WorldWideScience

Sample records for legal ontology based

  1. Direct: Ontology based discovery of responsibility and causality in legal case descriptions

    NARCIS (Netherlands)

    Breuker, J.A.P.J.; Hoekstra, R.J.; Gordon, T.

    2004-01-01

    In this paper we present DIRECT, a system forautomatic discovery of responsibility and causal relations in legal case descriptions based on LRI-Core, a core ontology that covers the main concepts that are common to all legal domains. These domains have a predominant common-sense character - the law

  2. A Legal Case OWL Ontology with an Instantiation of Popov v. Hayashi

    NARCIS (Netherlands)

    Wyner, A.Z.; Hoekstra, R.J.

    2012-01-01

    The paper provides an OWL ontology for legal cases with an instantiation of the legal case Popov v. Hayashi. The ontology makes explicit the conceptual knowledge of the legal case domain, supports reasoning about the domain, and can be used to annotate the text of cases, which in turn can be used to

  3. A legal case OWL ontology with an instantiation of Popov v. Hayashi

    NARCIS (Netherlands)

    Wyner, A.; Hoekstra, R.

    2012-01-01

    The paper provides an OWL ontology for legal cases with an instantiation of the legal case Popov v. Hayashi. The ontology makes explicit the conceptual knowledge of the legal case domain, supports reasoning about the domain, and can be used to annotate the text of cases, which in turn can be used to

  4. Medico legal and de ontological features of breast diagnosis

    International Nuclear Information System (INIS)

    Lopez, J. A.; Lopez, M. C.

    2001-01-01

    A medical and legal review of the literature in regards to the medico legal and de ontological features involved in Imaging Diagnosis of the breast was performed in order to elaborate a series of preventive measures to prevent or reduce the demands on the radiologist. Basically, the contents of the Spanish Medical De ontology Code as well the rules and laws in force in our country have been considered, both from the medical professional point of view as well as from that of the law professional. As a result of the review carried out, a series of preventive measures aimed at reducing the incidence of possible lawsuits against the radiologist who works in breast imaging diagnosis are proposed. The radiologist is regularly involved in lawsuits, especially related with the delay in the diagnosis of breast cancer. In the United States of America and Italy. he(she is the professional who receives the greatest number of lawsuits, being ahead of the gynecologist. The radiologist occupies and important place in the diagnosis of breast cancer, which converts him/her into the object of possible lawsuits. Within these, deadly in the diagnosis of cancer caused by several situations are included: these being, principally, non-detection by mammography, not using the complementary studies and not carrying out an integrated reading of the triad or binomial diagnosis. In some cases, these situations are favored by lack of experience (incompetence) of the radiologists as well as by lack of information from the patient. In order to avoid possible lawsuits, the most important preventive measures are: a) inform the patient; b) be competent in the material: c) follow an action Protocol according to the l ex artis: d) in the case of being staff, comply with the guidelines of Quality Control: e) elaborate clear and concise written reports, maintaining, if relevant, the limitations of the procedures used and suggestions for the professional clinician. (Author) 27 refs

  5. 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...

  6. Semoogle - An Ontology Based Search Engine

    OpenAIRE

    Aghajani, Nooshin

    2012-01-01

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

  7. 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

  8. Ontology-Based Multiple Choice Question Generation

    Directory of Open Access Journals (Sweden)

    Maha Al-Yahya

    2014-01-01

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

  9. Designing Network-based Business Model Ontology

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  10. Towards ontology based search and knowledgesharing using domain ontologies

    DEFF Research Database (Denmark)

    Zambach, Sine

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

  11. Modulated evaluation metrics for drug-based ontologies.

    Science.gov (United States)

    Amith, Muhammad; Tao, Cui

    2017-04-24

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

  12. 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

  13. Open Biomedical Ontology-based Medline exploration

    Science.gov (United States)

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

    2009-01-01

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

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

    Science.gov (United States)

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

    2010-06-03

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

  15. Construct Primary Education Semantic Ontology Library Based Mind Mapping

    Directory of Open Access Journals (Sweden)

    Hu Dong-Hong

    2016-01-01

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

  16. 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

  17. 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...

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

    Indian Academy of Sciences (India)

    B Sathiya

    2017-11-16

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

  19. 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...

  20. Model Validation in Ontology Based Transformations

    Directory of Open Access Journals (Sweden)

    Jesús M. Almendros-Jiménez

    2012-10-01

    Full Text Available Model Driven Engineering (MDE is an emerging approach of software engineering. MDE emphasizes the construction of models from which the implementation should be derived by applying model transformations. The Ontology Definition Meta-model (ODM has been proposed as a profile for UML models of the Web Ontology Language (OWL. In this context, transformations of UML models can be mapped into ODM/OWL transformations. On the other hand, model validation is a crucial task in model transformation. Meta-modeling permits to give a syntactic structure to source and target models. However, semantic requirements have to be imposed on source and target models. A given transformation will be sound when source and target models fulfill the syntactic and semantic requirements. In this paper, we present an approach for model validation in ODM based transformations. Adopting a logic programming based transformational approach we will show how it is possible to transform and validate models. Properties to be validated range from structural and semantic requirements of models (pre and post conditions to properties of the transformation (invariants. The approach has been applied to a well-known example of model transformation: the Entity-Relationship (ER to Relational Model (RM transformation.

  1. 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)

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

    Science.gov (United States)

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

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

  3. Statistical mechanics of ontology based annotations

    Science.gov (United States)

    Hoyle, David C.; Brass, Andrew

    2016-01-01

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

  4. Cross document ontology based information for multimedia retrieval

    NARCIS (Netherlands)

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

    2003-01-01

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

  5. Instance-Based Ontology Matching by Instance Enrichment

    NARCIS (Netherlands)

    Schopman, B.; Wang, S.; Isaac, A.H.J.C.A.; Schlobach, K.S.

    2012-01-01

    The ontology matching (OM) problem is an important barrier to achieve true Semantic Interoperability. Instance-based ontology matching (IBOM) uses the extension of concepts, the instances directly associated with a concept, to determine whether a pair of concepts is related or not. While IBOM has

  6. PSOM 2—partitioning-based scalable ontology matching using ...

    Indian Academy of Sciences (India)

    These sets of clusters or sub-ontologies are matched across the input ontologies to identify matchable cluster pairs, based on anchors that are efficiently discovered through a new light-weight linguistic matcher (EI-sub). However, in order to further increase the efficiency of the time-consuming anchor discovery process we ...

  7. An ontology based trust verification of software license agreement

    Science.gov (United States)

    Lu, Wenhuan; Li, Xiaoqing; Gan, Zengqin; Wei, Jianguo

    2017-08-01

    When we install software or download software, there will show up so big mass document to state the rights and obligations, for which lots of person are not patient to read it or understand it. That would may make users feel distrust for the software. In this paper, we propose an ontology based verification for Software License Agreement. First of all, this work proposed an ontology model for domain of Software License Agreement. The domain ontology is constructed by proposed methodology according to copyright laws and 30 software license agreements. The License Ontology can act as a part of generalized copyright law knowledge model, and also can work as visualization of software licenses. Based on this proposed ontology, a software license oriented text summarization approach is proposed which performances showing that it can improve the accuracy of software licenses summarizing. Based on the summarization, the underline purpose of the software license can be explicitly explored for trust verification.

  8. An Extensible, Ontology-based, Distributed Information System Architecture

    National Research Council Canada - National Science Library

    Chao, Alan I; Krikeles, Basil C; Lusignan, Angela E; Starczewski, Edward

    2003-01-01

    ...), which facilitates the construction of scalable, flexible distributed systems. XDA is based on a simple ontology mechanism that enables the definition and maintenance of high-level object models to capture the shared semantics necessary for interoperability...

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2017-01-01

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

  11. 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

  12. Conceptual Design of Compliant Mechanism Based on Port Ontology

    Directory of Open Access Journals (Sweden)

    Zhanwei Li

    2013-01-01

    Full Text Available It is an effective method for port-based ontology (PBO to be used to represent and organize product design information and, support product conceptualization. As port is used to map and link components together, it plays an important role in capturing component information. This paper establishes a design method of compliant mechanism based on port ontology. Firstly, the coding rules are constituted based on PBO, and knowledge base of compliant mechanism is constructed, which includes stiffness base and inherent frequency base of flexible cells. Secondly, incidence matrix is established to denote the relationship of components, and based on incidence matrix design, schemes are generated by adopting the genetic algorithm. Thirdly, by selecting suitable parameters, scheme populations are generated towards training neural network (NN, and the trained NN model is employed for choosing preferential schemes to be satisfied with users' demands. At last, an application case is given to demonstrate the conceptual design of compliant mechanism based on port ontology.

  13. 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.

  14. Ontology- and graph-based similarity assessment in biological networks.

    Science.gov (United States)

    Wang, Haiying; Zheng, Huiru; Azuaje, Francisco

    2010-10-15

    A standard systems-based approach to biomarker and drug target discovery consists of placing putative biomarkers in the context of a network of biological interactions, followed by different 'guilt-by-association' analyses. The latter is typically done based on network structural features. Here, an alternative analysis approach in which the networks are analyzed on a 'semantic similarity' space is reported. Such information is extracted from ontology-based functional annotations. We present SimTrek, a Cytoscape plugin for ontology-based similarity assessment in biological networks. http://rosalind.infj.ulst.ac.uk/SimTrek.html francisco.azuaje@crp-sante.lu Supplementary data are available at Bioinformatics online.

  15. SPATIAL DATA INTEGRATION USING ONTOLOGY-BASED APPROACH

    Directory of Open Access Journals (Sweden)

    S. Hasani

    2015-12-01

    Full Text Available In today's world, the necessity for spatial data for various organizations is becoming so crucial that many of these organizations have begun to produce spatial data for that purpose. In some circumstances, the need to obtain real time integrated data requires sustainable mechanism to process real-time integration. Case in point, the disater management situations that requires obtaining real time data from various sources of information. One of the problematic challenges in the mentioned situation is the high degree of heterogeneity between different organizations data. To solve this issue, we introduce an ontology-based method to provide sharing and integration capabilities for the existing databases. In addition to resolving semantic heterogeneity, better access to information is also provided by our proposed method. Our approach is consisted of three steps, the first step is identification of the object in a relational database, then the semantic relationships between them are modelled and subsequently, the ontology of each database is created. In a second step, the relative ontology will be inserted into the database and the relationship of each class of ontology will be inserted into the new created column in database tables. Last step is consisted of a platform based on service-oriented architecture, which allows integration of data. This is done by using the concept of ontology mapping. The proposed approach, in addition to being fast and low cost, makes the process of data integration easy and the data remains unchanged and thus takes advantage of the legacy application provided.

