WorldWideScience

Sample records for upper tag ontology

  1. 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

  2. Ontologies and tag-statistics

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  3. A Proposition Of Knowledge Management Methodology For The Purpose Of Reasoning With The Use Of An Upper-Ontology

    Directory of Open Access Journals (Sweden)

    Kamil Szymański

    2007-01-01

    Full Text Available This article describes a proposition of knowledge organization for the purpose of reasoningusing an upper-ontology. It presents a model of integrated ontologies architecture whichconsists of a domain ontologies layer with instances, a shared upper-ontology layer withadditional rules and a layer of ontologies mapping concrete domain ontologies with the upperontology.Thanks to the upper-ontology, new facts were concluded from domain ontologiesduring the reasoning process. A practical realization proposition is given as well. It is basedon some popular SemanticWeb technologies and tools, such as OWL, SWRL, nRQL, Prot´eg´eand Racer.

  4. Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus

    Science.gov (United States)

    Singh, Swati; Gupta, Sanchita; Mani, Ashutosh; Chaturvedi, Anoop

    2012-01-01

    Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function. PMID:22368382

  5. Pitfalls in alignment of observation models resolved using PROV as an upper ontology

    Science.gov (United States)

    Cox, S. J. D.

    2015-12-01

    A number of models for observation metadata have been developed in the earth and environmental science communities, including OGC's Observations and Measurements (O&M), the ecosystems community's Extensible Observation Ontology (OBOE), the W3C's Semantic Sensor Network Ontology (SSNO), and the CUAHSI/NSF Observations Data Model v2 (ODM2). In order to combine data formalized in the various models, mappings between these must be developed. In some cases this is straightforward: since ODM2 took O&M as its starting point, their terminology is almost completely aligned. In the eco-informatics world observations are almost never made in isolation of other observations, so OBOE pays particular attention to groupings, with multiple atomic 'Measurements' in each oboe:Observation which does not have a result of its own and thus plays a different role to an om:Observation. And while SSN also adopted terminology from O&M, mapping is confounded by the fact that SSN uses DOLCE as its foundation and places ssn:Observations as 'Social Objects' which are explicitly disjoint from 'Events', while O&M is formalized as part of the ISO/TC 211 harmonised (UML) model and sees om:Observations as value assignment activities. Foundational ontologies (such as BFO, GFO, UFO or DOLCE) can provide a framework for alignment, but different upper ontologies can be based in profoundly different worldviews and use of incommensurate frameworks can confound rather than help. A potential resolution is provided by comparing recent studies that align SSN and O&M, respectively, with the PROV-O ontology. PROV-O provides just three base classes: Entity, Activity and Agent. om:Observation is sub-classed from prov:Activity, while ssn:Observation is sub-classed from prov:Entity. This confirms that, despite the same name, om:Observation and ssn:Observation denote different aspects of the observation process: the observation event, and the record of the observation event, respectively. Alignment with the simple

  6. The Open-Multinet Upper Ontology Towards the Semantic-based Management of Federated Infrastructures

    Directory of Open Access Journals (Sweden)

    Alexander Willner

    2015-12-01

    Full Text Available The Internet remains an unfinished work. There are several approaches to enhancing it that have been experimentally validated within federated testbed environments. To best gain scientific knowledge from these studies, reproducibility and automation are needed in all areas of the experiment life cycle. Within the GENI and FIRE context, several architectures and protocols have been developed for this purpose. However, a major open research issue remains, namely the description and discovery of the heterogeneous resources involved. To remedy this, we propose a semantic information model that can be used to allow declarative interoperability, build dependency graphs, validate requests, infer knowledge and conduct complex queries. The requirements for such an information model have been extracted from current international Future Internet research projects and the practicality of the model is being evaluated through initial implementations. The main outcome of this work is the definition of the Open-Multinet Upper Ontology and related sub-ontologies, which can be used to describe and manage federated infrastructures and their resources.

  7. 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…

  8. Toward the Use of an Upper Ontology for U.S. Government and U.S. Military Domains: An Evaluation

    National Research Council Canada - National Science Library

    Semy, Salim K; Pulvermacher, Mary K; Obrst, Leo J

    2004-01-01

    ...) of data and ultimately of applications. Key to the vision of a Semantic Web is the ability to capture data and application semantics in ontologies and map these ontologies together via related concepts...

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

    OpenAIRE

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

    2008-01-01

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

  10. Tracing the contribution of debris flow-dominated channels to gravel-bed torrential river channel: implementing pit-tags in the upper Guil River (French Alps)

    Science.gov (United States)

    Arnaud-Fassetta, Gilles; Lissak, Candide; Fort, Monique; Bétard, François; Carlier, Benoit; Cossart, Etienne; Madelin, Malika; Viel, Vincent; Charnay, Bérengère; Bletterie, Xavier

    2014-05-01

    In the upper, wider reaches of Alpine valleys, shaping of active channels is usually subject to rapid change. It mostly depends upon hydro-climatic variability, runoff concentration and sediment supply, and may result in alternating sequences of fluvial and debris-flow pulses, as recorded in alluvial fans and terraces. Our study, carried in the frame of SAMCO (ANR) project, focuses on the upper Guil River Valley (Queyras, Southern French Alps) cut into the slaty shale "schistes lustrés". Steep, lower order drains carry a contrasted solid discharge, including predominantly sandy-loam particles mixed with gravels and boulders (sandstone schists, ophiolites). Abundant sediment supply by frost shattering, snow avalanche and landslides is then reworked during snowmelt or summer storm runoff events, and may result in catastrophic, very destructive floods along the main channel, as shown by historical records. Following the RI-30 year 2000 flood, our investigations included sediment budgets, i.e. balance of erosion and deposition, and the mapping of the source, transport and storage of various sediments (talus, colluvium, torrential fans, terraces). To better assess sediment fluxes and sediment delivery into the main channel network, we implemented tracers (pit-tags) in selected sub-catchments, significantly contributing to the sediment yield of the valley bottoms during the floods and/or avalanches: Maloqueste, Combe Morel, Bouchouse and Peyronnelle catchments. The first three are direct tributaries of the Guil River whereas the Peyronnelle is a left bank tributary of the Peynin River, which joins the Guil River via an alluvial cone with high human and material stakes. The Maloqueste and the Combe Morel are two tributaries facing each other in the Guil valley, representing a double lateral constraint for the road during flood events of the Guil River. After pit-tag initialisation in laboratory, we set them up along the four tributaries: Maloqueste (20 pit-tags), Combe

  11. Quantum ontologies

    International Nuclear Information System (INIS)

    Stapp, H.P.

    1988-12-01

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

  12. Billfish Tagging

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The SWFSC's constituent-based Billfish Tagging Program began in 1963 and since that time has provided conventional spaghetti type tags and tagging supplies to...

  13. Tag questions Tag questions

    Directory of Open Access Journals (Sweden)

    David Brazil

    2008-04-01

    Full Text Available The so-called 'tag' structures of English have received a lot of attention in language teaching programmes, attention that is not hard to justify when one considers the problems and anxiety they can occasion for many foreign learners. Most teachers one speaks to seem fairly willing to agree, however, that traditional treatments of the topic leave much to be desired. It happens, also, that, when considered collectively, the tags and some related phenomena have a special heoretical interest. For they constitute a field in which it seems essential to bring together insights that derive from the study of several aspects of linguistic organisation, aspects which in some recent work have been held to need distinctive kinds of descriptive category to handle. Traditional treatments have found it necessary to recognise different syntactic types (e.g. 'same polarity' and 'reversed polarity' tags and ifferent intonational treatments ("falling'and 'rising' tag; while the way the communicative significance of the various permutations is described normally requires reference to the expectations they signal regarding the immediately following behaviour of the other party (in the common phrase, 'What kind of answer they expect'. This last consideration places the matter squarely in the arena of recent work on the analysis of interactive discourse. The so-called 'tag' structures of English have received a lot of attention in language teaching programmes, attention that is not hard to justify when one considers the problems and anxiety they can occasion for many foreign learners. Most teachers one speaks to seem fairly willing to agree, however, that traditional treatments of the topic leave much to be desired. It happens, also, that, when considered collectively, the tags and some related phenomena have a special heoretical interest. For they constitute a field in which it seems essential to bring together insights that derive from the study of several aspects

  14. Ontological Planning

    Directory of Open Access Journals (Sweden)

    Ahmet Alkan

    2017-12-01

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

  15. 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...

  16. 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

  17. 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...

  18. Ontology authoring with Forza

    CSIR Research Space (South Africa)

    Keet, CM

    2014-11-01

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

  19. Ontological Surprises

    DEFF Research Database (Denmark)

    Leahu, Lucian

    2016-01-01

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

  20. 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.

  1. Didactical Ontologies

    Directory of Open Access Journals (Sweden)

    Steffen Mencke, Reiner Dumke

    2008-03-01

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

  2. Assessment Applications of Ontologies.

    Science.gov (United States)

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

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

  3. Ontologies vs. Classification Systems

    DEFF Research Database (Denmark)

    Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

    2009-01-01

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

  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. 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.

  6. 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.

  7. Yellowtail Tagging Data (MRDBS)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Yellowtail Flounder Tagging Program began in 2003 and works with commercial fishermen to tag and release yellowtaiI flounder with pink and yellow disc tags or...

  8. Constructive Ontology Engineering

    Science.gov (United States)

    Sousan, William L.

    2010-01-01

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

  9. Towards Agile Ontology Maintenance

    Science.gov (United States)

    Luczak-Rösch, Markus

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

  10. Conceptual querying through ontologies

    DEFF Research Database (Denmark)

    Andreasen, Troels; Bulskov, Henrik

    2009-01-01

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

  11. Survey on Ontology Mapping

    Science.gov (United States)

    Zhu, Junwu

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

  12. 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 ...

  13. Semi Automatic Ontology Instantiation in the domain of Risk Management

    Science.gov (United States)

    Makki, Jawad; Alquier, Anne-Marie; Prince, Violaine

    One of the challenging tasks in the context of Ontological Engineering is to automatically or semi-automatically support the process of Ontology Learning and Ontology Population from semi-structured documents (texts). In this paper we describe a Semi-Automatic Ontology Instantiation method from natural language text, in the domain of Risk Management. This method is composed from three steps 1 ) Annotation with part-of-speech tags, 2) Semantic Relation Instances Extraction, 3) Ontology instantiation process. It's based on combined NLP techniques using human intervention between steps 2 and 3 for control and validation. Since it heavily relies on linguistic knowledge it is not domain dependent which is a good feature for portability between the different fields of risk management application. The proposed methodology uses the ontology of the PRIMA1 project (supported by the European community) as a Generic Domain Ontology and populates it via an available corpus. A first validation of the approach is done through an experiment with Chemical Fact Sheets from Environmental Protection Agency2.

  14. Ontology Design of Influential People Identification Using Centrality

    Science.gov (United States)

    Maulana Awangga, Rolly; Yusril, Muhammad; Setyawan, Helmi

    2018-04-01

    Identifying influential people as a node in a graph theory commonly calculated by social network analysis. The social network data has the user as node and edge as relation forming a friend relation graph. This research is conducting different meaning of every nodes relation in the social network. Ontology was perfect match science to describe the social network data as conceptual and domain. Ontology gives essential relationship in a social network more than a current graph. Ontology proposed as a standard for knowledge representation for the semantic web by World Wide Web Consortium. The formal data representation use Resource Description Framework (RDF) and Web Ontology Language (OWL) which is strategic for Open Knowledge-Based website data. Ontology used in the semantic description for a relationship in the social network, it is open to developing semantic based relationship ontology by adding and modifying various and different relationship to have influential people as a conclusion. This research proposes a model using OWL and RDF for influential people identification in the social network. The study use degree centrality, between ness centrality, and closeness centrality measurement for data validation. As a conclusion, influential people identification in Facebook can use proposed Ontology model in the Group, Photos, Photo Tag, Friends, Events and Works data.

  15. Unintended consequences of existential quantifications in biomedical ontologies

    Directory of Open Access Journals (Sweden)

    Boeker Martin

    2011-11-01

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

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

    NARCIS (Netherlands)

    Stoelhorst, J.W.

    2008-01-01

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

  17. 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

  18. 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.

  19. Ontology of fractures

    Science.gov (United States)

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

    2009-03-01

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

  20. 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.

  1. The Electronic Notebook Ontology

    OpenAIRE

    Chalk, Stuart

    2016-01-01

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

  2. Ontology Update in the Cognitive Model of Ontology Learning

    Directory of Open Access Journals (Sweden)

    Zhang De-Hai

    2016-01-01

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

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

    Science.gov (United States)

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

    2012-09-21

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

  4. Gillnet Tag Program

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Certain fishery management programs require vessels to obtain gillnet tags to be used with their gillnet gear. Gillnet tag data is a collection of requests and...

  5. Cooperative Tagging Center (CTC)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Cooperative Tagging Center (CTC) began as the Cooperative Game Fish Tagging Program (GTP) at Woods Hole Oceanographic Institute (WHOI) in 1954. The GTP was...

  6. North Pacific Albacore Tagging

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Conventional tagging data are available from 1971 to 1996. Electronic tagging data are available from 2000 to present. The data are managed by SWFSC in Access...

  7. Supporting Better Treatments for Meeting Health Consumers' Needs: Extracting Semantics in Social Data for Representing a Consumer Health Ontology

    Science.gov (United States)

    Choi, Yunseon

    2016-01-01

    Introduction: The purpose of this paper is to provide a framework for building a consumer health ontology using social tags. This would assist health users when they are accessing health information and increase the number of documents relevant to their needs. Methods: In order to extract concepts from social tags, this study conducted an…

  8. Tagging vs. Controlled Vocabulary

    DEFF Research Database (Denmark)

    Bogers, Toine; Petras, Vivien

    2015-01-01

    The popularity of social tagging has sparked a great deal of debate on whether tags could replace or improve upon professional metadata as descriptors of books and other information objects. In this paper we present a large-scale empirical comparison of the contributions of individual information...... that tags and controlled vocabulary terms do not actually outperform each other consistently, but seem to provide complementary contributions: some information needs are best addressed using controlled vocabulary terms whereas other are best addressed using tags....

  9. Cutaneous skin tag

    Science.gov (United States)

    Skin tag; Acrochordon; Fibroepithelial polyp ... have diabetes. They are thought to occur from skin rubbing against skin. ... The tag sticks out of the skin and may have a short, narrow stalk connecting it to the surface of the skin. Some skin tags are as long as ...

  10. Towards Universal Semantic Tagging

    NARCIS (Netherlands)

    Abzianidze, Lasha; Bos, Johan

    2017-01-01

    The paper proposes the task of universal semantic tagging---tagging word tokens with language-neutral, semantically informative tags. We argue that the task, with its independent nature, contributes to better semantic analysis for wide-coverage multilingual text. We present the initial version of

  11. Extracting Tag Hierarchies

    Science.gov (United States)

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

    2013-01-01

    Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy between the tags for systems with a "flat", egalitarian organization of the tags, which is very common when the tags correspond to free words given by numerous independent people. Here we present a complete framework for automated tag hierarchy extraction based on tag occurrence statistics. Along with proposing new algorithms, we are also introducing different quality measures enabling the detailed comparison of competing approaches from different aspects. Furthermore, we set up a synthetic, computer generated benchmark providing a versatile tool for testing, with a couple of tunable parameters capable of generating a wide range of test beds. Beside the computer generated input we also use real data in our studies, including a biological example with a pre-defined hierarchy between the tags. The encouraging similarity between the pre-defined and reconstructed hierarchy, as well as the seemingly meaningful hierarchies obtained for other real systems indicate that tag hierarchy extraction is a very promising direction for further research with a great potential for practical applications. Tags have become very prevalent nowadays in various online platforms ranging from blogs through scientific publications to protein databases. Furthermore, tagging systems dedicated for voluntary tagging of photos, films, books, etc. with free words are also becoming popular. The emerging large collections of tags associated with different objects are often referred to as folksonomies, highlighting their collaborative origin and the “flat” organization of the tags opposed to traditional hierarchical categorization. Adding a tag hierarchy corresponding to a given folksonomy can very effectively help narrowing or broadening the scope of search

  12. Extracting tag hierarchies.

    Directory of Open Access Journals (Sweden)

    Gergely Tibély

    Full Text Available Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy between the tags for systems with a "flat", egalitarian organization of the tags, which is very common when the tags correspond to free words given by numerous independent people. Here we present a complete framework for automated tag hierarchy extraction based on tag occurrence statistics. Along with proposing new algorithms, we are also introducing different quality measures enabling the detailed comparison of competing approaches from different aspects. Furthermore, we set up a synthetic, computer generated benchmark providing a versatile tool for testing, with a couple of tunable parameters capable of generating a wide range of test beds. Beside the computer generated input we also use real data in our studies, including a biological example with a pre-defined hierarchy between the tags. The encouraging similarity between the pre-defined and reconstructed hierarchy, as well as the seemingly meaningful hierarchies obtained for other real systems indicate that tag hierarchy extraction is a very promising direction for further research with a great potential for practical applications. Tags have become very prevalent nowadays in various online platforms ranging from blogs through scientific publications to protein databases. Furthermore, tagging systems dedicated for voluntary tagging of photos, films, books, etc. with free words are also becoming popular. The emerging large collections of tags associated with different objects are often referred to as folksonomies, highlighting their collaborative origin and the "flat" organization of the tags opposed to traditional hierarchical categorization. Adding a tag hierarchy corresponding to a given folksonomy can very effectively help narrowing or broadening the scope of

  13. Extracting tag hierarchies.

    Science.gov (United States)

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

    2013-01-01

    Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy between the tags for systems with a "flat", egalitarian organization of the tags, which is very common when the tags correspond to free words given by numerous independent people. Here we present a complete framework for automated tag hierarchy extraction based on tag occurrence statistics. Along with proposing new algorithms, we are also introducing different quality measures enabling the detailed comparison of competing approaches from different aspects. Furthermore, we set up a synthetic, computer generated benchmark providing a versatile tool for testing, with a couple of tunable parameters capable of generating a wide range of test beds. Beside the computer generated input we also use real data in our studies, including a biological example with a pre-defined hierarchy between the tags. The encouraging similarity between the pre-defined and reconstructed hierarchy, as well as the seemingly meaningful hierarchies obtained for other real systems indicate that tag hierarchy extraction is a very promising direction for further research with a great potential for practical applications. Tags have become very prevalent nowadays in various online platforms ranging from blogs through scientific publications to protein databases. Furthermore, tagging systems dedicated for voluntary tagging of photos, films, books, etc. with free words are also becoming popular. The emerging large collections of tags associated with different objects are often referred to as folksonomies, highlighting their collaborative origin and the "flat" organization of the tags opposed to traditional hierarchical categorization. Adding a tag hierarchy corresponding to a given folksonomy can very effectively help narrowing or broadening the scope of search. Moreover

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

    Directory of Open Access Journals (Sweden)

    Daniel L Cook

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

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

    Science.gov (United States)

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

    2011-01-01

    As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities-molecules, cells, organs-are well-established, there are no principled ontologies of physical properties-energies, volumes, flow rates-of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB), a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration. © 2011 Cook et al.

  16. Ontological interpretation of biomedical database content.

    Science.gov (United States)

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

    2017-06-26

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

  17. 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

  18. Ontology: ambiguity and accuracy

    Directory of Open Access Journals (Sweden)

    Marcelo Schiessl

    2012-08-01

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

  19. Ontological engineering versus metaphysics

    Science.gov (United States)

    Tataj, Emanuel; Tomanek, Roman; Mulawka, Jan

    2011-10-01

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

  20. A Method for Building Personalized Ontology Summaries

    OpenAIRE

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

    2013-01-01

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

  1. Ontology and medical diagnosis.

    Science.gov (United States)

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

    2012-03-01

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

  2. Core Semantics for Public Ontologies

    National Research Council Canada - National Science Library

    Suni, Niranjan

    2005-01-01

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

  3. 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

  4. ONTOLOGY IN PHARMACY

    Directory of Open Access Journals (Sweden)

    L. Yu. Babintseva

    2015-05-01

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

  5. 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....

  6. Biomedical ontologies: toward scientific debate.

    Science.gov (United States)

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

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Wasila M Dahdul

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

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

    Science.gov (United States)

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

    2012-01-01

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

  9. A Unified Anatomy Ontology of the Vertebrate Skeletal System

    Science.gov (United States)

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

    2012-01-01

    The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity. PMID:23251424

  10. 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.

  11. 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 ...

  12. 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…

  13. Audit Validation Using Ontologies

    Directory of Open Access Journals (Sweden)

    Ion IVAN

    2015-01-01

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

  14. Biomedicine: an ontological dissection.

    Science.gov (United States)

    Baronov, David

    2008-01-01

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

  15. 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

  16. Approximation properties of haplotype tagging

    Directory of Open Access Journals (Sweden)

    Dreiseitl Stephan

    2006-01-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are locations at which the genomic sequences of population members differ. Since these differences are known to follow patterns, disease association studies are facilitated by identifying SNPs that allow the unique identification of such patterns. This process, known as haplotype tagging, is formulated as a combinatorial optimization problem and analyzed in terms of complexity and approximation properties. Results It is shown that the tagging problem is NP-hard but approximable within 1 + ln((n2 - n/2 for n haplotypes but not approximable within (1 - ε ln(n/2 for any ε > 0 unless NP ⊂ DTIME(nlog log n. A simple, very easily implementable algorithm that exhibits the above upper bound on solution quality is presented. This algorithm has running time O((2m - p + 1 ≤ O(m(n2 - n/2 where p ≤ min(n, m for n haplotypes of size m. As we show that the approximation bound is asymptotically tight, the algorithm presented is optimal with respect to this asymptotic bound. Conclusion The haplotype tagging problem is hard, but approachable with a fast, practical, and surprisingly simple algorithm that cannot be significantly improved upon on a single processor machine. Hence, significant improvement in computatational efforts expended can only be expected if the computational effort is distributed and done in parallel.

  17. Tags on healthcare information websites

    DEFF Research Database (Denmark)

    Lykke, Marianne; Ådland, Marit Kristine

    2018-01-01

    This paper explores tags and tagging behaviour on health information websites using an empirical, user-oriented, exploratory case study. Taggers and editors were interviewed about tags and tagging, while taggers solved tasks that included applying tags to a website. This qualitative data...... articles, request information, and value article content. Some of these show that tags are not only not only topical descriptions, but communicative by intent. This result can potentially inform the design of tagging features....

  18. 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.

  19. Ontology-based Information Retrieval

    DEFF Research Database (Denmark)

    Styltsvig, Henrik Bulskov

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

  20. An approach to development of ontological knowledge base in the field of scientific and research activity in Russia

    Science.gov (United States)

    Murtazina, M. Sh; Avdeenko, T. V.

    2018-05-01

    The state of art and the progress in application of semantic technologies in the field of scientific and research activity have been analyzed. Even elementary empirical comparison has shown that the semantic search engines are superior in all respects to conventional search technologies. However, semantic information technologies are insufficiently used in the field of scientific and research activity in Russia. In present paper an approach to construction of ontological model of knowledge base is proposed. The ontological model is based on the upper-level ontology and the RDF mechanism for linking several domain ontologies. The ontological model is implemented in the Protégé environment.

  1. Completeness, supervenience and ontology

    International Nuclear Information System (INIS)

    Maudlin, Tim W E

    2007-01-01

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

  2. Completeness, supervenience and ontology

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-03-23

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

  3. PIT Tagging Anurans

    Science.gov (United States)

    McCreary, Brome

    2008-01-01

    The following video demonstrates a procedure to insert a passive integrated transponder (PIT) tag under the skin of an anuran (frog or toad) for research and monitoring purposes. Typically, a 12.5 mm tag (0.5 in.) is used to uniquely identify individual anurans as smal as 40 mm (1.6 in.) in length from snout to vent. Smaller tags are also available and allow smaller anurans to be tagged. The procedure does not differ for other sizes of tages or other sizes of anurans. Anyone using this procedure should ensure that the tag is small enough to fit easily behind the sacral hump of the anuran, as shown in this video.

  4. LOGISTICS OPTIMIZATION USING ONTOLOGIES

    OpenAIRE

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

    2014-01-01

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

  5. Ontology evolution in physics

    OpenAIRE

    Chan, Michael

    2013-01-01

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

  6. Feasibility of automated foundational ontology interchangeability

    CSIR Research Space (South Africa)

    Khan, ZC

    2014-11-01

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

  7. 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…

  8. Flavour Tagging at LHCb

    CERN Multimedia

    Grabalosa Gandara, M

    2009-01-01

    To do precise CP violation measurements, the most possible accurate knowledge of the flavour at production of the reconstructed B meson is required. This poster summarizes the flavour tagging performances for the LHCb experiment. We use same side an opposite side algorithms to establish wheter the meson contained a b or a b\\bar quark. The final decision is obtained through a combination of several methods. The use of control channels, decays to a flavour specific final state, will allow to determine the wrong tag fraction \\omega (the probability of a tag to be wrong), which can be used as input for the determination of CKM unitary triangle angles.

