of domain ontology, formalization of ontology model, and development of supply chain knowledge management system based on ontology. Finally, taking vegetable supply chain as a case, complete the vegetable supply chain knowledge management system based on ontology. The bet...

  20. The Gene Ontology (GO) project in 2006

    National Research Council Canada - National Science Library

    2006-01-01

    The Gene Ontology (GO) project (http://www.geneontology.org) develops and uses a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://song.sourceforge.net...

  1. The Gene Ontology project in 2008

    National Research Council Canada - National Science Library

    The Gene Ontology (GO) project (http://www.geneontology.org/) provides a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://www.sequenceontology.org...

  2. 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...

  3. 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.)

  4. CSEO - the Cigarette Smoke Exposure Ontology

    National Research Council Canada - National Science Library

    Younesi, Erfan; Ansari, Sam; Guendel, Michaela; Ahmadi, Shiva; Coggins, Chris; Hoeng, Julia; Hofmann-Apitius, Martin; Peitsch, Manuel C

    2014-01-01

    ...) is composed of 20091 concepts. The ontology in its current form is able to capture a wide range of cigarette smoke exposure concepts within the knowledge domain of exposure science with a reasonable sensitivity and specificity...

  5. Combining machine learning and ontological data handling for multi-source classification of nature conservation areas

    Science.gov (United States)

    Moran, Niklas; Nieland, Simon; Tintrup gen. Suntrup, Gregor; Kleinschmit, Birgit

    2017-02-01

    Manual field surveys for nature conservation management are expensive and time-consuming and could be supplemented and streamlined by using Remote Sensing (RS). RS is critical to meet requirements of existing laws such as the EU Habitats Directive (HabDir) and more importantly to meet future challenges. The full potential of RS has yet to be harnessed as different nomenclatures and procedures hinder interoperability, comparison and provenance. Therefore, automated tools are needed to use RS data to produce comparable, empirical data outputs that lend themselves to data discovery and provenance. These issues are addressed by a novel, semi-automatic ontology-based classification method that uses machine learning algorithms and Web Ontology Language (OWL) ontologies that yields traceable, interoperable and observation-based classification outputs. The method was tested on European Union Nature Information System (EUNIS) grasslands in Rheinland-Palatinate, Germany. The developed methodology is a first step in developing observation-based ontologies in the field of nature conservation. The tests show promising results for the determination of the grassland indicators wetness and alkalinity with an overall accuracy of 85% for alkalinity and 76% for wetness.

  6. The pathway ontology - updates and applications.

    Science.gov (United States)

    Petri, Victoria; Jayaraman, Pushkala; Tutaj, Marek; Hayman, G Thomas; Smith, Jennifer R; De Pons, Jeff; Laulederkind, Stanley Jf; Lowry, Timothy F; Nigam, Rajni; Wang, Shur-Jen; Shimoyama, Mary; Dwinell, Melinda R; Munzenmaier, Diane H; Worthey, Elizabeth A; Jacob, Howard J

    2014-02-05

    The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hierarchical structure of a directed acyclic graph. The ontology allows for the standardized annotation of rat, and of human and mouse genes to pathway terms. It also constitutes a vehicle for easy navigation between gene and ontology report pages, between reports and interactive pathway diagrams, between pathways directly connected within a diagram and between those that are globally related in pathway suites and suite networks. Surveys of the literature and the development of the Pathway and Disease Portals are important sources for the ongoing development of the ontology. User requests and mapping of pathways in other databases to terms in the ontology further contribute to increasing its content. Recently built automated pipelines use the mapped terms to make available the annotations generated by other groups. The two released pipelines - the Pathway Interaction Database (PID) Annotation Import Pipeline and the Kyoto Encyclopedia of Genes and Genomes (KEGG) Annotation Import Pipeline, make available over 7,400 and 31,000 pathway gene annotations, respectively. Building the PID pipeline lead to the addition of new terms within the signaling node, also augmented by the release of the RGD "Immune and Inflammatory Disease Portal" at that time. Building the KEGG pipeline lead to a substantial increase in the number of disease pathway terms, such as those within the 'infectious disease pathway' parent term category. The 'drug pathway' node has also seen increases in the number of terms as well as a restructuring of the node. Literature surveys, disease portal deployments and user requests have contributed and continue to contribute additional new terms across the ontology. Since first presented, the content of PW has increased by over 75%. Ongoing development of

  7. The pathway ontology – updates and applications

    Science.gov (United States)

    2014-01-01

    Background The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hierarchical structure of a directed acyclic graph. The ontology allows for the standardized annotation of rat, and of human and mouse genes to pathway terms. It also constitutes a vehicle for easy navigation between gene and ontology report pages, between reports and interactive pathway diagrams, between pathways directly connected within a diagram and between those that are globally related in pathway suites and suite networks. Surveys of the literature and the development of the Pathway and Disease Portals are important sources for the ongoing development of the ontology. User requests and mapping of pathways in other databases to terms in the ontology further contribute to increasing its content. Recently built automated pipelines use the mapped terms to make available the annotations generated by other groups. Results The two released pipelines – the Pathway Interaction Database (PID) Annotation Import Pipeline and the Kyoto Encyclopedia of Genes and Genomes (KEGG) Annotation Import Pipeline, make available over 7,400 and 31,000 pathway gene annotations, respectively. Building the PID pipeline lead to the addition of new terms within the signaling node, also augmented by the release of the RGD “Immune and Inflammatory Disease Portal” at that time. Building the KEGG pipeline lead to a substantial increase in the number of disease pathway terms, such as those within the ‘infectious disease pathway’ parent term category. The ‘drug pathway’ node has also seen increases in the number of terms as well as a restructuring of the node. Literature surveys, disease portal deployments and user requests have contributed and continue to contribute additional new terms across the ontology. Since first presented, the content of PW has increased by

  8. GFVO: the Genomic Feature and Variation Ontology.

    Science.gov (United States)

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

    2015-01-01

    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.