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

    Science.gov (United States)

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

    2017-09-06

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

  17. Taxonomy-Based Approaches to Quality Assurance of Ontologies

    Directory of Open Access Journals (Sweden)

    Michael Halper

    2017-01-01

    Full Text Available Ontologies are important components of health information management systems. As such, the quality of their content is of paramount importance. It has been proven to be practical to develop quality assurance (QA methodologies based on automated identification of sets of concepts expected to have higher likelihood of errors. Four kinds of such sets (called QA-sets organized around the themes of complex and uncommonly modeled concepts are introduced. A survey of different methodologies based on these QA-sets and the results of applying them to various ontologies are presented. Overall, following these approaches leads to higher QA yields and better utilization of QA personnel. The formulation of additional QA-set methodologies will further enhance the suite of available ontology QA tools.

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

    Indian Academy of Sciences (India)

    This system proposes an -gram based approach to automatic Tamil lyric generation, by the ontological semantic interpretation of the input scene. The approach is based on identifying the semantics conveyed in the scenario, thereby making the system understand the situation and generate lyrics accordingly. The heart of ...

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

    Indian Academy of Sciences (India)

    Abstract. This system proposes an N-gram based approach to automatic Tamil lyric generation, by the ontological semantic interpretation of the input scene. The approach is based on identifying the semantics conveyed in the scenario, thereby mak- ing the system understand the situation and generate lyrics accordingly.

  20. A Case for Embedded Natural Logic for Ontological Knowledge Bases

    DEFF Research Database (Denmark)

    Andreasen, Troels; Nilsson, Jørgen Fischer

    2014-01-01

    We argue in favour of adopting a form of natural logic for ontology-structured knowledge bases as an alternative to description logic and rule based languages. Natural logic is a form of logic resembling natural language assertions, unlike description logic. This is essential e.g. in life sciences...

  1. Statistical algorithms for ontology-based annotation of scientific literature.

    Science.gov (United States)

    Chakrabarti, Chayan; Jones, Thomas B; Luger, George F; Xu, Jiawei F; Turner, Matthew D; Laird, Angela R; Turner, Jessica A

    2014-01-01

    Ontologies encode relationships within a domain in robust data structures that can be used to annotate data objects, including scientific papers, in ways that ease tasks such as search and meta-analysis. However, the annotation process requires significant time and effort when performed by humans. Text mining algorithms can facilitate this process, but they render an analysis mainly based upon keyword, synonym and semantic matching. They do not leverage information embedded in an ontology's structure. We present a probabilistic framework that facilitates the automatic annotation of literature by indirectly modeling the restrictions among the different classes in the ontology. Our research focuses on annotating human functional neuroimaging literature within the Cognitive Paradigm Ontology (CogPO). We use an approach that combines the stochastic simplicity of naïve Bayes with the formal transparency of decision trees. Our data structure is easily modifiable to reflect changing domain knowledge. We compare our results across naïve Bayes, Bayesian Decision Trees, and Constrained Decision Tree classifiers that keep a human expert in the loop, in terms of the quality measure of the F1-mirco score. Unlike traditional text mining algorithms, our framework can model the knowledge encoded by the dependencies in an ontology, albeit indirectly. We successfully exploit the fact that CogPO has explicitly stated restrictions, and implicit dependencies in the form of patterns in the expert curated annotations.

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

    OpenAIRE

    Yuan Xu; Chunhong Zhang; Yang Ji

    2014-01-01

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

  3. Ontology based heterogeneous materials database integration and semantic query

    Science.gov (United States)

    Zhao, Shuai; Qian, Quan

    2017-10-01

    Materials digital data, high throughput experiments and high throughput computations are regarded as three key pillars of materials genome initiatives. With the fast growth of materials data, the integration and sharing of data is very urgent, that has gradually become a hot topic of materials informatics. Due to the lack of semantic description, it is difficult to integrate data deeply in semantic level when adopting the conventional heterogeneous database integration approaches such as federal database or data warehouse. In this paper, a semantic integration method is proposed to create the semantic ontology by extracting the database schema semi-automatically. Other heterogeneous databases are integrated to the ontology by means of relational algebra and the rooted graph. Based on integrated ontology, semantic query can be done using SPARQL. During the experiments, two world famous First Principle Computational databases, OQMD and Materials Project are used as the integration targets, which show the availability and effectiveness of our method.

  4. An Ontology-Based Framework for Modeling User Behavior

    DEFF Research Database (Denmark)

    Razmerita, Liana

    2011-01-01

    This paper focuses on the role of user modeling and semantically enhanced representations for personalization. This paper presents a generic Ontology-based User Modeling framework (OntobUMf), its components, and its associated user modeling processes. This framework models the behavior of the users...... and classifies its users according to their behavior. The user ontology is the backbone of OntobUMf and has been designed according to the Information Management System Learning Information Package (IMS LIP). The user ontology includes a Behavior concept that extends IMS LIP specification and defines....... The results of this research may contribute to the development of other frameworks for modeling user behavior, other semantically enhanced user modeling frameworks, or other semantically enhanced information systems....

  5. Knowledge modeling of coal mining equipments based on ontology

    Science.gov (United States)

    Zhang, Baolong; Wang, Xiangqian; Li, Huizong; Jiang, Miaomiao

    2017-06-01

    The problems of information redundancy and sharing are universe in coal mining equipment management. In order to improve the using efficiency of knowledge of coal mining equipments, this paper proposed a new method of knowledge modeling based on ontology. On the basis of analyzing the structures and internal relations of coal mining equipment knowledge, taking OWL as ontology construct language, the ontology model of coal mining equipment knowledge is built with the help of Protégé 4.3 software tools. The knowledge description method will lay the foundation for the high effective knowledge management and sharing, which is very significant for improving the production management level of coal mining enterprises.

  6. Ontology-Based Method for Fault Diagnosis of Loaders.

    Science.gov (United States)

    Xu, Feixiang; Liu, Xinhui; Chen, Wei; Zhou, Chen; Cao, Bingwei

    2018-02-28

    This paper proposes an ontology-based fault diagnosis method which overcomes the difficulty of understanding complex fault diagnosis knowledge of loaders and offers a universal approach for fault diagnosis of all loaders. This method contains the following components: (1) An ontology-based fault diagnosis model is proposed to achieve the integrating, sharing and reusing of fault diagnosis knowledge for loaders; (2) combined with ontology, CBR (case-based reasoning) is introduced to realize effective and accurate fault diagnoses following four steps (feature selection, case-retrieval, case-matching and case-updating); and (3) in order to cover the shortages of the CBR method due to the lack of concerned cases, ontology based RBR (rule-based reasoning) is put forward through building SWRL (Semantic Web Rule Language) rules. An application program is also developed to implement the above methods to assist in finding the fault causes, fault locations and maintenance measures of loaders. In addition, the program is validated through analyzing a case study.

  7. Ontology-Based e-Assessment for Accounting Education

    Science.gov (United States)

    Litherland, Kate; Carmichael, Patrick; Martínez-García, Agustina

    2013-01-01

    This summary reports on a pilot of a novel, ontology-based e-assessment system in accounting. The system, OeLe, uses emerging semantic technologies to offer an online assessment environment capable of marking students' free text answers to questions of a conceptual nature. It does this by matching their response with a "concept map" or…

  8. 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

  9. Ontology of a scene based on Java 3D architecture.

    Directory of Open Access Journals (Sweden)

    Rubén González Crespo

    2009-12-01

    Full Text Available The present article seeks to make an approach to the class hierarchy of a scene built with the architecture Java 3D, to develop an ontology of a scene as from the semantic essential components for the semantic structuring of the Web3D. Java was selected because the language recommended by the W3C Consortium for the Development of the Web3D oriented applications as from X3D standard is Xj3D which compositionof their Schemas is based the architecture of Java3D In first instance identifies the domain and scope of the ontology, defining classes and subclasses that comprise from Java3D architecture and the essential elements of a scene, as its point of origin, the field of rotation, translation The limitation of the scene and the definition of shaders, then define the slots that are declared in RDF as a framework for describing the properties of the classes established from identifying thedomain and range of each class, then develops composition of the OWL ontology on SWOOP Finally, be perform instantiations of the ontology building for a Iconosphere object as from class expressions defined.

  10. Fish Ontology framework for taxonomy-based fish recognition

    Science.gov (United States)

    Ali, Najib M.; Khan, Haris A.; Then, Amy Y-Hui; Ving Ching, Chong; Gaur, Manas

    2017-01-01

    Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users. PMID:28929028

  11. Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia

    Science.gov (United States)

    Ong, Edison; He, Yongqun

    2016-01-01

    Hundreds of biological and biomedical ontologies have been developed to support data standardization, integration and analysis. Although ontologies are typically developed for community usage, community efforts in ontology development are limited. To support ontology visualization, distribution, and community-based annotation and development, we have developed Ontokiwi, an ontology extension to the MediaWiki software. Ontokiwi displays hierarchical classes and ontological axioms. Ontology classes and axioms can be edited and added using Ontokiwi form or MediaWiki source editor. Ontokiwi also inherits MediaWiki features such as Wikitext editing and version control. Based on the Ontokiwi/MediaWiki software package, we have developed Ontobedia, which targets to support community-based development and annotations of biological and biomedical ontologies. As demonstrations, we have loaded the Ontology of Adverse Events (OAE) and the Cell Line Ontology (CLO) into Ontobedia. Our studies showed that Ontobedia was able to achieve expected Ontokiwi features. PMID:27570653

  12. Mathematical modeling creation for curriculum based on ontology. Part 1

    OpenAIRE

    PIYAVSKY S.A.; LARUKHIN V.B.

    2012-01-01

    This article delivers a mathematical optimal formation model of curriculum based on the solution of multi-criteria optimization problem. A mathematical model of optimal curriculum shaping based on the solution of multi-criteria optimization. In combination with the previously developed ontology of the educational process, it allows us to offer information technology of forming curriculum at various levels of training in universities personalized for each students

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

    Science.gov (United States)

    2015-07-06

    ComTrustO: Composite Trust-based Ontology Framework for Information and Decision Fusion Alessandro Oltramari Carnegie Mellon University Pittsburgh... ontology -based framework for information fusion, as a support system for human decision makers. In particular, we build upon the concept of composite...multidimensional trust, we construct a composite trust ontology framework, called ComTrustO, that embraces four trust ontologies , one for each trust type. We

  14. Product line based ontology development for semantic web service

    DEFF Research Database (Denmark)

    Zhang, Weishan; Kunz, Thomas

    2006-01-01

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

  15. Evaluation of a frame-based ontology: a formalization-oriented approach

    NARCIS (Netherlands)

    Cornet, Ronald; Abu-Hanna, Ameen

    2002-01-01

    This paper describes the evaluation of our current frame-based ontology in Intensive Care. Our approach to the evaluation consists of formalizing the ontology. The motivation for formalization is twofold: a. The formalization process itself can shed light on the implicit ambiguities in the ontology

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

    Directory of Open Access Journals (Sweden)

    Wei Gao

    2017-01-01

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

  17. Ontology-based Software Architecture Documentation

    NARCIS (Netherlands)

    de Graaf, K.A.; Tang, A.; Liang, P.; van Vliet, J.C.