  9. ONSET: Automated foundational ontology selection and explanation

    CSIR Research Space (South Africa)

    Khan, Z

    2012-10-01

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

  10. Tagged Vector Contour (TVC)

    Data.gov (United States)

    Kansas Data Access and Support Center — The Kansas Tagged Vector Contour (TVC) dataset consists of digitized contours from the 7.5 minute topographic quadrangle maps. Coverage for the state is incomplete....

  11. 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

  12. Ontology-Based Approach to Social Data Sentiment Analysis: Detection of Adolescent Depression Signals.

    Science.gov (United States)

    Jung, Hyesil; Park, Hyeoun-Ae; Song, Tae-Min

    2017-07-24

    Social networking services (SNSs) contain abundant information about the feelings, thoughts, interests, and patterns of behavior of adolescents that can be obtained by analyzing SNS postings. An ontology that expresses the shared concepts and their relationships in a specific field could be used as a semantic framework for social media data analytics. The aim of this study was to refine an adolescent depression ontology and terminology as a framework for analyzing social media data and to evaluate description logics between classes and the applicability of this ontology to sentiment analysis. The domain and scope of the ontology were defined using competency questions. The concepts constituting the ontology and terminology were collected from clinical practice guidelines, the literature, and social media postings on adolescent depression. Class concepts, their hierarchy, and the relationships among class concepts were defined. An internal structure of the ontology was designed using the entity-attribute-value (EAV) triplet data model, and superclasses of the ontology were aligned with the upper ontology. Description logics between classes were evaluated by mapping concepts extracted from the answers to frequently asked questions (FAQs) onto the ontology concepts derived from description logic queries. The applicability of the ontology was validated by examining the representability of 1358 sentiment phrases using the ontology EAV model and conducting sentiment analyses of social media data using ontology class concepts. We developed an adolescent depression ontology that comprised 443 classes and 60 relationships among the classes; the terminology comprised 1682 synonyms of the 443 classes. In the description logics test, no error in relationships between classes was found, and about 89% (55/62) of the concepts cited in the answers to FAQs mapped onto the ontology class. Regarding applicability, the EAV triplet models of the ontology class represented about 91

  13. Ontology Based Model Transformation Infrastructure

    NARCIS (Netherlands)

    Göknil, Arda; Topaloglu, N.Y.

    2005-01-01

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

  14. 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.…

  15. The foundational ontology library ROMULUS

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-09-01

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

  16. Tracking Changes during Ontology Evolution

    NARCIS (Netherlands)

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

    2004-01-01

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

  17. Tagging in Volunteered Geographic Information: An Analysis of Tagging Practices for Cities and Urban Regions in OpenStreetMap

    Directory of Open Access Journals (Sweden)

    Nikola Davidovic

    2016-12-01

    Full Text Available In Volunteered Geographic Information (VGI projects, the tagging or annotation of objects is usually performed in a flexible and non-constrained manner. Contributors to a VGI project are normally free to choose whatever tags they feel are appropriate to annotate or describe a particular geographic object or place. In OpenStreetMap (OSM, the Map Features part of the OSM Wiki serves as the de-facto rulebook or ontology for the annotation of features in OSM. Within Map Features, suggestions and guidance on what combinations of tags to use for certain geographic objects are outlined. In this paper, we consider these suggestions and recommendations and analyse the OSM database for 40 cities around the world to ascertain if contributors to OSM in these urban areas are using this guidance in their tagging practices. Overall, we find that compliance with the suggestions and guidance in Map Features is generally average or poor. This leads us to conclude that contributors in these areas do not always tag features with the same level of annotation. Our paper also confirms anecdotal evidence that OSM Map Features is less influential in how OSM contributors tag objects.

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

    Science.gov (United States)

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

    2016-07-04

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

  19. Logic and Ontology

    Directory of Open Access Journals (Sweden)

    Newton C. A. da Costa

    2002-12-01

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

  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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Building a developmental toxicity ontology.

    Science.gov (United States)

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

    2018-04-03

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

  2. Inclusive Flavour Tagging Algorithm

    International Nuclear Information System (INIS)

    Likhomanenko, Tatiana; Derkach, Denis; Rogozhnikov, Alex

    2016-01-01

    Identifying the flavour of neutral B mesons production is one of the most important components needed in the study of time-dependent CP violation. The harsh environment of the Large Hadron Collider makes it particularly hard to succeed in this task. We present an inclusive flavour-tagging algorithm as an upgrade of the algorithms currently used by the LHCb experiment. Specifically, a probabilistic model which efficiently combines information from reconstructed vertices and tracks using machine learning is proposed. The algorithm does not use information about underlying physics process. It reduces the dependence on the performance of lower level identification capacities and thus increases the overall performance. The proposed inclusive flavour-tagging algorithm is applicable to tag the flavour of B mesons in any proton-proton experiment. (paper)

  3. 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.

  4. Personalization of tagging systems

    NARCIS (Netherlands)

    J. Wang (Jun); M. Clements (Maarten); J. Yang; A.P. de Vries (Arjen); M.J.T. Reinders

    2010-01-01

    htmlabstractSocial media systems have encouraged end user participation in the Internet, for the purpose of storing and distributing Internet content, sharing opinions and maintaining relationships. Collaborative tagging allows users to annotate the resulting user-generated content, and enables

  5. TagPad

    DEFF Research Database (Denmark)

    Bornoe, Nis; Barkhuus, Louise

    2013-01-01

    The area of cyberinfrastructures has looked extensively at research within the natural sciences, however, the social sciences have been largely overlooked in terms of novel data collection and analysis systems. We developed a probe tool, TagPad, to look at the process for social science data...

  6. development of ontological knowledge representation

    African Journals Online (AJOL)

    Preferred Customer

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

  7. A Mobile Army of Ontologies

    DEFF Research Database (Denmark)

    Juul, Jesper

    2015-01-01

    Presentation at the Ludo-ontologies panel. Do we need ludo-ontologies, and what are they? In this event several scholars of games and videogames discuss these questions from a variety of perspectives. What different game and videogame ontologies exist and could exist, and why they are important...... for game and videogame research? The round table is designed to promote ludo-ontological dialogue in order to make these questions visible and debated. A series of short presentations (approximately 10 minutes each) will be followed by an intense debate through freeform dialogue. After the industrial...... commercialization of games and videogames their study has shifted between approaches focused on players (ludic processes) and artifacts (ludic objects). Some attempts to analyze the relationship between the process and the object have occasionally been done in terms of ‘ontology’ (Zagal 2005; Leino 2010; Gualeni...

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

    OpenAIRE

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

    1999-01-01

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

  9. ``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.

  10. Incremental Ontology-Based Extraction and Alignment in Semi-structured Documents

    Science.gov (United States)

    Thiam, Mouhamadou; Bennacer, Nacéra; Pernelle, Nathalie; Lô, Moussa

    SHIRIis an ontology-based system for integration of semi-structured documents related to a specific domain. The system’s purpose is to allow users to access to relevant parts of documents as answers to their queries. SHIRI uses RDF/OWL for representation of resources and SPARQL for their querying. It relies on an automatic, unsupervised and ontology-driven approach for extraction, alignment and semantic annotation of tagged elements of documents. In this paper, we focus on the Extract-Align algorithm which exploits a set of named entity and term patterns to extract term candidates to be aligned with the ontology. It proceeds in an incremental manner in order to populate the ontology with terms describing instances of the domain and to reduce the access to extern resources such as Web. We experiment it on a HTML corpus related to call for papers in computer science and the results that we obtain are very promising. These results show how the incremental behaviour of Extract-Align algorithm enriches the ontology and the number of terms (or named entities) aligned directly with the ontology increases.

  11. GeoSciGraph: An Ontological Framework for EarthCube Semantic Infrastructure

    Science.gov (United States)

    Gupta, A.; Schachne, A.; Condit, C.; Valentine, D.; Richard, S.; Zaslavsky, I.

    2015-12-01

    The CINERGI (Community Inventory of EarthCube Resources for Geosciences Interoperability) project compiles an inventory of a wide variety of earth science resources including documents, catalogs, vocabularies, data models, data services, process models, information repositories, domain-specific ontologies etc. developed by research groups and data practitioners. We have developed a multidisciplinary semantic framework called GeoSciGraph semantic ingration of earth science resources. An integrated ontology is constructed with Basic Formal Ontology (BFO) as its upper ontology and currently ingests multiple component ontologies including the SWEET ontology, GeoSciML's lithology ontology, Tematres controlled vocabulary server, GeoNames, GCMD vocabularies on equipment, platforms and institutions, software ontology, CUAHSI hydrology vocabulary, the environmental ontology (ENVO) and several more. These ontologies are connected through bridging axioms; GeoSciGraph identifies lexically close terms and creates equivalence class or subclass relationships between them after human verification. GeoSciGraph allows a community to create community-specific customizations of the integrated ontology. GeoSciGraph uses the Neo4J,a graph database that can hold several billion concepts and relationships. GeoSciGraph provides a number of REST services that can be called by other software modules like the CINERGI information augmentation pipeline. 1) Vocabulary services are used to find exact and approximate terms, term categories (community-provided clusters of terms e.g., measurement-related terms or environmental material related terms), synonyms, term definitions and annotations. 2) Lexical services are used for text parsing to find entities, which can then be included into the ontology by a domain expert. 3) Graph services provide the ability to perform traversal centric operations e.g., finding paths and neighborhoods which can be used to perform ontological operations like

  12. 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

  13. Gold-standard evaluation of a folksonomy-based ontology learning model

    Science.gov (United States)

    Djuana, E.

    2018-03-01

    Folksonomy, as one result of collaborative tagging process, has been acknowledged for its potential in improving categorization and searching of web resources. However, folksonomy contains ambiguities such as synonymy and polysemy as well as different abstractions or generality problem. To maximize its potential, some methods for associating tags of folksonomy with semantics and structural relationships have been proposed such as using ontology learning method. This paper evaluates our previous work in ontology learning according to gold-standard evaluation approach in comparison to a notable state-of-the-art work and several baselines. The results show that our method is comparable to the state-of the art work which further validate our approach as has been previously validated using task-based evaluation approach.

  14. The role of tag suggestions in folksonomies

    NARCIS (Netherlands)

    Bollen, D.G.F.M.; Halpin, H.

    2009-01-01

    Most tagging systems support the user in the tag selection process by providing tag suggestions, or recommendations, based on a popularity measurement of tags other users provided when tagging the same resource. The majority of theories and mathematical models of tagging found in the literature

  15. Tag-elese or The Language of Tags

    Directory of Open Access Journals (Sweden)

    Jan Simons

    2008-01-01

    Full Text Available The core "meme" of Web 2.0 from which almost all other memes radiated was: 'You control your own data' (O'Reilly, 2005, 3. Key instruments for this user control are tagging systems that allow users to freely assign keywords of their own choosing to Internet resources of their own making as well as to documents produced by others. Of course, freely chosen keywords tags do not necessarily follow prefixed taxonomies or classification systems. But going by the maxim that interaction creates similarity and similarity creates interaction, the idea - or hope - is, however, that the tagging practices of individual users will eventually converge into an emergent common vocabulary or folksonomy (Merholz, 2004; Shirky, 2005; Vander Wal, 2005b; Mika, 2007. It is far from clear, however, that free tagging systems will eventually yield controlled vocabularies, and there are many incentives for idiosyncratic, ambiguous, and inconsistent uses of tags. Left to themselves, free tagging systems seem to be too wild and too chaotic for any order to emerge. But are these free tagging systems really as "feral" as they seem to be, or do they only look uncontrolled because one has been looking for order in the wrong place? I have done a quick-and-dirty" analysis of Flickr's tag cloud. The concept was: if folksonomies encourage users to tap on their own vernacular, everyday natural language must somehow "guide" the tagging practices of users of tagging systems. Flickr's tag cloud has been choosen because it may teach us something about tagging systems and folksonomies, and not - or not primarily - because of what tags may tell us about pictures.

  16. Inferring ontology graph structures using OWL reasoning

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel

    2018-01-05

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

  17. Inferring ontology graph structures using OWL reasoning.

    Science.gov (United States)

    Rodríguez-García, Miguel Ángel; Hoehndorf, Robert

    2018-01-05

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

  18. 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...

  19. 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.

  20. Geographic Ontologies, Gazetteers and Multilingualism

    Directory of Open Access Journals (Sweden)

    Robert Laurini

    2015-01-01

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

  1. Ontology Matching with Semantic Verification.

    Science.gov (United States)

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

    2009-09-01

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

  2. The use of external electronic tags on fish: an evaluation of tag retention and tagging effects

    DEFF Research Database (Denmark)

    Jepsen, Niels; Thorstad, Eva B.; Havn, Torgeir

    2015-01-01

    External tagging of fish with electronic tags has been used for decades for a wide range of marine and freshwater species. In the early years of fish telemetry research, it was the most commonly used attachment method, but later internal implants became preferred. Recently, the number of telemetry...... unsuitable for surgical implantation, or when using tags with sensors recording the external environment. The most commonly reported problems with external tags are tissue damage, premature tag loss, and decreased swimming capacity, but the effects are highly context dependent and species specific. Reduced......, but particularly there are few studies on predation risk, social interactions, and studies distinguishing capture and handling effects from tagging effects. For PSATs, especially those that are large relative to fish size, there are particular problems with a high proportion of premature tag losses, reduced...

  3. Markov Chain Ontology Analysis (MCOA).

    Science.gov (United States)

    Frost, H Robert; McCray, Alexa T

    2012-02-03

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

  4. Inferring ontology graph structures using OWL reasoning

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel; Hoehndorf, Robert

    2018-01-01

    ' semantic content remains a challenge.We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies

  5. Ontologies, Knowledge Bases and Knowledge Management

    National Research Council Canada - National Science Library

    Chalupsky, Hans

    2002-01-01

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

  6. 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...

  7. Technique for designing a domain ontology

    OpenAIRE

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

    2018-01-01

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

  8. Social Tagging of Mission Data

    Science.gov (United States)

    Norris, Jeffrey S.; Wallick, Michael N.; Joswig, Joseph C.; Powell, Mark W.; Torres, Recaredo J.; Mittman, David S.; Abramyan, Lucy; Crockett, Thomas M.; Shams, Khawaja S.; Fox, Jason M.; hide

    2010-01-01

    Mars missions will generate a large amount of data in various forms, such as daily plans, images, and scientific information. Often, there is a semantic linkage between images that cannot be captured automatically. Software is needed that will provide a method for creating arbitrary tags for this mission data so that items with a similar tag can be related to each other. The tags should be visible and searchable for all users. A new routine was written to offer a new and more flexible search option over previous applications. This software allows users of the MSLICE program to apply any number of arbitrary tags to a piece of mission data through a MSLICE search interface. The application of tags creates relationships between data that did not previously exist. These tags can be easily removed and changed, and contain enough flexibility to be specifically configured for any mission. This gives users the ability to quickly recall or draw attention to particular pieces of mission data, for example: Give a semantic and meaningful description to mission data; for example, tag all images with a rock in them with the tag "rock." Rapidly recall specific and useful pieces of data; for example, tag a plan as"driving template." Call specific data to a user s attention; for example, tag a plan as "for:User." This software is part of the MSLICE release, which was written in Java. It will run on any current Windows, Macintosh, or Linux system.

  9. 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

  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. Terminology representation guidelines for biomedical ontologies in the semantic web notations.

    Science.gov (United States)

    Tao, Cui; Pathak, Jyotishman; Solbrig, Harold R; Wei, Wei-Qi; Chute, Christopher G

    2013-02-01

    Terminologies and ontologies are increasingly prevalent in healthcare and biomedicine. However they suffer from inconsistent renderings, distribution formats, and syntax that make applications through common terminologies services challenging. To address the problem, one could posit a shared representation syntax, associated schema, and tags. We identified a set of commonly-used elements in biomedical ontologies and terminologies based on our experience with the Common Terminology Services 2 (CTS2) Specification as well as the Lexical Grid (LexGrid) project. We propose guidelines for precisely such a shared terminology model, and recommend tags assembled from SKOS, OWL, Dublin Core, RDF Schema, and DCMI meta-terms. We divide these guidelines into lexical information (e.g. synonyms, and definitions) and semantic information (e.g. hierarchies). The latter we distinguish for use by informal terminologies vs. formal ontologies. We then evaluate the guidelines with a spectrum of widely used terminologies and ontologies to examine how the lexical guidelines are implemented, and whether our proposed guidelines would enhance interoperability. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. Towards ontology based search and knowledgesharing using domain ontologies

    DEFF Research Database (Denmark)

    Zambach, Sine

    verbs for relations in the ontology modeling. For this work we use frequency lists from a biomedical text corpus of different genres as well as a study of the relations used in other biomedical text mining tools. In addition, we discuss how these relations can be used in broarder perspective....

  14. An Ontology for Knowledge Representation and Applications

    OpenAIRE

    Nhon Do

    2008-01-01

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

  15. On Algebraic Spectrum of Ontology Evaluation

    OpenAIRE

    Adekoya Adebayo Felix; kinwale Adio Taofiki; Sofoluwe Adetokunbo

    2011-01-01

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

  16. [Implementation of ontology-based clinical decision support system for management of interactions between antihypertensive drugs and diet].

    Science.gov (United States)

    Park, Jeong Eun; Kim, Hwa Sun; Chang, Min Jung; Hong, Hae Sook

    2014-06-01

    The influence of dietary composition on blood pressure is an important subject in healthcare. Interactions between antihypertensive drugs and diet (IBADD) is the most important factor in the management of hypertension. It is therefore essential to support healthcare providers' decision making role in active and continuous interaction control in hypertension management. The aim of this study was to implement an ontology-based clinical decision support system (CDSS) for IBADD management (IBADDM). We considered the concepts of antihypertensive drugs and foods, and focused on the interchangeability between the database and the CDSS when providing tailored information. An ontology-based CDSS for IBADDM was implemented in eight phases: (1) determining the domain and scope of ontology, (2) reviewing existing ontology, (3) extracting and defining the concepts, (4) assigning relationships between concepts, (5) creating a conceptual map with CmapTools, (6) selecting upper ontology, (7) formally representing the ontology with Protégé (ver.4.3), (8) implementing an ontology-based CDSS as a JAVA prototype application. We extracted 5,926 concepts, 15 properties, and formally represented them using Protégé. An ontology-based CDSS for IBADDM was implemented and the evaluation score was 4.60 out of 5. We endeavored to map functions of a CDSS and implement an ontology-based CDSS for IBADDM.

  17. An ontological approach to domain engineering

    NARCIS (Netherlands)

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

    2002-01-01

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

  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

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

    OpenAIRE

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

    2014-01-01

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

  20. A wireless sensor tag platform for container security and integrity

    Science.gov (United States)

    Amaya, Ivan A.; Cree, Johnathan V.; Mauss, Fredrick J.

    2011-04-01

    Cargo containers onboard ships are widely used in the global supply chain. The need for container security is evidenced by the Container Security Initiative launched by the U.S. Bureau of Customs and Border Protection (CBP). One method of monitoring cargo containers is using low power wireless sensor tags. The wireless sensor tags are used to set up a network that is comprised of tags internal to the container and a central device. The sensor network reports alarms and other anomalies to a central device, which then relays the message to an outside network upon arrival at the destination port. This allows the port authorities to have knowledge of potential security or integrity issues before physically examining the container. Challenges of using wireless sensor tag networks for container security include battery life, size, environmental conditions, information security, and cost among others. PNNL developed an active wireless sensor tag platform capable of reporting data wirelessly to a central node as well as logging data to nonvolatile memory. The tags, operate at 2.4 GHz over an IEEE 802.15.4 protocol, and were designed to be distributed throughout the inside of a shipping container in the upper support frame. The tags are mounted in a housing that allows for simple and efficient installation or removal prior to, during, or after shipment. The distributed tags monitor the entire container volume. The sensor tag platform utilizes low power electronics and provides an extensible sensor interface for incorporating a wide range of sensors including chemical, biological, and environmental sensors.

  1. Antenna for passive RFID tags

    Science.gov (United States)

    Schiopu, Paul; Manea, Adrian; Cristea, Ionica; Grosu, Neculai; Vladescu, Marian; Craciun, Anca-Ileana; Craciun, Alexandru

    2015-02-01

    Minuscule devices, called RFID tags are attached to objects and persons and emit information which positioned readers may capture wirelessly. Many methods of identification have been used, but that of most common is to use a unique serial number for identification of person or object. RFID tags can be characterized as either active or passive [1,2]. Traditional passive tags are typically in "sleep" state until awakened by the reader's emitted field. In passive tags, the reader's field acts to charge the capacitor that powers the badge and this can be a combination of antenna and barcodes obtained with SAW( Surface Acoustic Wave) devices [1,2,3] . The antenna in an RFID tag is a conductive element that permits the tag to exchange data with the reader. The paper contribution are targeted to antenna for passive RFID tags. The electromagnetic field generated by the reader is somehow oriented by the reader antenna and power is induced in the tag only if the orientation of the tag antenna is appropriate. A tag placed orthogonal to the reader yield field will not be read. This is the reason that guided manufacturers to build circular polarized antenna capable of propagating a field that is alternatively polarized on all planes passing on the diffusion axis. Passive RFID tags are operated at the UHF frequencies of 868MHz (Europe) and 915MHz (USA) and at the microwave frequencies of 2,45 GHz and 5,8 GHz . Because the tags are small dimensions, in paper, we present the possibility to use circular polarization microstrip antenna with fractal edge [2].

  2. Nuclear studies with tagged photons

    International Nuclear Information System (INIS)

    Axel, P.

    1979-01-01

    First, the photon tagging technique will be described schematically, and a brief history of photon tagging will be given, including the 20 year development of this technique at Illinois. In the second part some typical operating conditions will be indicated for our tagged photon facility. The final section of this paper will illustrate some types of experiments by showing data obtained recently. (KBE) 891 KBE/KBE 892 ARA

  3. 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

  4. 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…

  5. Quantum physics and relational ontology

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-01

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

  6. 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.

  7. An ontological approach to logistics

    NARCIS (Netherlands)

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

    2013-01-01

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

  8. Buddy Tag CONOPS and Requirements.

    Energy Technology Data Exchange (ETDEWEB)

    Brotz, Jay Kristoffer [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Deland, Sharon M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-12-01

    This document defines the concept of operations (CONOPS) and the requirements for the Buddy Tag, which is conceived and designed in collaboration between Sandia National Laboratories and Princeton University under the Department of State Key VerificationAssets Fund. The CONOPS describe how the tags are used to support verification of treaty limitations and is only defined to the extent necessary to support a tag design. The requirements define the necessary functions and desired non-functional features of the Buddy Tag at a high level

  9. Flavour tagging performance in LHCb

    International Nuclear Information System (INIS)

    Grabalosa Gandara, Marc

    2009-01-01

    To do precise CP violation measurements, the best possible determination of the flavour of the B-meson is necessary. This report summarizes the flavour tagging performances for the LHCb experiment. The flavour tagging is obtained through a combination of several methods, based on different signatures. The use of control channels, which are decays to flavour-specific final states, will allow to determine the wrong tag fraction ω (the probability of a tag to be wrong), which can be used as an input for the determination of CKM unitarity triangle angles.

  10. 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

  11. 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.

  12. History Matters: Incremental Ontology Reasoning Using Modules

    Science.gov (United States)

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

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

  13. ROLE OF ONTOLOGY IN THE SYSTEM OF FORMATION OF EDUCATIONAL AND COGNITIVE COMPETENCES ON PHYSICS OF SECONDARY SCHOOL PUPILS

    Directory of Open Access Journals (Sweden)

    Nataliia A. Ivanytska

    2014-02-01

    Full Text Available The article considers the structure of ontology on physics and its parts, which was built on the basis of webquest. We describe possibilities of modern computers program «GraphEditor», directing a route for pupils in their own theoretical research. Also, it was determined basic steps of the ontology and described how to use it in teaching. We analyzed didactic problems of the ontology application that establish visualization of ties when we use computers program «GraphEditor», as well as distinguished peculiarities of the ontology that organize an independent work of pupils. On the basis of regulatory documents proved the feasibility of the ontology as means of distance learning for upper-form pupils which are capable for research.