  9. WEB MINING BASED FRAMEWORK FOR ONTOLOGY LEARNING

    OpenAIRE

    Ramesh, C.; K.V.Chalapati Rao; Govardhan, A

    2015-01-01

    Today, the notion of Semantic Web has emerged as a prominent solution to the problem of organizing the immense information provided by World Wide Web, and its focus on supporting a better co-operation between humans and machines is noteworthy. Ontology forms the major component of Semantic Web in its realization. However, manual method of ontology construction is time-consuming, costly, error-prone and inflexible to change and in addition, it requires a complete participation o...

  10. A Chronostratigraphic Relational Database Ontology

    Science.gov (United States)

    Platon, E.; Gary, A.; Sikora, P.

    2005-12-01

    A chronostratigraphic research database was donated by British Petroleum to the Stratigraphy Group at the Energy and Geoscience Institute (EGI), University of Utah. These data consists of over 2,000 measured sections representing over three decades of research into the application of the graphic correlation method. The data are global and includes both microfossil (foraminifera, calcareous nannoplankton, spores, pollen, dinoflagellate cysts, etc) and macrofossil data. The objective of the donation was to make the research data available to the public in order to encourage additional chronostratigraphy studies, specifically regarding graphic correlation. As part of the National Science Foundation's Cyberinfrastructure for the Geosciences (GEON) initiative these data have been made available to the public at http://css.egi.utah.edu. To encourage further research using the graphic correlation method, EGI has developed a software package, StrataPlot that will soon be publicly available from the GEON website as a standalone software download. The EGI chronostratigraphy research database, although relatively large, has many data holes relative to some paleontological disciplines and geographical areas, so the challenge becomes how do we expand the data available for chronostratigrahic studies using graphic correlation. There are several public or soon-to-be public databases available to chronostratigraphic research, but they have their own data structures and modes of presentation. The heterogeneous nature of these database schemas hinders their integration and makes it difficult for the user to retrieve and consolidate potentially valuable chronostratigraphic data. The integration of these data sources would facilitate rapid and comprehensive data searches, thus helping advance studies in chronostratigraphy. The GEON project will host a number of databases within the geology domain, some of which contain biostratigraphic data. Ontologies are being developed to provide

  11. 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.

  12. 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.

  13. Microposts Ontology Construction Via Concept Extraction

    Directory of Open Access Journals (Sweden)

    Beenu Yadav

    2012-08-01

    Full Text Available The social networking website Facebook offers to its users a feature called “status updates” (or just “status”, which allows users to create Microposts directed to all their contacts, or a subset thereof. Readers can respond to Microposts, or in addition to that also click a “Like” button to show their appreciation for a certain Micropost. Adding semantic meaning in the sense of unambiguous intended ideas to such Microposts. We can make a start towards semantic web by adding semantic annotation to web resources. Ontology are used to specify meaning of annotations. Ontology provide a vocabulary for representing and communicating knowledge about some topic and a set of semantic relationships that hold among the terms in that vocabulary. For increasing the efficiency of ontology based application there is a need to develop a mechanism that reduces the manual work in developing ontology. In this paper, we proposed Microposts’ ontology construction. In this paper we present a method that extracts meaningfulknowledge from microposts shared in social platforms. This process involves different steps for the analysis of such microposts (extraction of keywords, named entities and their matching to ontological concepts.

  14. Ontological Modeling for Integrated Spacecraft Analysis

    Science.gov (United States)

    Wicks, Erica

    2011-01-01

    Current spacecraft work as a cooperative group of a number of subsystems. Each of these requiresmodeling software for development, testing, and prediction. It is the goal of my team to create anoverarching software architecture called the Integrated Spacecraft Analysis (ISCA) to aid in deploying the discrete subsystems' models. Such a plan has been attempted in the past, and has failed due to the excessive scope of the project. Our goal in this version of ISCA is to use new resources to reduce the scope of the project, including using ontological models to help link the internal interfaces of subsystems' models with the ISCA architecture.I have created an ontology of functions specific to the modeling system of the navigation system of a spacecraft. The resulting ontology not only links, at an architectural level, language specificinstantiations of the modeling system's code, but also is web-viewable and can act as a documentation standard. This ontology is proof of the concept that ontological modeling can aid in the integration necessary for ISCA to work, and can act as the prototype for future ISCA ontologies.

  15. Ontology Based Feature Driven Development Life Cycle

    Directory of Open Access Journals (Sweden)

    Farheen Siddiqui

    2012-01-01

    Full Text Available The upcoming technology support for semantic web promises fresh directions for Software Engineering community. Also semantic web has its roots in knowledge engineering that provoke software engineers to look for application of ontology applications throughout the Software Engineering lifecycle. The internal components of a semantic web are "light weight", and may be of less quality standards than the externally visible modules. In fact the internal components are generated from external (ontological component. That's the reason agile development approaches such as feature driven development are suitable for applications internal component development. As yet there is no particular procedure that describes the role of ontology in FDD processes. Therefore we propose an ontology based feature driven development for semantic web application that can be used form application model development to feature design and implementation. Features are precisely defined in the OWL-based domain model. Transition from OWL based domain model to feature list is directly defined in transformation rules. On the other hand the ontology based overall model can be easily validated through automated tools. Advantages of ontology-based feature Driven development are also discussed.