    2012-01-01

    A common approach to software architecture documentation in industry projects is the use of file-based documents. This approach offers a single-dimensional perspective on the architectural knowledge contained. Knowledge retrieval from file-based architecture documentation is efficient if the

  18. Ontology and modeling patterns for state-based behavior representation

    Science.gov (United States)

    Castet, Jean-Francois; Rozek, Matthew L.; Ingham, Michel D.; Rouquette, Nicolas F.; Chung, Seung H.; Kerzhner, Aleksandr A.; Donahue, Kenneth M.; Jenkins, J. Steven; Wagner, David A.; Dvorak, Daniel L.; hide

    2015-01-01

    This paper provides an approach to capture state-based behavior of elements, that is, the specification of their state evolution in time, and the interactions amongst them. Elements can be components (e.g., sensors, actuators) or environments, and are characterized by state variables that vary with time. The behaviors of these elements, as well as interactions among them are represented through constraints on state variables. This paper discusses the concepts and relationships introduced in this behavior ontology, and the modeling patterns associated with it. Two example cases are provided to illustrate their usage, as well as to demonstrate the flexibility and scalability of the behavior ontology: a simple flashlight electrical model and a more complex spacecraft model involving instruments, power and data behaviors. Finally, an implementation in a SysML profile is provided.

  19. Cardinal Direction Relations Query Modeling Based on Geo-Ontology

    Science.gov (United States)

    Zhu, X.; Chen, D.; Zhou, C.; Li, M.; Xiao, W.

    2012-08-01

    Direction relations, as an important spatial relationship, is simply expressed as object prosperity in traditional geo-ontology. The lacking of explicit specifications and reasoning rules of direction relations in geo-ontology result in the difficult or inflexible of spatial reasoning. Also, digital gazetteers provide information on named features, linking the feature's name with its location and its type. Although the location information is incomplete and not exact, the implicit spatial information, for example spatial relationships and spatial scale, can be extract using the appropriate models based on geo-ontology. In this paper, we proposed a novel conceptual framework of direction relations in order to formalize the semantics and implicit information of direction relations, and present an extraction algorithm of implicit information based on previous researches, which will produce a complete query instance of direction relations. At last, the most suitable direction physical model is recommended to calculation module according to relevant rules. And the experimental results show that this direction query model not only extracted the implicit information effectively, but also made a reasonable interpretation for the user's intention.

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

    International Nuclear Information System (INIS)

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

    2009-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-10-01

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

  2. Ontology Based Vocabulary Matching for Oceanographic Instruments

    Science.gov (United States)

    Chen, Yu; Shepherd, Adam; Chandler, Cyndy; Arko, Robert; Leadbetter, Adam

    2014-05-01

    Data integration act as the preliminary entry point as we enter the era of big data in many scientific domains. However the reusefulness of various dataset has met the hurdle due to different initial of interests of different parties, therefore different vocabularies in describing similar or semantically related concepts. In this scenario it is vital to devise an automatic or semi-supervised algorithm to facilitate the convergence of different vocabularies. The Ocean Data Interoperability Platform (ODIP) seeks to increase data sharing across scientific domains and international boundaries by providing a forum to harmonize diverse regional data systems. ODIP participants from the US include the Rolling Deck to Repository (R2R) program, whose mission is to capture, catalog, and describe the underway/environmental sensor data from US oceanographic research vessels and submit the data to public long-term archives. In an attempt to harmonize these regional data systems, especially vocabularies, R2R recognizes the value of the SeaDataNet vocabularies served by the NERC Vocabulary Server (NVS) hosted at the British Oceanographic Data Centre as a trusted, authoritative source for describing many oceanographic research concepts such as instrumentation. In this work, we make use of the semantic relations in the vocabularies served by NVS to build a Bayesian network and take advantage of the idea of entropy in evaluating the correlation between different concepts and keywords. The performance of the model is evaluated against matching instruments from R2R against the SeaDataNet instrument vocabularies based on calculated confidence scores in the instrument pairings. These pairings with their scores can then be analyzed for assertion growing the interoperability of the R2R vocabulary through its links to the SeaDataNet entities.

  3. Structure-based classification and ontology in chemistry

    Directory of Open Access Journals (Sweden)

    Hastings Janna

    2012-04-01

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

  4. Feature-based Ontology Mapping from an Information Receivers’ Viewpoint

    DEFF Research Database (Denmark)

    Glückstad, Fumiko Kano; Mørup, Morten

    2012-01-01

    This paper compares four algorithms for computing feature-based similarities between concepts respectively possessing a distinctive set of features. The eventual purpose of comparing these feature-based similarity algorithms is to identify a candidate term in a Target Language (TL) that can...... optimally convey the original meaning of a culturally-specific Source Language (SL) concept to a TL audience by aligning two culturally-dependent domain-specific ontologies. The results indicate that the Bayesian Model of Generalization [1] performs best, not only for identifying candidate translation terms...

  5. A Case for Embedded Natural Logic for Ontological Knowledge Bases

    DEFF Research Database (Denmark)

    Andreasen, Troels; Nilsson, Jørgen Fischer

    2014-01-01

    We argue in favour of adopting a form of natural logic for ontology-structured knowledge bases as an alternative to description logic and rule based languages. Natural logic is a form of logic resembling natural language assertions, unlike description logic. This is essential e.g. in life sciences......, where the large and evolving knowledge specifications should be directly accessible to domain experts. Moreover, natural logic comes with intuitive inference rules. The considered version of natural logic leans toward the closed world assumption (CWA) unlike the open world assumption with classical...

  6. Gene ontology based transfer learning for protein subcellular localization

    Directory of Open Access Journals (Sweden)

    Zhou Shuigeng

    2011-02-01

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

  7. Ontology-Based Data Mining in Digital Libraries

    Science.gov (United States)

    Kovačević, Ana

    The paper proposes matching short forms (abbreviated titles from the citation report) with their corresponding longer ones (journal titles in the digital library). The main problem is that there are often a number of syntactically different abbreviated forms for one abbreviated title in the citation report. We use character- and token-based similarity metrics to identify duplicate records. Also, we improve the process of identifying syntactically different data with the automated discovery of ontological knowledge representations such as thesauri from correctly matched data.

  8. An Approach for Composing Services Based on Environment Ontology

    Directory of Open Access Journals (Sweden)

    Guangjun Cai

    2013-01-01

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

  9. Law-Based Ontology for E-Government Services Construction - Case Study: The Specification of Services in Relationship with the Venture Creation in Switzerland

    Science.gov (United States)

    Khadraoui, Abdelaziz; Opprecht, Wanda; Léonard, Michel; Aïdonidis, Christine

    The compliance of e-government services with legal aspects is a crucial issue for administrations. This issue becomes more difficult with the fast-evolving dynamics of laws. This chapter presents our approach to describe and establish the link between e-government services and legal sources. This link is established by an ontology called “law-based ontology.” We use this ontology as means to define and to construct e-government services. The proposed approach is illustrated with one case study: the specification of services in relationship with the venture ­creation in Switzerland and in the State of Geneva. We have selected the Commercial Register area which mainly encompasses the registration of a new company and the modification of its registration.

  10. IBRI-CASONTO: Ontology-based semantic search engine

    Directory of Open Access Journals (Sweden)

    Awny Sayed

    2017-11-01

    Full Text Available The vast availability of information, that added in a very fast pace, in the data repositories creates a challenge in extracting correct and accurate information. Which has increased the competition among developers in order to gain access to technology that seeks to understand the intent researcher and contextual meaning of terms. While the competition for developing an Arabic Semantic Search systems are still in their infancy, and the reason could be traced back to the complexity of Arabic Language. It has a complex morphological, grammatical and semantic aspects, as it is a highly inflectional and derivational language. In this paper, we try to highlight and present an Ontological Search Engine called IBRI-CASONTO for Colleges of Applied Sciences, Oman. Our proposed engine supports both Arabic and English language. It is also employed two types of search which are a keyword-based search and a semantics-based search. IBRI-CASONTO is based on different technologies such as Resource Description Framework (RDF data and Ontological graph. The experiments represent in two sections, first it shows a comparison among Entity-Search and the Classical-Search inside the IBRI-CASONTO itself, second it compares the Entity-Search of IBRI-CASONTO with currently used search engines, such as Kngine, Wolfram Alpha and the most popular engine nowadays Google, in order to measure their performance and efficiency.

  11. Benchmarking the Applicability of Ontology in Geographic Object-Based Image Analysis

    Directory of Open Access Journals (Sweden)

    Sachit Rajbhandari

    2017-11-01

    Full Text Available In Geographic Object-based Image Analysis (GEOBIA, identification of image objects is normally achieved using rule-based classification techniques supported by appropriate domain knowledge. However, GEOBIA currently lacks a systematic method to formalise the domain knowledge required for image object identification. Ontology provides a representation vocabulary for characterising domain-specific classes. This study proposes an ontological framework that conceptualises domain knowledge in order to support the application of rule-based classifications. The proposed ontological framework is tested with a landslide case study. The Web Ontology Language (OWL is used to construct an ontology in the landslide domain. The segmented image objects with extracted features are incorporated into the ontology as instances. The classification rules are written in Semantic Web Rule Language (SWRL and executed using a semantic reasoner to assign instances to appropriate landslide classes. Machine learning techniques are used to predict new threshold values for feature attributes in the rules. Our framework is compared with published work on landslide detection where ontology was not used for the image classification. Our results demonstrate that a classification derived from the ontological framework accords with non-ontological methods. This study benchmarks the ontological method providing an alternative approach for image classification in the case study of landslides.

  12. Semantic Ontology Method of Learning Resource based on the Approximate Subgraph Isomorphism

    OpenAIRE

    Lili Zhang; Jinghua Ding

    2014-01-01

    Digital learning resource ontology is often based on different specification building. It is hard to find resources by linguistic ontology matching method. The existing structural matching method fails to solve the problem of calculation of structural similarity well. For the heterogeneity problem among learning resource ontology, an algorithm is presented based on subgraph approximate isomorphism. First of all, we can preprocess the resource of clustering algorithm through the semantic analy...

