WorldWideScience

Sample records for formal ontologies meet

  1. 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...

  2. 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.

  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. 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.

  5. Representations of spacetime: Formalism and ontological commitment

    Science.gov (United States)

    Bain, Jonathan Stanley

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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. An Ontology for a TripTych Formal Software Development

    DEFF Research Database (Denmark)

    Bjørner, Dines

    2003-01-01

    An ontology, ie., a formalised set of strongly interrelated definitions, is given for an approach to software development that spans domain engineering, requirements engineering and software design - and which is otherwise based on a judicious use of both informal and formal, mathematics-based te......An ontology, ie., a formalised set of strongly interrelated definitions, is given for an approach to software development that spans domain engineering, requirements engineering and software design - and which is otherwise based on a judicious use of both informal and formal, mathematics...

  11. Regaining the Square of Opposition in Formal Ontology Development

    DEFF Research Database (Denmark)

    Nilsson, Jørgen Fischer

    2014-01-01

    be held simply in the case that "all P are Q" does not hold. These default rules are routinely adopted in ontology development without mentioning. Appealing to these conventions, the 4 sentence forms in the square are effectively made at disposal. We discuss a first order metalogical formalization...... of the 4 sentence forms with classes reified as individual constants elucidating the logical relationships between the sentence forms. Our formalization appeals to non-provability. Non-provability incurs non-monotonicity, implying that extension of an ontology with additional subclass relationships may...

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

    DEFF Research Database (Denmark)

    Christensen, Jesper Vinther

    2007-01-01

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

  13. Towards a Formal Ontology of Information. Selected Ideas of K. Turek

    Directory of Open Access Journals (Sweden)

    Roman Krzanowski

    2016-12-01

    Full Text Available There are many ontologies of the world or of specific phenomena such as time, matter, space, and quantum mechanics1. However, ontologies of information are rather rare. One of the reasons behind this is that information is most frequently associated with communication and computing, and not with ‘the furniture of the world’. But what would be the nature of an ontology of information? For it to be of significant import it should be amenable to formalization in a logico-grammatical formalism. A candidate ontology satisfying such a requirement can be found in some of the ideas of K. Turek, presented in this paper. Turek outlines the ontology of information conceived of as a part of nature, and provides the ‘missing link’ to the Z axiomatic set theory, offering a proposal for developing a formal ontology of information both in its philosophical and logicogrammatical representations.

  14. Generative Graph Grammar of Neo-Vaiśeṣika Formal Ontology (NVFO)

    Science.gov (United States)

    Tavva, Rajesh; Singh, Navjyoti

    NLP applications for Sanskrit so far work within computational paradigm of string grammars. However, to compute 'meanings', as in traditional śā bdabodha prakriyā-s, there is a need to develop suitable graph grammars. Ontological structures are fundamentally graphs. We work within the formal framework of Neo-Vaiśeṣika Formal Ontology (NVFO) to propose a generative graph grammar. The proposed formal grammar only produces well-formed graphs that can be readily interpreted in accordance with Vaiśeṣ ika Ontology. We show that graphs not permitted by Vaiśeṣ ika ontology are not generated by the proposed grammar. Further, we write Interpreter of these graphical structures. This creates computational environment which can be deployed for writing computational applications of Vaiśeṣ ika ontology. We illustrate how this environment can be used to create applications like computing śā bdabodha of sentences.

  15. A formal ontological perspective on the behaviors and functions of technical artifacts

    NARCIS (Netherlands)

    Borgo, S.; Carrara, M.; Garbacz, P.; Vermaas, P.E.

    2008-01-01

    In this paper we present a formal characterization of the engineering concepts of behavior and function of technical artifacts. We capture the meanings that engineers attach to these concepts by formalizing, within the formal ontology DOLCE, the five meanings of artifact behavior and the two

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

    KAUST Repository

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

    2015-01-01

    underlying biophysical basis is currently in its infancy. In this commentary, we discuss some of the fundamental problems in designing and using behaviour ontologies, and present some of the best developed tools in this domain. © 2015 Springer Science

  17. Combining Archetypes, Ontologies and Formalization Enables Automated Computation of Quality Indicators.

    Science.gov (United States)

    Legaz-García, María Del Carmen; Dentler, Kathrin; Fernández-Breis, Jesualdo Tomás; Cornet, Ronald

    2017-01-01

    ArchMS is a framework that represents clinical information and knowledge using ontologies in OWL, which facilitates semantic interoperability and thereby the exploitation and secondary use of clinical data. However, it does not yet support the automated assessment of quality of care. CLIF is a stepwise method to formalize quality indicators. The method has been implemented in the CLIF tool which supports its users in generating computable queries based on a patient data model which can be based on archetypes. To enable the automated computation of quality indicators using ontologies and archetypes, we tested whether ArchMS and the CLIF tool can be integrated. We successfully automated the process of generating SPARQL queries from quality indicators that have been formalized with CLIF and integrated them into ArchMS. Hence, ontologies and archetypes can be combined for the execution of formalized quality indicators.

  18. Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

    Directory of Open Access Journals (Sweden)

    Mungall Christopher J

    2010-10-01

    Full Text Available Abstract Background The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all species, there are inherent taxon specificities in some branches. For example, the process 'lactation' is specific to mammals and the location 'mitochondrion' is specific to eukaryotes. The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation. Results We have formalized the taxonomic constraints implicit in some GO classes, and specified these at various levels in the ontology. We have also developed an inference system that can be used to check for violations of these constraints in annotations. Using the constraints in conjunction with the inference system, we have detected and removed errors in annotations and improved the structure of the ontology. Conclusions Detection of inconsistencies in taxon-specificity enables gradual improvement of the ontologies, the annotations, and the formalized constraints. This is progressively improving the quality of our data. The full system is available for download, and new constraints or proposed changes to constraints can be submitted online at https://sourceforge.net/tracker/?atid=605890&group_id=36855.

  19. An Ontology for State Analysis: Formalizing the Mapping to SysML

    Science.gov (United States)

    Wagner, David A.; Bennett, Matthew B.; Karban, Robert; Rouquette, Nicolas; Jenkins, Steven; Ingham, Michel

    2012-01-01

    State Analysis is a methodology developed over the last decade for architecting, designing and documenting complex control systems. Although it was originally conceived for designing robotic spacecraft, recent applications include the design of control systems for large ground-based telescopes. The European Southern Observatory (ESO) began a project to design the European Extremely Large Telescope (E-ELT), which will require coordinated control of over a thousand articulated mirror segments. The designers are using State Analysis as a methodology and the Systems Modeling Language (SysML) as a modeling and documentation language in this task. To effectively apply the State Analysis methodology in this context it became necessary to provide ontological definitions of the concepts and relations in State Analysis and greater flexibility through a mapping of State Analysis into a practical extension of SysML. The ontology provides the formal basis for verifying compliance with State Analysis semantics including architectural constraints. The SysML extension provides the practical basis for applying the State Analysis methodology with SysML tools. This paper will discuss the method used to develop these formalisms (the ontology), the formalisms themselves, the mapping to SysML and approach to using these formalisms to specify a control system and enforce architectural constraints in a SysML model.

  20. Development of Smart Sensors System Based on Formal Concept Analysis and Ontology Model

    Directory of Open Access Journals (Sweden)

    Hongsheng Xu

    2013-06-01

    Full Text Available The smart sensor is the product of the combination of one or more sensitive components, precision analog circuits, digital circuits, microprocessor, communication interface, intelligent software systems and hardware integration in a packaging component. Formal concept analysis is from the given data to automatically extract the classification relationship between the entire hidden concept and concept, formation of concept model. Ontology is a set of relations between concepts of the specific domain and concept, and it can effectively express the general knowledge of specific field. The paper proposes development of smart sensors system based on formal concept analysis and ontology model. Smart sensor is a micro processor, sensor with information detection, information processing, information memory, logical thinking and judging function. The methods can improve the effect of the smart sensors.

  1. Top-level categories of constitutively organized material entities--suggestions for a formal top-level ontology.

    Directory of Open Access Journals (Sweden)

    Lars Vogt

    2011-04-01

    Full Text Available Application oriented ontologies are important for reliably communicating and managing data in databases. Unfortunately, they often differ in the definitions they use and thus do not live up to their potential. This problem can be reduced when using a standardized and ontologically consistent template for the top-level categories from a top-level formal foundational ontology. This would support ontological consistency within application oriented ontologies and compatibility between them. The Basic Formal Ontology (BFO is such a foundational ontology for the biomedical domain that has been developed following the single inheritance policy. It provides the top-level template within the Open Biological and Biomedical Ontologies Foundry. If it wants to live up to its expected role, its three top-level categories of material entity (i.e., 'object', 'fiat object part', 'object aggregate' must be exhaustive, i.e. every concrete material entity must instantiate exactly one of them.By systematically evaluating all possible basic configurations of material building blocks we show that BFO's top-level categories of material entity are not exhaustive. We provide examples from biology and everyday life that demonstrate the necessity for two additional categories: 'fiat object part aggregate' and 'object with fiat object part aggregate'. By distinguishing topological coherence, topological adherence, and metric proximity we furthermore provide a differentiation of clusters and groups as two distinct subcategories for each of the three categories of material entity aggregates, resulting in six additional subcategories of material entity.We suggest extending BFO to incorporate two additional categories of material entity as well as two subcategories for each of the three categories of material entity aggregates. With these additions, BFO would exhaustively cover all top-level types of material entity that application oriented ontologies may use as templates. Our

  2. Dealing with Resilience Conceptualisation. Formal Ontologies as a Tool for Implementation of Intelligent Geographic Information Systems

    Directory of Open Access Journals (Sweden)

    Giampiero Lombardini

    2014-05-01

    Full Text Available The paper addresses the issue of the representation of the concept of resilience (urban, environmental and landscape resilience in the context of geographic information systems. In the current technical and scientific debate, resilience is configured as an intrinsic property of a system to switch from one equilibrium state to another without losing its basic internal structure, also definable in terms of "identity." The paths to success or stable growth as well as those of continuing and recursive crisis, although already explained in macroeconomic terms through the mechanisms of accumulation and multiplication (cumulative advantage, are also interpreted in terms of resilience. So, in the field of studies on spatial planning, the concept of resilience became particularly significant in an era characterized by great instability of social systems, deep economic and environmental crisis. In the process of urban and regional planning, conceive the development of an urban region in terms of resilience means using the logic of complex systems and then adapt in this way their methods of knowledge representation. The concept of resilience is multi-dimensional and vague, so its conceptualization is complex. The formal ontologies can be a useful tool to orient geographic information systems towards more complex forms of knowledge representation and to adapt them to the requirements of logic and formal complex systems, such as today's urban regions.

  3. The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions.

    Science.gov (United States)

    Wirkner, Christian S; Göpel, Torben; Runge, Jens; Keiler, Jonas; Klussmann-Fricke, Bastian-Jesper; Huckstorf, Katarina; Scholz, Stephan; Mikó, István; J Yoder, Matthew; Richter, Stefan

    2017-09-01

    Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the "linguistic problem of morphology", concerns the usage of terminology and also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use of phenotypic data in systematics and evolutionary biology. We therefore argue, that for morphological descriptions, the basis of all systematic and evolutionary interpretations, ontologies need to be utilized which are based exclusively on structural qualities/properties and which in no case include statements about homology and/or function. Statements about homology and function constitute interpretations on a different or higher level. Based on these "anatomy ontologies", further ontological dimensions (e.g., referring to functional properties or homology) may be exerted for a broad use in evolutionary phenomics. To this end we present the first organ-based ontology for the most species-rich animal group, the Arthropoda. Our Ontology of Arthropod Circulatory Systems (OArCS) contains a comprehensive collection of 383 terms (i.e., labels) tied to 296 concepts (i.e., definitions) collected from the literature on phenotypic aspects of circulatory organ features in arthropods. All of the concepts used in OArCS are based exclusively on structural features, and in the context of the ontology are independent of homology and functional assumptions. We cannot rule out that in some cases, terms are used which in traditional usage and previous accounts might have implied homology and/or function (e.g. heart, sternal artery). Concepts are composed of descriptive elements that are used to classify observed instances into the organizational framework of the

  4. 28 CFR 16.203 - Closed meetings-Formal procedure.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Closed meetings-Formal procedure. 16.203 Section 16.203 Judicial Administration DEPARTMENT OF JUSTICE PRODUCTION OR DISCLOSURE OF MATERIAL OR... involvement of any person in the commission of a crime, but only to the extent that the production of such...

  5. The ontological turn meets the certainty of death.

    Science.gov (United States)

    McDonald, Maryon

    2017-08-01

    The 'ontological turn' involves some anthropological points of long standing but the approaches recently coordinated into this turn have been presented as a 'call to arms', as shaking up 'mono-realist singularities' and as inherently political. This fighting talk has no doubt made important contributions to anthropology and insights from the ontological turn can help in anthropological understandings of medical practices. However, this paper contends that this helpfulness is also limited and that a call to arms may be inappropriate. This point is made through an ethnographic understanding of medical concern about the diagnosis of death.

  6. Combining Archetypes, Ontologies and Formalization Enables Automated Computation of Quality Indicators

    NARCIS (Netherlands)

    Legaz-García, María Del Carmen; Dentler, Kathrin; Fernández-Breis, Jesualdo Tomás; Cornet, Ronald

    2017-01-01

    ArchMS is a framework that represents clinical information and knowledge using ontologies in OWL, which facilitates semantic interoperability and thereby the exploitation and secondary use of clinical data. However, it does not yet support the automated assessment of quality of care. CLIF is a

  7. An Approach to Formalizing Ontology Driven Semantic Integration: Concepts, Dimensions and Framework

    Science.gov (United States)

    Gao, Wenlong

    2012-01-01

    The ontology approach has been accepted as a very promising approach to semantic integration today. However, because of the diversity of focuses and its various connections to other research domains, the core concepts, theoretical and technical approaches, and research areas of this domain still remain unclear. Such ambiguity makes it difficult to…

  8. Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature.

    Science.gov (United States)

    Arguello Casteleiro, Mercedes; Demetriou, George; Read, Warren; Fernandez Prieto, Maria Jesus; Maroto, Nava; Maseda Fernandez, Diego; Nenadic, Goran; Klein, Julie; Keane, John; Stevens, Robert

    2018-04-12

    Automatic identification of term variants or acceptable alternative free-text terms for gene and protein names from the millions of biomedical publications is a challenging task. Ontologies, such as the Cardiovascular Disease Ontology (CVDO), capture domain knowledge in a computational form and can provide context for gene/protein names as written in the literature. This study investigates: 1) if word embeddings from Deep Learning algorithms can provide a list of term variants for a given gene/protein of interest; and 2) if biological knowledge from the CVDO can improve such a list without modifying the word embeddings created. We have manually annotated 105 gene/protein names from 25 PubMed titles/abstracts and mapped them to 79 unique UniProtKB entries corresponding to gene and protein classes from the CVDO. Using more than 14 M PubMed articles (titles and available abstracts), word embeddings were generated with CBOW and Skip-gram. We setup two experiments for a synonym detection task, each with four raters, and 3672 pairs of terms (target term and candidate term) from the word embeddings created. For Experiment I, the target terms for 64 UniProtKB entries were those that appear in the titles/abstracts; Experiment II involves 63 UniProtKB entries and the target terms are a combination of terms from PubMed titles/abstracts with terms (i.e. increased context) from the CVDO protein class expressions and labels. In Experiment I, Skip-gram finds term variants (full and/or partial) for 89% of the 64 UniProtKB entries, while CBOW finds term variants for 67%. In Experiment II (with the aid of the CVDO), Skip-gram finds term variants for 95% of the 63 UniProtKB entries, while CBOW finds term variants for 78%. Combining the results of both experiments, Skip-gram finds term variants for 97% of the 79 UniProtKB entries, while CBOW finds term variants for 81%. This study shows performance improvements for both CBOW and Skip-gram on a gene/protein synonym detection task by

  9. Formalized Conflicts Detection Based on the Analysis of Multiple Emails: An Approach Combining Statistics and Ontologies

    Science.gov (United States)

    Zakaria, Chahnez; Curé, Olivier; Salzano, Gabriella; Smaïli, Kamel

    In Computer Supported Cooperative Work (CSCW), it is crucial for project leaders to detect conflicting situations as early as possible. Generally, this task is performed manually by studying a set of documents exchanged between team members. In this paper, we propose a full-fledged automatic solution that identifies documents, subjects and actors involved in relational conflicts. Our approach detects conflicts in emails, probably the most popular type of documents in CSCW, but the methods used can handle other text-based documents. These methods rely on the combination of statistical and ontological operations. The proposed solution is decomposed in several steps: (i) we enrich a simple negative emotion ontology with terms occuring in the corpus of emails, (ii) we categorize each conflicting email according to the concepts of this ontology and (iii) we identify emails, subjects and team members involved in conflicting emails using possibilistic description logic and a set of proposed measures. Each of these steps are evaluated and validated on concrete examples. Moreover, this approach's framework is generic and can be easily adapted to domains other than conflicts, e.g. security issues, and extended with operations making use of our proposed set of measures.

  10. 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…

  11. Artificial grammar learning meets formal language theory: an overview

    Science.gov (United States)

    Fitch, W. Tecumseh; Friederici, Angela D.

    2012-01-01

    Formal language theory (FLT), part of the broader mathematical theory of computation, provides a systematic terminology and set of conventions for describing rules and the structures they generate, along with a rich body of discoveries and theorems concerning generative rule systems. Despite its name, FLT is not limited to human language, but is equally applicable to computer programs, music, visual patterns, animal vocalizations, RNA structure and even dance. In the last decade, this theory has been profitably used to frame hypotheses and to design brain imaging and animal-learning experiments, mostly using the ‘artificial grammar-learning’ paradigm. We offer a brief, non-technical introduction to FLT and then a more detailed analysis of empirical research based on this theory. We suggest that progress has been hampered by a pervasive conflation of distinct issues, including hierarchy, dependency, complexity and recursion. We offer clarifications of several relevant hypotheses and the experimental designs necessary to test them. We finally review the recent brain imaging literature, using formal languages, identifying areas of convergence and outstanding debates. We conclude that FLT has much to offer scientists who are interested in rigorous empirical investigations of human cognition from a neuroscientific and comparative perspective. PMID:22688631

  12. Perceptions of Civility for Mobile Phone Use in Formal and Informal Meetings

    Science.gov (United States)

    Washington, Melvin C.; Okoro, Ephraim A.; Cardon, Peter W.

    2014-01-01

    We report our survey research about what American business professionals consider appropriate or civil mobile phone behavior during formal and informal meetings. The findings come from two of our recent research studies: an open-ended survey of 204 employees at a beverage distributor on the East Coast and a nationwide, random-sample survey of 350…

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

    Directory of Open Access Journals (Sweden)

    Hakenberg Jörg

    2009-01-01

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

  14. Ontologies vs. Classification Systems

    DEFF Research Database (Denmark)

    Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

    2009-01-01

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

  15. Scenario testing using formal ontologies

    CSIR Research Space (South Africa)

    Harmse, HF

    2014-09-01

    Full Text Available One of the challenges in the Software Development Life Cycle (SDLC) is to ensure that the requirements that drive the development of a software system are correct. However, establishing unambiguous and error-free requirements is not a trivial...

  16. 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....

  17. A document-centric approach for developing the tolAPC ontology.

    Science.gov (United States)

    Blfgeh, Aisha; Warrender, Jennifer; Hilkens, Catharien M U; Lord, Phillip

    2017-11-28

    There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometimes, an understanding of the philosophical background. In practice, it is very rare that an ontology can be completed by a single person, as they are unlikely to combine all of these skills. So people with these skills must collaborate. One solution to this is to use face-to-face meetings, but these can be expensive and time-consuming for teams that are not co-located. Remote collaboration is possible, of course, but one difficulty here is that domain specialists use a wide-variety of different "formalisms" to represent and share their data - by the far most common, however, is the "office file" either in the form of a word-processor document or a spreadsheet. Here we describe the development of an ontology of immunological cell types; this was initially developed by domain specialists using an Excel spreadsheet for collaboration. We have transformed this spreadsheet into an ontology using highly-programmatic and pattern-driven ontology development. Critically, the spreadsheet remains part of the source for the ontology; the domain specialists are free to update it, and changes will percolate to the end ontology. We have developed a new ontology describing immunological cell lines built by instantiating ontology design patterns written programmatically, using values from a spreadsheet catalogue. This method employs a spreadsheet that was developed by domain experts. The spreadsheet is unconstrained in its usage and can be freely updated resulting in a new ontology. This provides a general methodology for ontology development using data generated by domain specialists.

  18. The role of architecture and ontology for interoperability.

    Science.gov (United States)

    Blobel, Bernd; González, Carolina; Oemig, Frank; Lopéz, Diego; Nykänen, Pirkko; Ruotsalainen, Pekka

    2010-01-01

    Turning from organization-centric to process-controlled or even to personalized approaches, advanced healthcare settings have to meet special interoperability challenges. eHealth and pHealth solutions must assure interoperability between actors cooperating to achieve common business objectives. Hereby, the interoperability chain also includes individually tailored technical systems, but also sensors and actuators. For enabling corresponding pervasive computing and even autonomic computing, individualized systems have to be based on an architecture framework covering many domains, scientifically managed by specialized disciplines using their specific ontologies in a formalized way. Therefore, interoperability has to advance from a communication protocol to an architecture-centric approach mastering ontology coordination challenges.

  19. 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.

  20. 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

  1. 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.

  2. 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…

  3. 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.

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

    Science.gov (United States)

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

    2017-01-01

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

  5. 78 FR 19492 - Draft Guidance for Industry on Formal Meetings Between FDA and Biosimilar Biological Product...