  16. Utilizing Statistical Semantic Similarity Techniques for Ontology Mapping——with Applications to AEC Standard Models

    Institute of Scientific and Technical Information of China (English)

    Pan Jiayi; Chin-Pang Jack Cheng; Gloria T. Lau; Kincho H. Law

    2008-01-01

    The objective of this paper is to introduce three semi-automated approaches for ontology mapping using relatedness analysis techniques. In the architecture, engineering, and construction (AEC) industry, there exist a number of ontological standards to describe the semantics of building models. Although the standards share similar scopes of interest, the task of comparing and mapping concepts among standards is challenging due to their differences in terminologies and perspectives. Ontology mapping is therefore necessary to achieve information interoperability, which allows two or more information sources to exchange data and to re-use the data for further purposes. The attribute-based approach, corpus-based approach, and name-based approach presented in this paper adopt the statistical relatedness analysis techniques to discover related concepts from heterogeneous ontologies. A pilot study is conducted on IFC and CIS/2 ontologies to evaluate the approaches. Preliminary results show that the attribute-based approach outperforms the other two approaches in terms of precision and F-measure.

  17. 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

  18. Ontological Matchmaking in Recommender Systems

    CERN Document Server

    Bonifati, Angela; Sileo, Domenica; Summa, Gianvito

    2010-01-01

    The electronic marketplace offers great potential for the recommendation of supplies. In the so called recommender systems, it is crucial to apply matchmaking strategies that faithfully satisfy the predicates specified in the demand, and take into account as much as possible the user preferences. We focus on real-life ontology-driven matchmaking scenarios and identify a number of challenges, being inspired by such scenarios. A key challenge is that of presenting the results to the users in an understandable and clear-cut fashion in order to facilitate the analysis of the results. Indeed, such scenarios evoke the opportunity to rank and group the results according to specific criteria. A further challenge consists of presenting the results to the user in an asynchronous fashion, i.e. the 'push' mode, along with the 'pull' mode, in which the user explicitly issues a query, and displays the results. Moreover, an important issue to consider in real-life cases is the possibility of submitting a query to multiple p...

  19. 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.

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

    Science.gov (United States)

    Tao, Cui; He, Yongqun; Arabandi, Sivaram

    2014-03-20

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

  1. 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...... 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....... 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...

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

    Directory of Open Access Journals (Sweden)

    Robert Hoehndorf

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

  3. 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

  4. 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

  5. Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base

    Directory of Open Access Journals (Sweden)

    Smith Barry

    2010-06-01

    Full Text Available Abstract Background The Salivaomics Knowledge Base (SKB is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1 the saliva biomarker discovery and validation resources at UCLA with (2 the ontology resources developed by the OBO (Open Biomedical Ontologies Foundry, including a new Saliva Ontology (SALO. Results We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/ as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies Foundry. Conclusions The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging' of a representative corpus of salivaomics research literature that is to be incorporated into the SKB.

  6. 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…

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

    NARCIS (Netherlands)

    Blums, Ivar; Weigand, Hans

    2016-01-01

    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 Con

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

    Science.gov (United States)

    Peng, Yefei

    2010-01-01

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

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

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Oellrich, Anika; Rebholz-Schuhmann, Dietrich; Schofield, Paul N; Gkoutos, Georgios V

    2011-01-01

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

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

    NARCIS (Netherlands)

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

    2012-01-01

    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 pap

  11. Applying the functional abnormality ontology pattern to anatomical functions

    Directory of Open Access Journals (Sweden)

    Hoehndorf Robert

    2010-03-01

    Full Text Available Abstract Background Several biomedical ontologies cover the domain of biological functions, including molecular and cellular functions. However, there is currently no publicly available ontology of anatomical functions. Consequently, no explicit relation between anatomical structures and their functions is expressed in the anatomy ontologies that are available for various species. Such an explicit relation between anatomical structures and their functions would be useful both for defining the classes of the anatomy and the phenotype ontologies accurately. Results We provide an ontological analysis of functions and functional abnormalities. From this analysis, we derive an approach to the automatic extraction of anatomical functions from existing ontologies which uses a combination of natural language processing, graph-based analysis of the ontologies and formal inferences. Additionally, we introduce a new relation to link material objects to processes that realize the function of these objects. This relation is introduced to avoid a needless duplication of processes already covered by the Gene Ontology in a new ontology of anatomical functions. Conclusions Ontological considerations on the nature of functional abnormalities and their representation in current phenotype ontologies show that we can extract a skeleton for an ontology of anatomical functions by using a combination of process, phenotype and anatomy ontologies automatically. We identify several limitations of the current ontologies that still need to be addressed to ensure a consistent and complete representation of anatomical functions and their abnormalities. Availability The source code and results of our analysis are available at http://bioonto.de.

  12. 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.

  13. 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

  14. The cognitive paradigm ontology: design and application.

    Science.gov (United States)

    Turner, Jessica A; Laird, Angela R

    2012-01-01

    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.

  15. 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.