  13. An Ontology-Based Transformation Model for the Digital Forensics Domain

    OpenAIRE

    Grigaliunas, Sarunas; Toldinas, Jevgenijus; Venckauskas, Algimantas

    2017-01-01

    The creation of an ontology makes it possible to form common information structures, to reuse knowledge, to make assumptions within a domain and to analyse every piece of knowledge. In this paper, we aim to create an ontologybased transformation model and a framework to develop an ontology-based transformation system in the digital forensics domain. We describe the architecture of the ontology-based transformation system and its components for assisting computer forensics experts in the appro...

  14. Ontology-based topic clustering for online discussion data

    Science.gov (United States)

    Wang, Yongheng; Cao, Kening; Zhang, Xiaoming

    2013-03-01

    With the rapid development of online communities, mining and extracting quality knowledge from online discussions becomes very important for the industrial and marketing sector, as well as for e-commerce applications and government. Most of the existing techniques model a discussion as a social network of users represented by a user-based graph without considering the content of the discussion. In this paper we propose a new multilayered mode to analysis online discussions. The user-based and message-based representation is combined in this model. A novel frequent concept sets based clustering method is used to cluster the original online discussion network into topic space. Domain ontology is used to improve the clustering accuracy. Parallel methods are also used to make the algorithms scalable to very large data sets. Our experimental study shows that the model and algorithms are effective when analyzing large scale online discussion data.

  15. Validation test case generation based on safety analysis ontology

    International Nuclear Information System (INIS)

    Fan, Chin-Feng; Wang, Wen-Shing

    2012-01-01

    Highlights: ► Current practice in validation test case generation for nuclear system is mainly ad hoc. ► This study designs a systematic approach to generate validation test cases from a Safety Analysis Report. ► It is based on a domain-specific ontology. ► Test coverage criteria have been defined and satisfied. ► A computerized toolset has been implemented to assist the proposed approach. - Abstract: Validation tests in the current nuclear industry practice are typically performed in an ad hoc fashion. This study presents a systematic and objective method of generating validation test cases from a Safety Analysis Report (SAR). A domain-specific ontology was designed and used to mark up a SAR; relevant information was then extracted from the marked-up document for use in automatically generating validation test cases that satisfy the proposed test coverage criteria; namely, single parameter coverage, use case coverage, abnormal condition coverage, and scenario coverage. The novelty of this technique is its systematic rather than ad hoc test case generation from a SAR to achieve high test coverage.

  16. The Software Cost Estimation Method Based on Fuzzy Ontology

    Directory of Open Access Journals (Sweden)

    Plecka Przemysław

    2014-12-01

    Full Text Available In the course of sales process of Enterprise Resource Planning (ERP Systems, it turns out that the standard system must be extended or changed (modified according to specific customer’s requirements. Therefore, suppliers face the problem of determining the cost of additional works. Most methods of cost estimation bring satisfactory results only at the stage of pre-implementation analysis. However, suppliers need to know the estimated cost as early as at the stage of trade talks. During contract negotiations, they expect not only the information about the costs of works, but also about the risk of exceeding these costs or about the margin of safety. One method that gives more accurate results at the stage of trade talks is the method based on the ontology of implementation costs. This paper proposes modification of the method involving the use of fuzzy attributes, classes, instances and relations in the ontology. The result provides not only the information about the value of work, but also about the minimum and maximum expected cost, and the most likely range of costs. This solution allows suppliers to effectively negotiate the contract and increase the chances of successful completion of the project.

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

    DEFF Research Database (Denmark)

    Zhang, Weishan; Kunz, Thomas

    2006-01-01

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

  18. A Social Network System Based on an Ontology in the Korea Institute of Oriental Medicine

    Science.gov (United States)

    Kim, Sang-Kyun; Han, Jeong-Min; Song, Mi-Young

    We in this paper propose a social network based on ontology in Korea Institute of Oriental Medicine (KIOM). By using the social network, researchers can find collaborators and share research results with others so that studies in Korean Medicine fields can be activated. For this purpose, first, personal profiles, scholarships, careers, licenses, academic activities, research results, and personal connections for all of researchers in KIOM are collected. After relationship and hierarchy among ontology classes and attributes of classes are defined through analyzing the collected information, a social network ontology are constructed using FOAF and OWL. This ontology can be easily interconnected with other social network by FOAF and provide the reasoning based on OWL ontology. In future, we construct the search and reasoning system using the ontology. Moreover, if the social network is activated, we will open it to whole Korean Medicine fields.

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

    Directory of Open Access Journals (Sweden)

    Emanuel Santos

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2017-10-01

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

  2. The application of ontology information system based on rough formal concept analysis

    Science.gov (United States)

    Wang, Yi

    2011-10-01

    The role of this ontology is to provide a shared vocabulary and semantics between domain knowledge and vision. Ontology presents semantics for interpreting data instances. Formal concept lattices and rough set theory are two kinds of complementary mathematical tools for data analysis and data processing. The paper proposes the method of constructiong ontology nodes information system based on rough formal concept analysis in order to constructing the ontology model of knowledge management. Experimental studies are done with rough set and FCA in constructing the numbers of ontology nodes. The experimental results indicate that this method has great promise and is showing that ROUGH SET is superior to FCA in building the numbers of ontology nodes.

  3. Ontology-Based Vaccine Adverse Event Representation and Analysis.

    Science.gov (United States)

    Xie, Jiangan; He, Yongqun

    2017-01-01

    ), have been developed with a specific aim to standardize AE categorization. However, these controlled terminologies have many drawbacks, such as lack of textual definitions, poorly defined hierarchies, and lack of semantic axioms that provide logical relations among terms. A biomedical ontology is a set of consensus-based and computer and human interpretable terms and relations that represent entities in a specific biomedical domain and how they relate each other. To represent and analyze vaccine adverse events (VAEs), our research group has initiated and led the development of a community-based ontology: the Ontology of Adverse Events (OAE) (He et al., J Biomed Semant 5:29, 2014). The OAE has been found to have advantages to overcome the drawbacks of those controlled terminologies (He et al., Curr Pharmacol Rep :1-16. doi:10.1007/s40495-016-0055-0, 2014). By expanding the OAE and the community-based Vaccine Ontology (VO) (He et al., VO: vaccine ontology. In The 1st International Conference on Biomedical Ontology (ICBO-2009). Nature Precedings, Buffalo. http://precedings.nature.com/documents/3552/version/1 ; J Biomed Semant 2(Suppl 2):S8; J Biomed Semant 3(1):17, 2009; Ozgur et al., J Biomed Semant 2(2):S8, 2011; Lin Y, He Y, J Biomed Semant 3(1):17, 2012), we have also developed the Ontology of Vaccine Adverse Events (OVAE) to represent known VAEs associated with licensed vaccines (Marcos E, Zhao B, He Y, J Biomed Semant 4:40, 2013).In this book chapter, we will first introduce the basic information of VAEs, VAE safety surveillance systems, and how to specifically query and analyze VAEs using the US VAE database VAERS (Chen et al., Vaccine 12(10):960-960, 1994). In the second half of the chapter, we will introduce the development and applications of the OAE and OVAE. Throughout this chapter, we will use the influenza vaccine Flublok as the vaccine example to launch the corresponding elaboration (Huber VC, McCullers JA, Curr Opin Mol Ther 10(1):75-85, 2008). Flublok is a

  4. Ontology-based information visualization : Toward semantic web applications

    NARCIS (Netherlands)

    Fluit, Christiaan; Sabou, Marta; Van Harmelen, Frank

    2006-01-01

    This chapter has demonstrated an elegant way to visually represent ontological data. We have described how the Cluster Map visualization can use ontologies to create expressive information visualizations, with the attractive property that classes and objects that are semantically related are also

  5. Ontology-Based Information Extraction for Business Intelligence

    Science.gov (United States)

    Saggion, Horacio; Funk, Adam; Maynard, Diana; Bontcheva, Kalina

    Business Intelligence (BI) requires the acquisition and aggregation of key pieces of knowledge from multiple sources in order to provide valuable information to customers or feed statistical BI models and tools. The massive amount of information available to business analysts makes information extraction and other natural language processing tools key enablers for the acquisition and use of that semantic information. We describe the application of ontology-based extraction and merging in the context of a practical e-business application for the EU MUSING Project where the goal is to gather international company intelligence and country/region information. The results of our experiments so far are very promising and we are now in the process of building a complete end-to-end solution.

  6. 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

  7. An Ontology-Based Tourism Recommender System Based on Spreading Activation Model

    Science.gov (United States)

    Bahramian, Z.; Abbaspour, R. Ali

    2015-12-01

    A tourist has time and budget limitations; hence, he needs to select points of interest (POIs) optimally. Since the available information about POIs is overloading, it is difficult for a tourist to select the most appreciate ones considering preferences. In this paper, a new travel recommender system is proposed to overcome information overload problem. A recommender system (RS) evaluates the overwhelming number of POIs and provides personalized recommendations to users based on their preferences. A content-based recommendation system is proposed, which uses the information about the user's preferences and POIs and calculates a degree of similarity between them. It selects POIs, which have highest similarity with the user's preferences. The proposed content-based recommender system is enhanced using the ontological information about tourism domain to represent both the user profile and the recommendable POIs. The proposed ontology-based recommendation process is performed in three steps including: ontology-based content analyzer, ontology-based profile learner, and ontology-based filtering component. User's feedback adapts the user's preferences using Spreading Activation (SA) strategy. It shows the proposed recommender system is effective and improves the overall performance of the traditional content-based recommender systems.

  8. Ontology-based validation and identification of regulatory phenotypes

    KAUST Repository

    Kulmanov, Maxat

    2018-01-31

    Motivation: Function annotations of gene products, and phenotype annotations of genotypes, provide valuable information about molecular mechanisms that can be utilized by computational methods to identify functional and phenotypic relatedness, improve our understanding of disease and pathobiology, and lead to discovery of drug targets. Identifying functions and phenotypes commonly requires experiments which are time-consuming and expensive to carry out; creating the annotations additionally requires a curator to make an assertion based on reported evidence. Support to validate the mutual consistency of functional and phenotype annotations as well as a computational method to predict phenotypes from function annotations, would greatly improve the utility of function annotations Results: We developed a novel ontology-based method to validate the mutual consistency of function and phenotype annotations. We apply our method to mouse and human annotations, and identify several inconsistencies that can be resolved to improve overall annotation quality. Our method can also be applied to the rule-based prediction of phenotypes from functions. We show that the predicted phenotypes can be utilized for identification of protein-protein interactions and gene-disease associations. Based on experimental functional annotations, we predict phenotypes for 1,986 genes in mouse and 7,301 genes in human for which no experimental phenotypes have yet been determined.