    Science.gov (United States)

    2013-04-01

    ..., or Office of Communication, Outreach, and Development (HFM-40), Center for Biologics Evaluation and... biological product. This draft guidance describes the Agency's current thinking on how it intends to... review of biosimilar biological products. Because these meetings often will represent critical points in...

  6. 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...

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. Supplementary Material for: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

    KAUST Repository

    Hoehndorf, Robert; AlShahrani, Mona; Gkoutos, Georgios; Gosline, George; Groom, Quentin; Hamann, Thomas; Kattge, Jens; Oliveira, Sylvia de; Schmidt, Marco; Sierra, Soraya; Smets, Erik; Vos, Rutger; Weiland, Claus

    2016-01-01

    traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based

  12. Conference Scene: epigenetics eh! The first formal meeting of the Canadian epigenetics community.

    Science.gov (United States)

    Underhill, Alan; Hendzel, Michael J

    2011-08-01

    In recognition of Canada's longstanding interest in epigenetics - and a particular linguistic interjection - the inaugural 'Epigenetics, Eh!' conference was held between 4-7 May 2011 in London, Ontario. The meeting struck an excellent balance between Canadian and international leaders in epigenetic research while also providing a venue to showcase up-and-coming talent. Almost without exception, presentations touched on the wide-ranging and severe consequences of epigenetic dysfunction, as well as current and emerging therapeutic opportunities. While gaining a deeper understanding of how DNA and histone modifications, together with multiple classes of ncRNAs, act to functionalize our genome, participants were also provided with a glimpse of the astounding complexity of chromatin structure, challenging existing dogma.

  13. 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

  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. 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

  16. 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…

  17. SUGOI: automated ontology interchangeability

    CSIR Research Space (South Africa)

    Khan, ZC

    2015-04-01

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

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. Conceptual Model Formalization in a Semantic Interoperability Service Framework: Transforming Relational Database Schemas to OWL.

    Science.gov (United States)

    Bravo, Carlos; Suarez, Carlos; González, Carolina; López, Diego; Blobel, Bernd

    2014-01-01

    Healthcare information is distributed through multiple heterogeneous and autonomous systems. Access to, and sharing of, distributed information sources are a challenging task. To contribute to meeting this challenge, this paper presents a formal, complete and semi-automatic transformation service from Relational Databases to Web Ontology Language. The proposed service makes use of an algorithm that allows to transform several data models of different domains by deploying mainly inheritance rules. The paper emphasizes the relevance of integrating the proposed approach into an ontology-based interoperability service to achieve semantic interoperability.

  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. 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...

  6. 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...

  7. 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.

  8. 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

  9. Aber-OWL: a framework for ontology-based data access in biology

    KAUST Repository

    Hoehndorf, Robert

    2015-01-28

    Background: Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within these ontologies relies on the use of automated reasoning. Results: We have developed the Aber-OWL infrastructure that provides reasoning services for bio-ontologies. Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature. Aber-OWL is freely available at http://aber-owl.net. Conclusions: Aber-OWL provides a framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies. When using Aber-OWL, access to ontologies and data annotated with them is not merely based on class names or identifiers but rather on the knowledge the ontologies contain and the inferences that can be drawn from it.

  10. Beyond formalism

    Science.gov (United States)

    Denning, Peter J.

    1991-01-01

    The ongoing debate over the role of formalism and formal specifications in software features many speakers with diverse positions. Yet, in the end, they share the conviction that the requirements of a software system can be unambiguously specified, that acceptable software is a product demonstrably meeting the specifications, and that the design process can be carried out with little interaction between designers and users once the specification has been agreed to. This conviction is part of a larger paradigm prevalent in American management thinking, which holds that organizations are systems that can be precisely specified and optimized. This paradigm, which traces historically to the works of Frederick Taylor in the early 1900s, is no longer sufficient for organizations and software systems today. In the domain of software, a new paradigm, called user-centered design, overcomes the limitations of pure formalism. Pioneered in Scandinavia, user-centered design is spreading through Europe and is beginning to make its way into the U.S.

  11. 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].

  12. 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.

  13. Youth Clubs as Spaces of Non-Formal Learning: Professional Idealism Meets the Spatiality Experienced by Young People in Finland

    Science.gov (United States)

    Kiilakoski, Tomi; Kivijärvi, Antti

    2015-01-01

    For many young people, youth clubs constitute a key instrument for learning outside the school curriculum. In this article, we scrutinise Finnish youth clubs empirically as spaces of non-formal learning from the perspectives of both professional youth workers and young people themselves. We propose that youth workers tend to present an educational…

  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. 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...

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

    Science.gov (United States)

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

    2011-05-17

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

  17. Elements for an Ontology of Care in the Field of Artificial Intelligence.

    Science.gov (United States)

    González Aguña, Alexandra; Fernández Batalla, Marta; Cercas Duque, Adriana; Herrero Jaén, Sara; Monsalvo San Macario, Enrique; Jiménez Rodríguez, Ma Lourdes; Santamaría García, José Ma; Ramírez Sánchez, Sylvia Claudine; Vialart Vidal, Niurka; Condor Camara, Daniel Flavio

    2018-01-01

    An ontology of care is a formal, explicit specification of a shared conceptualization. Constructing an ontology is a process that requires four elements: knowledge object, subject that knows, knowledge operation and result. These elements configure theframework to generate ontologies that can be used in Artificial Intelligence systems for care.

  18. 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.

  19. 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

  20. ACL2 Meets the GPU: Formalizing a CUDA-based Parallelizable All-Pairs Shortest Path Algorithm in ACL2

    Directory of Open Access Journals (Sweden)

    David S. Hardin

    2013-04-01

    Full Text Available As Graphics Processing Units (GPUs have gained in capability and GPU development environments have matured, developers are increasingly turning to the GPU to off-load the main host CPU of numerically-intensive, parallelizable computations. Modern GPUs feature hundreds of cores, and offer programming niceties such as double-precision floating point, and even limited recursion. This shift from CPU to GPU, however, raises the question: how do we know that these new GPU-based algorithms are correct? In order to explore this new verification frontier, we formalized a parallelizable all-pairs shortest path (APSP algorithm for weighted graphs, originally coded in NVIDIA's CUDA language, in ACL2. The ACL2 specification is written using a single-threaded object (stobj and tail recursion, as the stobj/tail recursion combination yields the most straightforward translation from imperative programming languages, as well as efficient, scalable executable specifications within ACL2 itself. The ACL2 version of the APSP algorithm can process millions of vertices and edges with little to no garbage generation, and executes at one-sixth the speed of a host-based version of APSP coded in C – a very respectable result for a theorem prover. In addition to formalizing the APSP algorithm (which uses Dijkstra's shortest path algorithm at its core, we have also provided capability that the original APSP code lacked, namely shortest path recovery. Path recovery is accomplished using a secondary ACL2 stobj implementing a LIFO stack, which is proven correct. To conclude the experiment, we ported the ACL2 version of the APSP kernels back to C, resulting in a less than 5% slowdown, and also performed a partial back-port to CUDA, which, surprisingly, yielded a slight performance increase.

  1. 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…

  2. Development and Evaluation of an Ontology for Guiding Appropriate Antibiotic Prescribing

    Science.gov (United States)

    Furuya, E. Yoko; Kuperman, Gilad J.; Cimino, James J.; Bakken, Suzanne

    2011-01-01

    Objectives To develop and apply formal ontology creation methods to the domain of antimicrobial prescribing and to formally evaluate the resulting ontology through intrinsic and extrinsic evaluation studies. Methods We extended existing ontology development methods to create the ontology and implemented the ontology using Protégé-OWL. Correctness of the ontology was assessed using a set of ontology design principles and domain expert review via the laddering technique. We created three artifacts to support the extrinsic evaluation (set of prescribing rules, alerts and an ontology-driven alert module, and a patient database) and evaluated the usefulness of the ontology for performing knowledge management tasks to maintain the ontology and for generating alerts to guide antibiotic prescribing. Results The ontology includes 199 classes, 10 properties, and 1,636 description logic restrictions. Twenty-three Semantic Web Rule Language rules were written to generate three prescribing alerts: 1) antibiotic-microorganism mismatch alert; 2) medication-allergy alert; and 3) non-recommended empiric antibiotic therapy alert. The evaluation studies confirmed the correctness of the ontology, usefulness of the ontology for representing and maintaining antimicrobial treatment knowledge rules, and usefulness of the ontology for generating alerts to provide feedback to clinicians during antibiotic prescribing. Conclusions This study contributes to the understanding of ontology development and evaluation methods and addresses one knowledge gap related to using ontologies as a clinical decision support system component—a need for formal ontology evaluation methods to measure their quality from the perspective of their intrinsic characteristics and their usefulness for specific tasks. PMID:22019377

  3. 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)

  4. 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

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

    Science.gov (United States)

    Tahar, Kais; Xu, Jie; Herre, Heinrich

    2017-01-01

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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Formal matrices

    CERN Document Server

    Krylov, Piotr

    2017-01-01

    This monograph is a comprehensive account of formal matrices, examining homological properties of modules over formal matrix rings and summarising the interplay between Morita contexts and K theory. While various special types of formal matrix rings have been studied for a long time from several points of view and appear in various textbooks, for instance to examine equivalences of module categories and to illustrate rings with one-sided non-symmetric properties, this particular class of rings has, so far, not been treated systematically. Exploring formal matrix rings of order 2 and introducing the notion of the determinant of a formal matrix over a commutative ring, this monograph further covers the Grothendieck and Whitehead groups of rings. Graduate students and researchers interested in ring theory, module theory and operator algebras will find this book particularly valuable. Containing numerous examples, Formal Matrices is a largely self-contained and accessible introduction to the topic, assuming a sol...

  11. 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.

  12. Drug target ontology to classify and integrate drug discovery data

    DEFF Research Database (Denmark)

    Lin, Yu; Mehta, Saurabh; Küçük-McGinty, Hande

    2017-01-01

    using a new software tool to auto-generate most axioms from a database while supporting manual knowledge acquisition. A modular, hierarchical implementation facilitate ontology development and maintenance and makes use of various external ontologies, thus integrating the DTO into the ecosystem...... of biomedical ontologies. As a formal OWL-DL ontology, DTO contains asserted and inferred axioms. Modeling data from the Library of Integrated Network-based Cellular Signatures (LINCS) program illustrates the potential of DTO for contextual data integration and nuanced definition of important drug target...... characteristics. DTO has been implemented in the IDG user interface Portal, Pharos and the TIN-X explorer of protein target disease relationships. CONCLUSIONS: DTO was built based on the need for a formal semantic model for druggable targets including various related information such as protein, gene, protein...

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

    International Nuclear Information System (INIS)

    Buschmann, J.E.

    1988-01-01

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

  14. 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

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

    Directory of Open Access Journals (Sweden)

    Bernardo Gonçalves

    2009-04-01

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

  16. 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.

  17. Constructive Ontology Engineering

    Science.gov (United States)

    Sousan, William L.

    2010-01-01

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

  18. 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.

  19. 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.

  20. CoordSS: An Ontology Framework for Heterogeneous Networks Experimentation

    Directory of Open Access Journals (Sweden)

    V. Nejkovic

    2016-11-01

    Full Text Available Experimenting with HetNets environments is of importance because of the role that such environments have in next-generation cellular networks. In this paper, the CoordSS ontology experimentation framework is proposed with an aim to support experimenting with HetNets environments on wireless networking testbeds. In the framework, domain and system ontologies are adopted for formal representation of the knowledge about the context of the problem. This paper outlines implementation details of ontologies in the CoordSS experimentation framework. The synergy between semantic and cognitive computing is introduced as the theoretical foundation of the paper.

  1. Classification, thésaurus, ontologies, folksonomies : comparaisons du point de vue de la recherche ouverte d'information (ROI)

    OpenAIRE

    Zacklad , Manuel

    2007-01-01

    International audience; This paper compares several Knowledge Organisations Systems (classifications, thesaurus, formal ontology, semiotic ontology, folksonomy) according to different criteria in order to assess their relevance according to Open Information Research.; Cet article compare différents systèmes d'organisation des connaissances (classifications, thésaurus, ontologies formelles, ontologies sémiotiques, folksonomies) selon différents critères pour évaluer leur pertinence en regard d...

  2. USE OF ONTOLOGIES FOR KNOWLEDGE BASES CREATION TUTORING COMPUTER SYSTEMS

    Directory of Open Access Journals (Sweden)

    Cheremisina Lyubov

    2014-11-01

    Full Text Available This paper deals with the use of ontology for the use and development of intelligent tutoring systems. We consider the shortcomings of educational software and distance learning systems and the advantages of using ontology’s in their design. Actuality creates educational computer systems based on systematic knowledge. We consider classification of properties, use and benefits of ontology’s. Characterized approaches to the problem of ontology mapping, the first of which – manual mapping, the second – a comparison of the names of concepts based on their lexical similarity and using special dictionaries. The analysis of languages available for the formal description of ontology. Considered a formal mathematical model of ontology’s and ontology consistency problem, which is that different developers for the same domain ontology can be created, syntactically or semantically heterogeneous, and their use requires a compatible broadcast or display. An algorithm combining ontology’s. The characteristic of the practical value of developing an ontology for electronic educational resources and recommendations for further research and development, such as implementation of other components of the system integration, formalization of the processes of integration and development of a universal expansion algorithms ontology’s software

  3. Practical ontologies for information professionals

    CERN Document Server

    AUTHOR|(CDS)2071712

    2016-01-01

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

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. Distributed and Collaborative Knowledge Management Using an Ontology-Based System

    OpenAIRE

    Adrian , Weronika ,; Ligęza , Antoni; Nalepa , Grzegorz ,; Kaczor , Krzysztof

    2012-01-01

    International audience; Semantic annotations and formally grounded ontologies constitute flexible yet powerful methods of knowledge representation. Using them in a system allows to perform automated reasoning and can enhance the knowledge management. In the paper, we present a system for collaborative knowledge management, in which an ontology and ontological reasoning is used. The main objective of the application is to provide information for citizens about threats in an urban environment. ...

  9. 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.

  10. 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.

  11. 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.

  12. Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning

    KAUST Repository

    Slater, Luke

    2016-04-19

    Ontologies are widely used in biology and biomedicine for the annotation and integration of data, and hundreds of ontologies have been developed for this purpose. These ontologies also constitute large volumes of formalized domain knowledge, usually expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within them relies on the use of automated reasoning. We have developed Aber-OWL, an ontology repository that provides OWL EL reasoning to answer queries and verify the consistency of ontologies. Aber-OWL also provides a set of web services which provide ontology-based access to scientific literature in Pubmed and Pubmed Central, SPARQL query expansion to retrieve linked data, and integration with Bio2RDF. Here, we report on our experiences with Aber-OWL and outline a roadmap for future development. Aber-OWL is freely available at http://aber-owl.net.

  13. 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.

  14. 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...

  15. 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.

  16. Applying terminological methods and description logic for creating and implementing and ontology on inhibition

    DEFF Research Database (Denmark)

    Zambach, Sine; Madsen, Bodil Nistrup

    2009-01-01

    By applying formal terminological methods to model an ontology within the domain of enzyme inhibition, we aim to clarify concepts and to obtain consistency. Additionally, we propose a procedure for implementing this ontology in OWL with the aim of obtaining a strict structure which can form...

  17. Towards Building an AOP-based Prenatal Developmental Toxicity Ontology (CEFIC LRI Workshop - Brussels)

    Science.gov (United States)

    Ontologies are a way to formalize domain-specific scientific knowledge. A developmental ontology would help researchers describe the pathways and processes critical to embryonic development and provide a way to link their chemical disruption to adverse outcomes. Designing one for...

  18. A Semi-Automatic Approach to Construct Vietnamese Ontology from Online Text

    Science.gov (United States)

    Nguyen, Bao-An; Yang, Don-Lin

    2012-01-01

    An ontology is an effective formal representation of knowledge used commonly in artificial intelligence, semantic web, software engineering, and information retrieval. In open and distance learning, ontologies are used as knowledge bases for e-learning supplements, educational recommenders, and question answering systems that support students with…

  19. 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

  20. An Ontological Approach to Developing Information Operations Applications for use on the Semantic Web

    National Research Council Canada - National Science Library

    Clarke, Timothy L

    2008-01-01

    .... By expressing IO capabilities in a formal ontology suitable for use on the Semantic Web, conditions are set such that computational power can more efficiently be leveraged to better define required...

  1. An Ontological Approach to Developing Information Operations Applications for Use on the Semantic Web

    National Research Council Canada - National Science Library

    Clarke, Timothy L

    2008-01-01

    .... By expressing IO capabilities in a formal ontology suitable for use on the Semantic Web, conditions are set such that computational power can more efficiently be leveraged to better define required...

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

    National Research Council Canada - National Science Library

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

    2006-01-01

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

  3. Superfield formalism

    Indian Academy of Sciences (India)

    dimensional superfields, is a clear signature of the presence of the (anti-)BRST invariance in the original. 4D theory. Keywords. Non-Abelian 1-form gauge theory; Dirac fields; (anti-)Becchi–Roucet–Stora–. Tyutin invariance; superfield formalism; ...

  4. Drug target ontology to classify and integrate drug discovery data.

    Science.gov (United States)

    Lin, Yu; Mehta, Saurabh; Küçük-McGinty, Hande; Turner, John Paul; Vidovic, Dusica; Forlin, Michele; Koleti, Amar; Nguyen, Dac-Trung; Jensen, Lars Juhl; Guha, Rajarshi; Mathias, Stephen L; Ursu, Oleg; Stathias, Vasileios; Duan, Jianbin; Nabizadeh, Nooshin; Chung, Caty; Mader, Christopher; Visser, Ubbo; Yang, Jeremy J; Bologa, Cristian G; Oprea, Tudor I; Schürer, Stephan C

    2017-11-09

    One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome. As part of that effort, we have developed a framework to integrate, navigate, and analyze drug discovery data based on formalized and standardized classifications and annotations of druggable protein targets, the Drug Target Ontology (DTO). DTO was constructed by extensive curation and consolidation of various resources. DTO classifies the four major drug target protein families, GPCRs, kinases, ion channels and nuclear receptors, based on phylogenecity, function, target development level, disease association, tissue expression, chemical ligand and substrate characteristics, and target-family specific characteristics. The formal ontology was built using a new software tool to auto-generate most axioms from a database while supporting manual knowledge acquisition. A modular, hierarchical implementation facilitate ontology development and maintenance and makes use of various external ontologies, thus integrating the DTO into the ecosystem of biomedical ontologies. As a formal OWL-DL ontology, DTO contains asserted and inferred axioms. Modeling data from the Library of Integrated Network-based Cellular Signatures (LINCS) program illustrates the potential of DTO for contextual data integration and nuanced definition of important drug target characteristics. DTO has been implemented in the IDG user interface Portal, Pharos and the TIN-X explorer of protein target disease relationships. DTO was built based on the need for a formal semantic

  5. Applied Ontology Engineering in Cloud Services, Networks and Management Systems

    CERN Document Server

    Serrano Orozco, J Martín

    2012-01-01

    Metadata standards in today’s ICT sector are proliferating at unprecedented levels, while automated information management systems collect and process exponentially increasing quantities of data. With interoperability and knowledge exchange identified as a core challenge in the sector, this book examines the role ontology engineering can play in providing solutions to the problems of information interoperability and linked data. At the same time as introducing basic concepts of ontology engineering, the book discusses methodological approaches to formal representation of data and information models, thus facilitating information interoperability between heterogeneous, complex and distributed communication systems. In doing so, the text advocates the advantages of using ontology engineering in telecommunications systems. In addition, it offers a wealth of guidance and best-practice techniques for instances in which ontology engineering is applied in cloud services, computer networks and management systems. �...

  6. 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.

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

    Science.gov (United States)

    Berges, Idoia; Bermúdez, Jesus; Illarramendi, Arantza

    2018-02-01

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

  8. SWARMs Ontology: A Common Information Model for the Cooperation of Underwater Robots

    Science.gov (United States)

    Li, Xin; Bilbao, Sonia; Martín-Wanton, Tamara; Bastos, Joaquim; Rodriguez, Jonathan

    2017-01-01

    In order to facilitate cooperation between underwater robots, it is a must for robots to exchange information with unambiguous meaning. However, heterogeneity, existing in information pertaining to different robots, is a major obstruction. Therefore, this paper presents a networked ontology, named the Smart and Networking Underwater Robots in Cooperation Meshes (SWARMs) ontology, to address information heterogeneity and enable robots to have the same understanding of exchanged information. The SWARMs ontology uses a core ontology to interrelate a set of domain-specific ontologies, including the mission and planning, the robotic vehicle, the communication and networking, and the environment recognition and sensing ontology. In addition, the SWARMs ontology utilizes ontology constructs defined in the PR-OWL ontology to annotate context uncertainty based on the Multi-Entity Bayesian Network (MEBN) theory. Thus, the SWARMs ontology can provide both a formal specification for information that is necessarily exchanged between robots and a command and control entity, and also support for uncertainty reasoning. A scenario on chemical pollution monitoring is described and used to showcase how the SWARMs ontology can be instantiated, be extended, represent context uncertainty, and support uncertainty reasoning. PMID:28287468

  9. Ontology for E-Learning: A Case Study

    Science.gov (United States)

    Colace, Francesco; De Santo, Massimo; Gaeta, Matteo

    2009-01-01

    Purpose: The development of adaptable and intelligent educational systems is widely considered one of the great challenges in scientific research. Among key elements for building advanced training systems, an important role is played by methodologies chosen for knowledge representation. In this scenario, the introduction of ontology formalism can…

  10. LTSA Conformance Testing to Architectural Design of LMS Using Ontology

    Science.gov (United States)

    Sengupta, Souvik; Dasgupta, Ranjan

    2017-01-01

    This paper proposes a new methodology for checking conformance of the software architectural design of Learning Management System (LMS) to Learning Technology System Architecture (LTSA). In our approach, the architectural designing of LMS follows the formal modeling style of Acme. An ontology is built to represent the LTSA rules and the software…

  11. 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.