  16. GFVO: the Genomic Feature and Variation Ontology

    Directory of Open Access Journals (Sweden)

    Joachim Baran

    2015-05-01

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

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

    Directory of Open Access Journals (Sweden)

    Lin Yu

    2011-10-01

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

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

    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. Product line based ontology development for semantic web service

    DEFF Research Database (Denmark)

    Zhang, Weishan; Kunz, Thomas

    2006-01-01

    and evolution. In this paper, we present a product line based reuseoriented ontology development methodology which integrates ontology development with design by reuse and design for reuse. The basic building block in our approach is the meta-ontology. In the first stage, reengineering of existing ontologies...... 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...

  20. Measuring Incoherence in Description Logic-Based Ontologies

    Science.gov (United States)

    Qi, Guilin; Hunter, Anthony

    Ontologies play a core role in the success of the Semantic Web as they provide a shared vocabulary for different resources and applications. Developing an error-free ontology is a difficult task. A common kind of error for an ontology is logical contradiction or incoherence. In this paper, we propose some approaches to measuring incoherence in DL-based ontologies. These measures give an ontology engineer important information for maintaining and evaluating ontologies. We implement the proposed approaches using the KAON2 reasoner and provide some preliminary but encouraging empirical results.

  1. Meeting Skills Needs in a Market-Based Training System: A Study of Employer Perceptions and Responses to Training Challenges in the Australian Transport and Logistics Industry

    Science.gov (United States)

    Gekara, Victor O.; Snell, Darryn; Chhetri, Prem; Manzoni, Alex

    2014-01-01

    Many countries are adopting market-based training systems to address industry skills needs. This paper examines the marketisation of Australia's training system and the implications for training provision and outcomes in the Transport and Logistics industry. Drawing on qualitative interviews from industry employers and training providers, we…

  2. A RESTful way to Manage Ontologies

    Science.gov (United States)

    Lowry, R. K.; Lawrence, B. N.

    2009-04-01

    In 2005 BODC implemented the first version of a vocabulary server developed as a contribution to the NERC DataGrid project. Vocabularies were managed within an RDBMS environment and accessed through a SOAP Web Service API. This was designed as a database query interface with operations targeted at designated database fields and results returned as strings. At the end of 2007 a new version of the server was released capable of serving thesauri and ontologies as well as vocabularies. The SOAP API functionality was enhanced and the output format changed to XML. In addition, a pseudo-RESTful query interface was developed directly addressing terms and lists by URLs. This is in full operational use by projects such as SeaDataNet and will run for the foreseeable future. However, operational experience has exposed shortcomings in both the API and its document payload. Other ontology servers, notably at MMI and CSIRO, are coming on-line making now the time to unify ontology management. This paper presents a RESTful API and payload document schema. It is based on the lessons learned in four years of operational vocabulary serving, provides full ontology management functionality and has the potential to form the basis for an interoperable network of distributed ontologies.

  3. Shiva++: An Enhanced Graph based Ontology Matcher

    Science.gov (United States)

    Mathur, Iti; Joshi, Nisheeth; Darbari, Hemant; Kumar, Ajai

    2014-04-01

    With the web getting bigger and assimilating knowledge about different concepts and domains, it is becoming very difficult for simple database driven applications to capture the data for a domain. Thus developers have come out with ontology based systems which can store large amount of information and can apply reasoning and produce timely information. Thus facilitating effective knowledge management. Though this approach has made our lives easier, but at the same time has given rise to another problem. Two different ontologies assimilating same knowledge tend to use different terms for the same concepts. This creates confusion among knowledge engineers and workers, as they do not know which is a better term then the other. Thus we need to merge ontologies working on same domain so that the engineers can develop a better application over it. This paper shows the development of one such matcher which merges the concepts available in two ontologies at two levels; 1) at string level and 2) at semantic level; thus producing better merged ontologies. We have used a graph matching technique which works at the core of the system. We have also evaluated the system and have tested its performance with its predecessor which works only on string matching. Thus current approach produces better results.

  4. An Architectural Approach for Building Medical Ontologies

    Directory of Open Access Journals (Sweden)

    Mircea Adrian FOCŞA

    2016-07-01

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

  5. Integrating systems biology models and biomedical ontologies

    Directory of Open Access Journals (Sweden)

    de Bono Bernard

    2011-08-01

    Full Text Available Abstract Background 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. Results 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. Conclusions 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. Integrating systems biology models and biomedical ontologies

    Science.gov (United States)

    2011-01-01

    Background 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. Results 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. Conclusions 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. PMID:21835028

  7. Towards a core ontology for integrating ecological and environmental ontologies to enable improved data interoperability

    Science.gov (United States)

    Bowers, S.; Madin, J.; Jones, M.; Schildhauer, M.; Ludaescher, B.