  9. An ontological knowledge base for cyber network attack planning

    CSIR Research Space (South Africa)

    Chan, P

    2015-03-01

    Full Text Available . An ontology enables the representation of semantic information and automated reasoning that can support the complexity of planning cyber operations. It also contributes towards the sharing of information and the creation and maintenance of a common vocabulary...

  10. Suggesting Missing Relations in Biomedical Ontologies Based on Lexical Regularities.

    Science.gov (United States)

    Quesada-Martínez, Manuel; Fernández-Breis, Jesualdo Tomás; Karlsson, Daniel

    2016-01-01

    The number of biomedical ontologies has increased significantly in recent years. Many of such ontologies are the result of efforts of communities of domain experts and ontology engineers. The development and application of quality assurance (QA) methods should help these communities to develop useful ontologies for both humans and machines. According to previous studies, biomedical ontologies are rich in natural language content, but most of them are not so rich in axiomatic terms. Here, we are interested in studying the relation between content in natural language and content in axiomatic form. The analysis of the labels of the classes permits to identify lexical regularities (LRs), which are sets of words that are shared by labels of different classes. Our assumption is that the classes exhibiting an LR should be logically related through axioms, which is used to propose an algorithm to detect missing relations in the ontology. Here, we analyse a lexical regularity of SNOMED CT, congenital stenosis, which is reported as problematic by the SNOMED CT maintenance team.

  11. Ubiquitous Supervisory System Based on Social Contexts Using Ontology

    Directory of Open Access Journals (Sweden)

    Satoru Izumi

    2009-01-01

    Full Text Available As described in this paper, we propose a supervisory system that considers actual situations and social aspects of users in a ubiquitous computing environment. To realize gentle and safe supervision while providing efficient supervisory services, the system must recognize the situations of a watched person, such as the person's physical condition. To achieve this, we have proposed a ubiquitous supervisory system "uEyes", which introduces Social Context Awareness: a distinguishing feature for supervision. Using this feature, the system can combine environmental information acquired from sensors in the real world and common-sense knowledge related to human activities in daily life. As described in this paper, we specifically examine design of Social Context Awareness using ontology technologies. Based on this advanced feature, a live video streaming system is configured autonomously depending on the users' circumstances in runtime. We implemented a uEyes prototype for supervising elderly people and performed some experiments based on several scenarios. Based on those experimental results, we confirmed that the social contexts are handled effectively to support the supervision.

  12. The Plasmodium falciparum Sexual Development Transcriptome: A Microarray Analysis using Ontology-Based Pattern Identification

    National Research Council Canada - National Science Library

    Young, Jason A; Fivelman, Quinton L; Blair, Peter L; de la Vega, Patricia; Le Roch, Karine G; Zhou, Yingyao; Carucci, Daniel J; Baker, David A; Winzeler, Elizabeth A

    2005-01-01

    ... a full-genome high-density oligonucleotide microarray. The interpretation of this transcriptional data was aided by applying a novel knowledge-based data-mining algorithm termed ontology-based pattern identification (OPI...

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

    Science.gov (United States)

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

    2004-01-01

    . They are large (in total around 100kLoC Prolog), knowledge intensive systems that employ complex symbolic reasoning to generate a wide range of non-trivial programs for complex application do- mains. Their schemas can have complex interactions, which make it hard to change them in isolation or even understand what an existing schema actually does. Adding more capabilities by increasing the number of schemas will only worsen this situation, ultimately leading to the entropy death of the synthesis system. The root came of this problem is that the domain knowledge is scattered throughout the entire system and only represented implicitly in the schema implementations. In our current work, we are addressing this problem by making explicit the knowledge from Merent parts of the synthesis system. Here; we discuss how Gruber's definition of an ontology as an explicit specification of a conceptualization matches our efforts in identifying and explicating the domain-specific concepts. We outline the dual role ontologies play in schema-based synthesis and argue that they address different audiences and serve different purposes. Their first role is descriptive: they serve as explicit documentation, and help to understand the internal structure of the system. Their second role is prescriptive: they provide the formal basis against which the other parts of the system (e.g., schemas) can be checked. Their final role is referential: ontologies also provide semantically meaningful "hooks" which allow schemas and tools to access the internal state of the program derivation process (e.g., fragments of the generated code) in domain-specific rather than language-specific terms, and thus to modify it in a controlled fashion. For discussion purposes we use AUTOLINEAR, a small synthesis system we are currently experimenting with, which can generate code for solving a system of linear equations, Az = b.

  14. Legal Knowledge and Agility in Public Administration

    NARCIS (Netherlands)

    Boer, A.; van Engers, T.

    2013-01-01

    To address agility in public administration, we have developed a knowledge acquisition infrastructure for legal knowledge, based on an implementation-oriented conceptualization of the legal system. Our objective is to reframe legal knowledge as a knowledge source in a design-oriented task ontology,

  15. Using ontologies to model human navigation behavior in information networks: A study based on Wikipedia.

    Science.gov (United States)

    Lamprecht, Daniel; Strohmaier, Markus; Helic, Denis; Nyulas, Csongor; Tudorache, Tania; Noy, Natalya F; Musen, Mark A

    The need to examine the behavior of different user groups is a fundamental requirement when building information systems. In this paper, we present Ontology-based Decentralized Search (OBDS), a novel method to model the navigation behavior of users equipped with different types of background knowledge. Ontology-based Decentralized Search combines decentralized search, an established method for navigation in social networks, and ontologies to model navigation behavior in information networks. The method uses ontologies as an explicit representation of background knowledge to inform the navigation process and guide it towards navigation targets. By using different ontologies, users equipped with different types of background knowledge can be represented. We demonstrate our method using four biomedical ontologies and their associated Wikipedia articles. We compare our simulation results with base line approaches and with results obtained from a user study. We find that our method produces click paths that have properties similar to those originating from human navigators. The results suggest that our method can be used to model human navigation behavior in systems that are based on information networks, such as Wikipedia. This paper makes the following contributions: (i) To the best of our knowledge, this is the first work to demonstrate the utility of ontologies in modeling human navigation and (ii) it yields new insights and understanding about the mechanisms of human navigation in information networks.

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

    Science.gov (United States)

    Morstyn, Ron

    2013-08-01

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

  17. Designing and Implementing Basic Sciences Ontology Based on Concepts and Relationships of Relevant Thesauri

    Directory of Open Access Journals (Sweden)

    Molouk Sadat Hosseini Beheshti

    2015-05-01

    Full Text Available Currently, the main portion of knowledge is stored in electronic texts and documents and for transferring that knowledge effectively, we must use proper methods to gather and retrieve relevant information. Ontologies provide means to produce structured documents and use intelligent search instead of keyword search. Ontology defines the common words and concepts used to describe and represent an area of knowledge. However, developing ontologies is a time consuming and labor work, so many ontology developers try to facilitate and speed up this process by reusing other resources. In fact, thesaurus contains semantic information and hierarchical structure that make it an appropriate resource for ontology construction. Therefore, we determined to use the thesauri previously developed at Iranian Research Institute for Information Science and Technology (IRANDOC to construct ontology in basic sciences domain. At first, we synchronized common concepts in thesauri before integrating them as a macro thesaurus and removed inconsistencies. To reduce the amount of time and human resources which were needed for synchronizing process, Thesaurus Synchronizer was developed to illustrate differences between matched cases of two thesauri. It provides powerful tools for demonstrating differences and suggestions for each of the existing matters. Thus, domain experts synchronized each two thesaurus semi-automatically. Then we merged thesauri and transform the data format into ISO 25964 standard. The conceptual model have been designed based on the terms and their relationships in the integrated thesaurus and the concept maps that were designed by domain experts for each of basic sciences (Chemistry, Physics, Biology, Geology and Mathematics. We used the methodology called METHONTOLOGY in this stage. The main activity in this methodology is conceptualization and it enables the construction of ontologies at the knowledge level. Ultimately, the ontology was generated by

  18. Feature-based Ontology Mapping from an Information Receivers’ Viewpoint

    DEFF Research Database (Denmark)

    Glückstad, Fumiko Kano; Mørup, Morten

    2012-01-01

    optimally convey the original meaning of a culturally-specific Source Language (SL) concept to a TL audience by aligning two culturally-dependent domain-specific ontologies. The results indicate that the Bayesian Model of Generalization [1] performs best, not only for identifying candidate translation terms...

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

    Indian Academy of Sciences (India)

    B Sathiya

    2017-11-16

    Nov 16, 2017 ... algorithms generally do not scale well due to the massive number of complex computations required to achieve matching. One of the methods used .... Even though several ontology matching systems exist, there are only very few matching ...... in Computational Intelligence, vol. 292, pp. 251–269. [12] Hanif ...

  20. Multi-label literature classification based on the Gene Ontology graph

    Directory of Open Access Journals (Sweden)

    Lu Xinghua

    2008-12-01

    Full Text Available Abstract Background The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of text mining approaches to facilitate the process by automatically extracting the Gene Ontology annotation from literature. The task is usually cast as a text classification problem, and contemporary methods are confronted with unbalanced training data and the difficulties associated with multi-label classification. Results In this research, we investigated the methods of enhancing automatic multi-label classification of biomedical literature by utilizing the structure of the Gene Ontology graph. We have studied three graph-based multi-label classification algorithms, including a novel stochastic algorithm and two top-down hierarchical classification methods for multi-label literature classification. We systematically evaluated and compared these graph-based classification algorithms to a conventional flat multi-label algorithm. The results indicate that, through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods can significantly improve predictions of the Gene Ontology terms implied by the analyzed text. Furthermore, the graph-based multi-label classifiers are capable of suggesting Gene Ontology annotations (to curators that are closely related to the true annotations even if they fail to predict the true ones directly. A software package implementing the studied algorithms is available for the research community. Conclusion Through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods have better potential than the conventional flat multi-label classification approach to facilitate

  1. Multi-label literature classification based on the Gene Ontology graph.

    Science.gov (United States)

    Jin, Bo; Muller, Brian; Zhai, Chengxiang; Lu, Xinghua

    2008-12-08

    The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of text mining approaches to facilitate the process by automatically extracting the Gene Ontology annotation from literature. The task is usually cast as a text classification problem, and contemporary methods are confronted with unbalanced training data and the difficulties associated with multi-label classification. In this research, we investigated the methods of enhancing automatic multi-label classification of biomedical literature by utilizing the structure of the Gene Ontology graph. We have studied three graph-based multi-label classification algorithms, including a novel stochastic algorithm and two top-down hierarchical classification methods for multi-label literature classification. We systematically evaluated and compared these graph-based classification algorithms to a conventional flat multi-label algorithm. The results indicate that, through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods can significantly improve predictions of the Gene Ontology terms implied by the analyzed text. Furthermore, the graph-based multi-label classifiers are capable of suggesting Gene Ontology annotations (to curators) that are closely related to the true annotations even if they fail to predict the true ones directly. A software package implementing the studied algorithms is available for the research community. Through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods have better potential than the conventional flat multi-label classification approach to facilitate protein annotation based on the literature.