  14. LHCb Tag Collector

    International Nuclear Information System (INIS)

    Fernández, Paloma Fuente; Clemencic, Marco; Cousin, Nicolas

    2011-01-01

    The LHCb physics software consists of hundreds of packages, each of which is developed by one or more physicists. When the developers have some code changes that they would like released, they commit them to the version control system, and enter the revision number into a database. These changes have to be integrated into a new release of each of the physics analysis applications. Tests are then performed by a nightly build system, which rebuilds various configurations of the whole software stack and executes a suite of run-time functionality tests. A Tag Collector system has been developed using solid standard technologies to cover both the use cases of developers and integration managers. A simple Web interface, based on an AJAX-like technology, is available. Integration with SVN and Nightly Build System, is possible via a Python API. Data are stored in a relational database with the help of an ORM (Object-Relational Mapping) library.

  15. Internally readable identifying tag

    International Nuclear Information System (INIS)

    Jefferts, K.B.; Jefferts, E.R.

    1980-01-01

    A method of identifying non-metallic objects by means of X-ray equipment is described in detail. A small metal pin with a number of grooves cut in a pre-determined equi-spaced pattern is implanted into the non-metallic object and by decoding the groove patterns using X-ray equipment, the object is uniquely identified. A specific example of such an application is in studying the migratory habits of fish. The pin inserted into the snout of the fish is 0.010 inch in diameter, 0.040 inch in length with 8 possible positions for grooves if spaced 0.005 inch apart. With 6 of the groove positions available for data, the capacity is 2 6 or 64 combinations; clearly longer pins would increase the data capacity. This method of identification is a major advance over previous techniques which necessitated destruction of the fish in order to recover the identification tag. (UK)

  16. Building a biomedical ontology recommender web service

    Directory of Open Access Journals (Sweden)

    Jonquet Clement

    2010-06-01

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

  17. 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.

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

    Science.gov (United States)

    Smith, Barry; Ceusters, Werner

    2010-11-15

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

  19. Engineering the ATLAS TAG Browser

    CERN Document Server

    Zhang, Q; The ATLAS collaboration

    2011-01-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. TAGs from all ATLAS physics and Monte Carlo data sets are routinely loaded into Oracle databases as an integral part of event processing. As data volumes increase, more and more sites are joining the distributed TAG data hosting topology[1]. Meanwhile, TAG content and database schemata continue to evolve as new user requirements and additional sources of metadata emerge. All of this has posed many challenges to the development of ELSSI, which must support vast amounts of TAG data while source, content, geographic locations, and user query patterns may change over time. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary service...

  20. Engineering the ATLAS TAG Browser

    CERN Document Server

    Zhang, Q; The ATLAS collaboration

    2011-01-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. TAGs from all ATLAS physics and Monte Carlo data sets are routinely loaded into Oracle databases as an integral part of event processing. As data volumes increase, more and more sites are joining the distributed TAG data hosting topology. Meanwhile, TAG content and database schemata continue to evolve as new user requirements and additional sources of metadata emerge. All of this has posed many challenges to the development of ELSSI, which must support vast amounts of TAG data while source, content, geographic locations, and user query patterns may change over time. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services a...

  1. Formal Ontologies and Uncertainty. In Geographical Knowledge

    Directory of Open Access Journals (Sweden)

    Matteo Caglioni

    2014-05-01

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

  2. Automatic extraction of ontological relations from Arabic text

    Directory of Open Access Journals (Sweden)

    Mohammed G.H. Al Zamil

    2014-12-01

    The proposed methodology has been designed to analyze Arabic text using lexical semantic patterns of the Arabic language according to a set of features. Next, the features have been abstracted and enriched with formal descriptions for the purpose of generalizing the resulted rules. The rules, then, have formulated a classifier that accepts Arabic text, analyzes it, and then displays related concepts labeled with its designated relationship. Moreover, to resolve the ambiguity of homonyms, a set of machine translation, text mining, and part of speech tagging algorithms have been reused. We performed extensive experiments to measure the effectiveness of our proposed tools. The results indicate that our proposed methodology is promising for automating the process of extracting ontological relations.

  3. Knowledge Portals: Ontologies at Work

    OpenAIRE

    Staab, Steffen; Maedche, Alexander

    2001-01-01

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

  4. 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....

  5. Emotion Ontology for Context Awareness

    OpenAIRE

    Berthelon , Franck; Sander , Peter

    2013-01-01

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

  6. Towards an Ontology of Software

    OpenAIRE

    Wang, Xiaowei

    2016-01-01

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

  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. 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

  9. Polarized tagged photons

    International Nuclear Information System (INIS)

    Maximon, L.C.; Ganz, Eric; Aniel, Thierry; Miniac, Arlette de.

    1982-03-01

    We consider in detail the differential cross section for polarized bremsstrahlung for angles and energies in the range of interest for a tagging system and derive a high energy, small angle approximation for this cross section. We use these approximations to determine the maxima and minima of the cross sections for these two polarization states, dσperpendicular and dσparallel, and to evaluate these cross sections at the extrema. It is shown that both dσperpendicular and dσparallel have a very sharp dip in the region of small momentum transfers. However, their behavior in the region of the dip, as a function of the azimuthal angle phi, is quite different over most of the photon spectrum. The cross section dσperpendicular behaves similarly to the cross section for unpolarized photons in that as phi increases, the sharp dip vanishes, the minimum fuses with the second maximum, and the cross section then has only a single maximum. In contrast, the sharp dip in the cross section dσparallel remains as phi increases. Coulomb corrections to the Born approximation are considered, and do not fill in these dips

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

    International Nuclear Information System (INIS)

    McDaniel, Michael

    2014-01-01

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

  11. Database Concepts in a Domain Ontology

    Directory of Open Access Journals (Sweden)

    Gorskis Henrihs

    2017-12-01

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

  12. Ontology-aided Data Fusion (Invited)

    Science.gov (United States)

    Raskin, R.

    2009-12-01

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

  13. 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.

  14. Quantum tagging for tags containing secret classical data

    International Nuclear Information System (INIS)

    Kent, Adrian

    2011-01-01

    Various authors have considered schemes for quantum tagging, that is, authenticating the classical location of a classical tagging device by sending and receiving quantum signals from suitably located distant sites, in an environment controlled by an adversary whose quantum information processing and transmitting power is potentially unbounded. All of the schemes proposed elsewhere in the literature assume that the adversary is able to inspect the interior of the tagging device. All of these schemes have been shown to be breakable if the adversary has unbounded predistributed entanglement. We consider here the case in which the tagging device contains a finite key string shared with distant sites but kept secret from the adversary, and show this allows the location of the tagging device to be authenticated securely and indefinitely. Our protocol relies on quantum key distribution between the tagging device and at least one distant site, and demonstrates a new practical application of quantum key distribution. It also illustrates that the attainable security in position-based cryptography can depend crucially on apparently subtle details in the security scenario considered.

  15. An Ontological Architecture for Orbital Debris Data

    OpenAIRE

    Rovetto, Robert J.

    2017-01-01

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

  16. Versioning System for Distributed Ontology Development

    Science.gov (United States)

    2016-03-15

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

  17. 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

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

    DEFF Research Database (Denmark)

    Seibt, Johanna

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

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

    OpenAIRE

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

    2007-01-01

    Abstract Background Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. Results We have produced a tool, OntologyWidget, which allows users to r...

  20. The NASA Air Traffic Management Ontology (atmonto)

    Data.gov (United States)

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

  1. 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...

  2. 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.

  3. Finding the best visualization of an ontology

    DEFF Research Database (Denmark)

    Fabritius, Christina; Madsen, Nadia; Clausen, Jens

    2006-01-01

    An ontology is a classification model for a given domain.In information retrieval ontologies are used to perform broad searches.An ontology can be visualized as nodes and edges. Each node represents an element and each edge a relation between a parent and a child element. Working with an ontology....... One method uses a discrete location model to create an initial solution and we propose heuristic methods to further improve the visual result. We evaluate the visual results according to our success criteria and the feedback from users. Running times of the heuristic indicate that an improved version...

  4. Finding the best visualization of an ontology

    DEFF Research Database (Denmark)

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

    2004-01-01

    An ontology is a classification model for a given domain. In information retrieval ontologies are used to perform broad searches. An ontology can be visualized as nodes and edges. Each node represents an element and each edge a relation between a parent and a child element. Working with an ontology....... One method uses a discrete location model to create an initial solution and we propose heuristic methods to further improve the visual result. We evaluate the visual results according to our success criteria and the feedback from users. Running times of the heuristic indicate that an improved version...

  5. 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...

  6. DEPONTO: A Reusable Dependability Domain Ontology

    Directory of Open Access Journals (Sweden)

    Teodora Sanislav

    2015-08-01

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

  7. Learning Resources Organization Using Ontological Framework

    Science.gov (United States)

    Gavrilova, Tatiana; Gorovoy, Vladimir; Petrashen, Elena

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

  8. Ontological Engineering for the Cadastral Domain

    DEFF Research Database (Denmark)

    Stubkjær, Erik; Stuckenschmidt, Heiner

    2000-01-01

    conceptualization of the world is that much information remains implicit. Ontologies have set out to overcome the problem of implicit and hidden knowledge by making the conceptualization of a domain (e.g. mathematics) explicit. Ontological engineering is thus an approach to achieve a conceptual rigor...... that characterizes established academic disciplines, like geodesy. Many university courses address more application oriented fields, like cadastral law, and spatial planning, and they may benefit from the ontological engineering approach. The paper provides an introduction to the field of ontological engineering...

  9. 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.

  10. 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

  11. Behavioral tagging of extinction learning.

    Science.gov (United States)

    de Carvalho Myskiw, Jociane; Benetti, Fernando; Izquierdo, Iván

    2013-01-15

    Extinction of contextual fear in rats is enhanced by exposure to a novel environment at 1-2 h before or 1 h after extinction training. This effect is antagonized by administration of protein synthesis inhibitors anisomycin and rapamycin into the hippocampus, but not into the amygdala, immediately after either novelty or extinction training, as well as by the gene expression blocker 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole administered after novelty training, but not after extinction training. Thus, this effect can be attributed to a mechanism similar to synaptic tagging, through which long-term potentiation can be enhanced by other long-term potentiations or by exposure to a novel environment in a protein synthesis-dependent fashion. Extinction learning produces a tag at the appropriate synapses, whereas novelty learning causes the synthesis of plasticity-related proteins that are captured by the tag, strengthening the synapses that generated this tag.

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

    Science.gov (United States)

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

    2017-01-01

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

  13. 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.

  14. 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.

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

    Lifescience Database Archive (English)

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

    d'Aquin, Mathieu; Noy, Natalya F.

    2011-01-01

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

  18. 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…

  19. 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…

  20. 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

  1. Strep-Tagged Protein Purification.

    Science.gov (United States)

    Maertens, Barbara; Spriestersbach, Anne; Kubicek, Jan; Schäfer, Frank

    2015-01-01

    The Strep-tag system can be used to purify recombinant proteins from any expression system. Here, protocols for lysis and affinity purification of Strep-tagged proteins from E. coli, baculovirus-infected insect cells, and transfected mammalian cells are given. Depending on the amount of Strep-tagged protein in the lysate, a protocol for batch binding and subsequent washing and eluting by gravity flow can be used. Agarose-based matrices with the coupled Strep-Tactin ligand are the resins of choice, with a binding capacity of up to 9 mg ml(-1). For purification of lower amounts of Strep-tagged proteins, the use of Strep-Tactin magnetic beads is suitable. In addition, Strep-tagged protein purification can also be automated using prepacked columns for FPLC or other liquid-handling chromatography instrumentation, but automated purification is not discussed in this protocol. The protocols described here can be regarded as an update of the Strep-Tag Protein Handbook (Qiagen, 2009). © 2015 Elsevier Inc. All rights reserved.

  2. 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.

  3. 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

  4. Nosology, ontology and promiscuous realism.

    Science.gov (United States)

    Binney, Nicholas

    2015-06-01

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

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

    Science.gov (United States)

    Figdor, Carrie

    2011-04-01

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

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

    DEFF Research Database (Denmark)

    Ahmed, Saeema; Storga, M

    2009-01-01

    to developing the ontology engineering design integrated taxonomies (EDIT) with a theoretical approach in which concepts and relations are elicited from engineering design theories ontology (DO) The limitations and advantages of each approach are discussed. The research methodology adopted is to map......This paper presents a comparison of two previous and separate efforts to develop an ontology in the engineering design domain, together with an ontology proposal from which ontologies for a specific application may be derived. The research contrasts an empirical, user-centered approach...

  7. A Novel Method for Mining SaaS Software Tag via Community Detection in Software Services Network

    Science.gov (United States)

    Qin, Li; Li, Bing; Pan, Wei-Feng; Peng, Tao

    The number of online software services based on SaaS paradigm is increasing. However, users usually find it hard to get the exact software services they need. At present, tags are widely used to annotate specific software services and also to facilitate the searching of them. Currently these tags are arbitrary and ambiguous since mostly of them are generated manually by service developers. This paper proposes a method for mining tags from the help documents of software services. By extracting terms from the help documents and calculating the similarity between the terms, we construct a software similarity network where nodes represent software services, edges denote the similarity relationship between software services, and the weights of the edges are the similarity degrees. The hierarchical clustering algorithm is used for community detection in this software similarity network. At the final stage, tags are mined for each of the communities and stored as ontology.

  8. Editorial Tag Endogeneity for News Websites

    OpenAIRE

    Bruno Ribeiro; Ricardo Morla; Amílcar Correia

    2013-01-01

    Editors and journalists at some news websites label their articles with structure and content-related editorial tags. Each article can have more than one tag and each tag can be used in more than one article. A network of tags can be defined whose edges are all possible pairs of tags in each article. Because editorial tags relate to structure and content rather than individual articles, the analysis of a network of editorial tags could assist editorial decisions to prioritize types of content...

  9. Tempting To Tag: An Experimental Comparison Of Four Tagging Input Mechanisms

    Directory of Open Access Journals (Sweden)

    Mark Melenhorst

    2010-01-01

    Full Text Available Tagging helps achieve improved indexing and recommendation of resources (e.g., videos or pictures in large data collections. In order to reap the benefits of tagging, people must be persuaded to label the resources they consume. This paper reports on a study in which four different tagging input mechanisms and their effect on users' motivation to tag were compared. The mechanisms consisted of a standard tag input box, a chatbot-like environment, a bookmarking mechanism, and a "tag and vote" game. The results of our experiment show that the use of the nonstandard tagging input mechanisms does not affect users' motivation to tag. In some instances tagging mechanisms were found to distract users from their primary task: consuming resources. Persuading people to tag might be accomplished more effectively by using other motivating tagging mechanisms (e.g., tagging games, or motivation could be created by explaining the usefulness of tagging.

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

    Science.gov (United States)

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

    2014-08-01

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

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

    Science.gov (United States)

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

    2018-01-12

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

  12. Introduction to Semantic Web Ontology Languages

    NARCIS (Netherlands)

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

    2005-01-01

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

  13. 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.

  14. 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.

  15. Fuzzy knowledge bases integration based on ontology

    OpenAIRE

    Ternovoy, Maksym; Shtogrina, Olena

    2012-01-01

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

  16. C2 Domain Ontology within Our Lifetime

    Science.gov (United States)

    2009-06-01

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

  17. Recent changes in the Building Topology Ontology

    DEFF Research Database (Denmark)

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

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

  18. Critical Ontology for an Enactive Music Pedagogy

    Science.gov (United States)

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

    2016-01-01

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

  19. Integrity and change in modular ontologies

    NARCIS (Netherlands)

    Stuckenschmidt, Heiner; Klein, Michel

    2003-01-01

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

  20. 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

  1. Collaborative ontology development for the geosciences

    NARCIS (Netherlands)

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

    2014-01-01

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

  2. 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...

  3. 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.

  4. [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.

  5. Tagging the European eel Anguilla anguilla (L.) with coded wire tags

    DEFF Research Database (Denmark)

    Thomassen, S.; Pedersen, Michael Ingemann; Holdensgaard, G.

    2000-01-01

    The coded wire tag (CWT) system was examined as a possible tool for tagging European eels (Anguilla anguilla). Two size groups of eels (3.8 and 10.2 g) were tagged with CWTs in the dorsal musculature, Tag loss 28 days after tagging was 3.1% for the small and 0.7% for the large groups of eels...

  6. XML, Ontologies, and Their Clinical Applications.

    Science.gov (United States)

    Yu, Chunjiang; Shen, Bairong

    2016-01-01

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

  7. GFVO: the Genomic Feature and Variation Ontology

    KAUST Repository

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

    2015-01-01

    Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.

  8. 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...

  9. Model Driven Engineering with Ontology Technologies

    Science.gov (United States)

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

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

  10. A priorean approach to time ontologies

    DEFF Research Database (Denmark)

    Øhrstrøm, Peter; Schärfe, Henrik

    2004-01-01

    Any non-trivial top-level ontology should take temporal notions into account. The details of how this should be done, however, are frequently debated. In this paper it is argued that "the four grades of tense-logical involvement" suggested by A.N. Prior form a useful framework for discussing how...... various temporal notions are related in a top-level ontology. Furthermore, a number of modern ontologies are analysed with respect to their incorporation of temporal notions. It is argued that all of them correspond to Prior's first and second grade, and that none of them reflect the views which Prior......'s third and fourth grade represent. Finally, the paper deals with Prior's ideas on a tensed ontology and it is argued that a logic based on the third grade and will be useful in the further development of tensed ontology....

  11. Tagging, Encoding, and Jones Optimality

    DEFF Research Database (Denmark)

    Danvy, Olivier; Lopez, Pablo E. Martinez

    2003-01-01

    A partial evaluator is said to be Jones-optimal if the result of specializing a self-interpreter with respect to a source program is textually identical to the source program, modulo renaming. Jones optimality has already been obtained if the self-interpreter is untyped. If the selfinterpreter...... is typed, however, residual programs are cluttered with type tags. To obtain the original source program, these tags must be removed. A number of sophisticated solutions have already been proposed. We observe, however, that with a simple representation shift, ordinary partial evaluation is already Jones......-optimal, modulo an encoding. The representation shift amounts to reading the type tags as constructors for higherorder abstract syntax. We substantiate our observation by considering a typed self-interpreter whose input syntax is higher-order. Specializing this interpreter with respect to a source program yields...

  12. The MMI Device Ontology: Enabling Sensor Integration

    Science.gov (United States)

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

    2010-12-01

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

  13. Anthropological Component of Descartes’ Ontology

    Directory of Open Access Journals (Sweden)

    Anatolii M. Malivskyi

    2014-06-01

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

  14. ANTHROPOLOGICAL COMPONENT OF DESCARTES’ ONTOLOGY

    Directory of Open Access Journals (Sweden)

    Anatolii M. Malivskyi

    2014-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Seongwook Youn

    2014-01-01

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

  16. 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.

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

    Science.gov (United States)

    2014-01-01

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

  18. Tagging, Encoding, and Jones Optimality

    DEFF Research Database (Denmark)

    Danvy, Olivier; López, Pablo Ernesto Martínes

    2003-01-01

    A partial evaluator is said to be Jones-optimal if the result of specializing a self-interpreter with respect to a source program is textually identical to the source program, modulo renaming. Jones optimality has already been obtained if the self-interpreter is untyped. If the selfinterpreter...... is typed, however, residual programs are cluttered with type tags. To obtain the original source program, these tags must be removed. A number of sophisticated solutions have already been proposed. We observe, however, that with a simple representation shift, ordinary partial evaluation is already Jones...

  19. WebTag: Web browsing into sensor tags over NFC.

    Science.gov (United States)

    Echevarria, Juan Jose; Ruiz-de-Garibay, Jonathan; Legarda, Jon; Alvarez, Maite; Ayerbe, Ana; Vazquez, Juan Ignacio

    2012-01-01

    Information and Communication Technologies (ICTs) continue to overcome many of the challenges related to wireless sensor monitoring, such as for example the design of smarter embedded processors, the improvement of the network architectures, the development of efficient communication protocols or the maximization of the life cycle autonomy. This work tries to improve the communication link of the data transmission in wireless sensor monitoring. The upstream communication link is usually based on standard IP technologies, but the downstream side is always masked with the proprietary protocols used for the wireless link (like ZigBee, Bluetooth, RFID, etc.). This work presents a novel solution (WebTag) for a direct IP based access to a sensor tag over the Near Field Communication (NFC) technology for secure applications. WebTag allows a direct web access to the sensor tag by means of a standard web browser, it reads the sensor data, configures the sampling rate and implements IP based security policies. It is, definitely, a new step towards the evolution of the Internet of Things paradigm.

  20. Tempting to Tag : An Experimental Comparison of Four Tagging Input Mechanisms

    OpenAIRE

    Melenhorst, Mark; van Velsen, Lex

    2010-01-01

    Tagging helps achieve improved indexing and recommendation of resources (e.g., videos or pictures) in large data collections. In order to reap the benefits of tagging, people must be persuaded to label the resources they consume. This paper reports on a study in which four different tagging input mechanisms and their effect on users' motivation to tag were compared. The mechanisms consisted of a standard tag input box, a chatbot-like environment, a bookmarking mechanism, and a "tag and v...

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

    Science.gov (United States)

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

    2018-04-01

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

  3. Ontology Versioning and Change Detection on the Web

    NARCIS (Netherlands)

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

    2002-01-01

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

  4. 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,…

  5. 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.

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    Chao Wang

    2017-12-01

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

  8. 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.

  9. 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.

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

    OpenAIRE

    Paschke, Adrian

    2013-01-01

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

  11. Satellite Tags- Guam/CNMI EEZ

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Satellite tagging was implemented in 2013. Satellite tagging is conducted using a Dan Inject air rifle and deployment arrows designed by Wildlife Computers. Two...

  12. HMSRP Hawaiian Monk Seal Tag Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains records for all tags applied to Hawaiian monk seals since 1981. These tags were applied by PSD personnel and cooperating scientists as part of...

  13. 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.)

  14. Learning Ontology from Object-Relational Database

    Directory of Open Access Journals (Sweden)

    Kaulins Andrejs

    2015-12-01

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

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

    African Journals Online (AJOL)

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

  16. Interoperability between phenotype and anatomy ontologies.

    Science.gov (United States)

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

    2010-12-15

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

  17. 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...

  18. Ontology Enabled Generation of Embedded Web Services

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  19. Metadata and Ontologies in Learning Resources Design

    Science.gov (United States)

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

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

  20. A Bayesian Network Approach to Ontology Mapping

    National Research Council Canada - National Science Library

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

    2005-01-01

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

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

    African Journals Online (AJOL)

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

  2. Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference.

    Science.gov (United States)

    Hastings, Janna; Brass, Andy; Caine, Colin; Jay, Caroline; Stevens, Robert

    2014-01-01

    We evaluate the application of the Emotion Ontology (EM) to the task of self-reporting of emotional experience in the context of audience response to academic presentations at the International Conference on Biomedical Ontology (ICBO). Ontology evaluation is regarded as a difficult task. Types of ontology evaluation range from gauging adherence to some philosophical principles, following some engineering method, to assessing fitness for purpose. The Emotion Ontology (EM) represents emotions and all related affective phenomena, and should enable self-reporting or articulation of emotional states and responses; how do we know if this is the case? Here we use the EM 'in the wild' in order to evaluate the EM's ability to capture people's self-reported emotional responses to a situation through use of the vocabulary provided by the EM. To achieve this evaluation we developed a tool, EmOntoTag, in which audience members were able to capture their self-reported emotional responses to scientific presentations using the vocabulary offered by the EM. We furthermore asked participants using the tool to rate the appropriateness of an EM vocabulary term for capturing their self-assessed emotional response. Participants were also able to suggest improvements to the EM using a free-text feedback facility. Here, we present the data captured and analyse the EM's fitness for purpose in reporting emotional responses to conference talks. Based on our analysis of this data set, our primary finding is that the audience are able to articulate their emotional response to a talk via the EM, and reporting via the EM ontology is able to draw distinctions between the audience's response to a speaker and between the speakers (or talks) themselves. Thus we can conclude that the vocabulary provided at the leaves of the EM are fit for purpose in this setting. We additionally obtained interesting observations from the experiment as a whole, such as that the majority of emotions captured had

  3. Making methodology a matter of process ontology

    DEFF Research Database (Denmark)

    Revsbæk, Line

    2016-01-01

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

  4. 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.

  5. 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.

  6. Integrating phenotype ontologies with PhenomeNET

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel

    2017-12-19

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

  7. 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.