    2007-12-01

    Research in the ecological and environmental sciences increasingly relies on the integration of traditionally small, focused studies to form larger datasets for synthetic analyses. However, a broad range of data types, structures, and semantic subtleties occur in ecological data, making data discovery and integration a difficult and time-consuming task. Our work focuses on capturing the subtleties of scientific data through semantic annotations, which involve linking ecological data to concepts and relationships in domain-specific ontologies, thereby enabling more advanced forms of data discovery and integration. A variety of ontologies related to ecological data are actively being developed, ranging from low-level and highly focused vocabularies to high-level models and classifications. However, as the number of ontologies and their included terms increase, organizing these into a coherent framework useful for data annotation becomes increasingly complex (we note that similar issues have been recognized within the molecular biology and bioinformatics communities). We describe a core ontology model for semantic annotation that provides a structured approach for integrating the growing number of ecology-relevant ontologies. The ontology defines the notion of "scientific observation" as a unifying concept for capturing the basic semantics of ecological data. Observations are distinguished at the level of the entity (e.g., location, time, thing, concept), and characteristics of an entity (e.g., height, name, color) are measured (named or classified) as data. The ontology permits observations to be related via context (such as spatial or temporal containment), further supporting the discovery and automated comparison and alignment (e.g., merging) of heterogeneous data. The core ontology also defines a set of extension points that can be used to either directly build new domain ontologies (as extension ontologies), or to provide a common basis to which existing

  8. Air Pollution Analysis using Ontologies and Regression Models

    Directory of Open Access Journals (Sweden)

    Parul Choudhary

    2016-07-01

    Full Text Available Rapidly throughout the world economy, "the expansive Web" in the "world" explosive growth, rapidly growing market characterized by short product cycles exists and the demand for increased flexibility as well as the extensive use of a new data vision managed data society. A new socio-economic system that relies more and more on movement and allocation results in data whose daily existence, refinement, economy and adjust the exchange industry. Cooperative Engineering Co -operation and multi -disciplinary installed on people's cooperation is a good example. Semantic Web is a new form of Web content that is meaningful to computers and additional approved another example. Communication, vision sharing and exchanging data Society's are new commercial bet. Urban air pollution modeling and data processing techniques need elevated Association. Artificial intelligence in countless ways and breakthrough technologies can solve environmental problems from uneven offers. A method for data to formal ontology means a true meaning and lack of ambiguity to allow us to portray memo. In this work we survey regression model for ontologies and air pollution.

  9. 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.

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

    OpenAIRE

    Sokolova, Marina; Fernández Caballero, Antonio

    2007-01-01

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

  11. 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.

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

  13. 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.

  14. Integrated Semantic Similarity Model Based on Ontology

    Institute of Scientific and Technical Information of China (English)

    LIU Ya-Jun; ZHAO Yun

    2004-01-01

    To solve the problem of the inadequacy of semantic processing in the intelligent question answering system, an integrated semantic similarity model which calculates the semantic similarity using the geometric distance and information content is presented in this paper.With the help of interrelationship between concepts, the information content of concepts and the strength of the edges in the ontology network, we can calculate the semantic similarity between two concepts and provide information for the further calculation of the semantic similarity between user's question and answers in knowlegdge base.The results of the experiments on the prototype have shown that the semantic problem in natural language processing can also be solved with the help of the knowledge and the abundant semantic information in ontology.More than 90% accuracy with less than 50 ms average searching time in the intelligent question answering prototype system based on ontology has been reached.The result is very satisfied.

  15. 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.

  16. A Water Conservation Digital Library Using Ontologies

    Science.gov (United States)

    Ziemba, Lukasz; Cornejo, Camilo; Beck, Howard

    New technologies are emerging that assist in organizing and retrieving knowledge stored in a variety of forms (books, papers, models, decision support systems, databases), but they can only be evaluated through real world applications. Ontology has been used to manage the Water Conservation Digital Library holding a growing collection of various types of digital resources in the domain of urban water conservation in Florida, USA. The ontology based back-end powers a fully operational web interface, available at http://library.conservefloridawater.org library.conservefloridawater.org" TargetType="URL"/> . The system has already demonstrated numerous benefits of the ontology application, including: easier and more precise finding of resources, information sharing and reuse, and proved to effectively facilitate information management.

  17. 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....

  18. Ontology-enriched Visualization of Human Anatomy

    Energy Technology Data Exchange (ETDEWEB)

    Pouchard, LC

    2005-12-20

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

  19. Ontology Driven Piecemeal Development of Smart Spaces

    Science.gov (United States)

    Ovaska, Eila

    Software development is facing new challenges due to transformation from product based software engineering towards integration and collaboration based software engineering that embodies high degree of dynamism both at design time and run time. Short time-to-markets require cost reduction by maximizing software reuse; openness for new innovations presumes a flexible innovation platform and agile software development; and user satisfaction assumes high quality in a situation based manner. How to deal with these contradictory requirements in software engineering? The main contribution of this paper is a novel approach that is influenced by business innovation, human centered design, model driven development and ontology oriented design. The approach is called Ontology driven Piecemeal Software Engineering (OPSE). OPSE facilitates incremental software development based on software pieces that follow the design principles defined by means of ontologies. Its key elements are abstraction, aggregation and adaptivity. The approach is intended for and applied to the development of smart spaces.

  20. Query strategy for sequential ontology debugging

    CERN Document Server

    Shchekotykhina, Kostyantyn; Fleiss, Philipp; Rodler, Patrick

    2011-01-01

    Debugging of ontologies is an important prerequisite for their wide-spread application, especially in areas that rely upon everyday users to create and maintain knowledge bases, as in the case of the Semantic Web. Recent approaches use diagnosis methods to identify causes of inconsistent or incoherent ontologies. However, in most debugging scenarios these methods return many alternative diagnoses, thus placing the burden of fault localization on the user. This paper demonstrates how the target diagnosis can be identified by performing a sequence of observations, that is, by querying an oracle about entailments of the target ontology. We exploit a-priori probabilities of typical user errors to formulate information-theoretic concepts for query selection. Our evaluation showed that the proposed method significantly reduces the number of required queries compared to myopic strategies. We experimented with different probability distributions of user errors and different qualities of the a-priori probabilities. Ou...