  2. BioPortal: An Open-Source Community-Based Ontology Repository

    Science.gov (United States)

    Noy, N.; NCBO Team

    2011-12-01

    Advances in computing power and new computational techniques have changed the way researchers approach science. In many fields, one of the most fruitful approaches has been to use semantically aware software to break down the barriers among disparate domains, systems, data sources, and technologies. Such software facilitates data aggregation, improves search, and ultimately allows the detection of new associations that were previously not detectable. Achieving these analyses requires software systems that take advantage of the semantics and that can intelligently negotiate domains and knowledge sources, identifying commonality across systems that use different and conflicting vocabularies, while understanding apparent differences that may be concealed by the use of superficially similar terms. An ontology, a semantically rich vocabulary for a domain of interest, is the cornerstone of software for bridging systems, domains, and resources. However, as ontologies become the foundation of all semantic technologies in e-science, we must develop an infrastructure for sharing ontologies, finding and evaluating them, integrating and mapping among them, and using ontologies in applications that help scientists process their data. BioPortal [1] is an open-source on-line community-based ontology repository that has been used as a critical component of semantic infrastructure in several domains, including biomedicine and bio-geochemical data. BioPortal, uses the social approaches in the Web 2.0 style to bring structure and order to the collection of biomedical ontologies. It enables users to provide and discuss a wide array of knowledge components, from submitting the ontologies themselves, to commenting on and discussing classes in the ontologies, to reviewing ontologies in the context of their own ontology-based projects, to creating mappings between overlapping ontologies and discussing and critiquing the mappings. Critically, it provides web-service access to all its

  3. 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.

  4. Development of health information search engine based on metadata and ontology.

    Science.gov (United States)

    Song, Tae-Min; Park, Hyeoun-Ae; Jin, Dal-Lae

    2014-04-01

    The aim of the study was to develop a metadata and ontology-based health information search engine ensuring semantic interoperability to collect and provide health information using different application programs. Health information metadata ontology was developed using a distributed semantic Web content publishing model based on vocabularies used to index the contents generated by the information producers as well as those used to search the contents by the users. Vocabulary for health information ontology was mapped to the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT), and a list of about 1,500 terms was proposed. The metadata schema used in this study was developed by adding an element describing the target audience to the Dublin Core Metadata Element Set. A metadata schema and an ontology ensuring interoperability of health information available on the internet were developed. The metadata and ontology-based health information search engine developed in this study produced a better search result compared to existing search engines. Health information search engine based on metadata and ontology will provide reliable health information to both information producer and information consumers.

  5. Disease Compass- a navigation system for disease knowledge based on ontology and linked data techniques.

    Science.gov (United States)

    Kozaki, Kouji; Yamagata, Yuki; Mizoguchi, Riichiro; Imai, Takeshi; Ohe, Kazuhiko

    2017-06-19

    Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated mechanisms of diseases are related to concepts across various medical domains. The authors developed a River Flow Model (RFM) of diseases, which captures diseases as the causal chains of abnormal states. It represents causes of diseases, disease progression, and downstream consequences of diseases, which is compliant with the intuition of medical experts. In this paper, we discuss a fact repository for causal chains of disease based on the disease ontology. It could be a valuable knowledge base for advanced medical information systems. We developed the fact repository for causal chains of diseases based on our disease ontology and abnormality ontology. This section summarizes these two ontologies. It is developed as linked data so that information scientists can access it using SPARQL queries through an Resource Description Framework (RDF) model for causal chain of diseases. We designed the RDF model as an implementation of the RFM for the fact repository based on the ontological definitions of the RFM. 1554 diseases and 7080 abnormal states in six major clinical areas, which are extracted from the disease ontology, are published as linked data (RDF) with SPARQL endpoint (accessible API). Furthermore, the authors developed Disease Compass, a navigation system for disease knowledge. Disease Compass can browse the causal chains of a disease and obtain related information, including abnormal states, through two web services that provide general information from linked data, such as DBpedia, and 3D anatomical images. Disease Compass can provide a complete picture of disease-associated processes in such a way that fits with a clinician's understanding of diseases. Therefore, it supports user exploration of disease knowledge with access to pertinent information

  6. Linking human diseases to animal models using ontology-based phenotype annotation.

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    Nicole L Washington

    2009-11-01

    Full Text Available Scientists and clinicians who study genetic alterations and disease have traditionally described phenotypes in natural language. The considerable variation in these free-text descriptions has posed a hindrance to the important task of identifying candidate genes and models for human diseases and indicates the need for a computationally tractable method to mine data resources for mutant phenotypes. In this study, we tested the hypothesis that ontological annotation of disease phenotypes will facilitate the discovery of new genotype-phenotype relationships within and across species. To describe phenotypes using ontologies, we used an Entity-Quality (EQ methodology, wherein the affected entity (E and how it is affected (Q are recorded using terms from a variety of ontologies. Using this EQ method, we annotated the phenotypes of 11 gene-linked human diseases described in Online Mendelian Inheritance in Man (OMIM. These human annotations were loaded into our Ontology-Based Database (OBD along with other ontology-based phenotype descriptions of mutants from various model organism databases. Phenotypes recorded with this EQ method can be computationally compared based on the hierarchy of terms in the ontologies and the frequency of annotation. We utilized four similarity metrics to compare phenotypes and developed an ontology of homologous and analogous anatomical structures to compare phenotypes between species. Using these tools, we demonstrate that we can identify, through the similarity of the recorded phenotypes, other alleles of the same gene, other members of a signaling pathway, and orthologous genes and pathway members across species. We conclude that EQ-based annotation of phenotypes, in conjunction with a cross-species ontology, and a variety of similarity metrics can identify biologically meaningful similarities between genes by comparing phenotypes alone. This annotation and search method provides a novel and efficient means to identify

  7. Ontology or formal ontology

    Science.gov (United States)

    Žáček, Martin

    2017-07-01

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

  8. THE SPAСE OF EDUCATIONAL RESEARCH ACTIVITY OF STUDENTS BASED ON ASSOCIATION ONTOLOGICALLY INTERFACE AND GIS-TECHNOLOGIES

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    Maryna A. Popova

    2014-04-01

    Full Text Available This article discusses the ontologies and ontological computer interface use as an effective means of integration, aggregation and visualization of distributed information resources and systems through the use of semantic properties to create and use of information space in education and research activities of students. The approach of combining ontologies features and geospatial analytical tools functions of GIS is described. The technique of ontological interface applying by creating a thematic map layers in GIS environment based on thematic ontology is presented.

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

    Science.gov (United States)

    Magdalenić, Ivan; Vrdoljak, Boris; Schatten, Markus

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

  10. Expert System Based on an Ontology Method to Analyze Types of Arabica Coffee Beans

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    Michelle Angelica

    2017-07-01

    Full Text Available In the past few decades, the use of ontologies in information systems has become popular in many fields, such as website development, database integration, and natural language processing. Because many kinds of coffee beans can be used in coffee shops, the prospective coffee house entrepreneur meets obstacles in terms of choosing the right coffee beans because of multiple unique characteristics. In order to help this cohort make decisions, our study proposed a simulation ontology-based matching for coffee bean selection by inserting three parameters—aroma, flavor, and sour level—as inputs on the website. Arabica coffee bean is used as the principal object in this study and the outputs would be the beans matched with the parameters that had been inserted. In this study, the system model gained from the ontology method is shown in the implementation by using an example.Key Words—Arabica coffee beans, Ontology, OWL, Protégé, SPARQL

  11. 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)

  12. Evaluating the Relevance of Corporate Ontological Knowledge Base Documents Using Their Hierarchical Role Clustering

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    A. P. Karpenko

    2014-01-01

    Full Text Available The article considers a corporate knowledge base representing a set of the large number of various semi-structured documents, which describe to some detail precedents i.e. some situations and decisions made in these situations. The task is to find the decision in such knowledge base and search the most suitable precedents and their corresponding documents in it.The work continues a series of the authors’ works, which develop an original approach to the solution of this task. It is supposed that metadata of the knowledge base documents are based on the ontology of the corresponding subject domain specified as a semantic network. As opposed to the previous works it is necessary that ontology of subject domain, and thereby and corresponding semantic network, is hierarchically clustered based on the roles of concepts.Documents in the knowledge base, and also search queries are presented as frames, which are called ‘patterns of design and inquiry’, respectively. Slots of these patterns correspond to roles of concepts of the used ontology. Above-noted roles break concepts of ontology, document, and request to the knowledge base into clusters. It is supposed that semantic networks of the abovementioned clusters are designed by a technique for creation of a semantic network of the document. Thus, search images of the document and inquiry are presented as a set of the semantic networks corresponding to slots of a pattern of design and a pattern of inquiry.The work offers the model of a semantic network of the ontological knowledge base using a hierarchical role clustering of concepts of this ontology. The task for a multi-criteria evaluation of relevance of corporate ontological knowledge base documents using their hierarchical role clustering is set. The method is offered to solve the task using the original measures of proximity of role patterns of design of the required document and inquiry.

  13. 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.

  14. Building spatio-temporal database model based on ontological approach using relational database environment

    International Nuclear Information System (INIS)

    Mahmood, N.; Burney, S.M.A.

    2017-01-01

    Everything in this world is encapsulated by space and time fence. Our daily life activities are utterly linked and related with other objects in vicinity. Therefore, a strong relationship exist with our current location, time (including past, present and future) and event through with we are moving as an object also affect our activities in life. Ontology development and its integration with database are vital for the true understanding of the complex systems involving both spatial and temporal dimensions. In this paper we propose a conceptual framework for building spatio-temporal database model based on ontological approach. We have used relational data model for modelling spatio-temporal data content and present our methodology with spatio-temporal ontological accepts and its transformation into spatio-temporal database model. We illustrate the implementation of our conceptual model through a case study related to cultivated land parcel used for agriculture to exhibit the spatio-temporal behaviour of agricultural land and related entities. Moreover, it provides a generic approach for designing spatiotemporal databases based on ontology. The proposed model is capable to understand the ontological and somehow epistemological commitments and to build spatio-temporal ontology and transform it into a spatio-temporal data model. Finally, we highlight the existing and future research challenges. (author)

  15. Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis.