  12. 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.

  13. 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 ...

  14. 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...

  15. 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

  16. Standardized terminology for clinical trial protocols based on top-level ontological categories.

    Science.gov (United States)

    Heller, B; Herre, H; Lippoldt, K; Loeffler, M

    2004-01-01

    This paper describes a new method for the ontologically based standardization of concepts with regard to the quality assurance of clinical trial protocols. We developed a data dictionary for medical and trial-specific terms in which concepts and relations are defined context-dependently. The data dictionary is provided to different medical research networks by means of the software tool Onto-Builder via the internet. The data dictionary is based on domain-specific ontologies and the top-level ontology of GOL. The concepts and relations described in the data dictionary are represented in natural language, semi-formally or formally according to their use.

  17. Ontology development for provenance tracing in National Climate Assessment of the US Global Change Research Program

    Science.gov (United States)

    Fu, Linyun; Ma, Xiaogang; Zheng, Jin; Goldstein, Justin; Duggan, Brian; West, Patrick; Aulenbach, Steve; Tilmes, Curt; Fox, Peter

    2014-05-01

    This poster will show how we used a case-driven iterative methodology to develop an ontology to represent the content structure and the associated provenance information in a National Climate Assessment (NCA) report of the US Global Change Research Program (USGCRP). We applied the W3C PROV-O ontology to implement a formal representation of provenance. We argue that the use case-driven, iterative development process and the application of a formal provenance ontology help efficiently incorporate domain knowledge from earth and environmental scientists in a well-structured model interoperable in the context of the Web of Data.

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

    Science.gov (United States)

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

    2003-01-01

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

  19. 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....

  20. Research on presentation and query service of geo-spatial data based on ontology

    Science.gov (United States)

    Li, Hong-wei; Li, Qin-chao; Cai, Chang

    2008-10-01

    The paper analyzed the deficiency on presentation and query of geo-spatial data existed in current GIS, discussed the advantages that ontology possessed in formalization of geo-spatial data and the presentation of semantic granularity, taken land-use classification system as an example to construct domain ontology, and described it by OWL; realized the grade level and category presentation of land-use data benefited from the thoughts of vertical and horizontal navigation; and then discussed query mode of geo-spatial data based on ontology, including data query based on types and grade levels, instances and spatial relation, and synthetic query based on types and instances; these methods enriched query mode of current GIS, and is a useful attempt; point out that the key point of the presentation and query of spatial data based on ontology is to construct domain ontology that can correctly reflect geo-concept and its spatial relation and realize its fine formalization description.

  1. 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.

  2. 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

  3. 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.

  4. 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 ...

  5. 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…

  6. 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.

  7. 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

  8. IDEF5 Ontology Description Capture Method: Concepts and Formal Foundations

    Science.gov (United States)

    1992-11-01

    cutter comes to exist. The puzzle here goes back to Greek times iii the guise of the Ship of Theseus : if we bit by bit replace the planks of a ship...831 Barwise, J. and Perry, J., Situations and Attitudes, The MIT Press, Cambridge, 1983. [Burch 911 Burch, R., A Peircean Reduction Thesis : The

  9. A First-Language-First Multilingual Model to Meet the Quality Imperative in Formal Basic Education in Three "Francophone" West African Countries

    Science.gov (United States)

    Nikiema, Norbert

    2011-01-01

    This paper documents the new trend towards a first-language-first multilingual model in formal education in three former French colonies of West Africa, namely Burkina Faso, Mali and Niger. It compares the sociolinguistic situations, the conditions of the development of multilingual education and the achievements of mother-tongue-medium education…

  10. 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

  11. Invariance as a Tool for Ontology of Information

    Directory of Open Access Journals (Sweden)

    Marcin J. Schroeder

    2016-03-01

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

  12. Derivation of Event-B Models from OWL Ontologies

    Directory of Open Access Journals (Sweden)

    Alkhammash Eman H.

    2016-01-01

    Full Text Available The derivation of formal specifications from large and complex requirements is a key challenge in systems engineering. In this paper we present an approach that aims to address this challenge by building formal models from OWL ontologies. An ontology is used in the field of knowledge representation to capture a clear view of the domain and to produce a concise and unambiguous set of domain requirements. We harness the power of ontologies to handle inconsistency of domain requirements and produce clear, concise and unambiguous set of domain requirements for Event-B modelling. The proposed approach works by generating Attempto Controlled English (ACE from the OWL ontology and then maps the ACE requirements to develop Event-B models. ACE is a subset of English that can be unambiguously translated into first-order logic. There is an injective mapping between OWL ontology and a subset of ACE. ACE is a suitable interlingua for producing the mapping between OWL and Event-B models for many reasons. Firstly, ACE is easy to learn and understand, it hides the math of OWL and would be natural to use by everybody. Secondly ACE has a parser that converts ACE texts into Discourse Representation Structures (DRS. Finally, ACE can be extended to target a richer syntactic subset of Event-B which ultimately would facilitate the translation of ACE requirements to Event-B.

  13. 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...

  14. HuPSON: the human physiology simulation ontology.

    Science.gov (United States)

    Gündel, Michaela; Younesi, Erfan; Malhotra, Ashutosh; Wang, Jiali; Li, Hui; Zhang, Bijun; de Bono, Bernard; Mevissen, Heinz-Theodor; Hofmann-Apitius, Martin

    2013-11-22

    Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain. We propose a first version of a newly constructed ontology, HuPSON, as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles; the constructed ontology has been evaluated via structural features, competency questions and use case scenarios.The ontology is freely available at: http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads.html (owl files) and http://bishop.scai.fraunhofer.de/scaiview/ (browser). HuPSON provides a framework for a) annotating simulation experiments, b) retrieving relevant information that are required for modelling, c) enabling interoperability of algorithmic approaches used in biomedical simulation, d) comparing simulation results and e) linking knowledge-based approaches to simulation-based approaches. It is meant to foster a more rapid uptake of semantic technologies in the modelling and simulation domain, with particular focus on the VPH domain.

  15. Adding a little reality to building ontologies for biology.

    Directory of Open Access Journals (Sweden)

    Phillip Lord

    Full Text Available BACKGROUND: Many areas of biology are open to mathematical and computational modelling. The application of discrete, logical formalisms defines the field of biomedical ontologies. Ontologies have been put to many uses in bioinformatics. The most widespread is for description of entities about which data have been collected, allowing integration and analysis across multiple resources. There are now over 60 ontologies in active use, increasingly developed as large, international collaborations. There are, however, many opinions on how ontologies should be authored; that is, what is appropriate for representation. Recently, a common opinion has been the "realist" approach that places restrictions upon the style of modelling considered to be appropriate. METHODOLOGY/PRINCIPAL FINDINGS: Here, we use a number of case studies for describing the results of biological experiments. We investigate the ways in which these could be represented using both realist and non-realist approaches; we consider the limitations and advantages of each of these models. CONCLUSIONS/SIGNIFICANCE: From our analysis, we conclude that while realist principles may enable straight-forward modelling for some topics, there are crucial aspects of science and the phenomena it studies that do not fit into this approach; realism appears to be over-simplistic which, perversely, results in overly complex ontological models. We suggest that it is impossible to avoid compromise in modelling ontology; a clearer understanding of these compromises will better enable appropriate modelling, fulfilling the many needs for discrete mathematical models within computational biology.

  16. FCAIR 2012 Formal Concept Analysis Meets Information Retrieval Workshop co-located with the 35th European Conference on Information Retrieval (ECIR 2013) March 24, 2013, Moscow, Russia

    OpenAIRE

    Carpineto , Claudio; Kuznetsov , Sergei O.; Napoli , Amedeo

    2013-01-01

    International audience; Formal Concept Analysis (FCA) is a mathematically well-founded theory aimed at data analysis and classifiation. The area came into being in the early 1980s and has since then spawned over 10000 scientific publications and a variety of practically deployed tools. FCA allows one to build from a data table with objects in rows and attributes in columns a taxonomic data structure called concept lattice, which can be used for many purposes, especially for Knowledge Discover...

  17. Meeting

    Indian Academy of Sciences (India)

    July 1989 No.19 Newsletter of the Indian Academy of Sciences. 55th Annual. Meeting ... in the world, keeping alive atthe same time his research interests, abreast .... theory made a comeback with many new ideas and with the success of the ...

  18. 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

  19. 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.

  20. Developing an Ontology for Ocean Biogeochemistry Data

    Science.gov (United States)

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

    2010-12-01

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

  1. 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...

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

    Science.gov (United States)

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

    2014-03-01

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

  3. 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...

  4. 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…

  5. Knowledge management of eco-industrial park for efficient energy utilization through ontology-based approach

    International Nuclear Information System (INIS)

    Zhang, Chuan; Romagnoli, Alessandro; Zhou, Li; Kraft, Markus

    2017-01-01

    Highlights: •An intelligent energy management system for Eco-Industrial Park (EIP) is proposed. •An explicit domain ontology for EIP energy management is designed. •Ontology-based approach can increase knowledge interoperability within EIP. •Ontology-based approach can allow self-optimization without human intervention in EIP. •The proposed system harbours huge potential in the future scenario of Internet of Things. -- Abstract: An ontology-based approach for Eco-Industrial Park (EIP) knowledge management is proposed in this paper. The designed ontology in this study is formalized conceptualization of EIP. Based on such an ontological representation, a Knowledge-Based System (KBS) for EIP energy management named J-Park Simulator (JPS) is developed. By applying JPS to the solution of EIP waste heat utilization problem, the results of this study show that ontology is a powerful tool for knowledge management of complex systems such as EIP. The ontology-based approach can increase knowledge interoperability between different companies in EIP. The ontology-based approach can also allow intelligent decision making by using disparate data from remote databases, which implies the possibility of self-optimization without human intervention scenario of Internet of Things (IoT). It is shown through this study that KBS can bridge the communication gaps between different companies in EIP, sequentially more potential Industrial Symbiosis (IS) links can be established to improve the overall energy efficiency of the whole EIP.

  6. A four stage approach for ontology-based health information system design.

    Science.gov (United States)

    Kuziemsky, Craig E; Lau, Francis

    2010-11-01

    To describe and illustrate a four stage methodological approach to capture user knowledge in a biomedical domain area, use that knowledge to design an ontology, and then implement and evaluate the ontology as a health information system (HIS). A hybrid participatory design-grounded theory (GT-PD) method was used to obtain data and code them for ontology development. Prototyping was used to implement the ontology as a computer-based tool. Usability testing evaluated the computer-based tool. An empirically derived domain ontology and set of three problem-solving approaches were developed as a formalized model of the concepts and categories from the GT coding. The ontology and problem-solving approaches were used to design and implement a HIS that tested favorably in usability testing. The four stage approach illustrated in this paper is useful for designing and implementing an ontology as the basis for a HIS. The approach extends existing ontology development methodologies by providing an empirical basis for theory incorporated into ontology design. Copyright © 2010 Elsevier B.V. All rights reserved.

  7. 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...

  8. Self-organizing ontology of biochemically relevant small molecules.

    Science.gov (United States)

    Chepelev, Leonid L; Hastings, Janna; Ennis, Marcus; Steinbeck, Christoph; Dumontier, Michel

    2012-01-06

    The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. We conclude that the proposed methodology can ease the burden of chemical data annotators and

  9. Self-organizing ontology of biochemically relevant small molecules

    Science.gov (United States)

    2012-01-01

    Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology can ease the burden of

  10. Self-organizing ontology of biochemically relevant small molecules

    Directory of Open Access Journals (Sweden)

    Chepelev Leonid L

    2012-01-01

    Full Text Available Abstract Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology

  11. ONTOLOGY BASED MEANINGFUL SEARCH USING SEMANTIC WEB AND NATURAL LANGUAGE PROCESSING TECHNIQUES

    Directory of Open Access Journals (Sweden)

    K. Palaniammal

    2013-10-01

    Full Text Available The semantic web extends the current World Wide Web by adding facilities for the machine understood description of meaning. The ontology based search model is used to enhance efficiency and accuracy of information retrieval. Ontology is the core technology for the semantic web and this mechanism for representing formal and shared domain descriptions. In this paper, we proposed ontology based meaningful search using semantic web and Natural Language Processing (NLP techniques in the educational domain. First we build the educational ontology then we present the semantic search system. The search model consisting three parts which are embedding spell-check, finding synonyms using WordNet API and querying ontology using SPARQL language. The results are both sensitive to spell check and synonymous context. This paper provides more accurate results and the complete details for the selected field in a single page.

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

    Science.gov (United States)

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

    2015-09-22

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

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

    Science.gov (United States)

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

    2014-01-01

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

  14. Developing VISO: Vaccine Information Statement Ontology for patient education.

    Science.gov (United States)

    Amith, Muhammad; Gong, Yang; Cunningham, Rachel; Boom, Julie; Tao, Cui

    2015-01-01

    To construct a comprehensive vaccine information ontology that can support personal health information applications using patient-consumer lexicon, and lead to outcomes that can improve patient education. The authors composed the Vaccine Information Statement Ontology (VISO) using the web ontology language (OWL). We started with 6 Vaccine Information Statement (VIS) documents collected from the Centers for Disease Control and Prevention (CDC) website. Important and relevant selections from the documents were recorded, and knowledge triples were derived. Based on the collection of knowledge triples, the meta-level formalization of the vaccine information domain was developed. Relevant instances and their relationships were created to represent vaccine domain knowledge. The initial iteration of the VISO was realized, based on the 6 Vaccine Information Statements and coded into OWL2 with Protégé. The ontology consisted of 132 concepts (classes and subclasses) with 33 types of relationships between the concepts. The total number of instances from classes totaled at 460, along with 429 knowledge triples in total. Semiotic-based metric scoring was applied to evaluate quality of the ontology.

  15. 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

  16. 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.…

  17. 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...

  18. 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

  19. An Intelligent Information Retrieval Approach Based on Two Degrees of Uncertainty Fuzzy Ontology

    OpenAIRE

    Maryam Hourali; Gholam Ali Montazer

    2011-01-01

    In spite of the voluminous studies in the field of intelligent retrieval systems, effective retrieving of information has been remained an important unsolved problem. Implementations of different conceptual knowledge in the information retrieval process such as ontology have been considered as a solution to enhance the quality of results. Furthermore, the conceptual formalism supported by typical ontology may not be sufficient to represent uncertainty information due to the lack of clear-cut ...

  20. A Formal Semantics for Concept Understanding relying on Description Logics

    DEFF Research Database (Denmark)

    Badie, Farshad

    2017-01-01

    logical assumptions whose discovery may lead us to a better understanding of ‘concept understanding’. The Structure of Observed Learning Outcomes (SOLO) model as an appropriate model of increasing complexity of humans’ understanding has supported the formal analysis.......In this research, Description Logics (DLs) will be employed for logical description, logical characterisation, logical modelling and ontological description of concept understanding in terminological systems. It’s strongly believed that using a formal descriptive logic could support us in revealing...

  1. A Formal Semantics for Concept Understanding relying on Description Logics

    DEFF Research Database (Denmark)

    Badie, Farshad

    2017-01-01

    In this research, Description Logics (DLs) will be employed for logical description, logical characterisation, logical modelling and ontological description of concept understanding in terminological systems. It’s strongly believed that using a formal descriptive logic could support us in reveali...... logical assumptions whose discovery may lead us to a better understanding of ‘concept understanding’. The Structure of Observed Learning Outcomes (SOLO) model as an appropriate model of increasing complexity of humans’ understanding has supported the formal analysis....

  2. SBME : Exploring boundaries between formal, non-formal, and informal learning

    OpenAIRE

    Shahoumian, Armineh; Parchoma, Gale; Saunders, Murray; Hanson, Jacky; Dickinson, Mike; Pimblett, Mark

    2013-01-01

    In medical education learning extends beyond university settings into practice. Non-formal and informal learning support learners’ efforts to meet externally set and learner-identified objectives. In SBME research, boundaries between formal, non-formal, and informal learning have not been widely explored. Whether SBME fits within or challenges these categories can make a contribution. Formal learning is described in relation to educational settings, planning, assessment, and accreditation. In...

  3. [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.

  4. Masses of Formal Philosophy

    DEFF Research Database (Denmark)

    Masses of Formal Philosophy is an outgrowth of Formal Philosophy. That book gathered the responses of some of the most prominent formal philosophers to five relatively open and broad questions initiating a discussion of metaphilosophical themes and problems surrounding the use of formal methods i...... in philosophy. Including contributions from a wide range of philosophers, Masses of Formal Philosophy contains important new responses to the original five questions.......Masses of Formal Philosophy is an outgrowth of Formal Philosophy. That book gathered the responses of some of the most prominent formal philosophers to five relatively open and broad questions initiating a discussion of metaphilosophical themes and problems surrounding the use of formal methods...

  5. Integrating reasoning and clinical archetypes using OWL ontologies and SWRL rules.

    Science.gov (United States)

    Lezcano, Leonardo; Sicilia, Miguel-Angel; Rodríguez-Solano, Carlos

    2011-04-01

    Semantic interoperability is essential to facilitate the computerized support for alerts, workflow management and evidence-based healthcare across heterogeneous electronic health record (EHR) systems. Clinical archetypes, which are formal definitions of specific clinical concepts defined as specializations of a generic reference (information) model, provide a mechanism to express data structures in a shared and interoperable way. However, currently available archetype languages do not provide direct support for mapping to formal ontologies and then exploiting reasoning on clinical knowledge, which are key ingredients of full semantic interoperability, as stated in the SemanticHEALTH report [1]. This paper reports on an approach to translate definitions expressed in the openEHR Archetype Definition Language (ADL) to a formal representation expressed using the Ontology Web Language (OWL). The formal representations are then integrated with rules expressed with Semantic Web Rule Language (SWRL) expressions, providing an approach to apply the SWRL rules to concrete instances of clinical data. Sharing the knowledge expressed in the form of rules is consistent with the philosophy of open sharing, encouraged by archetypes. Our approach also allows the reuse of formal knowledge, expressed through ontologies, and extends reuse to propositions of declarative knowledge, such as those encoded in clinical guidelines. This paper describes the ADL-to-OWL translation approach, describes the techniques to map archetypes to formal ontologies, and demonstrates how rules can be applied to the resulting representation. We provide examples taken from a patient safety alerting system to illustrate our approach. Copyright © 2010 Elsevier Inc. All rights reserved.

  6. 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

  7. 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.

  8. 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.

  9. Ontology-supported research on vaccine efficacy, safety and integrative biological networks.

    Science.gov (United States)

    He, Yongqun

    2014-07-01

    While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including Vaccine Ontology, Ontology of Adverse Events and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network ('OneNet') Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms.

  10. An Intelligent Information Retrieval Approach Based on Two Degrees of Uncertainty Fuzzy Ontology

    Directory of Open Access Journals (Sweden)

    Maryam Hourali

    2011-01-01

    Full Text Available In spite of the voluminous studies in the field of intelligent retrieval systems, effective retrieving of information has been remained an important unsolved problem. Implementations of different conceptual knowledge in the information retrieval process such as ontology have been considered as a solution to enhance the quality of results. Furthermore, the conceptual formalism supported by typical ontology may not be sufficient to represent uncertainty information due to the lack of clear-cut boundaries between concepts of the domains. To tackle this type of problems, one possible solution is to insert fuzzy logic into ontology construction process. In this article, a novel approach for fuzzy ontology generation with two uncertainty degrees is proposed. Hence, by implementing linguistic variables, uncertainty level in domain's concepts (Software Maintenance Engineering (SME domain has been modeled, and ontology relations have been modeled by fuzzy theory consequently. Then, we combined these uncertain models and proposed a new ontology with two degrees of uncertainty both in concept expression and relation expression. The generated fuzzy ontology was implemented for expansion of initial user's queries in SME domain. Experimental results showed that the proposed model has better overall retrieval performance comparing to keyword-based or crisp ontology-based retrieval systems.

  11. Toward an Ontology of Simulated Social Interaction

    DEFF Research Database (Denmark)

    Seibt, Johanna

    2017-01-01

    and asymmetric modes of realizing Á, called the ‘simulatory expansion’ of interaction type Á. Simulatory expansions of social interactions can be used to map out different kinds and degrees of sociality in human-human and human-robot interaction, relative to current notions of sociality in philosophy......, anthropology, and linguistics. The classificatory framework developed (SISI) thus represents the field of possible simulated social interactions. SISI can be used to clarify which conceptual and empirical grounds we can draw on to evaluate capacities and affordances of robots for social interaction......The paper develops a general conceptual framework for the ontological classification of human-robot interaction. After arguing against fictionalist interpretations of human-robot interactions, I present five notions of simulation or partial realization, formally defined in terms of relationships...

  12. The Volcanism Ontology (VO): a model of the volcanic system

    Science.gov (United States)

    Myer, J.; Babaie, H. A.