  1. The ontology-based answers (OBA service: A connector for embedded usage of ontologies in applications

    Directory of Open Access Journals (Sweden)

    Jürgen eDönitz

    2012-10-01

    Full Text Available The semantic web depends on the use of ontologies to let electronic systems interpret contextualinformation. Optimally, the handling and access of ontologies should be completely transparent to theuser. As a means to this end, we have developed a service that attempts to bridge the gap betweenexperts in a certain knowledge domain, ontologists and application developers. The ontology-basedanswers (OBA service introduced here can be embedded into custom applications to grant access to theclasses of ontologies and their relations as most important structural features as well as to informationencoded in the relations between ontology classes. Thus computational biologists can benefit fromontologies without detailed knowledge about the respective ontology. The content of ontologies ismapped to a graph of connected objects which is compatible to the object-oriented programmingstyle in Java. Semantic functions implement knowledge about the complex semantics of anontology beyond the class hierarchy and partOf-relations. By using these OBA functions anapplication can, for example, provide a semantic search function, or (in the examples outlined mapan anatomical structure to the organs it belongs to. The semantic functions relieve the applicationdeveloper from the necessity of acquiring in-depth knowledge about the semantics and curationguidelines of the used ontologies by implementing the required knowledge. The architecture of theOBA service encapsulates the logic to process ontologies in order to achieve a separation from theapplication logic. A public server with the current plugins is available and can be used with theprovided connector in a custom application in scenarios analogous to the presented use cases. Theserver and the client are freely available if a project requires the use of custom plugins or nonpublicontologies.The OBA service and further documentation is available at: http://www.bioinf.med.unigoettingen.de/projects/oba

  2. Ontological metaphors for negative energy in an interdisciplinary context

    Science.gov (United States)

    Dreyfus, Benjamin W.; Geller, Benjamin D.; Gouvea, Julia; Sawtelle, Vashti; Turpen, Chandra; Redish, Edward F.

    2014-12-01

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

  3. Design of ontology mapping framework and improvement of similarity computation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Ontology heterogeneity is the primary obstacle for interoperation of ontologies.Ontology mapping is the best way to solve this problem.The key of ontology mapping is the similarity computation.At present,the method of similarity computation is imperfect.And the computation quantity is high.To solve these problems,an ontology-mapping framework with a kind of hybrid architecture is put forward.with an improvement in the method of similarity computation.Different areas have different local ontologies.Two ontologies are taken as examples,to explain the specific mapping framework and improved method of similarity computation.These two ontologies are about classes and teachers in a university.The experimental results show that using this framework and improved method can increase the accuracy of computation to a certain extent.Otherwise,the quantity of computation can be decreased.

  4. 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.

  5. Ontology and Epistemology in Management Research: An Islamic Perspective

    Directory of Open Access Journals (Sweden)

    Naail Mohammed KAMIL

    2011-09-01

    Full Text Available From the Western value system, two kinds of ontological and epistemological standpoints are characterized in Management and Social Sciences research;realist ontology and subjectivist ontology or objectivist epistemology and subjectivist epistemology. The kind of ontology and epistemology a researcher commits to has inherent effects towards the researcher’s way of contributing new knowledge. This short communication attempts to contribute new knowledge to the literature of philosophical standpoints in management research by discussing the ontological and epistemological stances with respect to Islam. It was shown that the Islamic viewpoint of ontology and epistemology is in the middle side between realist – subjectivist ontology and between objectivist – subjectivist epistemology. This stance of Islam on ontology andepistemology as elaborated in the Qur’an and the tradition of the Prophet Muhammad (peace be upon him increases the resilience with which knowledge is contributed in a holistic manner regardless of social, cultural or political backgrounds.

  6. Ontological metaphors for negative energy in an interdisciplinary context

    CERN Document Server

    Dreyfus, Benjamin W; Gouvea, Julia; Sawtelle, Vashti; Turpen, Chandra; Redish, Edward F

    2013-01-01

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

  7. Evolution of biomedical ontologies and mappings: Overview of recent approaches.

    Science.gov (United States)

    Groß, Anika; Pruski, Cédric; Rahm, Erhard

    2016-01-01

    Biomedical ontologies are heavily used to annotate data, and different ontologies are often interlinked by ontology mappings. These ontology-based mappings and annotations are used in many applications and analysis tasks. Since biomedical ontologies are continuously updated dependent artifacts can become outdated and need to undergo evolution as well. Hence there is a need for largely automated approaches to keep ontology-based mappings up-to-date in the presence of evolving ontologies. In this article, we survey current approaches and novel directions in the context of ontology and mapping evolution. We will discuss requirements for mapping adaptation and provide a comprehensive overview on existing approaches. We will further identify open challenges and outline ideas for future developments.

  8. The Ontology of Command and Control (C2)

    Science.gov (United States)

    2009-06-01

    semantic uniformity through application of a disciplined approach to ontology. An ontology is a consensus framework representing the types of...Recovery Operation Enforcement of Sanctions Irregular Warfare Peace Making Consequence Mangement Elimination of WMD Peace Enforcement Unconventional Warfare

  9. A Posteriori Ontology Engineering for Data-Driven Science

    Energy Technology Data Exchange (ETDEWEB)

    Gessler, Damian Dg; Joslyn, Cliff A.; Verspoor, Karin M.