    Science.gov (United States)

    Tao, Cui; He, Yongqun; Yang, Hannah; Poland, Gregory A; Chute, Christopher G

    2012-12-20

    The U.S. FDA/CDC Vaccine Adverse Event Reporting System (VAERS) provides a valuable data source for post-vaccination adverse event analyses. The structured data in the system has been widely used, but the information in the write-up narratives is rarely included in these kinds of analyses. In fact, the unstructured nature of the narratives makes the data embedded in them difficult to be used for any further studies. We developed an ontology-based approach to represent the data in the narratives in a "machine-understandable" way, so that it can be easily queried and further analyzed. Our focus is the time aspect in the data for time trending analysis. The Time Event Ontology (TEO), Ontology of Adverse Events (OAE), and Vaccine Ontology (VO) are leveraged for the semantic representation of this purpose. A VAERS case report is presented as a use case for the ontological representations. The advantages of using our ontology-based Semantic web representation and data analysis are emphasized. We believe that representing both the structured data and the data from write-up narratives in an integrated, unified, and "machine-understandable" way can improve research for vaccine safety analyses, causality assessments, and retrospective studies.

  16. Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis

    Directory of Open Access Journals (Sweden)

    Tao Cui

    2012-12-01

    Full Text Available Abstract Background The U.S. FDA/CDC Vaccine Adverse Event Reporting System (VAERS provides a valuable data source for post-vaccination adverse event analyses. The structured data in the system has been widely used, but the information in the write-up narratives is rarely included in these kinds of analyses. In fact, the unstructured nature of the narratives makes the data embedded in them difficult to be used for any further studies. Results We developed an ontology-based approach to represent the data in the narratives in a “machine-understandable” way, so that it can be easily queried and further analyzed. Our focus is the time aspect in the data for time trending analysis. The Time Event Ontology (TEO, Ontology of Adverse Events (OAE, and Vaccine Ontology (VO are leveraged for the semantic representation of this purpose. A VAERS case report is presented as a use case for the ontological representations. The advantages of using our ontology-based Semantic web representation and data analysis are emphasized. Conclusions We believe that representing both the structured data and the data from write-up narratives in an integrated, unified, and “machine-understandable” way can improve research for vaccine safety analyses, causality assessments, and retrospective studies.

  17. Ontology-Based Information Behaviour to Improve Web Search

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    Silvia Calegari

    2010-10-01

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

  18. Ontology-based data integration between clinical and research systems.

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    Sebastian Mate

    Full Text Available Data from the electronic medical record comprise numerous structured but uncoded elements, which are not linked to standard terminologies. Reuse of such data for secondary research purposes has gained in importance recently. However, the identification of relevant data elements and the creation of database jobs for extraction, transformation and loading (ETL are challenging: With current methods such as data warehousing, it is not feasible to efficiently maintain and reuse semantically complex data extraction and trans-formation routines. We present an ontology-supported approach to overcome this challenge by making use of abstraction: Instead of defining ETL procedures at the database level, we use ontologies to organize and describe the medical concepts of both the source system and the target system. Instead of using unique, specifically developed SQL statements or ETL jobs, we define declarative transformation rules within ontologies and illustrate how these constructs can then be used to automatically generate SQL code to perform the desired ETL procedures. This demonstrates how a suitable level of abstraction may not only aid the interpretation of clinical data, but can also foster the reutilization of methods for un-locking it.

  19. Deriving ontological semantic relations between Arabic compound nouns concepts

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    Imen Bouaziz Mezghanni

    2017-04-01

    Experiments carried out on Arabic legal dataset showed that the proposed approach reached encouraging performance through achieving high precision and recall scores. This performance affects positively the retrieval results of legal documents based on a powerful ontology, which presents our main objective.

  20. Ontology-based, Tissue MicroArray oriented, image centered tissue bank

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    Viti Federica

    2008-04-01

    Full Text Available Abstract Background Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many images which need to be properly managed, if possible with an infrastructure able to support tissue sharing between institutes. Moreover, the available frameworks oriented to Tissue MicroArray provide good storage for clinical patient, sample treatment and block construction information, but their utility is limited by the lack of data integration with biomolecular information. Results In this work we propose a Tissue MicroArray web oriented system to support researchers in managing bio-samples and, through the use of ontologies, enables tissue sharing aimed at the design of Tissue MicroArray experiments and results evaluation. Indeed, our system provides ontological description both for pre-analysis tissue images and for post-process analysis image results, which is crucial for information exchange. Moreover, working on well-defined terms it is then possible to query web resources for literature articles to integrate both pathology and bioinformatics data. Conclusions Using this system, users associate an ontology-based description to each image uploaded into the database and also integrate results with the ontological description of biosequences identified in every tissue. Moreover, it is possible to integrate the ontological description provided by the user with a full compliant gene ontology definition, enabling statistical studies about correlation between the analyzed pathology and the most commonly related biological processes.

  1. EEVADO-ontology based construction of a knowledge based system for handling radiation emergency

    International Nuclear Information System (INIS)

    Datta, D.; Hegde, A.G.

    2001-01-01

    The basic aim of handling a radiation emergency is to protect the site personnel and public in the off-site areas. Hence it is required to assess the accident to develop the protective action recommendations for the site personnel, members of the public and emergency workers. An explanation facility is required to analyze the emergency situation and make needful decision. Algorithmic based software cannot provide this support as it does not have any such facility. A knowledge based system (KBS) obviously would act as a special purpose intelligent agent on behalf or at the behest of the emergency organization. Knowledge of the KBS has been elicited on the basis of ontology, a set of definitions of classes, objects, attributes, relations and constraints. Ontology provides a vocabulary for the expression of domain knowledge. The present paper discusses the development and utility of a knowledge based system - EEVADO (Emergency Evaluation and Dosimetry). The present software is verified and validated by ontology and by conducting Desktop Exercise in training program on Emergency Preparedness. (author)

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

    Science.gov (United States)

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

    2015-02-21

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

  3. Unexpected rules using a conceptual distance based on fuzzy ontology

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    Mohamed Said Hamani

    2014-01-01

    Full Text Available One of the major drawbacks of data mining methods is that they generate a notably large number of rules that are often obvious or useless or, occasionally, out of the user’s interest. To address such drawbacks, we propose in this paper an approach that detects a set of unexpected rules in a discovered association rule set. Generally speaking, the proposed approach investigates the discovered association rules using the user’s domain knowledge, which is represented by a fuzzy domain ontology. Next, we rank the discovered rules according to the conceptual distances of the rules.

  4. Ontology-based automatic identification of public health-related Turkish tweets.

    Science.gov (United States)

    Küçük, Emine Ela; Yapar, Kürşad; Küçük, Dilek; Küçük, Doğan

    2017-04-01

    Social media analysis, such as the analysis of tweets, is a promising research topic for tracking public health concerns including epidemics. In this paper, we present an ontology-based approach to automatically identify public health-related Turkish tweets. The system is based on a public health ontology that we have constructed through a semi-automated procedure. The ontology concepts are expanded through a linguistically motivated relaxation scheme as the last stage of ontology development, before being integrated into our system to increase its coverage. The ultimate lexical resource which includes the terms corresponding to the ontology concepts is used to filter the Twitter stream so that a plausible tweet subset, including mostly public-health related tweets, can be obtained. Experiments are carried out on two million genuine tweets and promising precision rates are obtained. Also implemented within the course of the current study is a Web-based interface, to track the results of this identification system, to be used by the related public health staff. Hence, the current social media analysis study has both technical and practical contributions to the significant domain of public health. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Ontology-Based Representation and Reasoning in Building Construction Cost Estimation in China

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    Xin Liu

    2016-08-01

    Full Text Available Cost estimation is one of the most critical tasks for building construction project management. The existing building construction cost estimation methods of many countries, including China, require information from several sources, including material, labor, and equipment, and tend to be manual, time-consuming, and error-prone. To solve these problems, a building construction cost estimation model based on ontology representation and reasoning is established, which includes three major components, i.e., concept model ontology, work item ontology, and construction condition ontology. Using this model, the cost estimation information is modeled into OWL axioms and SWRL rules that leverage the semantically rich ontology representation to reason about cost estimation. Based on OWL axioms and SWRL rules, the cost estimation information can be translated into a set of concept models, work items, and construction conditions associated with the specific construction conditions. The proposed method is demonstrated in Protégé 3.4.8 through case studies based on the Measurement Specifications of Building Construction and Decoration Engineering taken from GB 50500-2013 (the Chinese national mandatory specifications. Finally, this research discusses the limitations of the proposed method and future research directions. The proposed method can help a building construction cost estimator extract information more easily and quickly.

  6. An ontology-based hierarchical semantic modeling approach to clinical pathway workflows.

    Science.gov (United States)

    Ye, Yan; Jiang, Zhibin; Diao, Xiaodi; Yang, Dong; Du, Gang

    2009-08-01

    This paper proposes an ontology-based approach of modeling clinical pathway workflows at the semantic level for facilitating computerized clinical pathway implementation and efficient delivery of high-quality healthcare services. A clinical pathway ontology (CPO) is formally defined in OWL web ontology language (OWL) to provide common semantic foundation for meaningful representation and exchange of pathway-related knowledge. A CPO-based semantic modeling method is then presented to describe clinical pathways as interconnected hierarchical models including the top-level outcome flow and intervention workflow level along a care timeline. Furthermore, relevant temporal knowledge can be fully represented by combing temporal entities in CPO and temporal rules based on semantic web rule language (SWRL). An illustrative example about a clinical pathway for cesarean section shows the applicability of the proposed methodology in enabling structured semantic descriptions of any real clinical pathway.

  7. Global polar geospatial information service retrieval based on search engine and ontology reasoning

    Science.gov (United States)

    Chen, Nengcheng; E, Dongcheng; Di, Liping; Gong, Jianya; Chen, Zeqiang

    2007-01-01

    In order to improve the access precision of polar geospatial information service on web, a new methodology for retrieving global spatial information services based on geospatial service search and ontology reasoning is proposed, the geospatial service search is implemented to find the coarse service from web, the ontology reasoning is designed to find the refined service from the coarse service. The proposed framework includes standardized distributed geospatial web services, a geospatial service search engine, an extended UDDI registry, and a multi-protocol geospatial information service client. Some key technologies addressed include service discovery based on search engine and service ontology modeling and reasoning in the Antarctic geospatial context. Finally, an Antarctica multi protocol OWS portal prototype based on the proposed methodology is introduced.