    2017-12-01

    We have modeled a part of the complex material and process entities and properties of the volcanic system in the Volcanism Ontology (VO) applying several top-level ontologies such as Basic Formal Ontology (BFO), SWEET, and Ontology of Physics for Biology (OPB) within a single framework. The continuant concepts in BFO describe features with instances that persist as wholes through time and have qualities (attributes) that may change (e.g., state, composition, and location). In VO, the continuants include lava, volcanic rock, and volcano. The occurrent concepts in BFO include processes, their temporal boundaries, and the spatio-temporal regions within which they occur. In VO, these include eruption (process), the onset of pyroclastic flow (temporal boundary), and the space and time span of the crystallization of lava in a lava tube (spatio-temporal region). These processes can be of physical (e.g., debris flow, crystallization, injection), atmospheric (e.g., vapor emission, ash particles blocking solar radiation), hydrological (e.g., diffusion of water vapor, hot spring), thermal (e.g., cooling of lava) and other types. The properties (predicates) relate continuants to other continuants, occurrents to continuants, and occurrents to occurrents. The ontology also models other concepts such as laboratory and field procedures by volcanologists, sampling by sensors, and the type of instruments applied in monitoring volcanic activity. When deployed on the web, VO will be used to explicitly and formally annotate data and information collected by volcanologists based on domain knowledge. This will enable the integration of global volcanic data and improve the interoperability of software that deal with such data.

  13. 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.

  14. An improved ontological representation of dendritic cells as a paradigm for all cell types

    Directory of Open Access Journals (Sweden)

    Mungall Chris

    2009-02-01

    Full Text Available Abstract Background Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL, designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal rigor of ontologies to better support computation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL's utility for computation and for cross-species data integration. Results To enhance the CL's utility for computational analyses, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL. DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. We avoid multiple uses of is_a by linking DC-CL terms to terms in other ontologies via additional, formally defined relations such as has_function. Conclusion This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. Accordingly, we propose our method as a general strategy for the ontological representation of cells. DC-CL is available from http://www.obofoundry.org.

  15. 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.

  16. 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...

  17. 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

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

    OpenAIRE

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

    1999-01-01

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

  19. ``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.

  20. An ontological knowledge framework for adaptive medical workflow.

    Science.gov (United States)

    Dang, Jiangbo; Hedayati, Amir; Hampel, Ken; Toklu, Candemir

    2008-10-01

    As emerging technologies, semantic Web and SOA (Service-Oriented Architecture) allow BPMS (Business Process Management System) to automate business processes that can be described as services, which in turn can be used to wrap existing enterprise applications. BPMS provides tools and methodologies to compose Web services that can be executed as business processes and monitored by BPM (Business Process Management) consoles. Ontologies are a formal declarative knowledge representation model. It provides a foundation upon which machine understandable knowledge can be obtained, and as a result, it makes machine intelligence possible. Healthcare systems can adopt these technologies to make them ubiquitous, adaptive, and intelligent, and then serve patients better. This paper presents an ontological knowledge framework that covers healthcare domains that a hospital encompasses-from the medical or administrative tasks, to hospital assets, medical insurances, patient records, drugs, and regulations. Therefore, our ontology makes our vision of personalized healthcare possible by capturing all necessary knowledge for a complex personalized healthcare scenario involving patient care, insurance policies, and drug prescriptions, and compliances. For example, our ontology facilitates a workflow management system to allow users, from physicians to administrative assistants, to manage, even create context-aware new medical workflows and execute them on-the-fly.

  1. ONS: an ontology for a standardized description of interventions and observational studies in nutrition.

    Science.gov (United States)

    Vitali, Francesco; Lombardo, Rosario; Rivero, Damariz; Mattivi, Fulvio; Franceschi, Pietro; Bordoni, Alessandra; Trimigno, Alessia; Capozzi, Francesco; Felici, Giovanni; Taglino, Francesco; Miglietta, Franco; De Cock, Nathalie; Lachat, Carl; De Baets, Bernard; De Tré, Guy; Pinart, Mariona; Nimptsch, Katharina; Pischon, Tobias; Bouwman, Jildau; Cavalieri, Duccio

    2018-01-01

    The multidisciplinary nature of nutrition research is one of its main strengths. At the same time, however, it presents a major obstacle to integrate data analysis, especially for the terminological and semantic interpretations that specific research fields or communities are used to. To date, a proper ontology to structure and formalize the concepts used for the description of nutritional studies is still lacking. We have developed the Ontology for Nutritional Studies (ONS) by harmonizing selected pre-existing de facto ontologies with novel health and nutritional terminology classifications. The ONS is the result of a scholarly consensus of 51 research centers in nine European countries. The ontology classes and relations are commonly encountered while conducting, storing, harmonizing, integrating, describing, and searching nutritional studies. The ONS facilitates the description and specification of complex nutritional studies as demonstrated with two application scenarios. The ONS is the first systematic effort to provide a solid and extensible formal ontology framework for nutritional studies. Integration of new information can be easily achieved by the addition of extra modules (i.e., nutrigenomics, metabolomics, nutrikinetics, and quality appraisal). The ONS provides a unified and standardized terminology for nutritional studies as a resource for nutrition researchers who might not necessarily be familiar with ontologies and standardization concepts.

  2. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

    KAUST Repository

    Hoehndorf, Robert

    2016-11-14

    Background The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text. Results We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities. Conclusions The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established

  3. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.

    Science.gov (United States)

    Hoehndorf, Robert; Alshahrani, Mona; Gkoutos, Georgios V; Gosline, George; Groom, Quentin; Hamann, Thomas; Kattge, Jens; de Oliveira, Sylvia Mota; Schmidt, Marco; Sierra, Soraya; Smets, Erik; Vos, Rutger A; Weiland, Claus

    2016-11-14

    The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text. We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities. The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established vocabularies or ontologies, but rather

  4. Initial implementation of a comparative data analysis ontology.

    Science.gov (United States)

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

    2009-07-03

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

  5. Concept Systems and Ontologies: Recommendations for Basic Terminology

    Science.gov (United States)

    Klein, Gunnar O.; Smith, Barry

    This essay concerns the problems surrounding the use of the term ``concept'' in current ontology and terminology research. It is based on the constructive dialogue between realist ontology on the one hand and the world of formal standardization of health informatics on the other, but its conclusions are not restricted to the domain of medicine. The term ``concept'' is one of the most misused even in literature and technical standards which attempt to bring clarity. In this paper we propose to use the term ``concept'' in the context of producing defined professional terminologies with one specific and consistent meaning which we propose for adoption as the agreed meaning of the term in future terminological research, and specifically in the development of formal terminologies to be used in computer systems. We also discuss and propose new definitions of a set of cognate terms. We describe the relations governing the realm of concepts, and compare these to the richer and more complex set of relations obtaining between entities in the real world. On this basis we also summarize an associated terminology for ontologies as representations of the real world and a partial mapping between the world of concepts and the world of reality.

  6. A Process for the Representation of openEHR ADL Archetypes in OWL Ontologies.

    Science.gov (United States)

    Porn, Alex Mateus; Peres, Leticia Mara; Didonet Del Fabro, Marcos

    2015-01-01

    ADL is a formal language to express archetypes, independent of standards or domain. However, its specification is not precise enough in relation to the specialization and semantic of archetypes, presenting difficulties in implementation and a few available tools. Archetypes may be implemented using other languages such as XML or OWL, increasing integration with Semantic Web tools. Exchanging and transforming data can be better implemented with semantics oriented models, for example using OWL which is a language to define and instantiate Web ontologies defined by W3C. OWL permits defining significant, detailed, precise and consistent distinctions among classes, properties and relations by the user, ensuring the consistency of knowledge than using ADL techniques. This paper presents a process of an openEHR ADL archetypes representation in OWL ontologies. This process consists of ADL archetypes conversion in OWL ontologies and validation of OWL resultant ontologies using the mutation test.

  7. An organizational model to support the flexible workflow based on ontology

    International Nuclear Information System (INIS)

    Yuan Feng; Li Xudong; Zhu Guangying; Zhang Xiankun

    2012-01-01

    Based on ontology theory, the paper addresses an organizational model for flexible workflow. Firstly, the paper describes the conceptual model of the organizational model on ontology chart, which provides a consistent semantic framework of organization. Secondly, the paper gives the formalization of the model and describes the six key ontology elements of the mode in detail. Finally, the paper discusses deeply how the model supports the flexible workflow and indicates that the model has the advantages of cross-area, cross-organization and cross-domain, multi-process support and scalability. Especially, because the model is represented by ontology, the paper produces the conclusion that the model has covered the defect of unshared feature in traditional models, at the same time, it is more capable and flexible. (authors)

  8. Ontology-Based Big Dimension Modeling in Data Warehouse Schema Design

    DEFF Research Database (Denmark)

    Iftikhar, Nadeem

    2013-01-01

    During data warehouse schema design, designers often encounter how to model big dimensions that typically contain a large number of attributes and records. To investigate effective approaches for modeling big dimensions is necessary in order to achieve better query performance, with respect...... partitioning, vertical partitioning and their hybrid. We formalize the design methods and propose an algorithm that describes the modeling process from an OWL ontology to a data warehouse schema. In addition, this paper also presents an effective ontology-based tool to automate the modeling process. The tool...... can automatically generate the data warehouse schema from the ontology of describing the terms and business semantics for the big dimension. In case of any change in the requirements, we only need to modify the ontology, and re-generate the schema using the tool. This paper also evaluates the proposed...

  9. A novel ontology approach to support design for reliability considering environmental effects.

    Science.gov (United States)

    Sun, Bo; Li, Yu; Ye, Tianyuan; Ren, Yi

    2015-01-01

    Environmental effects are not considered sufficiently in product design. Reliability problems caused by environmental effects are very prominent. This paper proposes a method to apply ontology approach in product design. During product reliability design and analysis, environmental effects knowledge reusing is achieved. First, the relationship of environmental effects and product reliability is analyzed. Then environmental effects ontology to describe environmental effects domain knowledge is designed. Related concepts of environmental effects are formally defined by using the ontology approach. This model can be applied to arrange environmental effects knowledge in different environments. Finally, rubber seals used in the subhumid acid rain environment are taken as an example to illustrate ontological model application on reliability design and analysis.

  10. 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

  11. Research on geo-ontology construction based on spatial affairs

    Science.gov (United States)

    Li, Bin; Liu, Jiping; Shi, Lihong

    2008-12-01

    Geo-ontology, a kind of domain ontology, is used to make the knowledge, information and data of concerned geographical science in the abstract to form a series of single object or entity with common cognition. These single object or entity can compose a specific system in some certain way and can be disposed on conception and given specific definition at the same time. Ultimately, these above-mentioned worked results can be expressed in some manners of formalization. The main aim of constructing geo-ontology is to get the knowledge of the domain of geography, and provide the commonly approbatory vocabularies in the domain, as well as give the definite definition about these geographical vocabularies and mutual relations between them in the mode of formalization at different hiberarchy. Consequently, the modeling tool of conception model of describing geographic Information System at the hiberarchy of semantic meaning and knowledge can be provided to solve the semantic conception of information exchange in geographical space and make them possess the comparatively possible characters of accuracy, maturity and universality, etc. In fact, some experiments have been made to validate geo-ontology. During the course of studying, Geo-ontology oriented to flood can be described and constructed by making the method based on geo-spatial affairs to serve the governmental departments at all levels to deal with flood. Thereinto, intelligent retrieve and service based on geoontology of disaster are main functions known from the traditional manner by using keywords. For instance, the function of dealing with disaster information based on geo-ontology can be provided when a supposed flood happened in a certain city. The correlative officers can input some words, such as "city name, flood", which have been realized semantic label, to get the information they needed when they browse different websites. The information, including basic geographical information and flood distributing

  12. Toward semantic interoperability with linked foundational ontologies in ROMULUS

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-06-01

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

  13. Formal Verification -26 ...

    Indian Academy of Sciences (India)

    by testing of the components and successful testing leads to the software being ... Formal verification is based on formal methods which are mathematically based ..... scenario under which a similar error could occur. There are various other ...

  14. Integrating the Ontological, Epistemological, and Sociocultural Aspects: A Holistic View of Teacher Education

    Science.gov (United States)

    Huang, Teng

    2016-01-01

    The three aspects of teacher change--ontological, epistemological, and sociocultural--are traditionally regarded as independent. Usually only the epistemological aspect is highlighted in formal teacher education. In this paper, I argue that a holistic and interdependent view of these aspects is needed. Thus, this paper aims to explore the process…

  15. A Distributed Database System for Developing Ontological and Lexical Resources in Harmony

    NARCIS (Netherlands)

    Horák, A.; Vossen, P.T.J.M.; Rambousek, A.; Gelbukh, A.

    2010-01-01

    In this article, we present the basic ideas of creating a new information-rich lexical database of Dutch, called Cornetto, that is interconnected with corresponding English synsets and a formal ontology. The Cornetto database is based on two existing electronic dictionaries - the Referentie Bestand

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

    CSIR Research Space (South Africa)

    Thomas, A

    2015-11-01

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

  17. Formalizing Informal Logic

    Directory of Open Access Journals (Sweden)

    Douglas Walton

    2015-12-01

    Full Text Available This paper presents a formalization of informal logic using the Carneades Argumentation System (CAS, a formal, computational model of argument that consists of a formal model of argument graphs and audiences. Conflicts between pro and con arguments are resolved using proof standards, such as preponderance of the evidence. CAS also formalizes argumentation schemes. Schemes can be used to check whether a given argument instantiates the types of argument deemed normatively appropriate for the type of dialogue.

  18. 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.

  19. 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.

  20. 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.

  1. Pragmatics for formal semantics

    DEFF Research Database (Denmark)

    Danvy, Olivier

    2011-01-01

    This tech talk describes how to write and how to inter-derive formal semantics for sequential programming languages. The progress reported here is (1) concrete guidelines to write each formal semantics to alleviate their proof obligations, and (2) simple calculational tools to obtain a formal...

  2. The ontologies of an environmental disaster

    Directory of Open Access Journals (Sweden)

    Francisco Ângelo Coutinho

    2017-04-01

    Full Text Available The paper intended to contribute to the understanding of the interrelationships between the so-called "academic knowledge" and the knowledge and experience of students of a Graduation in Rural Education, at a public university of southeastern Brazil. Specifically, we are interested in analyzing the discussions that emerged in lessons of Life Sciences, focusing on the elements of the controversies that happened at these meetings. Based on the actor-network theory, the research points to the fact that the students place themselves as active subjects who mobilize knowledge, practices and experiences that make them foster controversy in a training situation, towards a knowledge that is authorized by the university. It could be noticed the rich ontological elements related to dynamic relations of the economy, politics, international relations and social hierarchies. Thus, it was possible to discern elements that compose the material reality with which the licensees are amalgamated.

  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. Part-whole reasoning in medical ontologies revisited--introducing SEP triplets into classification-based description logics.

    OpenAIRE

    Schulz, S.; Romacker, M.; Hahn, U.

    1998-01-01

    The development of powerful and comprehensive medical ontologies that support formal reasoning on a large scale is one of the key requirements for clinical computing in the next millennium. Taxonomic medical knowledge, a major portion of these ontologies, is mainly characterized by generalization and part-whole relations between concepts. While reasoning in generalization hierarchies is quite well understood, no fully conclusive mechanism as yet exists for part-whole reasoning. The approach w...

  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. 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....

  13. 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 ...

  14. 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 ...

  15. Ontology modeling for generation of clinical pathways

    Directory of Open Access Journals (Sweden)

    Jasmine Tehrani

    2012-12-01

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

  16. Text Mining to inform construction of Earth and Environmental Science Ontologies

    Science.gov (United States)

    Schildhauer, M.; Adams, B.; Rebich Hespanha, S.

    2013-12-01

    There is a clear need for better semantic representation of Earth and environmental concepts, to facilitate more effective discovery and re-use of information resources relevant to scientists doing integrative research. In order to develop general-purpose Earth and environmental science ontologies, however, it is necessary to represent concepts and relationships that span usage across multiple disciplines and scientific specialties. Traditional knowledge modeling through ontologies utilizes expert knowledge but inevitably favors the particular perspectives of the ontology engineers, as well as the domain experts who interacted with them. This often leads to ontologies that lack robust coverage of synonymy, while also missing important relationships among concepts that can be extremely useful for working scientists to be aware of. In this presentation we will discuss methods we have developed that utilize statistical topic modeling on a large corpus of Earth and environmental science articles, to expand coverage and disclose relationships among concepts in the Earth sciences. For our work we collected a corpus of over 121,000 abstracts from many of the top Earth and environmental science journals. We performed latent Dirichlet allocation topic modeling on this corpus to discover a set of latent topics, which consist of terms that commonly co-occur in abstracts. We match terms in the topics to concept labels in existing ontologies to reveal gaps, and we examine which terms are commonly associated in natural language discourse, to identify relationships that are important to formally model in ontologies. Our text mining methodology uncovers significant gaps in the content of some popular existing ontologies, and we show how, through a workflow involving human interpretation of topic models, we can bootstrap ontologies to have much better coverage and richer semantics. Because we base our methods directly on what working scientists are communicating about their

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

    Directory of Open Access Journals (Sweden)

    Сергій Козіброда

    2014-04-01

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

  18. 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

  19. 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

  20. 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...

  1. Formalization of Many-Valued Logics

    DEFF Research Database (Denmark)

    Villadsen, Jørgen; Schlichtkrull, Anders

    2017-01-01

    Partiality is a key challenge for computational approaches to artificial intelligence in general and natural language in particular. Various extensions of classical two-valued logic to many-valued logics have been investigated in order to meet this challenge. We use the proof assistant Isabelle...... to formalize the syntax and semantics of many-valued logics with determinate as well as indeterminate truth values. The formalization allows for a concise presentation and makes automated verification possible....

  2. 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

  3. 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…

  4. 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.

  5. 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.

  6. 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

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

    Science.gov (United States)

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

    2010-03-01

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

  8. 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

  9. 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.

  10. 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.

  11. Industrial use of formal methods formal verification

    CERN Document Server

    Boulanger, Jean-Louis

    2012-01-01

    At present the literature gives students and researchers of the very general books on the formal technics. The purpose of this book is to present in a single book, a return of experience on the used of the "formal technics" (such proof and model-checking) on industrial examples for the transportation domain. This book is based on the experience of people which are completely involved in the realization and the evaluation of safety critical system software based.  The implication of the industrialists allows to raise the problems of confidentiality which could appear and so allow

  12. Axiomatic Ontology Learning Approaches for English Translation of the Meaning of Quranic Texts

    Directory of Open Access Journals (Sweden)

    Saad Saidah

    2017-01-01

    Full Text Available Ontology learning (OL is the computational task of generating a knowledge base in the form of an ontology, given an unstructured corpus in natural language (NL. While most works in the field of ontology learning have been primarily based on a statistical approach to extract lightweight OL, very few attempts have been made to extract axiomatic OL (called heavyweight OL from NL text documents. Axiomatic OL supports more precise formal logic-based reasoning when compared to lightweight OL. Lexico-syntactic pattern matching and statisticsal one cannot lead to very accurate learning, mostly because of several linguistic nuances in the NL. Axiomatic OL is an alternative methodology that has not been explored much, where a deep linguistics analysis in computational linguistics is used to generate formal axioms and definitions instead of simply inducing a taxonomy. The ontology that is created not only stores the information about the application domain in explicit knowledge, but also can deduce the implicit knowledge from this ontology. This research will explore the English translation of the meaning of Quranic texts.

  13. Measurement and Ontology: What Kind of Evidence Can We Have for Quantum Fields?

    Science.gov (United States)

    Falkenburg, Brigitte

    In the following, I deal with the ontology of quantum field theory (QFT) from a Kantian point of view, in terms of parts of empirical reality and their relations. In contradistinction to a formal ontology of QFT that is based primarily on the formal structure of the theory, I focus on the ways in which quantum fields can be measured, and on the structural features of empirical reality to which these measurements give rise. To approach the ontology of quantum fields in terms of measurement results in two paradoxes. First, ontology is about the structure of independent entities which belong to the furniture of the world, but measurements rely on interaction. Second, experimental evidence for quantum field theories is mainly based on particle tracks and other local phenomena. Thus, what kind of evidence can we have for the field structure of quantum fields? My paper attempts to unravel these paradoxes in the following steps. First, I give a rough sketch of the appearances of particle physics, the kinds of experimental evidence which count as tests of quantum electrodynamcs (QED) and the standard model of particle physics (1). In an intermezzo on Kant's view of scientific experience, I explain in which terms we might conceive of empirical reality beyond the claims of strict empiricism (2). Finally, I apply these ideas to the appearances of particle physics and suggest that they commit us to a relational ontology of QFT (3).

  14. Knowledge Management Framework for Emerging Infectious Diseases Preparedness and Response: Design and Development of Public Health Document Ontology.

    Science.gov (United States)

    Zhang, Zhizun; Gonzalez, Mila C; Morse, Stephen S; Venkatasubramanian, Venkat

    2017-10-11

    There are increasing concerns about our preparedness and timely coordinated response across the globe to cope with emerging infectious diseases (EIDs). This poses practical challenges that require exploiting novel knowledge management approaches effectively. This work aims to develop an ontology-driven knowledge management framework that addresses the existing challenges in sharing and reusing public health knowledge. We propose a systems engineering-inspired ontology-driven knowledge management approach. It decomposes public health knowledge into concepts and relations and organizes the elements of knowledge based on the teleological functions. Both knowledge and semantic rules are stored in an ontology and retrieved to answer queries regarding EID preparedness and response. A hybrid concept extraction was implemented in this work. The quality of the ontology was evaluated using the formal evaluation method Ontology Quality Evaluation Framework. Our approach is a potentially effective methodology for managing public health knowledge. Accuracy and comprehensiveness of the ontology can be improved as more knowledge is stored. In the future, a survey will be conducted to collect queries from public health practitioners. The reasoning capacity of the ontology will be evaluated using the queries and hypothetical outbreaks. We suggest the importance of developing a knowledge sharing standard like the Gene Ontology for the public health domain. ©Zhizun Zhang, Mila C Gonzalez, Stephen S Morse, Venkat Venkatasubramanian. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 11.10.2017.