  8. 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

  9. 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.

  10. Exploring autophagy with Gene Ontology

    Science.gov (United States)

    2018-01-01

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

  11. ATLAS boosted object tagging 2

    CERN Document Server

    Caudron, Julien; The ATLAS collaboration

    2015-01-01

    A detailed study into the optimal techniques for identifying boosted hadronically decaying W or Z bosons is presented. Various algorithms for reconstructing, grooming and tagging bosonic jets are compared for W bosons with a wide range of transverse momenta using 8 TeV data and 8 TeV and 13 TeV MC simulations. In addition, given that a hadronic jet has been identified as resulting from the hadronic decay of a W or Z, a technique is developed to discriminate between W and Z bosons. The modeling of the tagging variables used in this technique is studied using 8 TeV pp collision data and systematic uncertainties for the tagger efficiency and fake rates are evaluated.

  12. Predicting floods with Flickr tags.

    Science.gov (United States)

    Tkachenko, Nataliya; Jarvis, Stephen; Procter, Rob

    2017-01-01

    Increasingly, user generated content (UGC) in social media postings and their associated metadata such as time and location stamps are being used to provide useful operational information during natural hazard events such as hurricanes, storms and floods. The main advantage of these new sources of data are twofold. First, in a purely additive sense, they can provide much denser geographical coverage of the hazard as compared to traditional sensor networks. Second, they provide what physical sensors are not able to do: By documenting personal observations and experiences, they directly record the impact of a hazard on the human environment. For this reason interpretation of the content (e.g., hashtags, images, text, emojis, etc) and metadata (e.g., keywords, tags, geolocation) have been a focus of much research into social media analytics. However, as choices of semantic tags in the current methods are usually reduced to the exact name or type of the event (e.g., hashtags '#Sandy' or '#flooding'), the main limitation of such approaches remains their mere nowcasting capacity. In this study we make use of polysemous tags of images posted during several recent flood events and demonstrate how such volunteered geographic data can be used to provide early warning of an event before its outbreak.

  13. b-tagging in DELPHI at LEP

    CERN Document Server

    Abdallah, J; Adam, W; Adye, T; Adzic, P; Albrecht, T; Alderweireld, T; Alemany-Fernandez, R; Allmendinger, T; Allport, P P; Almehed, S; Amaldi, Ugo; Amapane, N; Amato, S; Anashkin, E; Andreazza, A; Andringa, S; Anjos, N; Antilogus, P; Apel, W D; Arnoud, Y; Ask, S; Åsman, B; Augustin, J E; Augustinus, A; Baillon, Paul; Ballestrero, A; Bambade, P; Barbier, R; Bardin, Dimitri Yuri; Barker, G; Baroncelli, A; Bates, M; Battaglia, Marco; Baubillier, M; Becks, K H; Begalli, M; Behrmann, A; Benekos, N C; Benvenuti, Alberto C; Bérat, C; Berggren, M; Berntzon, L; Bertrand, D; Besançon, M; Besson, N; Bibby, J; Biffi, P; Bloch, D; Blom, M; Bonesini, M; Boonekamp, M; Booth, P S L; Borisov, G; Botner, O; Bouquet, B; Bowcock, T J V; Boyko, I; Bracko, M; Branchini, P; Brenner, R; Brodet, E; Brückman, P; Brunet, J M; Bugge, L; Buschmann, P; Caccia, M; Calvi, M; Camporesi, T; Canale, V; Carena, F; Castro, N; Cavallo, F R; Chabaud, V; Chapkin, M M; Charpentier, P; Checchia, P; Chierici, R; Shlyapnikov, P; Chudoba, J; Chung, S U; Cieslik, K; Collins, P; Contri, R; Cosme, G; Cossutti, F; Costa, M J; Couchot, F; Crawley, B; Crennell, D J; Cuevas-Maestro, J; D'Almagne, B; D'Hondt, J; Dalmau, J; Da Silva, T; Da Silva, W; Della Ricca, G; De Angelis, A; de Boer, Wim; De Clercq, C; De Lotto, B; De Maria, N; De Min, A; De Paula, L S; Di Ciaccio, Lucia; Dijkstra, H; Di Simone, A; Doroba, K; Drees, J; Dris, M; Eigen, G; Ekelöf, T J C; Ellert, M; Elsing, M; Espirito-Santo, M C; Fanourakis, G K; Fassouliotis, D; Feindt, M; Fernández, J; Ferrer, A; Ferro, F; Flagmeyer, U; Föth, H; Fokitis, E; Fulda-Quenzer, F; Fuster, J A; Gandelman, M; García, C; Gavillet, P; Gazis, E N; Geralis, T; Gokieli, R; Golob, B; Gómez-Cadenas, J J; Gómez-Ceballos, G; Gonçalves, P; Graziani, E; Grosdidier, G; Grzelak, K; Guy, J; Haag, C; Hallgren, A; Hamacher, K; Hamilton, K; Hansen, J; Haug, S; Hauler, F; Hedberg, V; Hennecke, M; Hernando, J A; Herr, H; Heuser, J M; Holmgren, S O; Holt, P J; Houlden, M A; Hultqvist, K; Jackson, J N; Jalocha, P; Jarlskog, C; Jarlskog, G; Jarry, P; Jeans, D; Johansson, E K; Johansson, P D; Jonsson, P; Joram, C; Jungermann, L; Kapusta, F; Karlsson, M; Katsanevas, S; Katsoufis, E C; Keränen, R; Kernel, G; Kersevan, Borut P; Kiiskinen, A P; King, B T; Kjaer, N J; Kluit, P; Kokkinias, P; Kourkoumelis, C; Kuznetsov, O; Krumshtein, Z; Kucharczyk, M; Kucewicz, W; Kurowska, J; Lamsa, J; Leder, G; Ledroit, F; Leinonen, L; Leitner, R; Lemonne, J; Lepeltier, V; Lesiak, T; Liebig, W; Liko, D; Lipniacka, A; Lopes, J H; López, J M; Loukas, D; Lutz, P; Lyons, L; MacNaughton, J; Malek, A; Maltezos, S; Mandl, F; Marco, J; Marco, R; Maréchal, B; Margoni, M; Marin, J C; Mariotti, C; Markou, A; Martínez-Rivero, C; Martínez-Vidal, F; Masik, J; Mastroyiannopoulos, N; Matorras, F; Matteuzzi, C; Mazzucato, F; Mazzucato, M; McNulty, R; Meroni, C; Meyer, W T; Migliore, E; Mitaroff, W A; Mjörnmark, U; Moa, T; Moch, M; Mönig, K; Monge, R; Montenegro, J; Moraes, D; Moreno, S; Morettini, P; Müller, U; Münich, K; Mulders, M; Mundim, L; Murray, W; Muryn, B; Myatt, Gerald; Myklebust, T; Nassiakou, M; Navarria, Francesco Luigi; Nawrocki, K; Nicolaidou, R; Niezurawski, P; Nikolenko, M; Nomerotski, A; Norman, A; Nygren, A; Oblakowska-Mucha, A; Obraztsov, V F; Olshevskii, A G; Onofre, A; Orava, Risto; Österberg, K; Ouraou, A; Oyanguren, A; Paganoni, M; Paiano, S; Palacios, J P; Palka, H; Papadopoulou, T D; Pape, L; Parkes, C; Parodi, F; Parzefall, U; Passeri, A; Passon, O; Peralta, L; Perepelitsa, V F; Perrotta, A; Petrolini, A; Piedra, J; Pieri, L; Pierre, F; Pimenta, M; Piotto, E; Podobnik, T; Poireau, V; Pol, M E; Polok, G; Poropat, P; Pozdnyakov, V; Pukhaeva, N; Pullia, Antonio; Rames, J; Ramler, L; Read, A; Rebecchi, P; Rehn, J; Reid, D; Reinhardt, R; Renton, P B; Richard, F; Rídky, J; Rivero, M; Rodríguez, D; Romero, A; Ronchese, P; Rosenberg, E I; Roudeau, Patrick; Rovelli, T; Ruhlmann-Kleider, V; Ryabtchikov, D; Sadovskii, A; Salmi, L; Salt, J; Savoy-Navarro, A; Schwickerath, U; Segar, A; Sekulin, R L; Siebel, M; Sissakian, A N; Smadja, G; Smirnova, O G; Sokolov, A; Sopczak, A; Sosnowski, R; Spassoff, Tz; Stanitzki, M; Stavitski, I; Stocchi, A; Strauss, J; Stugu, B; Szczekowski, M; Szeptycka, M; Szumlak, T; Tabarelli de Fatis, T; Taffard, A C; Tegenfeldt, F; Timmermans, J; Tinti, N; Tkatchev, L G; Tobin, M; Todorovova, S; Tomaradze, A G; Tomé, B; Tonazzo, A; Tortosa, P; Travnicek, P; Treille, D; Trischuk, W; Tristram, G; Trochimczuk, M; Troncon, C; Turluer, M L; Tyapkin, I A; Tyapkin, P; Tyndel, M; Tzamarias, S; Uvarov, V; Valenti, G; van Dam, P; Van Eldik, J; Van Lysebetten, A; Van Remortel, N; Van Vulpen, I B; Vegni, G; Veloso, F; Venus, W A; Verbeure, F; Verdier, P; Verzi, V; Vilanova, D; Vitale, L; Vrba, V; Wahlen, H; Washbrook, A J; Weilhammer, Peter; Weiser, C; Wicke, D; Wickens, J H; Wilkinson, G; Winter, M; Witek, M; Yushchenko, O P; Zalewska-Bak, A; Zalewski, Piotr; Zavrtanik, D; Zimin, N I; Zinchenko, A I; Zupan, M

    2004-01-01

    The standard method used for tagging b-hadrons in the DELPHI experiment at the CERN LEP Collider is discussed in detail. The main ingredient of b-tagging is the impact parameters of tracks, which relies mostly on the vertex detector. Additional information, such as the mass of particles associated to a secondary vertex, significantly improves the selection efficiency and the background suppression. The paper describes various discriminating variables used for the tagging and the procedure of their combination. In addition, applications of b-tagging to some physics analyses, which depend crucially on the performance and reliability of b-tagging, are described briefly.

  14. ONTOGRABBING: Extracting Information from Texts Using Generative Ontologies

    DEFF Research Database (Denmark)

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

    2009-01-01

    We describe principles for extracting information from texts using a so-called generative ontology in combination with syntactic analysis. Generative ontologies are introduced as semantic domains for natural language phrases. Generative ontologies extend ordinary finite ontologies with rules...... for producing recursively shaped terms representing the ontological content (ontological semantics) of NL noun phrases and other phrases. We focus here on achieving a robust, often only partial, ontology-driven parsing of and ascription of semantics to a sentence in the text corpus. The aim of the ontological...... analysis is primarily to identify paraphrases, thereby achieving a search functionality beyond mere keyword search with synsets. We further envisage use of the generative ontology as a phrase-based rather than word-based browser into text corpora....

  15. 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…

  16. 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

  17. 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

  18. Gas tagging system development in Japan

    International Nuclear Information System (INIS)

    Sekiguchi, N.; Rindo, H.; Akiyama, T.; Miyazawa, T.; Heki, H.

    1981-05-01

    The Gas tagging method has been considered to be most desirable for a failed fuel location system for the fast breeder reactor, regarding the component reduction in the reactor vessel and rapid location during reactor operation. The gas tagging system has been designed by referring to R and D results obtained in Japan and other countries. The designed system is comprised of tag gas filling pins, cover gas sampling system, tag gas recovery and enrichment system, tag gas analyzer and system control and data handling computers. The main specifications for this system have been decided as follows; 1) Main function is location of failed fuels in core and a part of blanket region, 2) Identification capability is each subassembly, 3) Time for identification is within a few days, 4) Continuous operation with automatic start at fuel failure, 5) Detection sensitivity must cover both gas leak and pin burst. In designing the gas tagging system, the following R and D items were selected; 1) System design study, 2) Tag gas capsule development, 3) Modeling the tag gas behavior in reactor primary cooling system, 4) Tag gas recovery and enrichment system, 5) Computer code development for tag gas isotope ratio change estimation. Details of the Japanese gas tagging system development appear in this paper. (author)

  19. The Cognitive Paradigm Ontology: Design and Application

    Science.gov (United States)

    Laird, Angela R.

    2013-01-01

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

  20. 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.

  1. 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

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

    Science.gov (United States)

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

    2016-01-01

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

  3. Secure passive RFID tag with seal

    Science.gov (United States)

    Nekoogar, Faranak; Reynolds, Matthew; Lefton, Scott; Dowla, Farid; Twogood, Richard

    2017-11-14

    A secure passive RFID tag system comprises at least one base station and at least one passive RFID tag. The tag includes a fiber optic cable with the cable ends sealed within the tag and the middle portion forming an external loop. The loop may be secured to at least portions of an object. The tag transmits and receives an optical signal through the fiber optic cable, and the cable is configured to be damaged or broken in response to removal or tampering attempts, wherein the optical signal is significantly altered if the cable is damaged or broken. The tag transmits the optical signal in response to receiving a radio signal from the base station and compares the transmitted optical signal to the received optical signal. If the transmitted optical signal and the received optical signal are identical, the tag transmits an affirmative radio signal to the base station.

  4. 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

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  6. Product line based ontology development for semantic web service

    DEFF Research Database (Denmark)

    Zhang, Weishan; Kunz, Thomas

    2006-01-01

    Ontology is recognized as a key technology for the success of the Semantic Web. Building reusable and evolve-able ontologies in order to cope with ontology evolution and requirement changes is increasingly important. But the existing methodologies and tools fail to support effective ontology reuse...... will lead to the initial implementation of the meta-onotologies using design by reuse and with the objective of design for reuse. After that step new ontologies could be generated by reusing these meta-ontologies. We demonstrate our approach with a Semantic Web Service application to show how to build...

  7. A methodology for creating ontologies for engineering design

    DEFF Research Database (Denmark)

    Ahmed, Saeema; Kim, S.; Wallace, K.M.

    2007-01-01

    This paper describes a six-stage methodology for developing ontologies for engineering design, together with the research methods and evaluation of each stage. The methodology focuses upon understanding a user's domain models through empirical research. A case study of an ontology for searching......, indexing, and retrieving engineering knowledge is described. The root concepts of the ontology were elicited from engineering designers. Relationships between concepts are extracted as the ontology is populated. The contribution of this research is a methodology to allow researchers. and industry to create...... ontologies for their particular purpose and a thesaurus for the terms within the ontology....

  8. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

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

    2011-08-11

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

  9. Validating EHR clinical models using ontology patterns.

    Science.gov (United States)

    Martínez-Costa, Catalina; Schulz, Stefan

    2017-12-01

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

  10. Annotating breast cancer microarray samples using ontologies

    Science.gov (United States)

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

    2008-01-01

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

  11. Mining rare associations between biological ontologies.

    Science.gov (United States)

    Benites, Fernando; Simon, Svenja; Sapozhnikova, Elena

    2014-01-01

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

  12. Mining rare associations between biological ontologies.

    Directory of Open Access Journals (Sweden)

    Fernando Benites

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

  13. 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.

  14. 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.

  15. The Russian Quest for Ontological Security

    DEFF Research Database (Denmark)

    Pedersen, Jonas Gejl

    This paper argues that Russia’s decision to militarily intervene in the Kosovo crisis (1999) arose out of ontological, alongside material, insecurity. Whereas states’ material security essentially deals with national survival, ontological security concerns safety of the ‘national Self......’. By supplementing the existing theories of geopolitics and regime security with the conceptual lens of ontological security, my interpretivist case study demonstrates why Russia, despite great risk and material costs, decided to militarily intervene and traces how Russian senses of ‘national Self’ were...... fundamentally reconstructed during intervention. I find that the anxiety arising from a future scenario of an already weak post-Soviet ‘Russian Self’ gradually being engulfed by a confident ‘Western Self’ played a significant role in Russia’s decision to occupy Slatina airbase. My analysis paradoxically shows...

  16. Løgstrup’s Ontological Ethics

    DEFF Research Database (Denmark)

    Rabjerg, Bjørn

    2017-01-01

    aim is to provide a coherent exposition of Løgstrup’s ethics. However, the result is not a normative ethics upon which we may act, but rather a descriptive diagnosis of interdependence as the basic ontological condition of human social life, where the sovereign expressions of life may enable us to act.......The article explores K. E. Løgstrup’s ontological ethics, understood as an ethics rooted in interdependence. Interdependence, the fact that human beings always hold power over each other, has two very different aspects, which I will call negative and positive, each of them in turn leading...... to different aspects of ontological ethics. By negative and positive I mean the two opposing possibilities of all human interaction that we can either destroy the other person’s life (to a greater or smaller degree) or cause the other person’s life to flourish. We can either be a blessing in the other person’s...

  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. Player-Specific Conflict Handling Ontology

    Directory of Open Access Journals (Sweden)

    Charline Hondrou

    2014-09-01

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

  19. Using ontology network structure in text mining.

    Science.gov (United States)

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

    2010-11-13

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

  20. 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.

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

    Science.gov (United States)

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

    2017-12-02

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

  2. 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.

  3. 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

  4. Ontology-based Metadata Portal for Unified Semantics

    Data.gov (United States)

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

  5. 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.

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

    National Research Council Canada - National Science Library

    Obrst, Leo; Hughes, Todd; Ray, Steve

    2006-01-01

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

  7. Annotating Evidence Based Clinical Guidelines : A Lightweight Ontology

    NARCIS (Netherlands)

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

    2012-01-01

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

  8. Ontological Model of Business Process Management Systems

    Science.gov (United States)

    Manoilov, G.; Deliiska, B.

    2008-10-01

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

  9. Methodology of decreasing software complexity using ontology

    Science.gov (United States)

    DÄ browska-Kubik, Katarzyna

    2015-09-01

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

  10. 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.

  11. Scalable Faceted Ranking in Tagging Systems

    Science.gov (United States)

    Orlicki, José I.; Alvarez-Hamelin, J. Ignacio; Fierens, Pablo I.

    Nowadays, web collaborative tagging systems which allow users to upload, comment on and recommend contents, are growing. Such systems can be represented as graphs where nodes correspond to users and tagged-links to recommendations. In this paper we analyze the problem of computing a ranking of users with respect to a facet described as a set of tags. A straightforward solution is to compute a PageRank-like algorithm on a facet-related graph, but it is not feasible for online computation. We propose an alternative: (i) a ranking for each tag is computed offline on the basis of tag-related subgraphs; (ii) a faceted order is generated online by merging rankings corresponding to all the tags in the facet. Based on the graph analysis of YouTube and Flickr, we show that step (i) is scalable. We also present efficient algorithms for step (ii), which are evaluated by comparing their results with two gold standards.

  12. Building Tag Clouds in Perl and PHP

    CERN Document Server

    Bumgardner, Jim

    2006-01-01

    Tag clouds are everywhere on the web these days. First popularized by the web sites Flickr, Technorati, and del.icio.us, these amorphous clumps of words now appear on a slew of web sites as visual evidence of their membership in the elite corps of "Web 2.0." This PDF analyzes what is and isn't a tag cloud, offers design tips for using them effectively, and then goes on to show how to collect tags and display them in the tag cloud format. Scripts are provided in Perl and PHP. Yes, some have said tag clouds are a fad. But as you will see, tag clouds, when used properly, have real merits. More

  13. Understanding why users tag: A survey of tagging motivation literature and results from an empirical study.

    Science.gov (United States)

    Strohmaier, Markus; Körner, Christian; Kern, Roman

    2012-12-01

    While recent progress has been achieved in understanding the structure and dynamics of social tagging systems, we know little about the underlying user motivations for tagging, and how they influence resulting folksonomies and tags. This paper addresses three issues related to this question. (1) What distinctions of user motivations are identified by previous research, and in what ways are the motivations of users amenable to quantitative analysis? (2) To what extent does tagging motivation vary across different social tagging systems? (3) How does variability in user motivation influence resulting tags and folksonomies? In this paper, we present measures to detect whether a tagger is primarily motivated by categorizing or describing resources, and apply these measures to datasets from seven different tagging systems. Our results show that (a) users' motivation for tagging varies not only across, but also within tagging systems, and that (b) tag agreement among users who are motivated by categorizing resources is significantly lower than among users who are motivated by describing resources . Our findings are relevant for (1) the development of tag-based user interfaces, (2) the analysis of tag semantics and (3) the design of search algorithms for social tagging systems.

  14. Applications of the ACGT Master Ontology on Cancer

    OpenAIRE

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

    2008-01-01

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

  15. A collaborative recommendation framework for ontology evaluation and reuse

    OpenAIRE

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

    2006-01-01

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

  16. Learner Corpora without Error Tagging

    Directory of Open Access Journals (Sweden)

    Rastelli, Stefano

    2009-01-01

    Full Text Available The article explores the possibility of adopting a form-to-function perspective when annotating learner corpora in order to get deeper insights about systematic features of interlanguage. A split between forms and functions (or categories is desirable in order to avoid the "comparative fallacy" and because – especially in basic varieties – forms may precede functions (e.g., what resembles to a "noun" might have a different function or a function may show up in unexpected forms. In the computer-aided error analysis tradition, all items produced by learners are traced to a grid of error tags which is based on the categories of the target language. Differently, we believe it is possible to record and make retrievable both words and sequence of characters independently from their functional-grammatical label in the target language. For this purpose at the University of Pavia we adapted a probabilistic POS tagger designed for L1 on L2 data. Despite the criticism that this operation can raise, we found that it is better to work with "virtual categories" rather than with errors. The article outlines the theoretical background of the project and shows some examples in which some potential of SLA-oriented (non error-based tagging will be possibly made clearer.

  17. B-tagging in CMS at LHC

    CERN Document Server

    Cucciarelli, S

    2003-01-01

    This report provides a review of the main algorithms for offline inclusive b-tagging developed within the CMS community. Two b-tag algorithms, one based on the impact parameter measurement and the other based on the secondary vertices are discussed. The performance of these algorithms are presented for several jet transverse energies and pseudorapidity regions. An additional decay length based b-tag is also described and its preliminary performance is presented. (4 refs) .

  18. 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

  19. Conflict Resolution in Partially Ordered OWL DL Ontologies

    NARCIS (Netherlands)

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

    2014-01-01

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

  20. Methodology for Automatic Ontology Generation Using Database Schema Information

    Directory of Open Access Journals (Sweden)

    JungHyen An

    2018-01-01

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

  1. Construction of Engineering Ontologies for Knowledge Sharing and Reuse

    NARCIS (Netherlands)

    Borst, Willem Nico; Borst, W.N.

    1997-01-01

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

  2. 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

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

    DEFF Research Database (Denmark)

    Andreasen, Troels; Knappe, Rasmus; Bulskov, Henrik

    2005-01-01

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

  4. 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

  5. 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

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

    NARCIS (Netherlands)

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

    2016-01-01

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

  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. 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…

  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. Ontology-based intelligent fuzzy agent for diabetes application

    NARCIS (Netherlands)

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

    2009-01-01

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

  11. MultiFarm: A Benchmark for Multilingual Ontology Matching

    NARCIS (Netherlands)

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

    2012-01-01

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

  12. Sensor-based material tagging system

    International Nuclear Information System (INIS)

    Vercellotti, L.C.; Cox, R.W.; Ravas, R.J.; Schlotterer, J.C.

    1991-01-01

    Electronic identification tags are being developed for tracking material and personnel. In applying electronic identification tags to radioactive materials safeguards, it is important to measure attributes of the material to ensure that the tag remains with the material. The addition of a microcontroller with an on-board analog-to-digital converter to an electronic identification tag application-specific integrated-circuit has been demonstrated as means to provide the tag with sensor data. Each tag is assembled into a housing, which serves as a scale for measuring the weight of a paint-can-sized container and its contents. Temperature rise of the can above ambient is also measured, and a piezoelectric detector detects disturbances and immediately puts the tag into its alarm and beacon mode. Radiation measurement was also considered, but the background from nearby containers was found to be excessive. The sensor-based tagging system allows tracking of the material in cans as it is stored in vaults or is moved through the manufacturing process. The paper presents details of the sensor-based material tagging system and describes a demonstration system

  13. Graph based techniques for tag cloud generation

    DEFF Research Database (Denmark)

    Leginus, Martin; Dolog, Peter; Lage, Ricardo Gomes

    2013-01-01

    Tag cloud is one of the navigation aids for exploring documents. Tag cloud also link documents through the user defined terms. We explore various graph based techniques to improve the tag cloud generation. Moreover, we introduce relevance measures based on underlying data such as ratings...... or citation counts for improved measurement of relevance of tag clouds. We show, that on the given data sets, our approach outperforms the state of the art baseline methods with respect to such relevance by 41 % on Movielens dataset and by 11 % on Bibsonomy data set....