    2013-05-28

    Science—and biology in particular—has a rich tradition in categorical knowledge management. This continues today in the generation and use of formal ontologies. Unfortunately, the link between hard data and ontological content is predominately qualitative, not quantitative. The usual approach is to construct ontologies of qualitative concepts, and then annotate the data to the ontologies. This process has seen great value, yet it is laborious, and the success to which ontologies are managing and organizing the full information content of the data is uncertain. An alternative approach is the converse: use the data itself to quantitatively drive ontology creation. Under this model, one generates ontologies at the time they are needed, allowing them to change as more data influences both their topology and their concept space. We outline a combined approach to achieve this, taking advantage of two technologies, the mathematical approach of Formal Concept Analysis (FCA) and the semantic web technologies of the Web Ontology Language (OWL).

  10. 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

  11. Primitive Ontology and the Classical World

    Science.gov (United States)

    Allori, Valia

    In this chapter, I present the common structure of quantum theories with a primitive ontology (PO), and discuss in what sense the classical world emerges from quantum theories as understood in this framework. In addition, I argue that the PO approach is better at analyzing the classical limit than the rival wave function ontology approach or any other approach in which the classical world is non-reductively "emergent:" even if the classical limit within this framework needs to be fully developed, the difficulties are technical rather than conceptual, while this is not true for the alternatives.

  12. Practical Applications of the Gene Ontology Resource

    Science.gov (United States)

    Huntley, Rachael P.; Dimmer, Emily C.; Apweiler, Rolf

    The Gene Ontology (GO) is a controlled vocabulary that represents knowledge about the functional attributes of gene products in a structured manner and can be used in both computational and human analyses. This vocabulary has been used by diverse curation groups to associate functional information to individual gene products in the form of annotations. GO has proven an invaluable resource for evaluating and interpreting the biological significance of large data sets, enabling researchers to create hypotheses to direct their future research. This chapter provides an overview of the Gene Ontology, how it can be used, and tips on getting the most out of GO analyses.

  13. Quantum Physics in a different ontology

    CERN Document Server

    de Silva, Nalin

    2010-01-01

    It is shown that neither the wave picture nor the ordinary particle picture offers a satisfactory explanation of the double-slit experiment. The Physicists who have been successful in formulating theories in the Newtonian Paradigm with its corresponding ontology find it difficult to interpret Quantum Physics which deals with particles that are not sensory perceptible. A different interpretation of Quantum Physics based in a different ontology is presented in what follows. According to the new interpretation Quantum particles have different properties from those of Classical Newtonian particles. The interference patterns are explained in terms of particles each of which passes through both slits.

  14. Semi-automated ontology generation and evolution

    Science.gov (United States)

    Stirtzinger, Anthony P.; Anken, Craig S.

    2009-05-01

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

  15. 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...

  16. 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.

  17. An ontological view of advanced practice nursing.

    Science.gov (United States)

    Arslanian-Engoren, Cynthia; Hicks, Frank D; Whall, Ann L; Algase, Donna L

    2005-01-01

    Identifying, developing, and incorporating nursing's unique ontological and epistemological perspective into advanced practice nursing practice places priority on delivering care based on research-derived knowledge. Without a clear distinction of our metatheoretical space, we risk blindly adopting the practice values of other disciplines, which may not necessarily reflect those of nursing. A lack of focus may lead current advanced practice nursing curricula and emerging doctorate of nursing practice programs to mirror the logical positivist paradigm and perspective of medicine. This article presents an ontological perspective for advanced practice nursing education, practice, and research.

  18. ONSET: Automated foundational ontology selection and explanation

    CSIR Research Space (South Africa)

    Khan, Z

    2012-10-01

    Full Text Available ://www.meteck.org/files/onset/. Scenario 1: Semantic Management of Middleware. The tool was tested according to the requirements of [9] which is an application of the semantic web. Ontolog- ical choices of the test case include: descriptiveness, a multiplicative approach, possibilism... to use DOLCE only. Even when a domain ontology developer wants to consider using a FO, there is a prohibitive learning curve due to the considerable quantity of documentation and the new terminology it introduces. Seeing that FOs are bene cial...

  19. An Extended Ontology Model and Ontology Checking Based on Description Logics

    Institute of Scientific and Technical Information of China (English)

    王洪伟; 蒋馥; 吴家春

    2004-01-01

    Ontology is defined as an explicit specification of a conceptualization. In this paper, an extended ontology model was constructed using description logics, which is a 5-tuples including term set, individual set, term definition set, instantiation assertion set and term restriction set. Based on the extended model, the issue on ontology checking was studied with the conclusion that the four kinds of term checking, including term satisfiability checking, term subsumption checking, term equivalence checking and term disjointness checking, can be reduced to the satisfiability checking, and satisfiability checking can be transformed into instantiation consistence checking.

  20. The Theoretical Status of Ontologies in Natural Language Processing

    CERN Document Server

    Bateman, J A

    1997-01-01

    This paper discusses the use of `ontologies' in Natural Language Processing. It classifies various kinds of ontologies that have been employed in NLP and discusses various benefits and problems with those designs. Particular focus is then placed on experiences gained in the use of the Upper Model, a linguistically-motivated `ontology' originally designed for use with the Penman text generation system. Some proposals for further NLP ontology design criteria are then made.