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

    Science.gov (United States)

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

    2014-12-08

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

  16. Fear of the Formal

    DEFF Research Database (Denmark)

    du Gay, Paul; Lopdrup-Hjorth, Thomas

    Over recent decades, institutions exhibiting high degrees of formality have come in for severe criticism. From the private to the public sector, and across a whole spectrum of actors spanning from practitioners to academics, formal organization is viewed with increasing doubt and skepticism....... In a “Schumpetarian world” (Teece et al., 1997: 509) of dynamic competition and incessant reform, formal organization appears as well suited to survival as a fish out of water. Indeed, formal organization, and its closely overlapping semantic twin bureaucracy, are not only represented as ill suited to the realities...... is that formal organization is an obstacle to be overcome. For that very reason, critics, intellectuals and reformers alike have urged public and private organizations to break out of the stifling straightjacket of formality, to dispense with bureaucracy, and to tear down hierarchies. This could either be done...

  17. TermGenie - a web-application for pattern-based ontology class generation.

    Science.gov (United States)

    Dietze, Heiko; Berardini, Tanya Z; Foulger, Rebecca E; Hill, David P; Lomax, Jane; Osumi-Sutherland, David; Roncaglia, Paola; Mungall, Christopher J

    2014-01-01

    Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes. TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes. TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.

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

    Directory of Open Access Journals (Sweden)

    Lucia Manni

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

  19. An ontology for factors affecting tuberculosis treatment adherence behavior in sub-Saharan Africa.

    Science.gov (United States)

    Ogundele, Olukunle Ayodeji; Moodley, Deshendran; Pillay, Anban W; Seebregts, Christopher J

    2016-01-01

    Adherence behavior is a complex phenomenon influenced by diverse personal, cultural, and socioeconomic factors that may vary between communities in different regions. Understanding the factors that influence adherence behavior is essential in predicting which individuals and communities are at risk of nonadherence. This is necessary for supporting resource allocation and intervention planning in disease control programs. Currently, there is no known concrete and unambiguous computational representation of factors that influence tuberculosis (TB) treatment adherence behavior that is useful for prediction. This study developed a computer-based conceptual model for capturing and structuring knowledge about the factors that influence TB treatment adherence behavior in sub-Saharan Africa (SSA). An extensive review of existing categorization systems in the literature was used to develop a conceptual model that captured scientific knowledge about TB adherence behavior in SSA. The model was formalized as an ontology using the web ontology language. The ontology was then evaluated for its comprehensiveness and applicability in building predictive models. The outcome of the study is a novel ontology-based approach for curating and structuring scientific knowledge of adherence behavior in patients with TB in SSA. The ontology takes an evidence-based approach by explicitly linking factors to published clinical studies. Factors are structured around five dimensions: factor type, type of effect, regional variation, cross-dependencies between factors, and treatment phase. The ontology is flexible and extendable and provides new insights into the nature of and interrelationship between factors that influence TB adherence.

  20. 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.

  1. OMIT: dynamic, semi-automated ontology development for the microRNA domain.

    Directory of Open Access Journals (Sweden)

    Jingshan Huang

    Full Text Available As a special class of short non-coding RNAs, microRNAs (a.k.a. miRNAs or miRs have been reported to perform important roles in various biological processes by regulating respective target genes. However, significant barriers exist during biologists' conventional miR knowledge discovery. Emerging semantic technologies, which are based upon domain ontologies, can render critical assistance to this problem. Our previous research has investigated the construction of a miR ontology, named Ontology for MIcroRNA Target Prediction (OMIT, the very first of its kind that formally encodes miR domain knowledge. Although it is unavoidable to have a manual component contributed by domain experts when building ontologies, many challenges have been identified for a completely manual development process. The most significant issue is that a manual development process is very labor-intensive and thus extremely expensive. Therefore, we propose in this paper an innovative ontology development methodology. Our contributions can be summarized as: (i We have continued the development and critical improvement of OMIT, solidly based on our previous research outcomes. (ii We have explored effective and efficient algorithms with which the ontology development can be seamlessly combined with machine intelligence and be accomplished in a semi-automated manner, thus significantly reducing large amounts of human efforts. A set of experiments have been conducted to thoroughly evaluate our proposed methodology.

  2. OMIT: dynamic, semi-automated ontology development for the microRNA domain.

    Science.gov (United States)

    Huang, Jingshan; Dang, Jiangbo; Borchert, Glen M; Eilbeck, Karen; Zhang, He; Xiong, Min; Jiang, Weijian; Wu, Hao; Blake, Judith A; Natale, Darren A; Tan, Ming

    2014-01-01

    As a special class of short non-coding RNAs, microRNAs (a.k.a. miRNAs or miRs) have been reported to perform important roles in various biological processes by regulating respective target genes. However, significant barriers exist during biologists' conventional miR knowledge discovery. Emerging semantic technologies, which are based upon domain ontologies, can render critical assistance to this problem. Our previous research has investigated the construction of a miR ontology, named Ontology for MIcroRNA Target Prediction (OMIT), the very first of its kind that formally encodes miR domain knowledge. Although it is unavoidable to have a manual component contributed by domain experts when building ontologies, many challenges have been identified for a completely manual development process. The most significant issue is that a manual development process is very labor-intensive and thus extremely expensive. Therefore, we propose in this paper an innovative ontology development methodology. Our contributions can be summarized as: (i) We have continued the development and critical improvement of OMIT, solidly based on our previous research outcomes. (ii) We have explored effective and efficient algorithms with which the ontology development can be seamlessly combined with machine intelligence and be accomplished in a semi-automated manner, thus significantly reducing large amounts of human efforts. A set of experiments have been conducted to thoroughly evaluate our proposed methodology.

  3. The next generation of similarity measures that fully explore the semantics in biomedical ontologies.

    Science.gov (United States)

    Couto, Francisco M; Pinto, H Sofia

    2013-10-01

    There is a prominent trend to augment and improve the formality of biomedical ontologies. For example, this is shown by the current effort on adding description logic axioms, such as disjointness. One of the key ontology applications that can take advantage of this effort is the conceptual (functional) similarity measurement. The presence of description logic axioms in biomedical ontologies make the current structural or extensional approaches weaker and further away from providing sound semantics-based similarity measures. Although beneficial in small ontologies, the exploration of description logic axioms by semantics-based similarity measures is computational expensive. This limitation is critical for biomedical ontologies that normally contain thousands of concepts. Thus in the process of gaining their rightful place, biomedical functional similarity measures have to take the journey of finding how this rich and powerful knowledge can be fully explored while keeping feasible computational costs. This manuscript aims at promoting and guiding the development of compelling tools that deliver what the biomedical community will require in a near future: a next-generation of biomedical similarity measures that efficiently and fully explore the semantics present in biomedical ontologies.

  4. OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain

    Science.gov (United States)

    Huang, Jingshan; Dang, Jiangbo; Borchert, Glen M.; Eilbeck, Karen; Zhang, He; Xiong, Min; Jiang, Weijian; Wu, Hao; Blake, Judith A.; Natale, Darren A.; Tan, Ming

    2014-01-01

    As a special class of short non-coding RNAs, microRNAs (a.k.a. miRNAs or miRs) have been reported to perform important roles in various biological processes by regulating respective target genes. However, significant barriers exist during biologists' conventional miR knowledge discovery. Emerging semantic technologies, which are based upon domain ontologies, can render critical assistance to this problem. Our previous research has investigated the construction of a miR ontology, named Ontology for MIcroRNA Target Prediction (OMIT), the very first of its kind that formally encodes miR domain knowledge. Although it is unavoidable to have a manual component contributed by domain experts when building ontologies, many challenges have been identified for a completely manual development process. The most significant issue is that a manual development process is very labor-intensive and thus extremely expensive. Therefore, we propose in this paper an innovative ontology development methodology. Our contributions can be summarized as: (i) We have continued the development and critical improvement of OMIT, solidly based on our previous research outcomes. (ii) We have explored effective and efficient algorithms with which the ontology development can be seamlessly combined with machine intelligence and be accomplished in a semi-automated manner, thus significantly reducing large amounts of human efforts. A set of experiments have been conducted to thoroughly evaluate our proposed methodology. PMID:25025130

  5. Integrating semi-formal and formal requirements

    NARCIS (Netherlands)

    Wieringa, Roelf J.; Olivé, Antoni; Dubois, Eric; Pastor, Joan Antoni; Huyts, Sander

    1997-01-01

    In this paper, we report on the integration of informal, semiformal and formal requirements specification techniques. We present a framework for requirements specification called TRADE, within which several well-known semiformal specification techniques are placed. TRADE is based on an analysis of

  6. 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.

  7. 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.

  8. Part-whole reasoning in medical ontologies revisited--introducing SEP triplets into classification-based description logics.

    Science.gov (United States)

    Schulz, S; Romacker, M; Hahn, U

    1998-01-01

    The development of powerful and comprehensive medical ontologies that support formal reasoning on a large scale is one of the key requirements for clinical computing in the next millennium. Taxonomic medical knowledge, a major portion of these ontologies, is mainly characterized by generalization and part-whole relations between concepts. While reasoning in generalization hierarchies is quite well understood, no fully conclusive mechanism as yet exists for part-whole reasoning. The approach we take emulates part-whole reasoning via classification-based reasoning using SEP triplets, a special data structure for encoding part-whole relations that is fully embedded in the formal framework of standard description logics.

  9. THE CIDOC CRM GAME: A Serious Game Approach to Ontology Learning

    Science.gov (United States)

    Guillem, A.; Bruseker, G.

    2017-08-01

    Formal ontologies such as CIDOC CRM (Conceptual Reference Model) form part of the central strategy for the medium and longterm integration of cultural heritage data to allow for its greater valorization and dissemination. Despite this, uptake of CIDOC CRM at the ground level of Cultural Heriage (CH) practice is limited. Part of the reason behind this lack of uptake lies in the fact that ontologies are considered too complicated and abstract for application in real life scenarios. This paper presents the rationale behind and the design of a CIDOC CRM game, the intent of which is to provide a learning mechanism to allow learners of wide backgrounds and interests to approach CIDOC CRM in a hands-on and interactive fashion. The CIDOC CRM game consist of decks of cards and game boards that allow players to engage with the concepts of a formal ontology in relation to real data in an entertaining and informative way. It is argued that the CIDOC CRM Game can form an important part of introducing the basic elements of formal ontology and this standard to a wider audience in order to aid wider understanding and adoption of the same.

  10. 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.

  11. Teoría de conjuntos y ontología

    Directory of Open Access Journals (Sweden)

    Minhot, Leticia O.

    2011-02-01

    Full Text Available The question “what kind of entity is a scientific theory” is an ontological one. Its answer has to have ontological categories in order to submit theories. If these categories belong to set theory, then scientific theories are set theoretical entities. In this paper I develop three possible ways to explicate the claim that set theory is the ontology for scientific theories. The first one understands set theory as formal ontology in the sense of Husserl. The second one is based on Tugendhat (2003. Here set theory is interpreted as formal semantics. The third one has no relation to structuralist view of theories, but it shares with it the idea that set theory is ontology. This last way belongs to Badiou. The idea in this paper is to think the reconstruction of theories using set theory from a different way to the ontosemantic thesis.

    Preguntarse qué clase de entidad es una teoría científica es plantearse una pregunta ontológica. Su respuesta consistirá de categorías ontológicas que subsumirán a las teorías. Si tales son las de la teoría de conjuntos, esto significa que las teorías científicas son entidades conjuntistas, al menos en parte. En este trabajo construyo tres modos posibles de elucidar la pretensión de la teoría de conjuntos como ontología para las teorías científicas. La primera es una lectura de la teoría de conjuntos como ontología formal en el sentido de Husserl. En la segunda, en base a Tugendhat (2003, el uso de la teoría de conjuntos para la reconstrucción de teorías significa que ésta es una semántica formal. La tercera es la presentación de una lectura ajena al estructuralismo, pero que, sin embargo, considera a la teoría de conjuntos como ontología. Lo que hago aquí es utilizar la propuesta de Badiou para pensar, desde una vía alternativa a la tesis ontosemántica, la actividad de reconstruir teorías utilizando a la teoría de conjuntos

  12. Supporting the Bronze CastingThrough Information Structuring Based on Ontology application

    Directory of Open Access Journals (Sweden)

    Górny Z.

    2014-03-01

    Full Text Available A significant part of the knowledge used in the production processes is represented with natural language. Yet, the use of that knowledge in computer-assisted decision-making requires the application of appropriate formal and development tools. An interesting possibility is created by the use of an ontology that is understandable both for humans and for the computer. This paper presents a proposal for structuring the information about the foundry processes, based on the definition of ontology adapted to the physical structure of the ongoing technological operations that make up the process of producing castings.

  13. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

    Science.gov (United States)

    Hastings, Janna; Chepelev, Leonid; Willighagen, Egon; Adams, Nico; Steinbeck, Christoph; Dumontier, Michel

    2011-01-01

    Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).

  14. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

    Directory of Open Access Journals (Sweden)

    Janna Hastings

    Full Text Available Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA.

  15. A fuzzy-ontology-oriented case-based reasoning framework for semantic diabetes diagnosis.

    Science.gov (United States)

    El-Sappagh, Shaker; Elmogy, Mohammed; Riad, A M

    2015-11-01

    Case-based reasoning (CBR) is a problem-solving paradigm that uses past knowledge to interpret or solve new problems. It is suitable for experience-based and theory-less problems. Building a semantically intelligent CBR that mimic the expert thinking can solve many problems especially medical ones. Knowledge-intensive CBR using formal ontologies is an evolvement of this paradigm. Ontologies can be used for case representation and storage, and it can be used as a background knowledge. Using standard medical ontologies, such as SNOMED CT, enhances the interoperability and integration with the health care systems. Moreover, utilizing vague or imprecise knowledge further improves the CBR semantic effectiveness. This paper proposes a fuzzy ontology-based CBR framework. It proposes a fuzzy case-base OWL2 ontology, and a fuzzy semantic retrieval algorithm that handles many feature types. This framework is implemented and tested on the diabetes diagnosis problem. The fuzzy ontology is populated with 60 real diabetic cases. The effectiveness of the proposed approach is illustrated with a set of experiments and case studies. The resulting system can answer complex medical queries related to semantic understanding of medical concepts and handling of vague terms. The resulting fuzzy case-base ontology has 63 concepts, 54 (fuzzy) object properties, 138 (fuzzy) datatype properties, 105 fuzzy datatypes, and 2640 instances. The system achieves an accuracy of 97.67%. We compare our framework with existing CBR systems and a set of five machine-learning classifiers; our system outperforms all of these systems. Building an integrated CBR system can improve its performance. Representing CBR knowledge using the fuzzy ontology and building a case retrieval algorithm that treats different features differently improves the accuracy of the resulting systems. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

    Science.gov (United States)

    Hastings, Janna; Chepelev, Leonid; Willighagen, Egon; Adams, Nico; Steinbeck, Christoph; Dumontier, Michel

    2011-01-01

    Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA). PMID:21991315

  17. Geometry and Formal Linguistics.

    Science.gov (United States)

    Huff, George A.

    This paper presents a method of encoding geometric line-drawings in a way which allows sets of such drawings to be interpreted as formal languages. A characterization of certain geometric predicates in terms of their properties as languages is obtained, and techniques usually associated with generative grammars and formal automata are then applied…

  18. Software Formal Inspections Guidebook

    Science.gov (United States)

    1993-01-01

    The Software Formal Inspections Guidebook is designed to support the inspection process of software developed by and for NASA. This document provides information on how to implement a recommended and proven method for conducting formal inspections of NASA software. This Guidebook is a companion document to NASA Standard 2202-93, Software Formal Inspections Standard, approved April 1993, which provides the rules, procedures, and specific requirements for conducting software formal inspections. Application of the Formal Inspections Standard is optional to NASA program or project management. In cases where program or project management decide to use the formal inspections method, this Guidebook provides additional information on how to establish and implement the process. The goal of the formal inspections process as documented in the above-mentioned Standard and this Guidebook is to provide a framework and model for an inspection process that will enable the detection and elimination of defects as early as possible in the software life cycle. An ancillary aspect of the formal inspection process incorporates the collection and analysis of inspection data to effect continual improvement in the inspection process and the quality of the software subjected to the process.

  19. Formality in Brackets

    DEFF Research Database (Denmark)

    Garsten, Christina; Nyqvist, Anette

    Ethnographic work in formal organizations involves learning to recognize the many layers of front stage and back stage of organized life, and to bracket formality. It means to be alert to the fact that what is formal and front stage for one some actors, and in some situations, may in fact be back...... stage and informal for others. Walking the talk, donning the appropriate attire, wearing the proper suit, may be part of what is takes to figure out the code of formal organizational settings – an entrance ticket to the backstage, as it were. Oftentimes, it involves a degree of mimicry, of ‘following...... suits’ (Nyqvist 2013), and of doing ‘ethnography by failure’ (Garsten 2013). In this paper, we explore the layers of informality and formality in our fieldwork experiences among financial investors and policy experts, and discuss how to ethnographically represent embodied fieldwork practices. How do we...

  20. 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...

  1. 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....

  2. 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...

  3. 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 ...

  4. 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.

  5. 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

  6. A Concept Lattice for Semantic Integration of Geo-Ontologies Based on Weight of Inclusion Degree Importance and Information Entropy

    Directory of Open Access Journals (Sweden)

    Jia Xiao

    2016-11-01

    Full Text Available Constructing a merged concept lattice with formal concept analysis (FCA is an important research direction in the field of integrating multi-source geo-ontologies. Extracting essential geographical properties and reducing the concept lattice are two key points of previous research. A formal integration method is proposed to address the challenges in these two areas. We first extract essential properties from multi-source geo-ontologies and use FCA to build a merged formal context. Second, the combined importance weight of each single attribute of the formal context is calculated by introducing the inclusion degree importance from rough set theory and information entropy; then a weighted formal context is built from the merged formal context. Third, a combined weighted concept lattice is established from the weighted formal context with FCA and the importance weight value of every concept is defined as the sum of weight of attributes belonging to the concept’s intent. Finally, semantic granularity of concept is defined by its importance weight; we, then gradually reduce the weighted concept lattice by setting up diminishing threshold of semantic granularity. Additionally, all of those reduced lattices are organized into a regular hierarchy structure based on the threshold of semantic granularity. A workflow is designed to demonstrate this procedure. A case study is conducted to show feasibility and validity of this method and the procedure to integrate multi-source geo-ontologies.

  7. Initial Implementation of a comparative Data Analysis Ontology

    Directory of Open Access Journals (Sweden)

    Francisco Prosdocimi

    2009-01-01

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

  8. Initial Implementation of a Comparative Data Analysis Ontology

    Directory of Open Access Journals (Sweden)

    Francisco Prosdocimi

    2009-07-01

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

  9. Supplementary Material for: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

    KAUST Repository

    Hoehndorf, Robert

    2016-01-01

    Abstract Background The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text. Results We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities. Conclusions The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established

  10. Design and Implementation of Hydrologic Process Knowledge-base Ontology: A case study for the Infiltration Process

    Science.gov (United States)

    Elag, M.; Goodall, J. L.