  14. Flavour Tagging developments within the LHCb experiment

    CERN Document Server

    Grabalosa, Marc

    Flavour Tagging at the LHCb experiment is a fundamental tool for the measurement of B oscillations and the study of CP violation. This document explains the development of different tagging techniques and the different strategies used to combine them to determine the flavour of the B meson as precisely as possible. The response of the tagging algorithms also needs to be optimized and calibrated. Both procedures are described using the available LHCb datasets corresponding to various integrated luminosities. First results on the tagging performances are shown for different control channels and physics measurements.

  15. Using Interference to Block RFID Tags

    DEFF Research Database (Denmark)

    Krigslund, Rasmus; Popovski, Petar; Pedersen, Gert Frølund

    We propose a novel method to block RFID tags from responding, using intentional interference. We focus on the experimental evaluation, where we impose interference on the download and uplink, respectively. The results are positive, where modulated CCI shows most effective to block a tag.......We propose a novel method to block RFID tags from responding, using intentional interference. We focus on the experimental evaluation, where we impose interference on the download and uplink, respectively. The results are positive, where modulated CCI shows most effective to block a tag....

  16. Discharge residence of TLD tagged fish

    International Nuclear Information System (INIS)

    Romberg, G.P.; Prepejchal, W.

    1974-01-01

    Although visual observations suggested that fish remained in the discharge for considerable periods, temperature-sensitive tags indicated the majority of fish spend less than 50 hr or 10 percent of the time at discharge temperatures. During 1974 a second fish tagging study was conducted, using temperature-sensitive tags to yield discharge residence times of Lake Michigan salmonids at Point Beach thermal discharge. Preliminary results revealed that many fish tag values were close to Unit I line indicating that calculated maximum discharge residence times for these fish will be nearly 100 percent of the elapsed time

  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. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Contributions to a Conceptual Ontology for Wittgenstein

    DEFF Research Database (Denmark)

    Addis, Mark; Brock, Steen; Pichler, Alois

    2015-01-01

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

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

    A conceptually sound explanation, I claim, respects the ontological order between properties. A dependent property is to be explained in terms of its underlying property, not the other way around. The applicability of this point goes well beyond the realm of the debate between scientific realists and antirealists.

  2. The location problem in social ontology

    NARCIS (Netherlands)

    Hindriks, Frank

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

  3. Ontologies for commitment-based smart contracts

    NARCIS (Netherlands)

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

    2017-01-01

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

  4. 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...

  5. Ontological support for web courseware authoring

    NARCIS (Netherlands)

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

    2002-01-01

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

  6. Ontology matching evaluation : A statistical perspective

    NARCIS (Netherlands)

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

    2016-01-01

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

  7. Ontology matching evaluation : A statistical perspective

    NARCIS (Netherlands)

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

    2016-01-01

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

  8. Ontological semantics in modified categorial grammar

    DEFF Research Database (Denmark)

    Szymczak, Bartlomiej Antoni

    2009-01-01

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

  9. 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 ...

  10. Asian Educational Discourse: Construction of Ontological Security

    Science.gov (United States)

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

    2018-01-01

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

  11. Development of an Ontology for Occupational Exposure

    Science.gov (United States)

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

  12. In Defense of Chi's Ontological Incompatibility Hypothesis

    Science.gov (United States)

    Slotta, James D.

    2011-01-01

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

  13. Adaptive e-learning system using ontology

    OpenAIRE

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

    2011-01-01

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

  14. Ontology for cell-based geographic information

    Science.gov (United States)

    Zheng, Bin; Huang, Lina; Lu, Xinhai

    2009-10-01

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

  15. Mapping between the OBO and OWL ontology languages.

    Science.gov (United States)

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

    2011-03-07

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

  16. Engineering the ATLAS TAG Browser

    International Nuclear Information System (INIS)

    Zhang Qizhi

    2011-01-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services are discussed. We also describe strategies for dealing with data that may vary over time, such as run-dependent trigger decision decoding. Along with examples, we illustrate how programming techniques in multiple languages (PHP, JAVASCRIPT, XML, AJAX, and PL/SQL) have been blended to achieve the required results. Finally, we evaluate features of the ELSSI service in terms of functionality, scalability, and performance.

  17. To tag or not to tag: animal welfare, conservation and stakeholder considerations in fish tracking studies that use electronic tags

    Energy Technology Data Exchange (ETDEWEB)

    Cooke, Steven J.; Nguyen, Vivian M.; Murchie, Karen J.; Thiem, Jason D.; Donaldson, Michael R.; Hinch, Scott G.; Brown, Richard S.; Fisk, Aaron

    2013-11-01

    The advent and widespread adoption of electronic tags (including biotelemetry and biologging devices) for tracking animals has provided unprecedented information on the biology, management, and conservation of fish in the world’s oceans and inland waters. However, use of these tools is not without controversy. Even when scientific and management objectives may best be achieved using electronic tags, it is increasingly important to further consider other factors such as the welfare of tagged animals (i.e., the role of training and science-based surgical guidelines, anesthetic use, inability to maintain sterile conditions in field environments), the ethics of tagging threatened species vs. using surrogates, stakeholder perspectives on tagging (including aboriginals), as well as use of data emanating from such studies (e.g., by fishers to facilitate exploitation). Failure to do so will have the potential to create conflict and undermine scientific, management and public confidence in the use of this powerful tool. Indeed, there are already a number of examples of where tracking studies using electronic tags have been halted based on concerns raised by researchers, authorities, or stakeholders. Here we present a candid evaluation of several factors that should be considered when determining when to tag or not to tag fish with electronic devices. It is not our objective to judge the merit of previous studies. Rather, we hope to stimulate debate and discussion regarding the use of electronic tags to study fish. Relatedly, there is a need for more research to address these questions (e.g., what level of cleanliness is needed when conducting surgeries, what type of training should be required for fish surgery) including human dimensions studies to understand perspectives of different actors including society as a whole with respect to tagging and tracking studies.

  18. A histological ontology of the human cardiovascular system.

    Science.gov (United States)

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

    2017-10-02

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

  19. Methodology to build medical ontology from textual resources.

    Science.gov (United States)

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

    2006-01-01

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

  20. Exploring the Long Tail of Social Media Tags

    NARCIS (Netherlands)

    Kordumova, S.; van Gemert, J.; Snoek, C.G.M.; Tian, Q.; Sebe, N.; Qi, G.-J.; Huet, B.; Hong, R.; Liu, X.

    2016-01-01

    There are millions of users who tag multimedia content, generating a large vocabulary of tags. Some tags are frequent, while other tags are rarely used following a long tail distribution. For frequent tags, most of the multimedia methods that aim to automatically understand audio-visual content,

  1. Colonial waterbird predation on Lost River and shortnose suckers based on recoveries of passive integrated transponder tags

    Science.gov (United States)

    Evans, Allen; Payton, Quinn; Cramer, Bradley D.; Collis, Ken; Hewitt, David A.; Roby, Daniel D.

    2015-01-01

    We evaluated predation on Lost River suckers (Deltistes luxatus) and shortnose suckers (Chasmistes brevirostris), both listed under the Endangered Species Act (ESA), from American white pelicans (Pelecanus erythrorhynchos) and double-crested cormorants (Phalacrocorax auritus) nesting at mixed species colonies on Clear Lake Reservoir, CA and Upper Klamath Lake, OR during 2009-2014. Predation was evaluated by recovering passive integrated transponder (PIT) tags that were implanted in suckers, subsequently consumed by pelicans or cormorants, and deposited on the birds’ nesting colonies. Data from PIT tag recoveries were used to estimate predation rates (proportion of available tagged suckers consumed) by birds to evaluate the relative susceptibility of suckers to avian predation in Upper Klamath Basin. Data on the size of pelican and cormorant colonies (number of breeding adults) at Clear Lake and Upper Klamath Lake were also collected and reported in the context of predation on suckers.

  2. Method and apparatus for manufacturing gas tags

    International Nuclear Information System (INIS)

    Gross, K.C.; Laug, M.T.

    1996-01-01

    For use in the manufacture of gas tags employed in a gas tagging failure detection system for a nuclear reactor, a plurality of commercial feed gases each having a respective noble gas isotopic composition are blended under computer control to provide various tag gas mixtures having selected isotopic ratios which are optimized for specified defined conditions such as cost. Using a new approach employing a discrete variable structure rather than the known continuous-variable optimization problem, the computer controlled gas tag manufacturing process employs an analytical formalism from condensed matter physics known as stochastic relaxation, which is a special case of simulated annealing, for input feed gas selection. For a tag blending process involving M tag isotopes with N distinct feed gas mixtures commercially available from an enriched gas supplier, the manufacturing process calculates the cost difference between multiple combinations and specifies gas mixtures which approach the optimum defined conditions. The manufacturing process is then used to control tag blending apparatus incorporating tag gas canisters connected by stainless-steel tubing with computer controlled valves, with the canisters automatically filled with metered quantities of the required feed gases. 4 figs

  3. Flavour Tagging Algorithms and Performances in LHCb

    CERN Document Server

    Calvi, M; Musy, M

    2007-01-01

    In this note we describe the general characteristics of the LHCb flavour tagging algorithms and summarize the tagging performances on the Monte Carlo samples generated for the Data Challenge 2004 in different decay channels. We also discuss some systematics effects and possible methods to extract the mistag fraction in real data.

  4. Evaluation of PIT-tagging in cyprinids

    DEFF Research Database (Denmark)

    Skov, Christian; Brodersen, J.; Brönmark, C.

    2005-01-01

    Laboratory and field experiments were used to investigate how different marking procedures, with 23 mm PIT (passive integrated transponders) - tags. affected mortality, body condition and tag expulsion in small roach Rutilus rutilus and rudd Scardinus erythrophthalmus (117 to 163 mm total length...

  5. Tagging behaviour with support from controlled vocabulary

    DEFF Research Database (Denmark)

    Lykke, Marianne; Høj, Anne Lyhne; Madsen, Line Nørgaard

    2011-01-01

    ) and an enhanced tagging system (experimental system) that additionally offers suggestions from the Dewey Decimal Classification system (DDC). In the experimental study twenty-eight political students completed four tagging tasks, each comprising fifteen documents. The focus was to examine how suggestions from...

  6. Use artificial neural network to align biological ontologies.

    Science.gov (United States)

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

    2008-09-16

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

  7. Comparing Relational and Ontological Triple Stores in Healthcare Domain

    Directory of Open Access Journals (Sweden)

    Ozgu Can

    2017-01-01

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

  8. Crowdsourcing the verification of relationships in biomedical ontologies.

    Science.gov (United States)

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

    2013-01-01

    Biomedical ontologies are often large and complex, making ontology development and maintenance a challenge. To address this challenge, scientists use automated techniques to alleviate the difficulty of ontology development. However, for many ontology-engineering tasks, human judgment is still necessary. Microtask crowdsourcing, wherein human workers receive remuneration to complete simple, short tasks, is one method to obtain contributions by humans at a large scale. Previously, we developed and refined an effective method to verify ontology hierarchy using microtask crowdsourcing. In this work, we report on applying this method to find errors in the SNOMED CT CORE subset. By using crowdsourcing via Amazon Mechanical Turk with a Bayesian inference model, we correctly verified 86% of the relations from the CORE subset of SNOMED CT in which Rector and colleagues previously identified errors via manual inspection. Our results demonstrate that an ontology developer could deploy this method in order to audit large-scale ontologies quickly and relatively cheaply.

  9. Notes on SAW Tag Interrogation Techniques

    Science.gov (United States)

    Barton, Richard J.

    2010-01-01

    We consider the problem of interrogating a single SAW RFID tag with a known ID and known range in the presence of multiple interfering tags under the following assumptions: (1) The RF propagation environment is well approximated as a simple delay channel with geometric power-decay constant alpha >/= 2. (2) The interfering tag IDs are unknown but well approximated as independent, identically distributed random samples from a probability distribution of tag ID waveforms with known second-order properties, and the tag of interest is drawn independently from the same distribution. (3) The ranges of the interfering tags are unknown but well approximated as independent, identically distributed realizations of a random variable rho with a known probability distribution f(sub rho) , and the tag ranges are independent of the tag ID waveforms. In particular, we model the tag waveforms as random impulse responses from a wide-sense-stationary, uncorrelated-scattering (WSSUS) fading channel with known bandwidth and scattering function. A brief discussion of the properties of such channels and the notation used to describe them in this document is given in the Appendix. Under these assumptions, we derive the expression for the output signal-to-noise ratio (SNR) for an arbitrary combination of transmitted interrogation signal and linear receiver filter. Based on this expression, we derive the optimal interrogator configuration (i.e., transmitted signal/receiver filter combination) in the two extreme noise/interference regimes, i.e., noise-limited and interference-limited, under the additional assumption that the coherence bandwidth of the tags is much smaller than the total tag bandwidth. Finally, we evaluate the performance of both optimal interrogators over a broad range of operating scenarios using both numerical simulation based on the assumed model and Monte Carlo simulation based on a small sample of measured tag waveforms. The performance evaluation results not only

  10. Sentiment topic mining based on comment tags

    Science.gov (United States)

    Zhang, Daohai; Liu, Xue; Li, Juan; Fan, Mingyue

    2018-03-01

    With the development of e-commerce, various comments based on tags are generated, how to extract valuable information from these comment tags has become an important content of business management decisions. This study takes HUAWEI mobile phone tags as an example using the sentiment analysis and topic LDA mining method. The first step is data preprocessing and classification of comment tag topic mining. And then make the sentiment classification for comment tags. Finally, mine the comments again and analyze the emotional theme distribution under different sentiment classification. The results show that HUAWEI mobile phone has a good user experience in terms of fluency, cost performance, appearance, etc. Meanwhile, it should pay more attention to independent research and development, product design and development. In addition, battery and speed performance should be enhanced.

  11. Interpretations of Ontologies for Breast Cancer

    Directory of Open Access Journals (Sweden)

    Srinandan Dasmahapatra

    2008-07-01

    Full Text Available There are increasing efforts directed at providing formal frameworks to consolidate the widening net of terms and relations used in medical practice. While there are many reasons for this, the need for standardisation of protocol and terminology is critical, not only for the provision of uniform levels of health care, but also to facilitate medical science research. In the domain of breast cancer pathology, a summary of current practice by the World Health Organisation states that the variability of the evidence archive (inconsistencies in describing microscopic appearances of phenomena, different diagnostic thresholds for working pathologists is chief among the barriers to the medical understanding of the symptoms and development of early cancers. Such variability is acknowledged across specialist fields of medicine, motivating standardisation of terminologies for reporting medical practice. The desideratum of making these standards machine-readable has led to their formalisation as ontologies. Ontologies are computational artefacts designed to provide representations of a domain of interest. Thus, the representation must be a formal description so that it can be encoded, and reused, allowing navigation of the key concepts recorded and retrieval of information indexed against it. This brings the required standardisation by offering a set of labelling options to record observations and events encountered by medical professionals. Given the twin goals of ontologies -- representation and standardisation -- this paper will consider the key question of their design in the context of the use by experts, of information handling applications built around them. We build on our experience in developing ontologies for decision support software in the area of breast cancer diagnosis and treatment. We will also examine, from this perspective, the suggestion offered in the literature that a set of metaphysically motivated questions should form the basis of

  12. A UML profile for the OBO relation ontology

    Science.gov (United States)

    2012-01-01

    Background Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain. Results We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO). Conclusions The use of an established and well-known graphical language in the development of biomedical ontologies provides a more

  13. Tagged at first listen: an examination of social tagging practices in a music recommender system

    Directory of Open Access Journals (Sweden)

    Audrey Laplante

    2015-01-01

    Full Text Available http://dx.doi.org/10.5007/1518-2924.2015v20nesp1p33 Social tagging has become a very common way to index different types of resources on the web. Less prevalent in music than in other domains, social tagging is nevertheless used in a popular recommender system, Last.fm. Although the number of publications on tagging and folksonomies has exploded in the last few years, music tagging is still not well studied. In this paper, we present a study of tagging practices of Last.fm users. We examine the social tagging of songs during the first three months after their release. Our analysis shows that the release of a song triggers a burst in tagging activity that lasts two weeks, after what it decreases sharply and then remains fairly constant for the next ten weeks. We also find that a majority of songs do not get tagged during the first week and that tagging was positively related to popularity. Finally, we find that tags that have been frequently applied to a given song are more likely to be genre related, shorter in length, and relatively objective than tags that have been applied only once.

  14. Developing an Ontology for Ocean Biogeochemistry Data

    Science.gov (United States)

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

    2010-12-01

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

  15. PAV ontology: provenance, authoring and versioning.

    Science.gov (United States)

    Ciccarese, Paolo; Soiland-Reyes, Stian; Belhajjame, Khalid; Gray, Alasdair Jg; Goble, Carole; Clark, Tim

    2013-11-22

    Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple scientific claim with supportive evidence. Existing vocabularies such as Dublin Core Terms (DC Terms) and the W3C Provenance Ontology (PROV-O) are domain-independent and general-purpose and they allow and encourage for extensions to cover more specific needs. In particular, to track authoring and versioning information of web resources, PROV-O provides a basic methodology but not any specific classes and properties for identifying or distinguishing between the various roles assumed by agents manipulating digital artifacts, such as author, contributor and curator. We present the Provenance, Authoring and Versioning ontology (PAV, namespace http://purl.org/pav/): a lightweight ontology for capturing "just enough" descriptions essential for tracking the provenance, authoring and versioning of web resources. We argue that such descriptions are essential for digital scientific content. PAV distinguishes between contributors, authors and curators of content and creators of representations in addition to the provenance of originating resources that have been accessed, transformed and consumed. We explore five projects (and communities) that have adopted PAV illustrating their usage through concrete examples. Moreover, we present mappings that show how PAV extends the W3C PROV-O ontology to support broader interoperability. The initial design of the PAV ontology was driven by requirements from the AlzSWAN project with further requirements incorporated later from other projects detailed in this paper. The authors strived to keep PAV lightweight and compact by including only those terms that have demonstrated to be pragmatically useful in existing applications, and by recommending terms from existing ontologies when plausible. We analyze and compare PAV with related

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

    OpenAIRE

    Dragisic, Zlatan; Lambrix, Patrick; Blomqvist, Eva

    2015-01-01

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

  17. Pop-up Archival Transmitting (PAT) fish tag data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The cooperative tagging center (CTC) began deploying electronic tags in 2002. To date over 300 tags have been deployed. The following species have been monitored:...

  18. DICOM involving XML path-tag

    Science.gov (United States)

    Zeng, Qiang; Yao, Zhihong; Liu, Lei

    2011-03-01

    Digital Imaging and Communications in Medicine (DICOM) is a standard for handling, storing, printing, and transmitting information in medical imaging. XML (Extensible Markup Language) is a set of rules for encoding documents in machine-readable form which has become more and more popular. The combination of these two is very necessary and promising. Using XML tags instead of numeric labels in DICOM files will effectively increase the readability and enhance the clear hierarchical structure of DICOM files. However, due to the fact that the XML tags rely heavily on the orders of the tags, the strong data dependency has a lot of influence on the flexibility of inserting and exchanging data. In order to improve the extensibility and sharing of DICOM files, this paper introduces XML Path-Tag to DICOM. When a DICOM file is converted to XML format, adding simple Path-Tag into the DICOM file in place of complex tags will keep the flexibility of a DICOM file while inserting data elements and give full play to the advantages of the structure and readability of an XML file. Our method can solve the weak readability problem of DICOM files and the tedious work of inserting data into an XML file. In addition, we set up a conversion engine that can transform among traditional DICOM files, XML-DCM and XML-DCM files involving XML Path-Tag efficiently.

  19. Electricity Markets Ontology to Support MASCEM's Simulations

    DEFF Research Database (Denmark)

    Santos, Gabriel; Pinto, Tiago; Vale, Zita

    2016-01-01

    the several issues related to these systems, including the involved players that act in this domain. To take better advantage of these systems, their integration is mandatory. The main contribution of this paper is the development of the Electricity Markets Ontology, which integrates the essential concepts...... necessary to interpret all the available information related to electricity markets, while enabling an easier cooperation and adequate communication between related systems. Additionally, the concepts and rules defined by this ontology can be extended and complemented according to the needs of other......Power systems worldwide are complex and challenging environments. The increasing necessity for an adequate integration of renewable energy sources is resulting in a rising complexity in power systems operation. Multi-agent based simulation platforms have proven to be a good option to study...

  20. Ontological and Epistemological Foundations of Qualitative Research

    Directory of Open Access Journals (Sweden)

    Irene Vasilachis de Gialdino

    2009-05-01

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

  1. A Cognitive Support Framework for Ontology Mapping

    Science.gov (United States)

    Falconer, Sean M.; Storey, Margaret-Anne

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

  2. Discovering Diabetes Complications: an Ontology Based Model.

    Science.gov (United States)

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

    2015-12-01

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

  3. BiOSS: A system for biomedical ontology selection.

    Science.gov (United States)

    Martínez-Romero, Marcos; Vázquez-Naya, José M; Pereira, Javier; Pazos, Alejandro

    2014-04-01

    In biomedical informatics, ontologies are considered a key technology for annotating, retrieving and sharing the huge volume of publicly available data. Due to the increasing amount, complexity and variety of existing biomedical ontologies, choosing the ones to be used in a semantic annotation problem or to design a specific application is a difficult task. As a consequence, the design of approaches and tools addressed to facilitate the selection of biomedical ontologies is becoming a priority. In this paper we present BiOSS, a novel system for the selection of biomedical ontologies. BiOSS evaluates the adequacy of an ontology to a given domain according to three different criteria: (1) the extent to which the ontology covers the domain; (2) the semantic richness of the ontology in the domain; (3) the popularity of the ontology in the biomedical community. BiOSS has been applied to 5 representative problems of ontology selection. It also has been compared to existing methods and tools. Results are promising and show the usefulness of BiOSS to solve real-world ontology selection problems. BiOSS is openly available both as a web tool and a web service. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Rüegg Alexander

    2006-04-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2018-02-06

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

  7. Folksonomia: a linguagem das tags

    Directory of Open Access Journals (Sweden)

    Juliana de Assis

    2013-01-01

    Full Text Available A radicalização do potencial colaborativo da web atual aponta uma tendência de personalização da recuperação da informação através de ferramentas que exploram a linguagem natural na representação e no compartilhamento de conteúdos ao longo das redes sociais. Tal configuração sócio-técnica traz desafios aos profissionais da informação tanto para a descrição e compreensão dos fenômenos informacionais que ocorrem neste âmbito, quanto para a elaboração de produtos e serviços voltados para um usuário que se apresenta cada vez mais como sujeito informacional ao assumir um papel ativo diante da complexidade que caracteriza a organização da informação em contextos digitais. Este artigo apresenta conclusões de pesquisa, relacionadas às analises da linguagem utilizada em três ambientes colaborativos que utilizam a folksonomia (Social Tagging Systems. A partir de uma perspectiva fundamentada na Semiótica e na Análise de Redes Sociais, são identificadas e descritas as principais manifestações da linguagem gerada e compartilhada pelas redes sociais através destes ambientes.

  8. The Ontology of Knowledge Based Optimization

    OpenAIRE

    Nasution, Mahyuddin K. M.