  1. An Ontology for Insider Threat Indicators Development and Applications

    Science.gov (United States)

    2014-11-01

    J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, et al., " Gene Ontology : tool for the unification of biology," Nature genetics, vol. 25, pp. 25-29...An Ontology for Insider Threat Indicators Development and Applications Daniel L. Costa, Matthew L. Collins, Samuel J. Perl, Michael J. Albrethsen...cert.org Abstract—We describe our ongoing development of an insider threat indicator ontology . Our ontology is intended to serve as a standardized

  2. Geo-Information (Lake Data Service Based on Ontology

    Directory of Open Access Journals (Sweden)

    Long-hua He

    2007-12-01

    Full Text Available Recently ontology research has received much attention in geo-information science and the concept of ontology is very important for spatial information concept modeling and data sharing, classification of geographical classes. More importantly, it enriches the semantic theory of spatial information. Geo-information services and geo-information interpretation and extraction are the two main applications of geo-ontology. Ontologies have great application potential for geo-information service.

  3. Influences of Ontology on Saussure’s Linguistics

    Institute of Scientific and Technical Information of China (English)

    XIA Xiao-lin

    2013-01-01

    Ontology is a core theory in Western philosophy, the study of‘which is focus on language itself’in ontological philos-ophy of language promotes the development of philosophy of language. This paper studies the influences of ontology on Saussuri-an linguistics, which finds that langue as an abstract holistic system is the linguistic being created by Saussure based on his study of ontology.

  4. Special issue on bio-ontologies and phenotypes.

    Science.gov (United States)

    Soldatova, Larisa N; Collier, Nigel; Oellrich, Anika; Groza, Tudor; Verspoor, Karin; Rocca-Serra, Philippe; Dumontier, Michel; Shah, Nigam H

    2015-01-01

    The bio-ontologies and phenotypes special issue includes eight papers selected from the 11 papers presented at the Bio-Ontologies SIG (Special Interest Group) and the Phenotype Day at ISMB (Intelligent Systems for Molecular Biology) conference in Boston in 2014. The selected papers span a wide range of topics including the automated re-use and update of ontologies, quality assessment of ontological resources, and the systematic description of phenotype variation, driven by manual, semi- and fully automatic means.

  5. Semi-automatic creation and exploitation of competence ontologies for trend aware profiling, matching and planning

    Directory of Open Access Journals (Sweden)

    H. Ulrich Hoppe

    2013-03-01

    Full Text Available Human resource managers are confronted with the problem that they have to fulfil the enterprise’s competence needs either by developing their current staff or by recruiting new employees. In both cases decisions about who to select for the new position and more often which competences are crucial for the future success. This is especially true for highly dynamic industries like the IT industry. This article presents our work from the KoPIWA project in the Digital Economy. Our approach is based on a conceptual model that encompasses the market level, the social context and relations between competences. This model is the foundation for the ontology based decision support system for human resource managers presented in this article. To semi-automatically create and update the competence ontology methods from the areas data mining, social network analysis and information retrieval are employed. The results of these methods with regard to recruiting and learning processes are presented.

  6. Semantic-Driven e-Government: Application of Uschold and King Ontology Building Methodology for Semantic Ontology Models Development

    CERN Document Server

    Fonou-Dombeu, Jean Vincent; 10.5121/ijwest.2011.2401

    2011-01-01

    Electronic government (e-government) has been one of the most active areas of ontology development during the past six years. In e-government, ontologies are being used to describe and specify e-government services (e-services) because they enable easy composition, matching, mapping and merging of various e-government services. More importantly, they also facilitate the semantic integration and interoperability of e-government services. However, it is still unclear in the current literature how an existing ontology building methodology can be applied to develop semantic ontology models in a government service domain. In this paper the Uschold and King ontology building methodology is applied to develop semantic ontology models in a government service domain. Firstly, the Uschold and King methodology is presented, discussed and applied to build a government domain ontology. Secondly, the domain ontology is evaluated for semantic consistency using its semi-formal representation in Description Logic. Thirdly, an...

  7. 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…

  8. 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…

  9. 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…

  10. 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…

  11. 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

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

    NARCIS (Netherlands)

    Guizzardi, Giancarlo; Wagner, Gerd; Guarino, Nicola; Sinderen, van Marten; Persson, Anne; Stirna, Janis

    2004-01-01

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

  13. Comparing alternative data-driven ontological vistas of natural history

    NARCIS (Netherlands)

    van Erp, M.G.J.; Lendvai, P.K.; van den Bosch, A.; Bunt, H.; Petukhova, V.; Wubben, S.

    2009-01-01

    Traditionally, ontologies are created manually, based on human experts' view of the concepts and relations of the domain at hand. We present ongoing work on two approaches to the automatic construction of ontologies from a flat database of records, and compare them to a manually constructed ontology

  14. 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

  15. 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

  16. 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 an

  17. Towards ontological foundations for agent modeling concepts using UFO

    NARCIS (Netherlands)

    Guizzardi, Giancarlo; Wagner, Gerd

    2005-01-01

    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 synthesi

  18. Construction of Engineering Ontologies for Knowledge Sharing and Reuse

    NARCIS (Netherlands)

    Borst, Willem Nico

    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 r

  19. About Ontology Application to the Description of Syllabus

    OpenAIRE

    Eremin, Evgeny

    2008-01-01

    Publication describes the experience in application of ontology technique to structuring of educational materials. Several topics of physics were formalized by means of Protégé software tool. Some principal problems in building of knowledge structure were found, so the discussion may interest not only ontology users, but also the developers of ontology tools.

  20. 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