    2013-12-01

    Hydrologic modeling often requires the re-use and integration of models from different disciplines to simulate complex environmental systems. Component-based modeling introduces a flexible approach for integrating physical-based processes across disciplinary boundaries. Several hydrologic-related modeling communities have adopted the component-based approach for simulating complex physical systems by integrating model components across disciplinary boundaries in a workflow. However, it is not always straightforward to create these interdisciplinary models due to the lack of sufficient knowledge about a hydrologic process. This shortcoming is a result of using informal methods for organizing and sharing information about a hydrologic process. A knowledge-based ontology provides such standards and is considered the ideal approach for overcoming this challenge. The aims of this research are to present the methodology used in analyzing the basic hydrologic domain in order to identify hydrologic processes, the ontology itself, and how the proposed ontology is integrated with the Water Resources Component (WRC) ontology. The proposed ontology standardizes the definitions of a hydrologic process, the relationships between hydrologic processes, and their associated scientific equations. The objective of the proposed Hydrologic Process (HP) Ontology is to advance the idea of creating a unified knowledge framework for components' metadata by introducing a domain-level ontology for hydrologic processes. The HP ontology is a step toward an explicit and robust domain knowledge framework that can be evolved through the contribution of domain users. Analysis of the hydrologic domain is accomplished using the Formal Concept Approach (FCA), in which the infiltration process, an important hydrologic process, is examined. Two infiltration methods, the Green-Ampt and Philip's methods, were used to demonstrate the implementation of information in the HP ontology. Furthermore, a SPARQL

  11. Approaching the axiomatic enrichment of the Gene Ontology from a lexical perspective.

    Science.gov (United States)

    Quesada-Martínez, Manuel; Mikroyannidi, Eleni; Fernández-Breis, Jesualdo Tomás; Stevens, Robert

    2015-09-01

    The main goal of this work is to measure how lexical regularities in biomedical ontology labels can be used for the automatic creation of formal relationships between classes, and to evaluate the results of applying our approach to the Gene Ontology (GO). In recent years, we have developed a method for the lexical analysis of regularities in biomedical ontology labels, and we showed that the labels can present a high degree of regularity. In this work, we extend our method with a cross-products extension (CPE) metric, which estimates the potential interest of a specific regularity for axiomatic enrichment in the lexical analysis, using information on exact matches in external ontologies. The GO consortium recently enriched the GO by using so-called cross-product extensions. Cross-products are generated by establishing axioms that relate a given GO class with classes from the GO or other biomedical ontologies. We apply our method to the GO and study how its lexical analysis can identify and reconstruct the cross-products that are defined by the GO consortium. The label of the classes of the GO are highly regular in lexical terms, and the exact matches with labels of external ontologies affect 80% of the GO classes. The CPE metric reveals that 31.48% of the classes that exhibit regularities have fragments that are classes into two external ontologies that are selected for our experiment, namely, the Cell Ontology and the Chemical Entities of Biological Interest ontology, and 18.90% of them are fully decomposable into smaller parts. Our results show that the CPE metric permits our method to detect GO cross-product extensions with a mean recall of 62% and a mean precision of 28%. The study is completed with an analysis of false positives to explain this precision value. We think that our results support the claim that our lexical approach can contribute to the axiomatic enrichment of biomedical ontologies and that it can provide new insights into the engineering of

  12. Database Concepts in a Domain Ontology

    Directory of Open Access Journals (Sweden)

    Gorskis Henrihs

    2017-12-01

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

  13. 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. Necessity of Integral Formalism

    International Nuclear Information System (INIS)

    Tao Yong

    2011-01-01

    To describe the physical reality, there are two ways of constructing the dynamical equation of field, differential formalism and integral formalism. The importance of this fact is firstly emphasized by Yang in case of gauge field [Phys. Rev. Lett. 33 (1974) 445], where the fact has given rise to a deeper understanding for Aharonov-Bohm phase and magnetic monopole [Phys. Rev. D 12 (1975) 3845]. In this paper we shall point out that such a fact also holds in general wave function of matter, it may give rise to a deeper understanding for Berry phase. Most importantly, we shall prove a point that, for general wave function of matter, in the adiabatic limit, there is an intrinsic difference between its integral formalism and differential formalism. It is neglect of this difference that leads to an inconsistency of quantum adiabatic theorem pointed out by Marzlin and Sanders [Phys. Rev. Lett. 93 (2004) 160408]. It has been widely accepted that there is no physical difference of using differential operator or integral operator to construct the dynamical equation of field. Nevertheless, our study shows that the Schrödinger differential equation (i.e., differential formalism for wave function) shall lead to vanishing Berry phase and that the Schrödinger integral equation (i.e., integral formalism for wave function), in the adiabatic limit, can satisfactorily give the Berry phase. Therefore, we reach a conclusion: There are two ways of describing physical reality, differential formalism and integral formalism; but the integral formalism is a unique way of complete description. (general)

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

    Directory of Open Access Journals (Sweden)

    Dibowski Henrik

    2011-01-01

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

  1. The Knowledge Sharing Based on PLIB Ontology and XML for Collaborative Product Commerce

    Science.gov (United States)

    Ma, Jun; Luo, Guofu; Li, Hao; Xiao, Yanqiu

    Collaborative Product Commerce (CPC) has become a brand-new commerce mode for manufacture. In order to promote information communication with each other more efficiently in CPC, a knowledge-sharing framework based on PLIB (ISO 13584) ontology and XML was presented, and its implementation method was studied. At first, according to the methodology of PLIB (ISO 13584), a common ontology—PLIB ontology was put forward which provide a coherent conceptual meaning within the context of CPC domain. Meanwhile, for the sake of knowledge intercommunion via internet, the PLIB ontology formalization description by EXPRESS mode was converted into XML Schema, and two mapping methods were presented: direct mapping approach and meta-levels mapping approach, while the latter was adopted. Based on above work, a parts resource knowledge-sharing framework (CPC-KSF) was put forward and realized, which has been applied in the process of automotive component manufacturing collaborative product commerce.

  2. a Representation-Driven Ontology for Spatial Data Quality Elements, with Orthoimagery as Running Example

    Science.gov (United States)

    Hangouët, J.-F.

    2015-08-01

    The many facets of what is encompassed by such an expression as "quality of spatial data" can be considered as a specific domain of reality worthy of formal description, i.e. of ontological abstraction. Various ontologies for data quality elements have already been proposed in literature. Today, the system of quality elements is most generally used and discussed according to the configuration exposed in the "data dictionary for data quality" of international standard ISO 19157. Our communication proposes an alternative view. This is founded on a perspective which focuses on the specificity of spatial data as a product: the representation perspective, where data in the computer are meant to show things of the geographic world and to be interpreted as such. The resulting ontology introduces new elements, the usefulness of which will be illustrated by orthoimagery examples.

  3. 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...

  4. 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...

  5. 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.

  6. Finding the best visualization of an ontology

    DEFF Research Database (Denmark)

    Fabritius, Christina; Madsen, Nadia; Clausen, Jens

    2006-01-01

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

  7. 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...

  8. 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...

  9. 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.

  10. 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.

  11. 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...

  12. 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.

  13. 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

  14. Ontology for assessment studies of human-computer-interaction in surgery.

    Science.gov (United States)

    Machno, Andrej; Jannin, Pierre; Dameron, Olivier; Korb, Werner; Scheuermann, Gerik; Meixensberger, Jürgen

    2015-02-01

    New technologies improve modern medicine, but may result in unwanted consequences. Some occur due to inadequate human-computer-interactions (HCI). To assess these consequences, an investigation model was developed to facilitate the planning, implementation and documentation of studies for HCI in surgery. The investigation model was formalized in Unified Modeling Language and implemented as an ontology. Four different top-level ontologies were compared: Object-Centered High-level Reference, Basic Formal Ontology, General Formal Ontology (GFO) and Descriptive Ontology for Linguistic and Cognitive Engineering, according to the three major requirements of the investigation model: the domain-specific view, the experimental scenario and the representation of fundamental relations. Furthermore, this article emphasizes the distinction of "information model" and "model of meaning" and shows the advantages of implementing the model in an ontology rather than in a database. The results of the comparison show that GFO fits the defined requirements adequately: the domain-specific view and the fundamental relations can be implemented directly, only the representation of the experimental scenario requires minor extensions. The other candidates require wide-ranging extensions, concerning at least one of the major implementation requirements. Therefore, the GFO was selected to realize an appropriate implementation of the developed investigation model. The ensuing development considered the concrete implementation of further model aspects and entities: sub-domains, space and time, processes, properties, relations and functions. The investigation model and its ontological implementation provide a modular guideline for study planning, implementation and documentation within the area of HCI research in surgery. This guideline helps to navigate through the whole study process in the form of a kind of standard or good clinical practice, based on the involved foundational frameworks

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2017-01-04

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

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

    Science.gov (United States)

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

    2013-05-01

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

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

    Lifescience Database Archive (English)

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

    d'Aquin, Mathieu; Noy, Natalya F.

    2011-01-01

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

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

    Science.gov (United States)

    Bachore, Zelalem

    2012-01-01

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

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

    Science.gov (United States)

    Soares, Andrey

    2009-01-01

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

  3. Formalized Informal Learning

    DEFF Research Database (Denmark)

    Levinsen, Karin Tweddell; Sørensen, Birgitte Holm

    2013-01-01

    are examined and the relation between network society competences, learners’ informal learning strategies and ICT in formalized school settings over time is studied. The authors find that aspects of ICT like multimodality, intuitive interaction design and instant feedback invites an informal bricoleur approach....... When integrated into certain designs for teaching and learning, this allows for Formalized Informal Learning and support is found for network society competences building....

  4. Integrated formal operations plan

    Energy Technology Data Exchange (ETDEWEB)

    Cort, G.; Dearholt, W.; Donahue, S.; Frank, J.; Perkins, B.; Tyler, R.; Wrye, J.

    1994-01-05

    The concept of formal operations (that is, a collection of business practices to assure effective, accountable operations) has vexed the Laboratory for many years. To date most attempts at developing such programs have been based upon rigid, compliance-based interpretations of a veritable mountain of Department of Energy (DOE) orders, directives, notices, and standards. These DOE dictates seldom take the broad view but focus on highly specialized programs isolated from the overall context of formal operations. The result is a confusing array of specific, and often contradictory, requirements that produce a patchwork of overlapping niche programs. This unnecessary duplication wastes precious resources, dramatically increases the complexity of our work processes, and communicates a sense of confusion to our customers and regulators. Coupled with the artificial divisions that have historically existed among the Laboratory`s formal operations organizations (quality assurance, configuration management, records management, training, etc.), this approach has produced layers of increasingly vague and complex formal operations plans, each of which interprets its parent and adds additional requirements of its own. Organizational gridlock ensues whenever an activity attempts to implement these bureaucratic monstrosities. The integrated formal operations plan presented is to establish a set of requirements that must be met by an integrated formal operations program, assign responsibilities for implementation and operation of the program, and specify criteria against which the performance of the program will be measured. The accountable line manager specifies the items, processes, and information (the controlled elements) to which the formal operations program specified applies. The formal operations program is implemented using a graded approach based on the level of importance of the various controlled elements and the scope of the activities in which they are involved.

  5. 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

  6. A method of constructing geo-object ontology in disaster system for prevention and decrease

    Science.gov (United States)

    Li, Bin; Liu, Jiping; Shi, Lihong; Wang, Zhenfeng

    2009-10-01

    A kind of formal system, which can express clearly a certain entity or information, is needed to express geographical concept. Besides, some rules explaining the interrelationship and action between different components are also required. Therefore, the conception of geo-object ontology is introduced. It is a shared formalization and display specification of conceptual knowledge system in the field of concrete application of spatial information science. It can constitute hierarchy structure, which derives from the concept classification system in the geographical area. Its concepts can be described by the property. Property sets can form a vector space with multi-dimensional characteristics. Geographic space is composed of different types of geographic entities. And its concept is formed by a series of geographic entities with the same properties and actions. Moreover, each of the geographic entities can be mapped to an object, and each object has its spatial property, time information and topology, semantic relationships associated with other objects. The biggest difference between ecumenical information ontology and geo-ontology is that the latter has the spatial characteristics. During the construction process of geo-object ontology, some important components, such as geographic type, spatial relation, spatial entity type and coordinates, time, should be included to make further research. Here, taking disaster as an example, by using Protégé and OWL, combined methods used by constructing the geo-object ontology in the form of being manual made by domanial experts and semi-automatic are investigated oriented to disaster to serve ultimately geographic information retrieval service driven by ontology.

  7. Ontology-Driven Search and Triage: Design of a Web-Based Visual Interface for MEDLINE.

    Science.gov (United States)

    Demelo, Jonathan; Parsons, Paul; Sedig, Kamran

    2017-02-02

    Diverse users need to search health and medical literature to satisfy open-ended goals such as making evidence-based decisions and updating their knowledge. However, doing so is challenging due to at least two major difficulties: (1) articulating information needs using accurate vocabulary and (2) dealing with large document sets returned from searches. Common search interfaces such as PubMed do not provide adequate support for exploratory search tasks. Our objective was to improve support for exploratory search tasks by combining two strategies in the design of an interactive visual interface by (1) using a formal ontology to help users build domain-specific knowledge and vocabulary and (2) providing multi-stage triaging support to help mitigate the information overload problem. We developed a Web-based tool, Ontology-Driven Visual Search and Triage Interface for MEDLINE (OVERT-MED), to test our design ideas. We implemented a custom searchable index of MEDLINE, which comprises approximately 25 million document citations. We chose a popular biomedical ontology, the Human Phenotype Ontology (HPO), to test our solution to the vocabulary problem. We implemented multistage triaging support in OVERT-MED, with the aid of interactive visualization techniques, to help users deal with large document sets returned from searches. Formative evaluation suggests that the design features in OVERT-MED are helpful in addressing the two major difficulties described above. Using a formal ontology seems to help users articulate their information needs with more accurate vocabulary. In addition, multistage triaging combined with interactive visualizations shows promise in mitigating the information overload problem. Our strategies appear to be valuable in addressing the two major problems in exploratory search. Although we tested OVERT-MED with a particular ontology and document collection, we anticipate that our strategies can be transferred successfully to other contexts.

  8. Development of description framework of pharmacodynamics ontology and its application to possible drug-drug interaction reasoning.

    Science.gov (United States)

    Imai, Takeshi; Hayakawa, Masayo; Ohe, Kazuhiko

    2013-01-01

    Prediction of synergistic or antagonistic effects of drug-drug interaction (DDI) in vivo has been of considerable interest over the years. Formal representation of pharmacological knowledge such as ontology is indispensable for machine reasoning of possible DDIs. However, current pharmacology knowledge bases are not sufficient to provide formal representation of DDI information. With this background, this paper presents: (1) a description framework of pharmacodynamics ontology; and (2) a methodology to utilize pharmacodynamics ontology to detect different types of possible DDI pairs with supporting information such as underlying pharmacodynamics mechanisms. We also evaluated our methodology in the field of drugs related to noradrenaline signal transduction process and 11 different types of possible DDI pairs were detected. The main features of our methodology are the explanation capability of the reason for possible DDIs and the distinguishability of different types of DDIs. These features will not only be useful for providing supporting information to prescribers, but also for large-scale monitoring of drug safety.

  9. 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.

  10. 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

  11. 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.

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

    Science.gov (United States)

    Glick, David

    2016-10-01

    In this paper I elicit a prediction from structural realism and compare it, not to a historical case, but to a contemporary scientific theory. If structural realism is correct, then we should expect physics to develop theories that fail to provide an ontology of the sort sought by traditional realists. If structure alone is responsible for instrumental success, we should expect surplus ontology to be eliminated. Quantum field theory (QFT) provides the framework for some of the best confirmed theories in science, but debates over its ontology are vexed. Rather than taking a stand on these matters, the structural realist can embrace QFT as an example of just the kind of theory SR should lead us to expect. Yet, it is not clear that QFT meets the structuralist's positive expectation by providing a structure for the world. In particular, the problem of unitarily inequivalent representations threatens to undermine the possibility of QFT providing a unique structure for the world. In response to this problem, I suggest that the structuralist should endorse pluralism about structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. 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.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

  16. Ontology-based classification of remote sensing images using spectral rules

    Science.gov (United States)

    Andrés, Samuel; Arvor, Damien; Mougenot, Isabelle; Libourel, Thérèse; Durieux, Laurent

    2017-05-01

    Earth Observation data is of great interest for a wide spectrum of scientific domain applications. An enhanced access to remote sensing images for "domain" experts thus represents a great advance since it allows users to interpret remote sensing images based on their domain expert knowledge. However, such an advantage can also turn into a major limitation if this knowledge is not formalized, and thus is difficult for it to be shared with and understood by other users. In this context, knowledge representation techniques such as ontologies should play a major role in the future of remote sensing applications. We implemented an ontology-based prototype to automatically classify Landsat images based on explicit spectral rules. The ontology is designed in a very modular way in order to achieve a generic and versatile representation of concepts we think of utmost importance in remote sensing. The prototype was tested on four subsets of Landsat images and the results confirmed the potential of ontologies to formalize expert knowledge and classify remote sensing images.

  17. 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...

  18. Combining the Generic Entity-Attribute-Value Model and Terminological Models into a Common Ontology to Enable Data Integration and Decision Support.

    Science.gov (United States)

    Bouaud, Jacques; Guézennec, Gilles; Séroussi, Brigitte

    2018-01-01

    The integration of clinical information models and termino-ontological models into a unique ontological framework is highly desirable for it facilitates data integration and management using the same formal mechanisms for both data concepts and information model components. This is particularly true for knowledge-based decision support tools that aim to take advantage of all facets of semantic web technologies in merging ontological reasoning, concept classification, and rule-based inferences. We present an ontology template that combines generic data model components with (parts of) existing termino-ontological resources. The approach is developed for the guideline-based decision support module on breast cancer management within the DESIREE European project. The approach is based on the entity attribute value model and could be extended to other domains.

  19. TrOn: an anatomical ontology for the beetle Tribolium castaneum.

    Directory of Open Access Journals (Sweden)

    Jürgen Dönitz

    Full Text Available In a morphological ontology the expert's knowledge is represented in terms, which describe morphological structures and how these structures relate to each other. With the assistance of ontologies this expert knowledge is made processable by machines, through a formal and standardized representation of terms and their relations to each other. The red flour beetle Tribolium castaneum, a representative of the most species rich animal taxon on earth (the Coleoptera, is an emerging model organism for development, evolution, physiology, and pest control. In order to foster Tribolium research, we have initiated the Tribolium Ontology (TrOn, which describes the morphology of the red flour beetle. The content of this ontology comprises so far most external morphological structures as well as some internal ones. All modeled structures are consistently annotated for the developmental stages larva, pupa and adult. In TrOn all terms are grouped into three categories: Generic terms represent morphological structures, which are independent of a developmental stage. In contrast, downstream of such terms are concrete terms which stand for a dissectible structure of a beetle at a specific life stage. Finally, there are mixed terms describing structures that are only found at one developmental stage. These terms combine the characteristics of generic and concrete terms with features of both. These annotation principles take into account the changing morphology of the beetle during development and provide generic terms to be used in applications or for cross linking with other ontologies and data resources. We use the ontology for implementing an intuitive search function at the electronic iBeetle-Base, which stores morphological defects found in a genome wide RNA interference (RNAi screen. The ontology is available for download at http://ibeetle-base.uni-goettingen.de.

  20. TrOn: an anatomical ontology for the beetle Tribolium castaneum.

    Science.gov (United States)

    Dönitz, Jürgen; Grossmann, Daniela; Schild, Inga; Schmitt-Engel, Christian; Bradler, Sven; Prpic, Nikola-Michael; Bucher, Gregor

    2013-01-01

    In a morphological ontology the expert's knowledge is represented in terms, which describe morphological structures and how these structures relate to each other. With the assistance of ontologies this expert knowledge is made processable by machines, through a formal and standardized representation of terms and their relations to each other. The red flour beetle Tribolium castaneum, a representative of the most species rich animal taxon on earth (the Coleoptera), is an emerging model organism for development, evolution, physiology, and pest control. In order to foster Tribolium research, we have initiated the Tribolium Ontology (TrOn), which describes the morphology of the red flour beetle. The content of this ontology comprises so far most external morphological structures as well as some internal ones. All modeled structures are consistently annotated for the developmental stages larva, pupa and adult. In TrOn all terms are grouped into three categories: Generic terms represent morphological structures, which are independent of a developmental stage. In contrast, downstream of such terms are concrete terms which stand for a dissectible structure of a beetle at a specific life stage. Finally, there are mixed terms describing structures that are only found at one developmental stage. These terms combine the characteristics of generic and concrete terms with features of both. These annotation principles take into account the changing morphology of the beetle during development and provide generic terms to be used in applications or for cross linking with other ontologies and data resources. We use the ontology for implementing an intuitive search function at the electronic iBeetle-Base, which stores morphological defects found in a genome wide RNA interference (RNAi) screen. The ontology is available for download at http://ibeetle-base.uni-goettingen.de.

  1. The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain

    Directory of Open Access Journals (Sweden)

    Groza Tudor

    2012-03-01

    Full Text Available Abstract Background Skeletal dysplasias are a rare and heterogeneous group of genetic disorders affecting skeletal development. Patients with skeletal dysplasias suffer from many complex medical issues including degenerative joint disease and neurological complications. Because the data and expertise associated with this field is both sparse and disparate, significant benefits will potentially accrue from the availability of an ontology that provides a shared conceptualisation of the domain knowledge and enables data integration, cross-referencing and advanced reasoning across the relevant but distributed data sources. Results We introduce the design considerations and implementation details of the Bone Dysplasia Ontology. We also describe the different components of the ontology, including a comprehensive and formal representation of the skeletal dysplasia domain as well as the related genotypes and phenotypes. We then briefly describe SKELETOME, a community-driven knowledge curation platform that is underpinned by the Bone Dysplasia Ontology. SKELETOME enables domain experts to use, refine and extend and apply the ontology without any prior ontology engineering experience--to advance the body of knowledge in the skeletal dysplasia field. Conclusions The Bone Dysplasia Ontology represents the most comprehensive structured knowledge source for the skeletal dysplasias domain. It provides the means for integrating and annotating clinical and research data, not only at the generic domain knowledge level, but also at the level of individual patient case studies. It enables links between individual cases and publicly available genotype and phenotype resources based on a community-driven curation process that ensures a shared conceptualisation of the domain knowledge and its continuous incremental evolution.

  2. An ontology for factors affecting tuberculosis treatment adherence behavior in sub-Saharan Africa

    Directory of Open Access Journals (Sweden)

    Ogundele OA

    2016-04-01

    Full Text Available Olukunle Ayodeji Ogundele,1 Deshendran Moodley,1 Anban W Pillay,1 Christopher J Seebregts1,2 1UKZN/CSIR Meraka Centre for Artificial Intelligence Research and Health Architecture Laboratory, School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, KwaZulu-Natal, 2Jembi Health Systems NPC, Cape Town, South Africa Purpose: Adherence behavior is a complex phenomenon influenced by diverse personal, cultural, and socioeconomic factors that may vary between communities in different regions. Understanding the factors that influence adherence behavior is essential in predicting which individuals and communities are at risk of nonadherence. This is necessary for supporting resource allocation and intervention planning in disease control programs. Currently, there is no known concrete and unambiguous computational representation of factors that influence tuberculosis (TB treatment adherence behavior that is useful for prediction. This study developed a computer-based conceptual model for capturing and structuring knowledge about the factors that influence TB treatment adherence behavior in sub-Saharan Africa (SSA.Methods: An extensive review of existing categorization systems in the literature was used to develop a conceptual model that captured scientific knowledge about TB adherence behavior in SSA. The model was formalized as an ontology using the web ontology language. The ontology was then evaluated for its comprehensiveness and applicability in building predictive models. Conclusion: The outcome of the study is a novel ontology-based approach for curating and structuring scientific knowledge of adherence behavior in patients with TB in SSA. The ontology takes an evidence-based approach by explicitly linking factors to published clinical studies. Factors are structured around five dimensions: factor type, type of effect, regional variation, cross-dependencies between factors, and treatment phase. The ontology is

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

    Directory of Open Access Journals (Sweden)

    Stefan TRAUSAN-MATU

    2009-01-01

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

  4. 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.