    2012-01-01

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

  9. Business Ontology for Evaluating Corporate Social Responsibility

    OpenAIRE

    Ion Smeureanu; Andreea Dioşteanu; Camelia Delcea; Liviu Cotfas

    2011-01-01

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

  10. Representing the Quantum Object through Fiction in Teaching: The Ontological Contribution of Gamow's Narrative as Part of an Introduction to Quantum Physics

    Science.gov (United States)

    Héraud, Jean-Loup; Lautesse, Philippe; Ferlin, Fabrice; Chabot, Hugues

    2017-01-01

    Our work extends a previous study of epistemological presuppositions in teaching quantum physics in upper scientific secondary school in France. Here, the problematic reference of quantum theory's concepts is treated at the ontological level (the counterintuitive nature of quantum objects). We consider the approach of using narratives describing…

  11. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

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

    2018-06-01

    The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

  12. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

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

    2018-03-01

    The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

  13. Defining functional distances over Gene Ontology

    Directory of Open Access Journals (Sweden)

    del Pozo Angela

    2008-01-01

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

  14. A Uniform Ontology for Software Interfaces

    Science.gov (United States)

    Feyock, Stefan

    2002-01-01

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

  15. The Human Phenotype Ontology in 2017

    International Nuclear Information System (INIS)

    Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark; Foster, Erin; McMurry, Julie

    2016-01-01

    Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human PhenotypeOntology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

  16. Cyber Forensics Ontology for Cyber Criminal Investigation

    Science.gov (United States)

    Park, Heum; Cho, Sunho; Kwon, Hyuk-Chul

    We developed Cyber Forensics Ontology for the criminal investigation in cyber space. Cyber crime is classified into cyber terror and general cyber crime, and those two classes are connected with each other. The investigation of cyber terror requires high technology, system environment and experts, and general cyber crime is connected with general crime by evidence from digital data and cyber space. Accordingly, it is difficult to determine relational crime types and collect evidence. Therefore, we considered the classifications of cyber crime, the collection of evidence in cyber space and the application of laws to cyber crime. In order to efficiently investigate cyber crime, it is necessary to integrate those concepts for each cyber crime-case. Thus, we constructed a cyber forensics domain ontology for criminal investigation in cyber space, according to the categories of cyber crime, laws, evidence and information of criminals. This ontology can be used in the process of investigating of cyber crime-cases, and for data mining of cyber crime; classification, clustering, association and detection of crime types, crime cases, evidences and criminals.

  17. Phenex: ontological annotation of phenotypic diversity.

    Directory of Open Access Journals (Sweden)

    James P Balhoff

    2010-05-01

    Full Text Available Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

  18. Phenex: ontological annotation of phenotypic diversity.

    Science.gov (United States)

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

    2010-05-05

    Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

  19. Annotating the human genome with Disease Ontology

    Science.gov (United States)

    Osborne, John D; Flatow, Jared; Holko, Michelle; Lin, Simon M; Kibbe, Warren A; Zhu, Lihua (Julie); Danila, Maria I; Feng, Gang; Chisholm, Rex L

    2009-01-01

    Background The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases. Results We used the Unified Medical Language System (UMLS) MetaMap Transfer tool (MMTx) to discover gene-disease relationships from the GeneRIF database. We utilized a comprehensive subset of UMLS, which is disease-focused and structured as a directed acyclic graph (the Disease Ontology), to filter and interpret results from MMTx. The results were validated against the Homayouni gene collection using recall and precision measurements. We compared our results with the widely used Online Mendelian Inheritance in Man (OMIM) annotations. Conclusion The validation data set suggests a 91% recall rate and 97% precision rate of disease annotation using GeneRIF, in contrast with a 22% recall and 98% precision using OMIM. Our thesaurus-based approach allows for comparisons to be made between disease containing databases and allows for increased accuracy in disease identification through synonym matching. The much higher recall rate of our approach demonstrates that annotating human genome with Disease Ontology and GeneRIF for diseases dramatically increases the coverage of the disease annotation of human genome. PMID:19594883

  20. W/Top/Higgs-tagging in ATLAS

    CERN Document Server

    Norjoharuddeen, Nurfikri; The ATLAS collaboration

    2017-01-01

    We present updates of W, Top and Higgs tagging studies with the ATLAS detector. The performance of 2 variable taggers, HEPTopTagger and shower deconstruction are compared in Monte Carlo simulations. To asses the modelling of the taggers’ performance, the tagging efficiencies are measured, with the full 2015+2016 dataset, in semi-leptonic top quark pair events and the background rejections are measured in dijet and photon+jet topologies. Recent developments in subjet reconstruction techniques for high transverse momentum Higgs->bb tagging are also presented.

  1. Linking descriptive geology and quantitative machine learning through an ontology of lithological concepts

    Science.gov (United States)

    Klump, J. F.; Huber, R.; Robertson, J.; Cox, S. J. D.; Woodcock, R.

    2014-12-01

    Despite the recent explosion of quantitative geological data, geology remains a fundamentally qualitative science. Numerical data only constitute a certain part of data collection in the geosciences. In many cases, geological observations are compiled as text into reports and annotations on drill cores, thin sections or drawings of outcrops. The observations are classified into concepts such as lithology, stratigraphy, geological structure, etc. These descriptions are semantically rich and are generally supported by more quantitative observations using geochemical analyses, XRD, hyperspectral scanning, etc, but the goal is geological semantics. In practice it has been difficult to bring the different observations together due to differing perception or granularity of classification in human observation, or the partial observation of only some characteristics using quantitative sensors. In the past years many geological classification schemas have been transferred into ontologies and vocabularies, formalized using RDF and OWL, and published through SPARQL endpoints. Several lithological ontologies were compiled by stratigraphy.net and published through a SPARQL endpoint. This work is complemented by the development of a Python API to integrate this vocabulary into Python-based text mining applications. The applications for the lithological vocabulary and Python API are automated semantic tagging of geochemical data and descriptions of drill cores, machine learning of geochemical compositions that are diagnostic for lithological classifications, and text mining for lithological concepts in reports and geological literature. This combination of applications can be used to identify anomalies in databases, where composition and lithological classification do not match. It can also be used to identify lithological concepts in the literature and infer quantitative values. The resulting semantic tagging opens new possibilities for linking these diverse sources of data.

  2. Development and Evaluation of an Adolescents' Depression Ontology for Analyzing Social Data.

    Science.gov (United States)

    Jung, Hyesil; Park, Hyeoun-Ae; Song, Tae-Min

    2016-01-01

    This study aims to develop and evaluate an ontology for adolescents' depression to be used for collecting and analyzing social data. The ontology was developed according to the 'ontology development 101' methodology. Concepts were extracted from clinical practice guidelines and related literatures. The ontology is composed of five sub-ontologies which represent risk factors, sign and symptoms, measurement, diagnostic result and management care. The ontology was evaluated in four different ways: First, we examined the frequency of ontology concept appeared in social data; Second, the content coverage of ontology was evaluated by comparing ontology concepts with concepts extracted from the youth depression counseling records; Third, the structural and representational layer of the ontology were evaluated by 5 ontology and psychiatric nursing experts; Fourth, the scope of the ontology was examined by answering 59 competency questions. The ontology was improved by adding new concepts and synonyms and revising the level of structure.

  3. Comparative Performance of Acoustic-tagged and PIT-tagged Juvenile Salmonids

    Energy Technology Data Exchange (ETDEWEB)

    Hockersmith, Eric E.; Brown, Richard S.; Liedtke, Theresa L.

    2008-02-01

    Numerous research tools and technologies are currently being used to evaluate fish passage and survival to determine the impacts of the Federal Columbia River Power System (FCRPS) on endangered and threatened juvenile salmonids, including PIT tags, balloon tags, hydroacoustic evaluations, radio telemetry, and acoustic telemetry. Each has advantages and disadvantages, but options are restricted in some situations because of limited capabilities of a specific technology, lack of detection capability downstream, or availability of adequate numbers of fish. However, there remains concern about the comparative effects of the tag or the tagging procedure on fish performance. The recently developed Juvenile Salmonid Acoustic Telemetry System (JSATS) acoustic transmitter is the smallest active acoustic tag currently available. The goal of this study was to determine whether fish tagged with the JSATS acoustic-telemetry tag can provide unbiased estimates of passage behavior and survival within the performance life of the tag. We conducted both field and laboratory studies to assess tag effects. For the field evaluation we released a total of 996 acoustic-tagged fish in conjunction with 21,026 PIT-tagged fish into the tailrace of Lower Granite Dam on 6 and 13 May. Travel times between release and downstream dams were not significantly different for the majority of the reaches between acoustic-tagged and PIT-tagged fish. In addition to the field evaluation, a series of laboratory experiments were conducted to determine if growth and survival of juvenile Chinook salmon surgically implanted with acoustic transmitters is different than untagged or PIT tagged juvenile Chinook salmon. Only yearling fish with integrated and non-integrated transmitters experienced mortalities, and these were low (<4.5%). Mortality among sub-yearling control and PIT-tag treatments ranged up to 7.7% while integrated and non-integrated treatments had slightly higher rates (up to 8.3% and 7

  4. Web Approach for Ontology-Based Classification, Integration, and Interdisciplinary Usage of Geoscience Metadata

    Directory of Open Access Journals (Sweden)

    B Ritschel

    2012-10-01

    Full Text Available The Semantic Web is a W3C approach that integrates the different sources of semantics within documents and services using ontology-based techniques. The main objective of this approach in the geoscience domain is the improvement of understanding, integration, and usage of Earth and space science related web content in terms of data, information, and knowledge for machines and people. The modeling and representation of semantic attributes and relations within and among documents can be realized by human readable concept maps and machine readable OWL documents. The objectives for the usage of the Semantic Web approach in the GFZ data center ISDC project are the design of an extended classification of metadata documents for product types related to instruments, platforms, and projects as well as the integration of different types of metadata related to data product providers, users, and data centers. Sources of content and semantics for the description of Earth and space science product types and related classes are standardized metadata documents (e.g., DIF documents, publications, grey literature, and Web pages. Other sources are information provided by users, such as tagging data and social navigation information. The integration of controlled vocabularies as well as folksonomies plays an important role in the design of well formed ontologies.

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

    Science.gov (United States)

    2015-07-06

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

  6. Nuclear component design ontology building based on ASME codes

    International Nuclear Information System (INIS)

    Bao Shiyi; Zhou Yu; He Shuyan

    2005-01-01

    The adoption of ontology analysis in the study of concept knowledge acquisition and representation for the nuclear component design process based on computer-supported cooperative work (CSCW) makes it possible to share and reuse numerous concept knowledge of multi-disciplinary domains. A practical ontology building method is accordingly proposed based on Protege knowledge model in combination with both top-down and bottom-up approaches together with Formal Concept Analysis (FCA). FCA exhibits its advantages in the way it helps establish and improve taxonomic hierarchy of concepts and resolve concept conflict occurred in modeling multi-disciplinary domains. With Protege-3.0 as the ontology building tool, a nuclear component design ontology based ASME codes is developed by utilizing the ontology building method. The ontology serves as the basis to realize concept knowledge sharing and reusing of nuclear component design. (authors)

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

    Science.gov (United States)

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

    2005-04-01

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

  8. An Ontology for Modeling Complex Inter-relational Organizations

    Science.gov (United States)

    Wautelet, Yves; Neysen, Nicolas; Kolp, Manuel

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

  9. Ontology matters: a commentary on contribution to cultural historical activity

    Science.gov (United States)

    Martin, Jenny

    2017-10-01

    This commentary promotes discussion on the imaginary provided by Sanaz Farhangi in her article entitled, Contribution to activity: a lens for understanding students' potential and agency in physics education. The commentary is concerned with aligning ontological assumptions in research accounts of learning and development with transformative aims. A broad definition of ontology as the theory of existence is preferred. Sociocultural approaches share relational ontology as a common foundation. I agree with scholars elaborating Vygotsky's Transformative Activist Stance that a relational ontology does not imply activism. However, I argue that relational ontology provides a necessary and sufficient theoretical grounding for intentional transformation. I draw upon positioning theory to elaborate the moral aspects of language use and to illustrate that a theory of being as relational already eliminates the transcendental position. I draw on Farhangi's article to further the discussion on the necessity and sufficiency of relational ontology and associated grammars in accounting for activism.

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

    Science.gov (United States)

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

    2015-10-01

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

  11. NanoParticle Ontology for Cancer Nanotechnology Research

    Science.gov (United States)

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

    2010-01-01

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

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

    KAUST Repository

    Gkoutos, Georgios V.

    2015-07-28

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

  13. Comparing the hierarchy of author given tags and repository given tags in a large document archive

    Science.gov (United States)

    Tibély, Gergely; Pollner, Péter; Palla, Gergely

    2016-10-01

    Folksonomies - large databases arising from collaborative tagging of items by independent users - are becoming an increasingly important way of categorizing information. In these systems users can tag items with free words, resulting in a tripartite item-tag-user network. Although there are no prescribed relations between tags, the way users think about the different categories presumably has some built in hierarchy, in which more special concepts are descendants of some more general categories. Several applications would benefit from the knowledge of this hierarchy. Here we apply a recent method to check the differences and similarities of hierarchies resulting from tags given by independent individuals and from tags given by a centrally managed repository system. The results from our method showed substantial differences between the lower part of the hierarchies, and in contrast, a relatively high similarity at the top of the hierarchies.

  14. User Interface Program for secure electronic tags

    International Nuclear Information System (INIS)

    Cai, Y.; Koehl, E.R.; Carlson, R.D.; Raptis, A.C.

    1995-05-01

    This report summarizes and documents the efforts of Argonne National Laboratory (ANL) in developing a secure tag communication user interface program comprising a tag monitor and a communication tool. This program can perform the same functions as the software that was developed at the Lawrence Livermore National Laboratory (LLNL), but it is enhanced with a user-friendly screen. It represents the first step in updating the TRANSCOM Tracking System (TRANSCOM) by incorporating a tag communication screen menu into the main menu of the TRANSCOM user program. A working version of TRANSCOM, enhanced with ANL secure-tag graphics, will strongly support the Department of Energy Warhead Dismantlement/Special Nuclear Materials Control initiatives. It will allow commercial satellite tracking of the movements and operational activities of treaty-limited items and transportation vehicles throughout Europe and the former USSR, as well as the continental US

  15. Flavour Tagging with the LHCb experiment

    CERN Multimedia

    Birnkraut, Alex

    2015-01-01

    Measurements of flavour oscillations and time-dependent CP asymmetries in neutral B meson systems require knowledge of the b quark production flavour. This identification is performed by the Flavour Tagging.

  16. Magnetic vector field tag and seal

    Science.gov (United States)

    Johnston, Roger G.; Garcia, Anthony R.

    2004-08-31

    One or more magnets are placed in a container (preferably on objects inside the container) and the magnetic field strength and vector direction are measured with a magnetometer from at least one location near the container to provide the container with a magnetic vector field tag and seal. The location(s) of the magnetometer relative to the container are also noted. If the position of any magnet inside the container changes, then the measured vector fields at the these locations also change, indicating that the tag has been removed, the seal has broken, and therefore that the container and objects inside may have been tampered with. A hollow wheel with magnets inside may also provide a similar magnetic vector field tag and seal. As the wheel turns, the magnets tumble randomly inside, removing the tag and breaking the seal.

  17. Expressed sequence tags (ESTs) and single nucleotide ...

    African Journals Online (AJOL)

    SERVER

    2008-02-19

    Feb 19, 2008 ... the discovery of the DNA, a new area of modern plant biotechnology begun. In plant ... Marker Assisted Breeding and Sequence Tagged Sites. (STS) are all in use in modern ...... and behaviour in the honey bee. Genome Res.

  18. 50 CFR 635.33 - Archival tags.

    Science.gov (United States)

    2010-10-01

    ... landing; furnish all requested information regarding the location and method of capture; and, as... recovery of the tag by a NMFS scientist, enforcement agent, or other person designated in writing by NMFS...

  19. Folksonomia: a linguagem das tags

    Directory of Open Access Journals (Sweden)

    Juliana de Assis

    2013-04-01

    Full Text Available http://dx.doi.org/10.5007/1518-2924.2013v18n36p85   A radicalização do potencial colaborativo da web atual aponta uma tendência de personalização da recuperação da informação através de ferramentas que exploram a linguagem natural na representação e no compartilhamento de conteúdos ao longo das redes sociais. Tal configuração sócio-técnica traz desafios aos profissionais da informação tanto para a descrição e compreensão dos fenômenos informacionais que ocorrem neste âmbito, quanto para a elaboração de produtos e serviços voltados para um usuário que se apresenta cada vez mais como sujeito informacional ao assumir um papel ativo diante da complexidade que caracteriza a organização da informação em contextos digitais. Este artigo apresenta conclusões de pesquisa, relacionadas às analises da linguagem utilizada em três ambientes colaborativos que utilizam a folksonomia (Social Tagging Systems. A partir de uma perspectiva fundamentada na Semiótica e na Análise de Redes Sociais, são identificadas e descritas as principais manifestações da linguagem gerada e compartilhada pelas redes sociais através destes ambientes.

  20. b-flavour tagging in pp collisions

    CERN Multimedia

    Birnkraut, Alex

    2015-01-01

    An essential ingredient of all time-dependent CP violation studies of B mesons is the ability to tag the initial flavour of the B meson. The harsh environment of 7 and 8 TeV pp collisions makes this a particularly difficult enterprise. We report progresses in the flavour tagging of B0 and Bs mesons, including developments of novel techniques like the use of an opposite side charm tagger.

  1. Logical Characterisation of Ontology Construction using Fuzzy Description Logics

    DEFF Research Database (Denmark)

    Badie, Farshad; Götzsche, Hans

    had the extension of ontologies with Fuzzy Logic capabilities which plan to make proper backgrounds for ontology driven reasoning and argumentation on vague and imprecise domains. This presentation conceptualises learning from fuzzy classes using the Inductive Logic Programming framework. Then......, employs Description Logics in characterising and analysing fuzzy statements. And finally, provides a conceptual framework describing fuzzy concept learning in ontologies using the Inductive Logic Programming....

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

    OpenAIRE

    Cristina NICULESCU; Stefan TRAUSAN-MATU

    2009-01-01

    The paper presents a generic framework of an intelligent information system for competence management based on ontologies for information technology companies. The advantage of using an ontology-based system is the possibility of the identification of new relations among concepts based on inferences starting from the existing knowledge. The inferences may be performed in our approach by a reasoning engine, using classifiers in the Descriptions Logics tab associated with the Protégé ontology e...

  3. Vector boson tagged jets and jet substructure

    Directory of Open Access Journals (Sweden)

    Vitev Ivan

    2018-01-01

    Full Text Available In these proceedings, we report on recent results related to vector boson-tagged jet production in heavy ion collisions and the related modification of jet substructure, such as jet shapes and jet momentum sharing distributions. Z0-tagging and γ-tagging of jets provides new opportunities to study parton shower formation and propagation in the quark-gluon plasma and has been argued to provide tight constrains on the energy loss of reconstructed jets. We present theoretical predictions for isolated photon-tagged and electroweak boson-tagged jet production in Pb+Pb collisions at √sNN = 5.02 TeV at the LHC, addressing the modification of their transverse momentum and transverse momentum imbalance distributions. Comparison to recent ATLAS and CMS experimental measurements is performed that can shed light on the medium-induced radiative corrections and energy dissipation due to collisional processes of predominantly quark-initiated jets. The modification of parton splitting functions in the QGP further implies that the substructure of jets in heavy ion collisions may differ significantly from the corresponding substructure in proton-proton collisions. Two such observables and the implication of tagging on their evaluation is also discussed.

  4. Clone tag detection in distributed RFID systems

    Science.gov (United States)

    Kamaludin, Hazalila; Mahdin, Hairulnizam

    2018-01-01

    Although Radio Frequency Identification (RFID) is poised to displace barcodes, security vulnerabilities pose serious challenges for global adoption of the RFID technology. Specifically, RFID tags are prone to basic cloning and counterfeiting security attacks. A successful cloning of the RFID tags in many commercial applications can lead to many serious problems such as financial losses, brand damage, safety and health of the public. With many industries such as pharmaceutical and businesses deploying RFID technology with a variety of products, it is important to tackle RFID tag cloning problem and improve the resistance of the RFID systems. To this end, we propose an approach for detecting cloned RFID tags in RFID systems with high detection accuracy and minimal overhead thus overcoming practical challenges in existing approaches. The proposed approach is based on consistency of dual hash collisions and modified count-min sketch vector. We evaluated the proposed approach through extensive experiments and compared it with existing baseline approaches in terms of execution time and detection accuracy under varying RFID tag cloning ratio. The results of the experiments show that the proposed approach outperforms the baseline approaches in cloned RFID tag detection accuracy. PMID:29565982

  5. Clone tag detection in distributed RFID systems.

    Science.gov (United States)

    Kamaludin, Hazalila; Mahdin, Hairulnizam; Abawajy, Jemal H

    2018-01-01

    Although Radio Frequency Identification (RFID) is poised to displace barcodes, security vulnerabilities pose serious challenges for global adoption of the RFID technology. Specifically, RFID tags are prone to basic cloning and counterfeiting security attacks. A successful cloning of the RFID tags in many commercial applications can lead to many serious problems such as financial losses, brand damage, safety and health of the public. With many industries such as pharmaceutical and businesses deploying RFID technology with a variety of products, it is important to tackle RFID tag cloning problem and improve the resistance of the RFID systems. To this end, we propose an approach for detecting cloned RFID tags in RFID systems with high detection accuracy and minimal overhead thus overcoming practical challenges in existing approaches. The proposed approach is based on consistency of dual hash collisions and modified count-min sketch vector. We evaluated the proposed approach through extensive experiments and compared it with existing baseline approaches in terms of execution time and detection accuracy under varying RFID tag cloning ratio. The results of the experiments show that the proposed approach outperforms the baseline approaches in cloned RFID tag detection accuracy.

  6. A hypergraph model of social tagging networks

    International Nuclear Information System (INIS)

    Zhang, Zi-Ke; Liu, Chuang

    2010-01-01

    The past few years have witnessed the great success of a new family of paradigms, so-called folksonomy, which allows users to freely associate tags with resources and efficiently manage them. In order to uncover the underlying structures and user behaviors in folksonomy, in this paper, we propose an evolutionary hypergraph model for explaining the emerging statistical properties. The present model introduces a novel mechanism that can not only assign tags to resources, but also retrieve resources via collaborative tags. We then compare the model with a real-world data set: Del.icio.us. Indeed, the present model shows considerable agreement with the empirical data in the following aspects: power-law hyperdegree distributions, negative correlation between clustering coefficients and hyperdegrees, and small average distances. Furthermore, the model indicates that most tagging behaviors are motivated by labeling tags on resources, and the tag plays a significant role in effectively retrieving interesting resources and making acquaintances with congenial friends. The proposed model may shed some light on the in-depth understanding of the structure and function of folksonomy

  7. Smart-tag Based Data Dissemination

    DEFF Research Database (Denmark)

    Bonnet, Philippe; Beaufour, Allan; Leopold, Martin

    2002-01-01

    Monitoring wide, hostile areas requires disseminating data between fixed, disconnected clusters of sensor nodes. It is not always possible to install long-range radios in order to cover the whole area. We propose to leverage the movement of mobile individuals, equipped with smart-tags, to dissemi......-tag based data dissemination. We use simulation to study the characteristics of the model we propose. Finally, we present an implementation based on Bluetooth smart-tags.......Monitoring wide, hostile areas requires disseminating data between fixed, disconnected clusters of sensor nodes. It is not always possible to install long-range radios in order to cover the whole area. We propose to leverage the movement of mobile individuals, equipped with smart......-tags, to disseminate data across disconnected static nodes spread across a wide area. Static nodes and mobile smart-tags exchange data when they are in the vicinity of each other; smart-tags disseminate data as they move around. In this paper, we propose an algorithm for update propagation and a model for smart...

  8. Multi-Threaded DNA Tag/Anti-Tag Library Generator for Multi-Core Platforms

    Science.gov (United States)

    2009-05-01

    base pair)  Watson ‐ Crick  strand pairs that bind perfectly within pairs, but poorly across pairs. A variety  of  DNA  strand hybridization metrics...AFRL-RI-RS-TR-2009-131 Final Technical Report May 2009 MULTI-THREADED DNA TAG/ANTI-TAG LIBRARY GENERATOR FOR MULTI-CORE PLATFORMS...TYPE Final 3. DATES COVERED (From - To) Jun 08 – Feb 09 4. TITLE AND SUBTITLE MULTI-THREADED DNA TAG/ANTI-TAG LIBRARY GENERATOR FOR MULTI-CORE

  9. Improving Recommendations in Tag-based Systems with Spectral Clustering of Tag Neighbors

    DEFF Research Database (Denmark)

    Pan, Rong; Xu, Guandong; Dolog, Peter

    2012-01-01

    Tag as a useful metadata reflects the collaborative and conceptual features of documents in social collaborative annotation systems. In this paper, we propose a collaborative approach for expanding tag neighbors and investigate the spectral clustering algorithm to filter out noisy tag neighbors...... in order to get appropriate recommendation for users. The preliminary experiments have been conducted on MovieLens dataset to compare our proposed approach with the traditional collaborative filtering recommendation approach and naive tag neighbors expansion approach in terms of precision, and the result...... demonstrates that our approach could considerably improve the performance of recommendations....