  5. 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).

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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...

  11. 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,…

  12. 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

  13. Ontologies and Information Systems: A Literature Survey

    Science.gov (United States)

    2011-06-01

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

  14. 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

  15. 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...

  16. [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.

  17. 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.

  18. 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.

  19. 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...

  20. 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....

  1. Formalizing Probabilistic Safety Claims

    Science.gov (United States)

    Herencia-Zapana, Heber; Hagen, George E.; Narkawicz, Anthony J.

    2011-01-01

    A safety claim for a system is a statement that the system, which is subject to hazardous conditions, satisfies a given set of properties. Following work by John Rushby and Bev Littlewood, this paper presents a mathematical framework that can be used to state and formally prove probabilistic safety claims. It also enables hazardous conditions, their uncertainties, and their interactions to be integrated into the safety claim. This framework provides a formal description of the probabilistic composition of an arbitrary number of hazardous conditions and their effects on system behavior. An example is given of a probabilistic safety claim for a conflict detection algorithm for aircraft in a 2D airspace. The motivation for developing this mathematical framework is that it can be used in an automated theorem prover to formally verify safety claims.

  2. Integrating ontologies and argumentation for decision-making in breast cancer

    OpenAIRE

    Williams, M. H.

    2009-01-01

    This thesis describes some of the problems in providing care for patients with breast cancer. These are then used to motivate the development of an extension to an existing theory of argumentation, which I call the Ontology-based Argumentation Formalism (OAF). The work is assessed in both theoretical and empirical ways. From a clinical perspective, there is a problem with the provision of care. Numerous reports have noted the failure to provide uniformly high quality care, as w...

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. Fear of the Formal

    DEFF Research Database (Denmark)

    du Gay, Paul; Lopdrup-Hjorth, Thomas

    2016-01-01

    term this ‘fear of the formal’, outlining key elements of its genealogy and exploring its contemporary manifestation in relation to recent and ongoing reforms of organisational life in a range of contexts. At the same time, we seek to indicate the continuing constitutive significance of formality...

  12. Formalization of Medical Guidelines

    Czech Academy of Sciences Publication Activity Database

    Peleška, Jan; Anger, Z.; Buchtela, David; Šebesta, K.; Tomečková, Marie; Veselý, Arnošt; Zvára, K.; Zvárová, Jana

    2005-01-01

    Roč. 1, - (2005), s. 133-141 ISSN 1801-5603 R&D Projects: GA AV ČR 1ET200300413 Institutional research plan: CEZ:AV0Z10300504 Keywords : GLIF model * formalization of guidelines * prevention of cardiovascular diseases Subject RIV: IN - Informatics, Computer Science

  13. Readings in Formal Epistemology

    DEFF Research Database (Denmark)

    Formal epistemology’ is a term coined in the late 1990s for a new constellation of interests in philosophy,the roots of which are found in earlier works of epistemologists, philosophers of science, and logicians. It addresses a growing agenda of problems concerning knowledge, belief, certainty, ...

  14. Criteria for logical formalization

    Czech Academy of Sciences Publication Activity Database

    Peregrin, Jaroslav; Svoboda, Vladimír

    2013-01-01

    Roč. 190, č. 14 (2013), s. 2897-2924 ISSN 0039-7857 R&D Projects: GA ČR(CZ) GAP401/10/1279 Institutional support: RVO:67985955 Keywords : logic * logical form * formalization * reflective equilibrium Subject RIV: AA - Philosophy ; Religion Impact factor: 0.637, year: 2013

  15. IDEF3 Formalization Report

    Science.gov (United States)

    1991-10-01

    SUBJECT TERMS 15. NUMBER OF PAGES engineering management information systems method formalization 60 information engineering process modeling 16 PRICE...CODE information systems requirements definition methods knowlede acquisition methods systems engineering 17. SECURITY CLASSIFICATION ji. SECURITY... Management , Inc., Santa Monica, California. CORYNEN, G. C., 1975, A Mathematical Theory of Modeling and Simula- tion. Ph.D. Dissertation, Department

  16. The Benefits of Formalization

    DEFF Research Database (Denmark)

    Rand, John; Torm, Nina Elisabeth

    2012-01-01

    Based on unique panel data consisting of both formal and informal firms, this paper uses a matched double difference approach to examine the relationship between legal status and firm level outcomes in micro, small and medium manufacturing enterprises (SMEs) in Vietnam. Controlling for determinin...

  17. Formalizing physical security procedures

    NARCIS (Netherlands)

    Meadows, C.; Pavlovic, Dusko

    Although the problems of physical security emerged more than 10,000 years before the problems of computer security, no formal methods have been developed for them, and the solutions have been evolving slowly, mostly through social procedures. But as the traffic on physical and social networks is now

  18. Remedial action programs annual meeting: Meeting notes

    International Nuclear Information System (INIS)

    1987-01-01

    The US Department of Energy Grand Junction Projects Office was pleased to host the 1987 Remedial Action programs Annual Meeting and herein presents notes from that meeting as prepared (on relatively short notice) by participants. These notes are a summary of the information derived from the workshops, case studies, and ad hoc committee reports rather than formal proceedings. The order of the materials in this report follows the actual sequence of presentations during the annual meeting

  19. Ontolojik Boyutta ‘Döngüsel Süreklilik’ & ‘Değişim ve Dönüşüm’ü İmleyen Görsel Sembollerle Şiirin Biçim Düzeyinde Bilinçli Deformasyonu: Divan Şiirinde Deyişbilimsel Bir Önceleme Alanı Olarak Biçimsel Sapmalar The Conscious Deformation Of The Poetry At The Formal Level With Visual Symbols Alluding To 'Cyclical Continuity' And 'Change And Transformation' At The Ontological Dimension: Formal Deviations In The Divan Poetry As A Field Of Stylistic Foregroundings

    Directory of Open Access Journals (Sweden)

    Özge ÖZTEKİN

    2012-09-01

    Full Text Available Within the context of multiple aesthetics, the attempt of the art toattain the deep/unchanging truth and the holistic/universal aims atsearching for the invisible “core” of the object, in other words, the originof existence. In The reflections of this quest pursued with introspectionon the artwork, one might find a set of symbols which may go unnoticedat first sight. For instance, the lines of visual centred texts which bringtogether the verse and the picture are placed in a way to form afigure/pattern. This special form is also called as “visual poetry”,“concrete poetry”, “pattern poetry” and “figurative poetry”. The Divanpoetry, which constitutes an important branch of the Turkish poetrytradition contains examples of the visual poetry. They takes nameaccording to their forms. For example müşeccer/teşcîr, mücessem,müdevver, murabba. Classical codes of the poetic structure have beenaltered and visual experiments on formal level have been conducted.With plays on letters, words and form, extraordinary examples pushingthe limits of Divan poetry have been given. Meticulous interpretationswill demonstrate that visual poetry of the old literature -as the oldliterature itself- is open to multiple readings because academic analysisof old Turkish literature, along with the usual text annotation practices,allow for a language-use oriented stylistic evaluation of poetry andevaluations based on the ontological point-of-view within the context ofpoetry-philosophy-existence. Çoğul estetik bağlamında sanatın derin/değişmez bir gerçekliğe ve bütüne/evrensel olana ulaşma çabası, aslında nesnenin görünmeyen „öz‟ünü yani varlığın kökenini aramaya yöneliktir. İçe yoğunlaşma ile yapılan bu arayış yolculuğundan sanat eserine yansıyanlarda, herkesin ilk anda göremediği bir takım semboller yer alabilir. Örneğin şiir ve resmi buluşturan görüntü merkezli metinlerdeki dizeler, birer fig

  20. FORMAL MODELLING OF BUSINESS RULES: WHAT KIND OF TOOL TO USE?

    Directory of Open Access Journals (Sweden)

    Sandra Lovrenčić

    2006-12-01

    Full Text Available Business rules are today essential parts of a business system model. But presently, there are still various approaches to, definitions and classifications of this concept. Similarly, there are also different approaches in business rules formalization and implementation. This paper investigates formalization using formal language in association with easy domain modelling. Two of the tools that enable such approach are described and compared according to several factors. They represent ontology modelling and UML, nowadays widely used standard for object-oriented modelling. A simple example is also presented.

  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. Building a semi-automatic ontology learning and construction system for geosciences

    Science.gov (United States)

    Babaie, H. A.; Sunderraman, R.; Zhu, Y.

    2013-12-01

    We are developing an ontology learning and construction framework that allows continuous, semi-automatic knowledge extraction, verification, validation, and maintenance by potentially a very large group of collaborating domain experts in any geosciences field. The system brings geoscientists from the side-lines to the center stage of ontology building, allowing them to collaboratively construct and enrich new ontologies, and merge, align, and integrate existing ontologies and tools. These constantly evolving ontologies can more effectively address community's interests, purposes, tools, and change. The goal is to minimize the cost and time of building ontologies, and maximize the quality, usability, and adoption of ontologies by the community. Our system will be a domain-independent ontology learning framework that applies natural language processing, allowing users to enter their ontology in a semi-structured form, and a combined Semantic Web and Social Web approach that lets direct participation of geoscientists who have no skill in the design and development of their domain ontologies. A controlled natural language (CNL) interface and an integrated authoring and editing tool automatically convert syntactically correct CNL text into formal OWL constructs. The WebProtege-based system will allow a potentially large group of geoscientists, from multiple domains, to crowd source and participate in the structuring of their knowledge model by sharing their knowledge through critiquing, testing, verifying, adopting, and updating of the concept models (ontologies). We will use cloud storage for all data and knowledge base components of the system, such as users, domain ontologies, discussion forums, and semantic wikis that can be accessed and queried by geoscientists in each domain. We will use NoSQL databases such as MongoDB as a service in the cloud environment. MongoDB uses the lightweight JSON format, which makes it convenient and easy to build Web applications using

  3. Ontological Realism for the Research Domain Criteria for Mental Disorders.

    Science.gov (United States)

    Ceusters, Werner; Jensen, Mark; Diehl, Alexander D

    2017-01-01

    At the heart of the Research Domain Criteria for Mental Disorders is a matrix in which functional aspects of behavior are related to genotypic and (endo-)phenotypic research findings, and the various techniques through which they can been observed. The matrix is work in progress. As such it currently suffers from several shortcomings, the resolution of which, we contend, are essential to success of NIMH's goal of fostering translational science on mental disorders. Using well-established criteria for assessing the terminological and ontological quality of biomedical representations we identified the major problems to be (1) the abundant presence of terms that lack face value, (2) the absence of what the exact nature of the represented relationships are, and (3) referential imprecision with respect to the intended granularity of what the terms denote. We propose to eliminate these shortcomings by resorting to definitions and formal representations under the umbrella of Ontological Realism as they already have been developed in the areas of mental health, anatomy and biological functions.

  4. 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.

  5. 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

  6. 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,…

  7. 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.

  8. Hierarchical Analysis of the Omega Ontology

    Energy Technology Data Exchange (ETDEWEB)

    Joslyn, Cliff A.; Paulson, Patrick R.

    2009-12-01

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

  9. Automated Predictive Big Data Analytics Using Ontology Based Semantics.

    Science.gov (United States)

    Nural, Mustafa V; Cotterell, Michael E; Peng, Hao; Xie, Rui; Ma, Ping; Miller, John A

    2015-10-01

    Predictive analytics in the big data era is taking on an ever increasingly important role. Issues related to choice on modeling technique, estimation procedure (or algorithm) and efficient execution can present significant challenges. For example, selection of appropriate and optimal models for big data analytics often requires careful investigation and considerable expertise which might not always be readily available. In this paper, we propose to use semantic technology to assist data analysts and data scientists in selecting appropriate modeling techniques and building specific models as well as the rationale for the techniques and models selected. To formally describe the modeling techniques, models and results, we developed the Analytics Ontology that supports inferencing for semi-automated model selection. The SCALATION framework, which currently supports over thirty modeling techniques for predictive big data analytics is used as a testbed for evaluating the use of semantic technology.

  10. Symmetry, Invariance and Ontology in Physics and Statistics

    Directory of Open Access Journals (Sweden)

    Julio Michael Stern

    2011-09-01

    Full Text Available This paper has three main objectives: (a Discuss the formal analogy between some important symmetry-invariance arguments used in physics, probability and statistics. Specifically, we will focus on Noether’s theorem in physics, the maximum entropy principle in probability theory, and de Finetti-type theorems in Bayesian statistics; (b Discuss the epistemological and ontological implications of these theorems, as they are interpreted in physics and statistics. Specifically, we will focus on the positivist (in physics or subjective (in statistics interpretations vs. objective interpretations that are suggested by symmetry and invariance arguments; (c Introduce the cognitive constructivism epistemological framework as a solution that overcomes the realism-subjectivism dilemma and its pitfalls. The work of the physicist and philosopher Max Born will be particularly important in our discussion.

  11. 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.

  12. Development of National Map ontologies for organization and orchestration of hydrologic observations

    Science.gov (United States)

    Lieberman, J. E.

    2014-12-01

    Feature layers in the National Map program (TNM) are a fundamental context for much of the data collection and analysis conducted by the USGS and other governmental and nongovernmental organizations. Their computational usefulness, though, has been constrained by the lack of formal relationships besides superposition between TNM layers, as well as limited means of representing how TNM datasets relate to additional attributes, datasets, and activities. In the field of Geospatial Information Science, there has been a growing recognition of the value of semantic representation and technology for addressing these limitations, particularly in the face of burgeoning information volume and heterogeneity. Fundamental to this approach is the development of formal ontologies for concepts related to that information that can be processed computationally to enhance creation and discovery of new geospatial knowledge. They offer a means of making much of the presently innate knowledge about relationships in and between TNM features accessible for machine processing and distributed computation.A full and comprehensive ontology of all knowledge represented by TNM features is still impractical. The work reported here involves elaboration and integration of a number of small ontology design patterns (ODP's) that represent limited, discrete, but commonly accepted and broadly applicable physical theories for the behavior of TNM features representing surface water bodies and landscape surfaces and the connections between them. These ontology components are validated through use in applications for discovery and aggregation of water science observational data associated with National Hydrography Data features, features from the National Elevation Dataset (NED) and Water Boundary Dataset (WBD) that constrain water occurrence in the continental US. These applications emphasize workflows which are difficult or impossible to automate using existing data structures. Evaluation of the

  13. 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.

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

    Science.gov (United States)

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

    2014-01-01

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

  15. Linked data meets ontology matching: enhancing data linking through ontology alignments

    OpenAIRE

    Scharffe , François; Euzenat , Jérôme

    2011-01-01

    scharffe2011b; International audience; The Web of data consists of publishing data on the Web in such a way that they can be connected together and interpreted. It is thus critical to establish links between these data, both for the Web of data and for the Semantic Web that it contributes to feed. We consider here the various techniques which have been developed for that purpose and analyze their commonalities and differences. This provides a general framework that the diverse data linking sy...

  16. Flexible receiver adapter formal design review

    International Nuclear Information System (INIS)

    Krieg, S.A.

    1995-01-01

    This memo summarizes the results of the Formal (90%) Design Review process and meetings held to evaluate the design of the Flexible Receiver Adapters, support platforms, and associated equipment. The equipment is part of the Flexible Receiver System used to remove, transport, and store long length contaminated equipment and components from both the double and single-shell underground storage tanks at the 200 area tank farms

  17. Organization model and formalized description of nuclear enterprise information system

    International Nuclear Information System (INIS)

    Yuan Feng; Song Yafeng; Li Xudong

    2012-01-01

    Organization model is one of the most important models of Nuclear Enterprise Information System (NEIS). Scientific and reasonable organization model is the prerequisite that NEIS has robustness and extendibility, and is also the foundation of the integration of heterogeneous system. Firstly, the paper describes the conceptual model of the NEIS on ontology chart, which provides a consistent semantic framework of organization. Then it discusses the relations between the concepts in detail. Finally, it gives the formalized description of the organization model of NEIS based on six-tuple array. (authors)

  18. An empirical analysis of ontology reuse in BioPortal.

    Science.gov (United States)

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

    2017-07-01

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

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

    Science.gov (United States)

    Dönitz, Jürgen; Wingender, Edgar

    2012-01-01

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

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

    OpenAIRE

    Paschke, Adrian

    2013-01-01

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

  1. The missions and means framework as an ontology

    Science.gov (United States)

    Deitz, Paul H.; Bray, Britt E.; Michaelis, James R.

    2016-05-01

    The analysis of warfare frequently suffers from an absence of logical structure for a] specifying explicitly the military mission and b] quantitatively evaluating the mission utility of alternative products and services. In 2003, the Missions and Means Framework (MMF) was developed to redress these shortcomings. The MMF supports multiple combatants, levels of war and, in fact, is a formal embodiment of the Military Decision-Making Process (MDMP). A major effect of incomplete analytic discipline in military systems analyses is that they frequently fall into the category of ill-posed problems in which they are under-specified, under-determined, or under-constrained. Critical context is often missing. This is frequently the result of incomplete materiel requirements analyses which have unclear linkages to higher levels of warfare, system-of-systems linkages, tactics, techniques and procedures, and the effect of opposition forces. In many instances the capabilities of materiel are assumed to be immutable. This is a result of not assessing how platform components morph over time due to damage, logistics, or repair. Though ill-posed issues can be found many places in military analysis, probably the greatest challenge comes in the disciplines of C4ISR supported by ontologies in which formal naming and definition of the types, properties, and interrelationships of the entities are fundamental to characterizing mission success. Though the MMF was not conceived as an ontology, over the past decade some workers, particularly in the field of communication, have labelled the MMF as such. This connection will be described and discussed.

  2. Magic Learning Pill: Ontological and Instrumental Learning in Order to Speed Up Education.

    Science.gov (United States)

    Matusov, Eugene; Baker, Daniella; Fan, Yueyue; Choi, Hye Jung; L Hampel, Robert

    2017-09-01

    The purpose of this research is to investigate the phenomenology of learning - people"s attitudes toward their learning experiences that have inherent worth in themselves (i.e., ontological learning) or have value outside of the learning itself (i.e., instrumental learning). In order to explore this topic, 58 participants from the U.S., Russia, and Brazil were interviewed with a central question derived from the science fiction writer Isaac Asimov's short story "Profession": whether participants would take a "Magic Learning Pill" (MLP) to avoid the process of learning, and instead magically acquire the knowledge. The MLP would guarantee the immediate learning by skipping the process of learning while achieving the same effect of gaining skills and knowledge. Almost all participants could think of some learning experiences for which they would take MLP and others for which they would not. Many participants would not take MLP for ontological learning, which is learning experiences that have inherent value for the people, while they would take MLP for instrumental learning, which is learning that mainly serves some other non-educational purposes. The main finding suggests that both instrumental and ontological types of learning are recognized by a wide range of people from diverse cultures as present and valued in their lives. This is especially significant in light of the overwhelmingly instrumental tone of public discourse about education. In the context of formal education, ontological learning was mentioned 35 times (28.0%) while instrumental learning was mentioned 74 times (60.2%). Although ontological learning was often mentioned as taking place outside of school, incorporating pedagogy supporting ontological learning at school deserves consideration.

  3. Scientific Reproducibility in Biomedical Research: Provenance Metadata Ontology for Semantic Annotation of Study Description.

    Science.gov (United States)

    Sahoo, Satya S; Valdez, Joshua; Rueschman, Michael

    2016-01-01

    Scientific reproducibility is key to scientific progress as it allows the research community to build on validated results, protect patients from potentially harmful trial drugs derived from incorrect results, and reduce wastage of valuable resources. The National Institutes of Health (NIH) recently published a systematic guideline titled "Rigor and Reproducibility " for supporting reproducible research studies, which has also been accepted by several scientific journals. These journals will require published articles to conform to these new guidelines. Provenance metadata describes the history or origin of data and it has been long used in computer science to capture metadata information for ensuring data quality and supporting scientific reproducibility. In this paper, we describe the development of Provenance for Clinical and healthcare Research (ProvCaRe) framework together with a provenance ontology to support scientific reproducibility by formally modeling a core set of data elements representing details of research study. We extend the PROV Ontology (PROV-O), which has been recommended as the provenance representation model by World Wide Web Consortium (W3C), to represent both: (a) data provenance, and (b) process provenance. We use 124 study variables from 6 clinical research studies from the National Sleep Research Resource (NSRR) to evaluate the coverage of the provenance ontology. NSRR is the largest repository of NIH-funded sleep datasets with 50,000 studies from 36,000 participants. The provenance ontology reuses ontology concepts from existing biomedical ontologies, for example the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT), to model the provenance information of research studies. The ProvCaRe framework is being developed as part of the Big Data to Knowledge (BD2K) data provenance project.

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

    Directory of Open Access Journals (Sweden)

    Lidia BAJENARU

    2015-01-01

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

  5. 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.)

  6. 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.

  7. 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 ...

  8. 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...

  9. Ontology Enabled Generation of Embedded Web Services

    DEFF Research Database (Denmark)

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

    2008-01-01

    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...

  10. 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.

  11. 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...

  12. 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.

  13. 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....

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. Using Ontologies in Cybersecurity Field

    Directory of Open Access Journals (Sweden)

    Tiberiu Marian GEORGESCU

    2017-01-01

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

  20. 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

  1. 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.