  10. Toward a general ontology for digital forensic disciplines.

    Science.gov (United States)

    Karie, Nickson M; Venter, Hein S

    2014-09-01

    Ontologies are widely used in different disciplines as a technique for representing and reasoning about domain knowledge. However, despite the widespread ontology-related research activities and applications in different disciplines, the development of ontologies and ontology research activities is still wanting in digital forensics. This paper therefore presents the case for establishing an ontology for digital forensic disciplines. Such an ontology would enable better categorization of the digital forensic disciplines, as well as assist in the development of methodologies and specifications that can offer direction in different areas of digital forensics. This includes such areas as professional specialization, certifications, development of digital forensic tools, curricula, and educational materials. In addition, the ontology presented in this paper can be used, for example, to better organize the digital forensic domain knowledge and explicitly describe the discipline's semantics in a common way. Finally, this paper is meant to spark discussions and further research on an internationally agreed ontological distinction of the digital forensic disciplines. Digital forensic disciplines ontology is a novel approach toward organizing the digital forensic domain knowledge and constitutes the main contribution of this paper. © 2014 American Academy of Forensic Sciences.

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

    Directory of Open Access Journals (Sweden)

    Daniël van Helden

    2018-05-01

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

  12. Matching biomedical ontologies based on formal concept analysis.

    Science.gov (United States)

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

    2018-03-19

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

  13. Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

    Directory of Open Access Journals (Sweden)

    Emanuel Santos

    Full Text Available Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

  14. Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

    Science.gov (United States)

    Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M

    2015-01-01

    Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

  15. Knowledge Representation in Patient Safety Reporting: An Ontological Approach

    Directory of Open Access Journals (Sweden)

    Liang Chen

    2016-10-01

    Full Text Available Purpose: The current development of patient safety reporting systems is criticized for loss of information and low data quality due to the lack of a uniformed domain knowledge base and text processing functionality. To improve patient safety reporting, the present paper suggests an ontological representation of patient safety knowledge. Design/methodology/approach: We propose a framework for constructing an ontological knowledge base of patient safety. The present paper describes our design, implementation, and evaluation of the ontology at its initial stage. Findings: We describe the design and initial outcomes of the ontology implementation. The evaluation results demonstrate the clinical validity of the ontology by a self-developed survey measurement. Research limitations: The proposed ontology was developed and evaluated using a small number of information sources. Presently, US data are used, but they are not essential for the ultimate structure of the ontology. Practical implications: The goal of improving patient safety can be aided through investigating patient safety reports and providing actionable knowledge to clinical practitioners. As such, constructing a domain specific ontology for patient safety reports serves as a cornerstone in information collection and text mining methods. Originality/value: The use of ontologies provides abstracted representation of semantic information and enables a wealth of applications in a reporting system. Therefore, constructing such a knowledge base is recognized as a high priority in health care.

  16. FOCIH: Form-Based Ontology Creation and Information Harvesting

    Science.gov (United States)

    Tao, Cui; Embley, David W.; Liddle, Stephen W.

    Creating an ontology and populating it with data are both labor-intensive tasks requiring a high degree of expertise. Thus, scaling ontology creation and population to the size of the web in an effort to create a web of data—which some see as Web 3.0—is prohibitive. Can we find ways to streamline these tasks and lower the barrier enough to enable Web 3.0? Toward this end we offer a form-based approach to ontology creation that provides a way to create Web 3.0 ontologies without the need for specialized training. And we offer a way to semi-automatically harvest data from the current web of pages for a Web 3.0 ontology. In addition to harvesting information with respect to an ontology, the approach also annotates web pages and links facts in web pages to ontological concepts, resulting in a web of data superimposed over the web of pages. Experience with our prototype system shows that mappings between conceptual-model-based ontologies and forms are sufficient for creating the kind of ontologies needed for Web 3.0, and experiments with our prototype system show that automatic harvesting, automatic annotation, and automatic superimposition of a web of data over a web of pages work well.

  17. Development of an Adolescent Depression Ontology for Analyzing Social Data.

    Science.gov (United States)

    Jung, Hyesil; Park, Hyeoun-Ae; Song, Tae-Min; Jeon, Eunjoo; Kim, Ae Ran; Lee, Joo Yun

    2015-01-01

    Depression in adolescence is associated with significant suicidality. Therefore, it is important to detect the risk for depression and provide timely care to adolescents. This study aims to develop an ontology for collecting and analyzing social media data about adolescent depression. This ontology was developed using the 'ontology development 101'. The important terms were extracted from several clinical practice guidelines and postings on Social Network Service. We extracted 777 terms, which were categorized into 'risk factors', 'sign and symptoms', 'screening', 'diagnosis', 'treatment', and 'prevention'. An ontology developed in this study can be used as a framework to understand adolescent depression using unstructured data from social media.

  18. Passive micromechanical tags. An investigation into writing information at nanometer resolution on micrometer size objects

    International Nuclear Information System (INIS)

    Schmieder, R.W.; Bastasz, R.J.

    1995-01-01

    The authors have completed a 3-year study of the technology related to the development of micron-sized passive micromechanical tags. The project was motivated by the discovery in 1990 by the present authors that low energy, high charge state ions (e.g., Xe +44 ) can produce nanometer-size damage sites on solid surfaces, and the realization that a pattern of these sites represents information. It was envisioned that extremely small, chemically inert, mechanical tags carrying a large label could be fabricated for a variety of applications, including tracking of controlled substances, document verification, process control, research, and engineering. Potential applications exist in the data storage, chemical, food, security, and other industries. The goals of this project were fully accomplished, and they are fully documented here. The work was both experimental and developmental. Most of the experimental effort was a search for appropriate tag materials. Several good materials were found, and the upper limits of information density were determined (ca. 10 12 bit/cm 2 ). Most of the developmental work involved inventing systems and strategies for using these tags, and compiling available technologies for implementing them. The technology provided herein is application-specific: first, the application must be specified, then the tag can be developed for it. The project was not intended to develop a single tag for a single application or for all possible applications. Rather, it was meant to provide the enabling technology for fabricating tags for a range of applications. The results of this project provide sufficient information to proceed directly with such development

  19. Passive micromechanical tags. An investigation into writing information at nanometer resolution on micrometer size objects

    Energy Technology Data Exchange (ETDEWEB)

    Schmieder, R.W.; Bastasz, R.J.

    1995-01-01

    The authors have completed a 3-year study of the technology related to the development of micron-sized passive micromechanical tags. The project was motivated by the discovery in 1990 by the present authors that low energy, high charge state ions (e.g., Xe{sup +44}) can produce nanometer-size damage sites on solid surfaces, and the realization that a pattern of these sites represents information. It was envisioned that extremely small, chemically inert, mechanical tags carrying a large label could be fabricated for a variety of applications, including tracking of controlled substances, document verification, process control, research, and engineering. Potential applications exist in the data storage, chemical, food, security, and other industries. The goals of this project were fully accomplished, and they are fully documented here. The work was both experimental and developmental. Most of the experimental effort was a search for appropriate tag materials. Several good materials were found, and the upper limits of information density were determined (ca. 10{sup 12} bit/cm{sup 2}). Most of the developmental work involved inventing systems and strategies for using these tags, and compiling available technologies for implementing them. The technology provided herein is application-specific: first, the application must be specified, then the tag can be developed for it. The project was not intended to develop a single tag for a single application or for all possible applications. Rather, it was meant to provide the enabling technology for fabricating tags for a range of applications. The results of this project provide sufficient information to proceed directly with such development.

  20. Human-Centered Implicit Tagging: Overview and Perspectives

    NARCIS (Netherlands)

    Soleymani, Mohammad; Pantic, Maja

    2012-01-01

    Tags are an effective form of metadata which help users to locate and browse multimedia content of interest. Tags can be generated by users (user-generated explicit tags), automatically from the content (content-based tags), or assigned automatically based on non-verbal behavioral reactions of users

  1. Overview of the recombinant proteins purification by affinity tags and ...

    African Journals Online (AJOL)

    From protein within isolation process which the same matter increases labor costs further and prevents application of these tags in industrial scale. Therefore proper replacement is emphasized for enzymatic removal of purification tags. Keywords: protein purification; recombinant proteins; self-cleavable tags; Intein tags; ...

  2. Annotating images by harnessing worldwide user-tagged photos

    NARCIS (Netherlands)

    Li, X.; Snoek, C.G.M.; Worring, M.

    2009-01-01

    Automatic image tagging is important yet challenging due to the semantic gap and the lack of learning examples to model a tag's visual diversity. Meanwhile, social user tagging is creating rich multimedia content on the Web. In this paper, we propose to combine the two tagging approaches in a

  3. DermO; an ontology for the description of dermatologic disease

    KAUST Repository

    Fisher, Hannah M.

    2016-06-13

    Background There have been repeated initiatives to produce standard nosologies and terminologies for cutaneous disease, some dedicated to the domain and some part of bigger terminologies such as ICD-10. Recently, formally structured terminologies, ontologies, have been widely developed in many areas of biomedical research. Primarily, these address the aim of providing comprehensive working terminologies for domains of knowledge, but because of the knowledge contained in the relationships between terms they can also be used computationally for many purposes. Results We have developed an ontology of cutaneous disease, constructed manually by domain experts. With more than 3000 terms, DermO represents the most comprehensive formal dermatological disease terminology available. The disease entities are categorized in 20 upper level terms, which use a variety of features such as anatomical location, heritability, affected cell or tissue type, or etiology, as the features for classification, in line with professional practice and nosology in dermatology. Available in OBO flatfile and OWL 2 formats, it is integrated semantically with other ontologies and terminologies describing diseases and phenotypes. We demonstrate the application of DermO to text mining the biomedical literature and in the creation of a network describing the phenotypic relationships between cutaneous diseases. Conclusions DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders. We envision that in the future it may be applied to the creation and mining of electronic health records, clinical training and basic research, as it supports automated inference and reasoning, and for the broader integration of skin disease information with that from other domains.

  4. Automated Ontology Alignment with Fuselets for Community of Interest (COI) Integration

    National Research Council Canada - National Science Library

    Starz, James; Roberts, Joe

    2008-01-01

    Discusses the ontology alignment problem by presenting a tool called Ontrapro-the Ontology Translation Protocol, which allows users to apply a myriad of ontology alignment algorithms in an iterative fashion...

  5. Methodologies for Improved Tag Cloud Generation with Clustering

    DEFF Research Database (Denmark)

    Leginus, Martin; Dolog, Peter; Lage, Ricardo Gomes

    2012-01-01

    Tag clouds are useful means for navigation in the social web systems. Usually the systems implement the tag cloud generation based on tag popularity which is not always the best method. In this paper we propose methodologies on how to combine clustering into the tag cloud generation to improve...... coverage and overlap. We study several clustering algorithms to generate tag clouds. We show that by extending cloud generation based on tag popularity with clustering we slightly improve coverage. We also show that if the cloud is generated by clustering independently of the tag popularity baseline we...

  6. 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.

  7. The federated ontology of the pal project interfacing ontologies and integrating time-dependent data

    NARCIS (Netherlands)

    Krieger, H.U.; Peters, R.; Kiefer, B.; Van Bekkum, M.A.; Kaptein, F.; Neerincx, M.A.

    2016-01-01

    This paper describes ongoing work carried out in the European project PAL which will support childre in their diabetes self-management as well as assist health professionals and parents involved in the diabete regimen of the child. Here, we will focus on the construction of the PAL ontology which

  8. Associated Particle Tagging (APT) in Magnetic Spectrometers

    Energy Technology Data Exchange (ETDEWEB)

    Jordan, David V.; Baciak, James E.; Stave, Sean C.; Chichester, David; Dale, Daniel; Kim, Yujong; Harmon, Frank

    2012-10-16

    Summary In Brief The Associated Particle Tagging (APT) project, a collaboration of Pacific Northwest National Laboratory (PNNL), Idaho National Laboratory (INL) and the Idaho State University (ISU)/Idaho Accelerator Center (IAC), has completed an exploratory study to assess the role of magnetic spectrometers as the linchpin technology in next-generation tagged-neutron and tagged-photon active interrogation (AI). The computational study considered two principle concepts: (1) the application of a solenoidal alpha-particle spectrometer to a next-generation, large-emittance neutron generator for use in the associated particle imaging technique, and (2) the application of tagged photon beams to the detection of fissile material via active interrogation. In both cases, a magnetic spectrometer momentum-analyzes charged particles (in the neutron case, alpha particles accompanying neutron generation in the D-T reaction; in the tagged photon case, post-bremsstrahlung electrons) to define kinematic properties of the relevant neutral interrogation probe particle (i.e. neutron or photon). The main conclusions of the study can be briefly summarized as follows: Neutron generator: • For the solenoidal spectrometer concept, magnetic field strengths of order 1 Tesla or greater are required to keep the transverse size of the spectrometer smaller than 1 meter. The notional magnetic spectrometer design evaluated in this feasibility study uses a 5-T magnetic field and a borehole radius of 18 cm. • The design shows a potential for 4.5 Sr tagged neutron solid angle, a factor of 4.5 larger than achievable with current API neutron-generator designs. • The potential angular resolution for such a tagged neutron beam can be less than 0.5o for modest Si-detector position resolution (3 mm). Further improvement in angular resolution can be made by using Si-detectors with better position resolution. • The report documents several features of a notional generator design incorporating the

  9. Energy Ontologies: Wind, Biomass, and Fossil Transportation

    Directory of Open Access Journals (Sweden)

    Heidi Scott

    2016-06-01

    Full Text Available This article uses literary sources to draw ontological distinctions among three distinct energy sources: wind power, biomass, and fossil fuels. The primary aim is to demonstrate how radically our fossil fuel regime has changed human ontology in the last two centuries during which we have entered the Anthropocene. Because this radical transformation contains myriad elements, this article will focus on transportation: the speed, quality, and quantity of travel permitted by successive energy sources. To consider the comparative literatures of energy as they relate to transportation, we will begin with wind, then consider muscle-driven biomass giving way to coal locomotion, and conclude with the highest octane fuel, petroleum. The central interest is in how the fuel depicted in literature illuminates historical moments in which the interfaces between self, society, and nature are configured by specific energy regimes. By using literature as a source text, we may arrive at an emotionally and philosophically more robust synthesis of energy history than the social and natural sciences, relying upon objective accounts and statistics, are able to provide. By re-reading literature through the lens of the Anthropocene, we gain perspective on how earlier insights into the relationship between energy and experience can inform our explorations of today’s ontological reality. Energy literature instructs us out of the fossil fuel mindset of world domination and back to a physical realm in which we are small actors in a world guided by capricious forces. Such a reality requires hard muscular work and emotional immersion to restore an ethic of care and sustainability.

  10. Ontology Based Quality Evaluation for Spatial Data

    Science.gov (United States)

    Yılmaz, C.; Cömert, Ç.

    2015-08-01

    Many institutions will be providing data to the National Spatial Data Infrastructure (NSDI). Current technical background of the NSDI is based on syntactic web services. It is expected that this will be replaced by semantic web services. The quality of the data provided is important in terms of the decision-making process and the accuracy of transactions. Therefore, the data quality needs to be tested. This topic has been neglected in Turkey. Data quality control for NSDI may be done by private or public "data accreditation" institutions. A methodology is required for data quality evaluation. There are studies for data quality including ISO standards, academic studies and software to evaluate spatial data quality. ISO 19157 standard defines the data quality elements. Proprietary software such as, 1Spatial's 1Validate and ESRI's Data Reviewer offers quality evaluation based on their own classification of rules. Commonly, rule based approaches are used for geospatial data quality check. In this study, we look for the technical components to devise and implement a rule based approach with ontologies using free and open source software in semantic web context. Semantic web uses ontologies to deliver well-defined web resources and make them accessible to end-users and processes. We have created an ontology conforming to the geospatial data and defined some sample rules to show how to test data with respect to data quality elements including; attribute, topo-semantic and geometrical consistency using free and open source software. To test data against rules, sample GeoSPARQL queries are created, associated with specifications.

  11. Improving the interoperability of biomedical ontologies with compound alignments.

    Science.gov (United States)

    Oliveira, Daniela; Pesquita, Catia

    2018-01-09

    Ontologies are commonly used to annotate and help process life sciences data. Although their original goal is to facilitate integration and interoperability among heterogeneous data sources, when these sources are annotated with distinct ontologies, bridging this gap can be challenging. In the last decade, ontology matching systems have been evolving and are now capable of producing high-quality mappings for life sciences ontologies, usually limited to the equivalence between two ontologies. However, life sciences research is becoming increasingly transdisciplinary and integrative, fostering the need to develop matching strategies that are able to handle multiple ontologies and more complex relations between their concepts. We have developed ontology matching algorithms that are able to find compound mappings between multiple biomedical ontologies, in the form of ternary mappings, finding for instance that "aortic valve stenosis"(HP:0001650) is equivalent to the intersection between "aortic valve"(FMA:7236) and "constricted" (PATO:0001847). The algorithms take advantage of search space filtering based on partial mappings between ontology pairs, to be able to handle the increased computational demands. The evaluation of the algorithms has shown that they are able to produce meaningful results, with precision in the range of 60-92% for new mappings. The algorithms were also applied to the potential extension of logical definitions of the OBO and the matching of several plant-related ontologies. This work is a first step towards finding more complex relations between multiple ontologies. The evaluation shows that the results produced are significant and that the algorithms could satisfy specific integration needs.

  12. Applications of Ontologies in Knowledge Management Systems

    Science.gov (United States)

    Rehman, Zobia; Kifor, Claudiu V.

    2014-12-01

    Enterprises are realizing that their core asset in 21st century is knowledge. In an organization knowledge resides in databases, knowledge bases, filing cabinets and peoples' head. Organizational knowledge is distributed in nature and its poor management causes repetition of activities across the enterprise. To get true benefits from this asset, it is important for an organization to "know what they know". That's why many organizations are investing a lot in managing their knowledge. Artificial intelligence techniques have a huge contribution in organizational knowledge management. In this article we are reviewing the applications of ontologies in knowledge management realm

  13. The Digital Exhibition and Keyimage Ontology

    OpenAIRE

    Airchinnigh, Mícheál Mac an; Sotirova, Kalina

    2008-01-01

    The Age of Image predates and is currently contemporaneous with the Information Age. In our times the explosive expansion of Web 2.0 Social Space, typified by the phenomena of De.licio.us, Flickr, MySpace, YouTube…, and the concomitant emergence of folksonomy, present interesting challenges in the management of this information. One key process by which to accomplish this in Social Space, is the wedding of folksonomy (of the people) with ontology (of the machine). Such a wedding must necessar...

  14. CYBERCULTURE AND PHYSICAL EDUCATION: some ontological considerations

    Directory of Open Access Journals (Sweden)

    Fabio Zoboli

    2010-12-01

    Full Text Available This work is a synthesis of a philosophical inquiry about epistemological impasses provoked by social and cultural changes in sports cyberculture of electronic games and robotic and its implications in physical education. We define philosophy like a justification and signification of the human questions drawn by the limits of the conscience while experience of the world and the implications of the material conflicts over social relationships. So, our theoretical and methodological horizon derives from materialism dialect (Adorno, ontology (Merleau-Ponty and the semiotics (Peirce and Lévy.

  15. Ontological and epistemological foundations of qualitative research

    OpenAIRE

    Vasilachis, Irene

    2016-01-01

    The purpose of this paper is to describe the most relevant features of qualitative research in order to show how, from the Epistemology of the Known Subject perspective I propose, it is necessary to review first the ontological and then the epistemological grounds of this type of inquiry. I begin by following the path that leads from the Epistemology of the Knowing Subject to the Epistemology of the Known Subject, proposed as a new and non exclusive way of knowing. I pass on to describe the p...

  16. Terminological Ontologies for Risk and Vulnerability Analysis

    DEFF Research Database (Denmark)

    Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

    2014-01-01

    Risk and vulnerability analyses are an important preliminary stage in civil contingency planning. The Danish Emergency Management Agency has developed a generic model and a set of tools that may be used in the preparedness planning, i.e. for identifying and describing society’s critical functions......, for formulating threat scenarios and for assessing consequences. Terminological ontologies, which are systems of domain specific concepts comprising concept relations and characteristics, are useful, both when describing the central concepts of risk and vulnerability analysis (meta concepts), and for further...

  17. Handbook of metadata, semantics and ontologies

    CERN Document Server

    Sicilia, Miguel-Angel

    2013-01-01

    Metadata research has emerged as a discipline cross-cutting many domains, focused on the provision of distributed descriptions (often called annotations) to Web resources or applications. Such associated descriptions are supposed to serve as a foundation for advanced services in many application areas, including search and location, personalization, federation of repositories and automated delivery of information. Indeed, the Semantic Web is in itself a concrete technological framework for ontology-based metadata. For example, Web-based social networking requires metadata describing people and

  18. A brief examination of optical tagging technologies.

    Energy Technology Data Exchange (ETDEWEB)

    Ackermann, Mark R.; Cahill, Paul A. (Aspecular Optics, Dayton, OH); Drummond, Timothy J.; Wilcoxon, Jess Patrick

    2003-07-01

    Presented within this report are the results of a brief examination of optical tagging technologies funded by the Laboratory Directed Research and Development (LDRD) program at Sandia National Laboratories. The work was performed during the summer months of 2002 with total funding of $65k. The intent of the project was to briefly examine a broad range of approaches to optical tagging concentrating on the wavelength range between ultraviolet (UV) and the short wavelength infrared (SWIR, {lambda} < 2{micro}m). Tagging approaches considered include such things as simple combinations of reflective and absorptive materials closely spaced in wavelength to give a high contrast over a short range of wavelengths, rare-earth oxides in transparent binders to produce a narrow absorption line hyperspectral tag, and fluorescing materials such as phosphors, dies and chemically precipitated particles. One technical approach examined in slightly greater detail was the use of fluorescing nano particles of metals and semiconductor materials. The idea was to embed such nano particles in an oily film or transparent paint binder. When pumped with a SWIR laser such as that produced by laser diodes at {lambda}=1.54{micro}m, the particles would fluoresce at slightly longer wavelengths, thereby giving a unique signal. While it is believed that optical tags are important for military, intelligence and even law enforcement applications, as a business area, tags do not appear to represent a high on return investment. Other government agencies frequently shop for existing or mature tag technologies but rarely are interested enough to pay for development of an untried technical approach. It was hoped that through a relatively small investment of laboratory R&D funds, enough technologies could be identified that a potential customers requirements could be met with a minimum of additional development work. Only time will tell if this proves to be correct.

  19. Towards an Ontology to Describe the Taxonomy of Common Modules in Learning Management Systems

    Directory of Open Access Journals (Sweden)

    Carlos E. Montenegro Marin

    2011-12-01

    Full Text Available This article have the objective a create ontology for "common modules in a Learning Management Systems", the steps for the build Ontology were: Determine the domain and scope of the ontology, Consider reusing existing ontology, Enumerate important terms in the ontology, Define the classes and the class hierarch, Define the properties of classes—slot and Define the facets of the slot, finally be explained how the ontology is composed.

  20. Peptide-tagged proteins in aqueous two-phase systems

    OpenAIRE

    Nilsson, Anna

    2002-01-01

    This thesis deals with proteins containing peptide tags for improved partitioning in aqueous two-phase systems. Qualitatively the peptide-tagged protein partitioning could be predicted from peptide data, i.e. partitioning trends found for peptides were also found for the peptide-tagged proteins. However, full effect of the tag as expected from peptide partitioning was not found in the tagged protein. When alkyl-ethylene oxide surfactant was included in a two-polymer system, almost full effect...

  1. Tag and Neighbor based Recommender systems for Medical events

    DEFF Research Database (Denmark)

    Bayyapu, Karunakar Reddy; Dolog, Peter

    2010-01-01

    This paper presents an extension of a multifactor recommendation approach based on user tagging with term neighbours. Neighbours of words in tag vectors and documents provide for hitting larger set of documents and not only those matching with direct tag vectors or content of the documents. Tag...... in the situations where the quality of tags is lower. We discuss the approach on the examples from the existing Medworm system to indicate the usefulness of the approach....

  2. Evaluation of visible implant elastomer tags in zebrafish (Danio rerio

    Directory of Open Access Journals (Sweden)

    Claudia Hohn

    2013-11-01

    The use of the visible implant elastomer (VIE tagging system in zebrafish (Danio rerio was examined. Two tag orientations (horizontal and vertical at the dorsal fin base were tested for tag retention, tag fragmentation and whether VIE tags affected growth and survival of juvenile zebrafish (1–4 month post hatch. Six tag locations (abdomen, anal fin base, caudal peduncle, dorsal fin base, pectoral fin base, isthmus and 5 tag colors (yellow, red, pink, orange, blue were evaluated for ease of VIE tag application and tag visibility in adult zebrafish. Long-term retention (1 year and multiple tagging sites (right and left of dorsal fin and pectoral fin base were examined in adult zebrafish. Lastly, survival of recombination activation gene 1−/− (rag1−/− zebrafish was evaluated after VIE tagging. The best tag location was the dorsal fin base, and the most visible tag color was pink. Growth rate of juvenile zebrafish was not affected by VIE tagging. Horizontal tagging is recommended in early stages of fish growth (1–2 months post hatch. VIE tags were retained for 1 year and tagging did not interfere with long-term growth and survival. There was no mortality associated with VIE tagging in rag1−/− zebrafish. The VIE tagging system is highly suitable for small-sized zebrafish. When familiar with the procedure, 120 adult zebrafish can be tagged in one hour. It does not increase mortality in adult zebrafish or interfere with growth in juvenile or adult zebrafish.

  3. EnTagRec : an enhanced tag recommendation system for software information sites

    NARCIS (Netherlands)

    Wang, S.; Lo, D.; Vasilescu, B.N.; Serebrenik, A.

    2014-01-01

    Software engineers share experiences with modern technologies by means of software information sites, such as STACK OVERFLOW. These sites allow developers to label posted content, referred to as software objects, with short descriptions, known as tags. However, tags assigned to objects tend to be

  4. Tag-to-Tag Interference Suppression Technique Based on Time Division for RFID

    Directory of Open Access Journals (Sweden)

    Grishma Khadka

    2017-01-01

    Full Text Available Radio-frequency identification (RFID is a tracking technology that enables immediate automatic object identification and rapid data sharing for a wide variety of modern applications using radio waves for data transmission from a tag to a reader. RFID is already well established in technical areas, and many companies have developed corresponding standards and measurement techniques. In the construction industry, effective monitoring of materials and equipment is an important task, and RFID helps to improve monitoring and controlling capabilities, in addition to enabling automation for construction projects. However, on construction sites, there are many tagged objects and multiple RFID tags that may interfere with each other’s communications. This reduces the reliability and efficiency of the RFID system. In this paper, we propose an anti-collision algorithm for communication between multiple tags and a reader. In order to suppress interference signals from multiple neighboring tags, the proposed algorithm employs the time-division (TD technique, where tags in the interrogation zone are assigned a specific time slot so that at every instance in time, a reader communicates with tags using the specific time slot. We present representative computer simulation examples to illustrate the performance of the proposed anti-collision technique for multiple RFID tags.

  5. Topical tags vs non-topical tags : Towards a bipartite classification?

    NARCIS (Netherlands)

    Basile, Valerio; Peroni, Silvio; Tamburini, Fabio; Vitali, Fabio

    2015-01-01

    In this paper we investigate whether it is possible to create a computational approach that allows us to distinguish topical tags (i.e. talking about the topic of a resource) and non-topical tags (i.e. describing aspects of a resource that are not related to its topic) in folksonomies, in a way that

  6. Extracting Usage Patterns and the Analysis of Tag Connection Dynamics within Collaborative Tagging Systems

    Directory of Open Access Journals (Sweden)

    Daniel MICAN

    2013-01-01

    Full Text Available Collaborative tagging has become a very popular way of annotation, thanks to the fact that any entity may be labeled by any individual based on his own reason. In this paper we present the results of the case study carried out on the basis of data gathered at different time intervals from the social tagging system developed and implemented on Întelepciune.ro. Analyzing collective data referring to the way in which community members associate different tags, we have observed that between tags, links are formed which become increasingly stable with the passing of time. Following the application of methodology specific to network analysis, we have managed to extract information referring to tag popularity, their influence within the network and the degree to which a tag depends upon another. As such, we have succeeded in determining different semantic structures within the collective tagging system and see their evolution at different stages in time. Furthermore, we have pictured the way in which tag rec-ommendations can be executed and that they can be integrated within recommendation sys-tems. Thus, we will be able to identify experts and trustworthy content based on different cat-egories of interest.

  7. Sequence tagging reveals unexpected modifications in toxicoproteomics

    Science.gov (United States)

    Dasari, Surendra; Chambers, Matthew C.; Codreanu, Simona G.; Liebler, Daniel C.; Collins, Ben C.; Pennington, Stephen R.; Gallagher, William M.; Tabb, David L.

    2010-01-01

    Toxicoproteomic samples are rich in posttranslational modifications (PTMs) of proteins. Identifying these modifications via standard database searching can incur significant performance penalties. Here we describe the latest developments in TagRecon, an algorithm that leverages inferred sequence tags to identify modified peptides in toxicoproteomic data sets. TagRecon identifies known modifications more effectively than the MyriMatch database search engine. TagRecon outperformed state of the art software in recognizing unanticipated modifications from LTQ, Orbitrap, and QTOF data sets. We developed user-friendly software for detecting persistent mass shifts from samples. We follow a three-step strategy for detecting unanticipated PTMs in samples. First, we identify the proteins present in the sample with a standard database search. Next, identified proteins are interrogated for unexpected PTMs with a sequence tag-based search. Finally, additional evidence is gathered for the detected mass shifts with a refinement search. Application of this technology on toxicoproteomic data sets revealed unintended cross-reactions between proteins and sample processing reagents. Twenty five proteins in rat liver showed signs of oxidative stress when exposed to potentially toxic drugs. These results demonstrate the value of mining toxicoproteomic data sets for modifications. PMID:21214251

  8. Electronic tagging and integrated product intelligence

    Science.gov (United States)

    Swerdlow, Martin; Weeks, Brian

    1996-03-01

    The advent of 'intelligent,' electronic data bearing tags is set to revolutionize the way industrial and retail products are identified and tracked throughout their life cycles. The dominant system for unique identification today is the bar code, which is based on printed symbology and regulated by the International Article Numbering Association. Bar codes provide users with significant operational advantages and generate considerable added value to packaging companies, product manufacturers, distributors and retailers, across supply chains in many different sectors, from retailing, to baggage handling and industrial components, e.g., for vehicles or aircraft. Electronic tags offer the potential to: (1) record and store more complex data about the product or any modifications which occur during its life cycle; (2) access (and up-date) stored data in real time in a way which does not involve contact with the product or article; (3) overcome the limitations imposed by systems which rely on line-of-sight access to stored data. Companies are now beginning to consider how electronic data tags can be used, not only to improve the efficiency of their supply chain processes, but also to revolutionize the way they do business. This paper reviews the applications and business opportunities for electronic tags and outlines CEST's strategy for achieving an 'open' standard which will ensure that tags from different vendors can co-exist on an international basis.

  9. Tagging: An Organization Scheme for the Internet

    Directory of Open Access Journals (Sweden)

    Marijke A. Visser

    2010-03-01

    Full Text Available How should the information on the Internet be organized? This question and the possible solutions spark debates among people concerned with how we identify, classify, and retrieve Internet content. This paper discusses the benefits and the controversies of using a tagging system to organize Internet resources. Tagging refers to a classification system where individual Internet users apply labels, or tags, to digital resources. Tagging increased in popularity with the advent of Web 2.0 applications that encourage interaction among users. As more information is available digitally, the challenge to find an organizational system scalable to the Internet will continue to require forward thinking. Trained to ensure access to a range of informational resources, librarians need to be concerned with access to Internet content. Librarians can play a pivotal role by advocating for a system that supports the user at the moment of need. Tagging may just be the necessary system.

  10. War of ontology worlds: mathematics, computer code, or Esperanto?

    Science.gov (United States)

    Rzhetsky, Andrey; Evans, James A

    2011-09-01

    The use of structured knowledge representations-ontologies and terminologies-has become standard in biomedicine. Definitions of ontologies vary widely, as do the values and philosophies that underlie them. In seeking to make these views explicit, we conducted and summarized interviews with a dozen leading ontologists. Their views clustered into three broad perspectives that we summarize as mathematics, computer code, and Esperanto. Ontology as mathematics puts the ultimate premium on rigor and logic, symmetry and consistency of representation across scientific subfields, and the inclusion of only established, non-contradictory knowledge. Ontology as computer code focuses on utility and cultivates diversity, fitting ontologies to their purpose. Like computer languages C++, Prolog, and HTML, the code perspective holds that diverse applications warrant custom designed ontologies. Ontology as Esperanto focuses on facilitating cross-disciplinary communication, knowledge cross-referencing, and computation across datasets from diverse communities. We show how these views align with classical divides in science and suggest how a synthesis of their concerns could strengthen the next generation of biomedical ontologies.

  11. An algorithm, implementation and execution ontology design pattern

    NARCIS (Netherlands)

    Lawrynowicz, A.; Esteves, D.; Panov, P.; Soru, T.; Dzeroski, S.; Vanschoren, J.

    2016-01-01

    This paper describes an ontology design pattern for modeling algorithms, their implementations and executions. This pattern is derived from the research results on data mining/machine learning ontologies, but is more generic. We argue that the proposed pattern will foster the development of

  12. 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

  13. Cross document ontology based information for multimedia retrieval

    NARCIS (Netherlands)

    Reidsma, Dennis; Kuper, Jan; Declerck, T.; Saggion, H.; Cunningham, H.; Ganter, B.; de Moor, A.

    2003-01-01

    This paper describes the MUMIS project, which applies ontology based Information Extraction to improve the results of Information Retrieval in multimedia archives. It makes use of a domain specific ontology, multilingual lexicons and reasoning algorithms to automatically create a semantic annotation

  14. Computing an Ontological Semantics for a Natural Language Fragment

    DEFF Research Database (Denmark)

    Szymczak, Bartlomiej Antoni

    tried to establish a domain independent “ontological semantics” for relevant fragments of natural language. The purpose of this research is to develop methods and systems for taking advantage of formal ontologies for the purpose of extracting the meaning contents of texts. This functionality...

  15. Asouzu's Complementary Ontology as a Foundation for a Viable ...

    African Journals Online (AJOL)

    This paper on “Asouzu's Complementary Ontology as a foundation for a viable Ethic of the Environment”, posits that an ethic of the environment can be seen as viable if it considers the whole of reality as ontologically relevant. This point of view would free environmental ethics of anthropocentric bias and its attendant ...

  16. Design Ontology-Contrasting an empirical and a theoritical approach

    DEFF Research Database (Denmark)

    Ahmed, Saeema; Storga, Mario

    2007-01-01

    This paper presents the result of the research that compares two previous and separate efforts of the authors to develop engineering design ontologies with a longer-term aim to produce a useable and theoretical sound ontology. The research methodology adopted was to examine each of the concepts a...

  17. 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.

  18. 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.

  19. The Ontological Politics of Evidence and Policy Enablement

    Science.gov (United States)

    Carusi, F. Tony; Rawlins, Peter; Ashton, Karen

    2018-01-01

    Ontological politics has received increasing attention within education policy studies, particularly as a support for the notion of policy enactment. While policy enactment offers serious challenges to traditional approaches toward policy implementation, this paper takes up ontological politics as a concept that extends beyond implementation and…

  20. Ontological Choices and the Value-Free Ideal

    NARCIS (Netherlands)

    Ludwig, D.J.

    2015-01-01

    The aim of this article is to argue that ontological choices in scientific practice undermine common formulations of the value-free ideal in science. First, I argue that the truth values of scientific statements depend on ontological choices. For example, statements about entities such as species,

  1. Ontological Choices and the Value-Free Ideal

    NARCIS (Netherlands)

    Ludwig, David

    2016-01-01

    The aim of this article is to argue that ontological choices in scientific practice undermine common formulations of the value-free ideal in science. First, I argue that the truth values of scientific statements depend on ontological choices. For example, statements about entities such as species,

  2. Interpreting XML documents via an RDF schema ontology

    NARCIS (Netherlands)

    Klein, Michel

    2002-01-01

    Many business documents are represented in XML. However XML only describes the structure of data, not its meaning. The meaning of data is required for advanced automated processing, as is envisaged in the "Semantic Web". Ontologies are often used to describe the meaning of data items. Many ontology

  3. Using semantic distances for reasoning with inconsistent ontologies

    NARCIS (Netherlands)

    Huang, Zhisheng; van Harmelen, Frank

    2009-01-01

    Re-using and combining multiple ontologies on the Web is bound to lead to inconsistencies between the combined vocabularies. Even many of the ontologies that are in use today turn out to be inconsistent once some of their implicit knowledge is made explicit. However, robust and efficient methods to

  4. An Ontology for Learning Services on the Shop Floor

    Science.gov (United States)

    Ullrich, Carsten

    2016-01-01

    An ontology expresses a common understanding of a domain that serves as a basis of communication between people or systems, and enables knowledge sharing, reuse of domain knowledge, reasoning and thus problem solving. In Technology-Enhanced Learning, especially in Intelligent Tutoring Systems and Adaptive Learning Environments, ontologies serve as…

  5. Ontology Extraction Tools: An Empirical Study with Educators

    Science.gov (United States)

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

    2012-01-01

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

  6. ExO: An Ontology for Exposure Science

    Science.gov (United States)

    An ontology is a formal representation of knowledge within a domain and typically consists of classes, the properties of those classes, and the relationships between them. Ontologies are critically important for specifying data of interest in a consistent manner, thereby enablin...

  7. The mouse-human anatomy ontology mapping project.

    Science.gov (United States)

    Hayamizu, Terry F; de Coronado, Sherri; Fragoso, Gilberto; Sioutos, Nicholas; Kadin, James A; Ringwald, Martin

    2012-01-01

    The overall objective of the Mouse-Human Anatomy Project (MHAP) was to facilitate the mapping and harmonization of anatomical terms used for mouse and human models by Mouse Genome Informatics (MGI) and the National Cancer Institute (NCI). The anatomy resources designated for this study were the Adult Mouse Anatomy (MA) ontology and the set of anatomy concepts contained in the NCI Thesaurus (NCIt). Several methods and software tools were identified and evaluated, then used to conduct an in-depth comparative analysis of the anatomy ontologies. Matches between mouse and human anatomy terms were determined and validated, resulting in a highly curated set of mappings between the two ontologies that has been used by other resources. These mappings will enable linking of data from mouse and human. As the anatomy ontologies have been expanded and refined, the mappings have been updated accordingly. Insights are presented into the overall process of comparing and mapping between ontologies, which may prove useful for further comparative analyses and ontology mapping efforts, especially those involving anatomy ontologies. Finally, issues concerning further development of the ontologies, updates to the mapping files, and possible additional applications and significance were considered. DATABASE URL: http://obofoundry.org/cgi-bin/detail.cgi?id=ma2ncit.

  8. FML-based ontological agent for healthcare application with diabetes

    NARCIS (Netherlands)

    Acampora, G.; Lee, C.-S.; Wang, M.-H.

    2009-01-01

    It is well-known that classical ontologies are not sufficient to deal with imprecise and vague knowledge. On the other hand, fuzzy ontologies can effectively solve data and knowledge with uncertainty, most importantly, if they are integrated with innovative methods for developing agents’

  9. An ontology design pattern for surface water features

    Science.gov (United States)

    Sinha, Gaurav; Mark, David; Kolas, Dave; Varanka, Dalia; Romero, Boleslo E.; Feng, Chen-Chieh; Usery, E. Lynn; Liebermann, Joshua; Sorokine, Alexandre

    2014-01-01

    Surface water is a primary concept of human experience but concepts are captured in cultures and languages in many different ways. Still, many commonalities exist due to the physical basis of many of the properties and categories. An abstract ontology of surface water features based only on those physical properties of landscape features has the best potential for serving as a foundational domain ontology for other more context-dependent ontologies. The Surface Water ontology design pattern was developed both for domain knowledge distillation and to serve as a conceptual building-block for more complex or specialized surface water ontologies. A fundamental distinction is made in this ontology between landscape features that act as containers (e.g., stream channels, basins) and the bodies of water (e.g., rivers, lakes) that occupy those containers. Concave (container) landforms semantics are specified in a Dry module and the semantics of contained bodies of water in a Wet module. The pattern is implemented in OWL, but Description Logic axioms and a detailed explanation is provided in this paper. The OWL ontology will be an important contribution to Semantic Web vocabulary for annotating surface water feature datasets. Also provided is a discussion of why there is a need to complement the pattern with other ontologies, especially the previously developed Surface Network pattern. Finally, the practical value of the pattern in semantic querying of surface water datasets is illustrated through an annotated geospatial dataset and sample queries using the classes of the Surface Water pattern.

  10. LKIF Core: principled ontology development for the legal domain

    NARCIS (Netherlands)

    Hoekstra, R.; Breuker, J.; Di Bello, M.; Boer, A.; Breuker, J.; Casanovas, P.; Klein, M.C.A.; Francesconi, E.

    2009-01-01

    In this paper we describe a legal core ontology that is part of the Legal Knowledge Interchange Format: a knowledge representation formalism that enables the translation of legal knowledge bases written in different representation formats and formalisms. A legal (core) ontology can play an important

  11. Validating Domain Ontologies: A Methodology Exemplified for Concept Maps

    Science.gov (United States)

    Steiner, Christina M.; Albert, Dietrich

    2017-01-01

    Ontologies play an important role as knowledge domain representations in technology-enhanced learning and instruction. Represented in form of concept maps they are commonly used as teaching and learning material and have the potential to enhance positive educational outcomes. To ensure the effective use of an ontology representing a knowledge…

  12. Ontology mapping specification in description logics for cooperative ...

    African Journals Online (AJOL)

    Furthermore, the resolution of differences among ontologies is necessary to process queries or use web services in distributed heterogeneous environments. Mapping discovery is a key issue to allow efficient resolution of heterogeneity. We develop an architecture for mapping different systems associated with ontologies.

  13. ONTOLOGY-DRIVEN TOOL FOR UTILIZING PROGRAMMING STYLES

    Directory of Open Access Journals (Sweden)

    Nikolay Sidorov

    2017-07-01

    Full Text Available Activities of a programmer will be more effective and the software will be more understandable when within the process of software development, programming styles (standards are used, providing clarity of software texts. Purpose: In this research, we present the tool for the realization of new ontology-based methodology automated reasoning techniques for utilizing programming styles. In particular, we focus on representing programming styles in the form of formal ontologies, and study how description logic reasoner can assist programmers in utilizing programming standards. Our research hypothesis is as follows: ontological representation of programming styles can provide additional benefits over existing approaches in utilizing programmer of programming standards. Our research goal is to develop a tool to support the ontology-based utilizing programming styles. Methods: ontological representation of programming styles; object-oriented programming; ontology-driven utilizing of programming styles. Results: the architecture was obtained and the tool was developed in the Java language, which provide tool support of ontology-driven programming styles application method. On the example of naming of the Java programming language standard, features of implementation and application of the tool are provided. Discussion: application of programming styles in coding of program; lack of automated tools for the processes of programming standards application; tool based on new method of ontology-driven application of programming styles; an example of the implementation of tool architecture for naming rules of the Java language standard.

  14. Spatial cyberinfrastructures, ontologies, and the humanities.

    Science.gov (United States)

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

    2011-04-05

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

  15. Spatial cyberinfrastructures, ontologies, and the humanities

    Science.gov (United States)

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

    2011-01-01

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

  16. Science Fiction and Ontologies of Leadership

    Directory of Open Access Journals (Sweden)

    Jana Vizmuller-Zocco

    2014-12-01

    Full Text Available The role of leadership in science fiction receives a particular analysis which is based on what can be termed transhumanist novels published in Italy between 2008 and 2013. The main purpose of this study is to answer the following question: What happens to (the nature of leadership in a technologically-driven society? Four novels form the backbone of the description of futuristic leadership. The four conclusions drawn from this analysis regarding the nature of leadership in a technologically-driven society point to a much greater need for leadership studies to pay attention to technological advances (and the philosophical underpinnings of, specifically, transhumanism. The impact of nano-bio-technology affecting the role of leaders, followers, goals, alignment, commitment has ontological repercussions on the manner in which (augmented and unaugmented humans deal with each other. If early augmented humans/cyborgs and any other sentient beings are in fact comparable to Giambattista Vico’s brutes, and if his corsi e ricorsi (ebbs and flows of human history can apply to non-human, sentient beings’ history, then the work is cut out for all disciplines, but especially for those which deal with ontologies of leadership.

  17. Amphibious Worlds:Environments, Infrastructures, Ontologies

    Directory of Open Access Journals (Sweden)

    CASPER BRUUN JENSEN

    2017-05-01

    Full Text Available Presently, we are witness to a global intensification of water-related disasters related to flooding, sinking erosion, and drought, reflecting changes in global water circulation, rising sea levels and changing weather patterns. Indeed, water is often the medium through which the message of climate change is delivered. Conventionally, water-related engineering projects have managed amphibious spaces through terrestrial approaches premised on removing or controlling water, for example by land reclamation and drainage. They can be contrasted with amphibious approaches that take water flows as a given and organize life around it––as exemplified by living in floating villages or houses on stilts, using water as a primary mode of transportation, or growing crops in water. Yet, the amphibious is gaining new life, as water seems to be increasingly flowing back into land, everywhere giving rise to emergencies that call for creative response. Thus, urban planners, engineers, and architects devise new infrastructures and models adaptive to environments that are becoming amphibious once again, or for the first time, and people living in watery environments everywhere find ways of adapting to increasingly amphibious circumstances. Doing so, they are contributing to the ongoing ontological transformation of amphibious worlds. This introduction to the thematic collection on “Amphibious Worlds: Environments, Infrastructures, Ontologies,” outlines some of the key issues facing STS and anthropological studies of such worlds, and introduces the papers that follow.

  18. Multicriteria analysis of ontologically represented information

    Science.gov (United States)

    Wasielewska, K.; Ganzha, M.; Paprzycki, M.; Bǎdicǎ, C.; Ivanovic, M.; Lirkov, I.

    2014-11-01

    Our current work concerns the development of a decision support system for the software selection problem. The main idea is to utilize expert knowledge to help the user in selecting the best software / method / computational resource to solve a computational problem. Obviously, this involves multicriterial decision making and the key open question is: which method to choose. The context of the work is provided by the Agents in Grid (AiG) project, where the software selection (and thus multicriterial analysis) is to be realized when all information concerning the problem, the hardware and the software is ontologically represented. Initially, we have considered the Analytical Hierarchy Process (AHP), which is well suited for the hierarchical data structures (e.g., such that have been formulated in terms of ontologies). However, due to its well-known shortcomings, we have decided to extend our search for the multicriterial analysis method best suited for the problem in question. In this paper we report results of our search, which involved: (i) TOPSIS (Technique for Order Preference by Similarity to Ideal Solution), (ii) PROMETHEE, and (iii) GRIP (Generalized Regression with Intensities of Preference). We also briefly argue why other methods have not been considered as valuable candidates.

  19. PERSONALIZATION SISTEM E-LEARNING BERBASIS ONTOLOGY

    Directory of Open Access Journals (Sweden)

    Ahmad Ashari

    2010-11-01

    Full Text Available Personalization of Ontology Based E-learning System. Today, a form of technology known as Web 2.0 thatthoroughly supports web-to-web interactions is present. Interactions, such as information sharing in the forms ofdocument sharing (slideshare, picture sharing (flickr, video sharing (youtube, Wikis, and online networking (weblogand web-forum are principally accomodating community empowerment services. These factors cause the appearanceof social interaction through Internet as well as learning interaction and anywhere-anytime training which is recentlycalled e-Learning. Basically, e-Learning needs a self-employed learning method and learning habits that emphasize onthe learner as the most important role. However, e-learning system which is expected to boost the intensity of selfemployedlearning is uncapable to represent the importance. This is proven with the current e-Learning system inIndonesia that only accomodates the delivery of learning materials identical to all active learners, ignores the cognitiveaspects and does not offer any approach or experience of interactive self-learning and disregards the aspect of users’ability to adapt. The proposed e-learning system which is Web 2.0-based utilizes ontology as the representation ofmeaning of knowledge formed by the learner.

  20. Ontology patterns for complex topographic feature yypes

    Science.gov (United States)

    Varanka, Dalia E.

    2011-01-01

    Complex feature types are defined as integrated relations between basic features for a shared meaning or concept. The shared semantic concept is difficult to define in commonly used geographic information systems (GIS) and remote sensing technologies. The role of spatial relations between complex feature parts was recognized in early GIS literature, but had limited representation in the feature or coverage data models of GIS. Spatial relations are more explicitly specified in semantic technology. In this paper, semantics for topographic feature ontology design patterns (ODP) are developed as data models for the representation of complex features. In the context of topographic processes, component assemblages are supported by resource systems and are found on local landscapes. The topographic ontology is organized across six thematic modules that can account for basic feature types, resource systems, and landscape types. Types of complex feature attributes include location, generative processes and physical description. Node/edge networks model standard spatial relations and relations specific to topographic science to represent complex features. To demonstrate these concepts, data from The National Map of the U. S. Geological Survey was converted and assembled into ODP.