  2. Desiderata for ontologies to be used in semantic annotation of biomedical documents.

    Science.gov (United States)

    Bada, Michael; Hunter, Lawrence

    2011-02-01

    A wealth of knowledge valuable to the translational research scientist is contained within the vast biomedical literature, but this knowledge is typically in the form of natural language. Sophisticated natural-language-processing systems are needed to translate text into unambiguous formal representations grounded in high-quality consensus ontologies, and these systems in turn rely on gold-standard corpora of annotated documents for training and testing. To this end, we are constructing the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-text biomedical journal articles that are being manually annotated with the entire sets of terms from select vocabularies, predominantly from the Open Biomedical Ontologies (OBO) library. Our efforts in building this corpus has illuminated infelicities of these ontologies with respect to the semantic annotation of biomedical documents, and we propose desiderata whose implementation could substantially improve their utility in this task; these include the integration of overlapping terms across OBOs, the resolution of OBO-specific ambiguities, the integration of the BFO with the OBOs and the use of mid-level ontologies, the inclusion of noncanonical instances, and the expansion of relations and realizable entities. Copyright © 2010 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2017-02-01

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

  4. Formalizing the concept of sound.

    Energy Technology Data Exchange (ETDEWEB)

    Kaper, H. G.; Tipei, S.

    1999-08-03

    The notion of formalized music implies that a musical composition can be described in mathematical terms. In this article we explore some formal aspects of music and propose a framework for an abstract approach.

  5. Formal Analysis of Domain Models

    National Research Council Canada - National Science Library

    Bharadwaj, Ramesh

    2002-01-01

    Recently, there has been a great deal of interest in the application of formal methods, in particular, precise formal notations and automatic analysis tools for the creation and analysis of requirements specifications (i.e...

  6. 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....

  7. 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…

  8. 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

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

    NARCIS (Netherlands)

    Blums, Ivar; Weigand, Hans

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

  10. Formalization of Database Systems -- and a Formal Definition of {IMS}

    DEFF Research Database (Denmark)

    Bjørner, Dines; Løvengreen, Hans Henrik

    1982-01-01

    Drawing upon an analogy between Programming Language Systems and Database Systems we outline the requirements that architectural specifications of database systems must futfitl, and argue that only formal, mathematical definitions may 6atisfy these. Then we illustrate home aspects and touch upon...... come ueee of formal definitions of data models and databaee management systems. A formal model of INS will carry this discussion. Finally we survey some of the exkting literature on formal definitions of database systems. The emphasis will be on constructive definitions in the denotationul semantics...... style of the VCM: Vienna Development Nethd. The role of formal definitions in international standardiaation efforts is briefly mentioned....

  11. OntoCheck: verifying ontology naming conventions and metadata completeness in Protégé 4.

    Science.gov (United States)

    Schober, Daniel; Tudose, Ilinca; Svatek, Vojtech; Boeker, Martin

    2012-09-21

    Although policy providers have outlined minimal metadata guidelines and naming conventions, ontologies of today still display inter- and intra-ontology heterogeneities in class labelling schemes and metadata completeness. This fact is at least partially due to missing or inappropriate tools. Software support can ease this situation and contribute to overall ontology consistency and quality by helping to enforce such conventions. We provide a plugin for the Protégé Ontology editor to allow for easy checks on compliance towards ontology naming conventions and metadata completeness, as well as curation in case of found violations. In a requirement analysis, derived from a prior standardization approach carried out within the OBO Foundry, we investigate the needed capabilities for software tools to check, curate and maintain class naming conventions. A Protégé tab plugin was implemented accordingly using the Protégé 4.1 libraries. The plugin was tested on six different ontologies. Based on these test results, the plugin could be refined, also by the integration of new functionalities. The new Protégé plugin, OntoCheck, allows for ontology tests to be carried out on OWL ontologies. In particular the OntoCheck plugin helps to clean up an ontology with regard to lexical heterogeneity, i.e. enforcing naming conventions and metadata completeness, meeting most of the requirements outlined for such a tool. Found test violations can be corrected to foster consistency in entity naming and meta-annotation within an artefact. Once specified, check constraints like name patterns can be stored and exchanged for later re-use. Here we describe a first version of the software, illustrate its capabilities and use within running ontology development efforts and briefly outline improvements resulting from its application. Further, we discuss OntoChecks capabilities in the context of related tools and highlight potential future expansions. The OntoCheck plugin facilitates

  12. GFVO: the Genomic Feature and Variation Ontology

    KAUST Repository

    Baran, Joachim

    2015-05-05

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

  13. Application of Ontologies for Big Earth Data

    Science.gov (United States)

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

    2014-12-01

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

  14. 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.

  15. Topical Roots of Formal Dialectic

    NARCIS (Netherlands)

    Krabbe, Erik C. W.

    Formal dialectic has its roots in ancient dialectic. We can trace this influence in Charles Hamblin's book on fallacies, in which he introduced his first formal dialectical systems. Earlier, Paul Lorenzen proposed systems of dialogical logic, which were in fact formal dialectical systems avant la

  16. 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.

  17. 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...

  18. 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....

  19. Formal representation of complex SNOMED CT expressions

    Directory of Open Access Journals (Sweden)

    Markó Kornél

    2008-10-01

    Full Text Available Abstract Background Definitory expressions about clinical procedures, findings and diseases constitute a major benefit of a formally founded clinical reference terminology which is ontologically sound and suited for formal reasoning. SNOMED CT claims to support formal reasoning by description-logic based concept definitions. Methods On the basis of formal ontology criteria we analyze complex SNOMED CT concepts, such as "Concussion of Brain with(out Loss of Consciousness", using alternatively full first order logics and the description logic ℰℒ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae8hmHuKae8NeHWeaaa@37B1@. Results Typical complex SNOMED CT concepts, including negations or not, can be expressed in full first-order logics. Negations cannot be properly expressed in the description logic ℰℒ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae8hmHuKae8NeHWeaaa@37B1@ underlying SNOMED CT. All concepts concepts the meaning of which implies a temporal scope may be subject to diverging interpretations, which are often unclear in SNOMED CT as their contextual determinants are not made explicit. Conclusion The description of complex medical occurrents is ambiguous, as the same situations can be described as (i a complex occurrent C that has A and B as temporal parts, (ii a simple occurrent A' defined as a kind of A followed by some B, or (iii a simple occurrent B' defined as a kind of B preceded by some A. As negative statements in SNOMED CT cannot be exactly represented without

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. Formal aspects of resilience

    Directory of Open Access Journals (Sweden)

    Diana-Maria Drigă

    2015-12-01

    Full Text Available The concept of resilience has represented during the recent years a leading concern both in Romania, within the European Union and worldwide. Specialists in economics, management, finance, legal sciences, political sciences, sociology, psychology, grant a particular interest to this concept. Multidisciplinary research of resilience has materialized throughout the time in multiple conceptualizations and theorizing, but without being a consensus between specialists in terms of content, specificity and scope. Through this paper it is intended to clarify the concept of resilience, achieving an exploration of the evolution of this concept in ecological, social and economic environment. At the same time, the paper presents aspects of feedback mechanisms and proposes a formalization of resilience using the logic and mathematical analysis.

  5. Formalized informal learning

    DEFF Research Database (Denmark)

    Levinsen, Karin; Sørensen, Birgitte Holm

    2011-01-01

    and other relevant stakeholders, as well as participant observations in the classroom documented by thick descriptions, formal and informal interviews and focus group interviews. The aim of the study was to explore and identify relations between designs for teaching and learning and the students' learning......This paper presents findings from a large-scale longitudinal, qualitative study - Project ICT and Learning (PIL) - that engaged the participation of eight primary schools in Denmark, and was conducted between 2006 and 2008. The research design was based on action research, involving teachers...... of school subjects within defined learning goals and curricula, along with various implementations of ICT in the pedagogical everyday practice (Levinsen & Sørensen 2008). However, another research strand - the topic of this paper - emerged during the project's life cycle as a consequence of ongoing changes...

  6. An Ontology for Identifying Cyber Intrusion Induced Faults in Process Control Systems

    Science.gov (United States)

    Hieb, Jeffrey; Graham, James; Guan, Jian

    This paper presents an ontological framework that permits formal representations of process control systems, including elements of the process being controlled and the control system itself. A fault diagnosis algorithm based on the ontological model is also presented. The algorithm can identify traditional process elements as well as control system elements (e.g., IP network and SCADA protocol) as fault sources. When these elements are identified as a likely fault source, the possibility exists that the process fault is induced by a cyber intrusion. A laboratory-scale distillation column is used to illustrate the model and the algorithm. Coupled with a well-defined statistical process model, this fault diagnosis approach provides cyber security enhanced fault diagnosis information to plant operators and can help identify that a cyber attack is underway before a major process failure is experienced.

  7. 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.

  8. The Russian Quest for Ontological Security

    DEFF Research Database (Denmark)

    Pedersen, Jonas Gejl

    This paper argues that Russia’s decision to militarily intervene in the Kosovo crisis (1999) arose out of ontological, alongside material, insecurity. Whereas states’ material security essentially deals with national survival, ontological security concerns safety of the ‘national Self......’. By 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...

  9. 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...

  10. 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....

  11. 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.

  12. 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.

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

    Science.gov (United States)

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

    2014-01-01

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

  14. 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.

  15. Using formal ontologies for the development of consistent and unambiguous financial accounting standards

    CSIR Research Space (South Africa)

    Gerber, MC

    2011-11-01

    Full Text Available The purpose of accounting is to gather financial data of a business or entity,to interpret this data and to report the results in financial statements to the different users thereof. The interpretation off financial data is regulated by financial...

  16. Knowledge Representation and Data Mining of Neuronal Morphologies Using Neuroinformatics Tools and Formal Ontologies

    Science.gov (United States)

    Polavaram, Sridevi

    2016-01-01

    Neuroscience can greatly benefit from using novel methods in computer science and informatics, which enable knowledge discovery in unexpected ways. Currently one of the biggest challenges in Neuroscience is to map the functional circuitry of the brain. The applications of this goal range from understanding structural reorganization of neurons to…

  17. 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.

  18. 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

  19. 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...

  20. 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.

  1. 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...

  2. 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

  3. 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

  4. Spinor formalism and complex-vector formalism of general relativity

    International Nuclear Information System (INIS)

    Han-ying, G.; Yong-shi, W.; Gendao, L.

    1974-01-01

    In this paper, using E. Cartan's exterior calculus, we give the spinor form of the structure equations, which leads naturally to the Newman--Penrose equations. Furthermore, starting from the spinor spaces and the el (2C) algebra, we construct the general complex-vector formalism of general relativity. We find that both the Cahen--Debever--Defrise complex-vector formalism and that of Brans are its special cases. Thus, the spinor formalism and the complex-vector formalism of general relativity are unified on the basis of the uni-modular group SL(2C) and its Lie algebra

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. A Prototype Ontology Tool and Interface for Coastal Atlas Interoperability

    Science.gov (United States)

    Wright, D. J.; Bermudez, L.; O'Dea, L.; Haddad, T.; Cummins, V.

    2007-12-01

    While significant capacity has been built in the field of web-based coastal mapping and informatics in the last decade, little has been done to take stock of the implications of these efforts or to identify best practice in terms of taking lessons learned into consideration. This study reports on the second of two transatlantic workshops that bring together key experts from Europe, the United States and Canada to examine state-of-the-art developments in coastal web atlases (CWA), based on web enabled geographic information systems (GIS), along with future needs in mapping and informatics for the coastal practitioner community. While multiple benefits are derived from these tailor-made atlases (e.g. speedy access to multiple sources of coastal data and information; economic use of time by avoiding individual contact with different data holders), the potential exists to derive added value from the integration of disparate CWAs, to optimize decision-making at a variety of levels and across themes. The second workshop focused on the development of a strategy to make coastal web atlases interoperable by way of controlled vocabularies and ontologies. The strategy is based on web service oriented architecture and an implementation of Open Geospatial Consortium (OGC) web services, such as Web Feature Services (WFS) and Web Map Service (WMS). Atlases publishes Catalog Web Services (CSW) using ISO 19115 metadata and controlled vocabularies encoded as Uniform Resource Identifiers (URIs). URIs allows the terminology of each atlas to be uniquely identified and facilitates mapping of terminologies using semantic web technologies. A domain ontology was also created to formally represent coastal erosion terminology as a use case, and with a test linkage of those terms between the Marine Irish Digital Atlas and the Oregon Coastal Atlas. A web interface is being developed to discover coastal hazard themes in distributed coastal atlases as part of a broader International Coastal

  10. 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...

  11. 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...

  12. 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...

  13. ONTOLOGICAL MODEL OF STRATEGIC ECONOMIC SECURITY OF ENTERPRISE

    Directory of Open Access Journals (Sweden)

    L. A. Zaporozhtseva

    2014-01-01

    Full Text Available Article explains the necessity the application of the ontological approach to modeling the strategic economic security in the formalization of the basic categories of domain company recognized its benefits. Among the advantages of the model distinguishes its versatility and ability to describe various aspects of strategic security - the system strategies and goals of the organization and business processes; possibility of its use at different levels of detail - from the top-level description of the basic categories of management, to design-level analytic applications; as well as the adaptability of the model, with depth on particular aspects determined by practical necessity and not regulated methodology. The model integrates various aspects of the concept of enterprise architecture and organizes conceptual apparatus. Ontological model easy to understand and adjust as business architects and specialists in designing systems of economic security and offers many categories of verbal representation of the domain of the enterprise. Proved the feasibility of using process-functional approach in providing strategic economic security, according to which the components of such a security company proposed as business processes, finance, staff and contractors. The article presents the author's ontological model of strategic economic security, including endangered sites, the presence of factors that threaten the security of the object and the subject of providing security. Further, it is proved that in the subjects of security impact on the object using the tools, measures and activities within the strategy formed the mechanism is implemented managerial decisions to strengthen the strategic economic security. The process of diagnosis, detection, identification of threats of economic security, and the development of enterprise development strategies, taking into account its level of economic security must be under the constant supervision of the process of

  14. Ontological Encoding of GeoSciML and INSPIRE geological standard vocabularies and schemas: application to geological mapping

    Science.gov (United States)

    Lombardo, Vincenzo; Piana, Fabrizio; Mimmo, Dario; Fubelli, Giandomenico; Giardino, Marco

    2016-04-01

    Encoding of geologic knowledge in formal languages is an ambitious task, aiming at the interoperability and organic representation of geological data, and semantic characterization of geologic maps. Initiatives such as GeoScience Markup Language (last version is GeoSciML 4, 2015[1]) and INSPIRE "Data Specification on Geology" (an operative simplification of GeoSciML, last version is 3.0 rc3, 2013[2]), as well as the recent terminological shepherding of the Geoscience Terminology Working Group (GTWG[3]) have been promoting information exchange of the geologic knowledge. There have also been limited attempts to encode the knowledge in a machine-readable format, especially in the lithology domain (see e.g. the CGI_Lithology ontology[4]), but a comprehensive ontological model that connect the several knowledge sources is still lacking. This presentation concerns the "OntoGeonous" initiative, which aims at encoding the geologic knowledge, as expressed through the standard vocabularies, schemas and data models mentioned above, through a number of interlinked computational ontologies, based on the languages of the Semantic Web and the paradigm of Linked Open Data. The initiative proceeds in parallel with a concrete case study, concerning the setting up of a synthetic digital geological map of the Piemonte region (NW Italy), named "GEOPiemonteMap" (developed by the CNR Institute of Geosciences and Earth Resources, CNR IGG, Torino), where the description and classification of GeologicUnits has been supported by the modeling and implementation of the ontologies. We have devised a tripartite ontological model called OntoGeonous that consists of: 1) an ontology of the geologic features (in particular, GeologicUnit, GeomorphologicFeature, and GeologicStructure[5], modeled from the definitions and UML schemata of CGI vocabularies[6], GeoScienceML and INSPIRE, and aligned with the Planetary realm of NASA SWEET ontology[7]), 2) an ontology of the Earth materials (as defined by the

  15. 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

  16. 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.

  17. 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

  18. 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...

  19. ContoExam: an ontology on context-aware examinations

    NARCIS (Netherlands)

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

    2014-01-01

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

  20. 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

  1. 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

  2. The Relationship between User Expertise and Structural Ontology Characteristics

    Science.gov (United States)

    Waldstein, Ilya Michael

    2014-01-01

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

  3. 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…

  4. 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),

  5. 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

  6. Ontology development for provenance tracing in National Climate Assessment of the US Global Change Research Program

    Science.gov (United States)

    Ma, X.; Zheng, J. G.; Goldstein, J.; Duggan, B.; Xu, J.; Du, C.; Akkiraju, A.; Aulenbach, S.; Tilmes, C.; Fox, P. A.

    2013-12-01

    The periodical National Climate Assessment (NCA) of the US Global Change Research Program (USGCRP) [1] produces reports about findings of global climate change and the impacts of climate change on the United States. Those findings are of great public and academic concerns and are used in policy and management decisions, which make the provenance information of findings in those reports especially important. The USGCRP is developing a Global Change Information System (GCIS), in which the NCA reports and associated provenance information are the primary records. We were modeling and developing Semantic Web applications for the GCIS. By applying a use case-driven iterative methodology [2], we developed an ontology [3] to represent the content structure of a report and the associated provenance information. We also mapped the classes and properties in our ontology into the W3C PROV-O ontology [4] to realize the formal presentation of provenance. We successfully implemented the ontology in several pilot systems for a recent National Climate Assessment report (i.e., the NCA3). They provide users the functionalities to browse and search provenance information with topics of interest. Provenance information of the NCA3 has been made structured and interoperable by applying the developed ontology. Besides the pilot systems we developed, other tools and services are also able to interact with the data in the context of the 'Web of data' and thus create added values. Our research shows that the use case-driven iterative method bridges the gap between Semantic Web researchers and earth and environmental scientists and is able to be deployed rapidly for developing Semantic Web applications. Our work also provides first-hand experience for re-using the W3C PROV-O ontology in the field of earth and environmental sciences, as the PROV-O ontology is recently ratified (on 04/30/2013) by the W3C as a recommendation and relevant applications are still rare. [1] http

  7. Clinical data integration model. Core interoperability ontology for research using primary care data.

    Science.gov (United States)

    Ethier, J-F; Curcin, V; Barton, A; McGilchrist, M M; Bastiaens, H; Andreasson, A; Rossiter, J; Zhao, L; Arvanitis, T N; Taweel, A; Delaney, B C; Burgun, A

    2015-01-01

    This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". Primary care data is the single richest source of routine health care data. However its use, both in research and clinical work, often requires data from multiple clinical sites, clinical trials databases and registries. Data integration and interoperability are therefore of utmost importance. TRANSFoRm's general approach relies on a unified interoperability framework, described in a previous paper. We developed a core ontology for an interoperability framework based on data mediation. This article presents how such an ontology, the Clinical Data Integration Model (CDIM), can be designed to support, in conjunction with appropriate terminologies, biomedical data federation within TRANSFoRm, an EU FP7 project that aims to develop the digital infrastructure for a learning healthcare system in European Primary Care. TRANSFoRm utilizes a unified structural / terminological interoperability framework, based on the local-as-view mediation paradigm. Such an approach mandates the global information model to describe the domain of interest independently of the data sources to be explored. Following a requirement analysis process, no ontology focusing on primary care research was identified and, thus we designed a realist ontology based on Basic Formal Ontology to support our framework in collaboration with various terminologies used in primary care. The resulting ontology has 549 classes and 82 object properties and is used to support data integration for TRANSFoRm's use cases. Concepts identified by researchers were successfully expressed in queries using CDIM and pertinent terminologies. As an example, we illustrate how, in TRANSFoRm, the Query Formulation Workbench can capture eligibility criteria in a computable representation, which is based on CDIM. A unified mediation approach to semantic interoperability provides a

  8. First formal ITER negotiations make excellent progress

    International Nuclear Information System (INIS)

    Barnard, P.

    2001-01-01

    November 8 and 9 2001 marked the historic beginning of formal negotiations meetings on the ITER project. Delegations from Canada, the European Union, Japan and the Russian Federation met in Toronto, Canada, for the first in a series of Negotiations that is expected to lead, by the end of 2002, to an agreement on the joint implementation of ITER. This agreement will govern, under international law, the construction, operation and decommissioning of ITER. The Negotiations concluded by issuing a joint news release, reflecting a commitment to share the progress reports on the efforts to implement ITER

  9. Formal System Verification - Extension 2

    Science.gov (United States)

    2012-08-08

    vision of truly trustworthy systems has been to provide a formally verified microkernel basis. We have previously developed the seL4 microkernel...together with a formal proof (in the theorem prover Isabelle/HOL) of its functional correctness [6]. This means that all the behaviours of the seL4 C...source code are included in the high-level, formal specification of the kernel. This work enabled us to provide further formal guarantees about seL4 , in

  10. Formalized Epistemology, Logic, and Grammar

    Science.gov (United States)

    Bitbol, Michel

    The task of a formal epistemology is defined. It appears that a formal epistemology must be a generalization of "logic" in the sense of Wittgenstein's Tractatus. The generalization is required because, whereas logic presupposes a strict relation between activity and language, this relation may be broken in some domains of experimental enquiry (e.g., in microscopic physics). However, a formal epistemology should also retain a major feature of Wittgenstein's "logic": It must not be a discourse about scientific knowledge, but rather a way of making manifest the structures usually implicit in knowledge-gaining activity. This strategy is applied to the formalism of quantum mechanics.

  11. 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.

  12. Formal, Non-Formal and Informal Learning in the Sciences

    Science.gov (United States)

    Ainsworth, Heather L.; Eaton, Sarah Elaine

    2010-01-01

    This research report investigates the links between formal, non-formal and informal learning and the differences between them. In particular, the report aims to link these notions of learning to the field of sciences and engineering in Canada and the United States, including professional development of adults working in these fields. It offers…

  13. 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...

  14. 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 ...

  15. 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 ...

  16. 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.

  17. 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

  18. 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

  19. 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...

  20. 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