  8. Domain XML semantic integration based on extraction rules and ontology mapping

    Directory of Open Access Journals (Sweden)

    Huayu LI

    2016-08-01

    Full Text Available A plenty of XML documents exist in petroleum engineering field, but traditional XML integration solution can’t provide semantic query, which leads to low data use efficiency. In light of WeXML(oil&gas well XML data semantic integration and query requirement, this paper proposes a semantic integration method based on extraction rules and ontology mapping. The method firstly defines a series of extraction rules with which elements and properties of WeXML Schema are mapped to classes and properties in WeOWL ontology, respectively; secondly, an algorithm is used to transform WeXML documents into WeOWL instances. Because WeOWL provides limited semantics, ontology mappings between two ontologies are then built to explain class and property of global ontology with terms of WeOWL, and semantic query based on global domain concepts model is provided. By constructing a WeXML data semantic integration prototype system, the proposed transformational rule, the transfer algorithm and the mapping rule are tested.

  9. [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.

  10. 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.

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

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    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.

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

    Science.gov (United States)

    Gao, Wei; Zhu, Linli; Wang, Kaiyun

    2015-12-01

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

  13. Ontological model for predicting cyberattacks based on virtualized Honeynets

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    Gaona-García, Pablo

    2016-12-01

    Full Text Available The honeynets security tools are widely used today for the purpose of gathering information from potential attackers about vulnerabilities in our network. For performing correct use of them is necessary to understand the existing types, structures raised, the tools used and current developments. However, poor planning honeypot or honeynet one could provide unwanted users an access point to the network we want to protect. The purpose of this article is to carry out the approach of an ontological model for identifying the most common attacks types from the use of honeynets, and its implementation on working scenarios. This model will facilitate decision-making for the location of elements and components to computer level in an organization.

  14. In Pursuit of Natural Logics for Ontology-Structured Knowledge Bases

    DEFF Research Database (Denmark)

    Nilsson, Jørgen Fischer

    2015-01-01

    We argue for adopting a form of natural logic for ontology-structured knowledge bases with complex sentences. This serves to ease reading of knowledge base for domain experts and to make reasoning and querying and path-finding more comprehensible. We explain natural logic as a development from...

  15. The Design and Engineering of Mobile Data Services: Developing an Ontology Based on Business Model Thinking

    Science.gov (United States)

    Al-Debei, Mutaz M.; Fitzgerald, Guy

    This paper addresses the design and engineering problem related to mobile data services. The aim of the research is to inform and advise mobile service design and engineering by looking at this issue from a rigorous and holistic perspective. To this aim, this paper develops an ontology based on business model thinking. The developed ontology identifies four primary dimensions in designing business models of mobile data services: value proposition, value network, value architecture, and value finance. Within these dimensions, 15 key design concepts are identified along with their interrelationships and rules in the telecommunication service business model domain and unambiguous semantics are produced. The developed ontology is of value to academics and practitioners alike, particularly those interested in strategic-oriented IS/IT and business developments in telecommunications. Employing the developed ontology would systemize mobile service engineering functions and make them more manageable, effective, and creative. The research approach to building the mobile service business model ontology essentially follows the design science paradigm. Within this paradigm, we incorporate a number of different research methods, so the employed methodology might be better characterized as a pluralist approach.

  16. An Ontology-Based Temporal Scheduling and Complexity Reduction Model for Timetabling Knowledge Management

    Directory of Open Access Journals (Sweden)

    Patience Usoro Usip

    2017-08-01

    Full Text Available Technological tools such as Semantic Web and ontologies have contributed immensely to the reduction of most managerial complexities on daily basis. However, most resolved complexities are solely dependent on the emerging issues which are not general enough to accommodate some specific domain challenges. Temporal scheduling complexities occur in several domains including timetabling, but inter-departmental courses allocation on a general institutional timetable has not been considered. This poses serious managerial concerns and threats to the academic performance of any institution. This paper is aimed at formalizing an ontology model for analyzing temporal scheduling complexities in an existing schedule and giving optimal possible time scheduling resolutions showing their reduction rates for efficient and intelligent knowledge management. Protégé was used in modeling the domain ontology described in the resulted ontograf. The semantics of the formal ontology model is described based on Allen’s interval temporal relations. The use of ontologies make way for easy and intelligent reasoning with knowledge and exposes the need for such knowledge management tool to manage the influx of the numerous data.

  17. An ontology based information system for the management of institutional repository's collections

    Science.gov (United States)

    Tsolakidis, A.; Kakoulidis, P.; Skourlas, C.

    2015-02-01

    In this paper we discuss a simple methodological approach to create, and customize institutional repositories for the domain of the technological education. The use of the open source software platform of DSpace is proposed to build up the repository application and provide access to digital resources including research papers, dissertations, administrative documents, educational material, etc. Also the use of owl ontologies is proposed for indexing and accessing the various, heterogeneous items stored in the repository. Customization and operation of a platform for the selection and use of terms or parts of similar existing owl ontologies is also described. This platform could be based on the open source software Protégé that supports owl, is widely used, and also supports visualization, SPARQL etc. The combined use of the owl platform and the DSpace repository form a basis for creating customized ontologies, accommodating the semantic metadata of items and facilitating searching.

  18. Ant-based extraction of rules in simple decision systems over ontological graphs

    Directory of Open Access Journals (Sweden)

    Pancerz Krzysztof

    2015-06-01

    Full Text Available In the paper, the problem of extraction of complex decision rules in simple decision systems over ontological graphs is considered. The extracted rules are consistent with the dominance principle similar to that applied in the dominancebased rough set approach (DRSA. In our study, we propose to use a heuristic algorithm, utilizing the ant-based clustering approach, searching the semantic spaces of concepts presented by means of ontological graphs. Concepts included in the semantic spaces are values of attributes describing objects in simple decision systems

  19. A rule-based ontological framework for the classification of molecules.

    Science.gov (United States)

    Magka, Despoina; Krötzsch, Markus; Horrocks, Ian

    2014-01-01

    A variety of key activities within life sciences research involves integrating and intelligently managing large amounts of biochemical information. Semantic technologies provide an intuitive way to organise and sift through these rapidly growing datasets via the design and maintenance of ontology-supported knowledge bases. To this end, OWL-a W3C standard declarative language- has been extensively used in the deployment of biochemical ontologies that can be conveniently organised using the classification facilities of OWL-based tools. One of the most established ontologies for the chemical domain is ChEBI, an open-access dictionary of molecular entities that supplies high quality annotation and taxonomical information for biologically relevant compounds. However, ChEBI is being manually expanded which hinders its potential to grow due to the limited availability of human resources. In this work, we describe a prototype that performs automatic classification of chemical compounds. The software we present implements a sound and complete reasoning procedure of a formalism that extends datalog and builds upon an off-the-shelf deductive database system. We capture a wide range of chemical classes that are not expressible with OWL-based formalisms such as cyclic molecules, saturated molecules and alkanes. Furthermore, we describe a surface 'less-logician-like' syntax that allows application experts to create ontological descriptions of complex biochemical objects without prior knowledge of logic. In terms of performance, a noticeable improvement is observed in comparison with previous approaches. Our evaluation has discovered subsumptions that are missing from the manually curated ChEBI ontology as well as discrepancies with respect to existing subclass relations. We illustrate thus the potential of an ontology language suitable for the life sciences domain that exhibits a favourable balance between expressive power and practical feasibility. Our proposed methodology can

  20. 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.

  1. Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research.

    Science.gov (United States)

    Sahoo, Satya S; Ramesh, Priya; Welter, Elisabeth; Bukach, Ashley; Valdez, Joshua; Tatsuoka, Curtis; Bamps, Yvan; Stoll, Shelley; Jobst, Barbara C; Sajatovic, Martha

    2016-10-01

    We present Insight as an integrated database and analysis platform for epilepsy self-management research as part of the national Managing Epilepsy Well Network. Insight is the only available informatics platform for accessing and analyzing integrated data from multiple epilepsy self-management research studies with several new data management features and user-friendly functionalities. The features of Insight include, (1) use of Common Data Elements defined by members of the research community and an epilepsy domain ontology for data integration and querying, (2) visualization tools to support real time exploration of data distribution across research studies, and (3) an interactive visual query interface for provenance-enabled research cohort identification. The Insight platform contains data from five completed epilepsy self-management research studies covering various categories of data, including depression, quality of life, seizure frequency, and socioeconomic information. The data represents over 400 participants with 7552 data points. The Insight data exploration and cohort identification query interface has been developed using Ruby on Rails Web technology and open source Web Ontology Language Application Programming Interface to support ontology-based reasoning. We have developed an efficient ontology management module that automatically updates the ontology mappings each time a new version of the Epilepsy and Seizure Ontology is released. The Insight platform features a Role-based Access Control module to authenticate and effectively manage user access to different research studies. User access to Insight is managed by the Managing Epilepsy Well Network database steering committee consisting of representatives of all current collaborating centers of the Managing Epilepsy Well Network. New research studies are being continuously added to the Insight database and the size as well as the unique coverage of the dataset allows investigators to conduct

  2. BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology

    Directory of Open Access Journals (Sweden)

    Gregorio Sergio E

    2009-05-01

    Full Text Available Abstract Motivation Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. Results We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. Availability The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

  3. ELE: An Ontology-Based System Integrating Semantic Search and E-Learning Technologies

    Science.gov (United States)

    Barbagallo, A.; Formica, A.

    2017-01-01

    ELSE (E-Learning for the Semantic ECM) is an ontology-based system which integrates semantic search methodologies and e-learning technologies. It has been developed within a project of the CME (Continuing Medical Education) program--ECM (Educazione Continua nella Medicina) for Italian participants. ELSE allows the creation of e-learning courses…

  4. Ontology-based high-level context inference for human behavior identification

    NARCIS (Netherlands)

    Villalonga, Claudia; Razzaq, Muhammad Asif; Ali Khan, Wajahat; Pomares, Hector; Rojas, Ignacio; Lee, Sungyoung; Banos Legran, Oresti

    2016-01-01

    Recent years have witnessed a huge progress in the utomatic identification of individual primitives of human behavior, such as activities or locations. However, the complex nature of human behavior demands more abstract contextual information for its analysis. This work presents an ontology-based

  5. Ontological Knowledge Base of Physical and Technical Effects for Conceptual Design of Sensors

    International Nuclear Information System (INIS)

    ASTRAKHAN CIVIL ENGINEERING INSTITUTE, Astrakhan (Russian Federation))" data-affiliation=" (Department of CAD Systems, State Autonomous Educational Institution of Astrakhan Region of Higher Professional Education ASTRAKHAN CIVIL ENGINEERING INSTITUTE, Astrakhan (Russian Federation))" >Zaripova, V M; ASTRAKHAN CIVIL ENGINEERING INSTITUTE, Astrakhan (Russian Federation))" data-affiliation=" (Department of CAD Systems, State Autonomous Educational Institution of Astrakhan Region of Higher Professional Education ASTRAKHAN CIVIL ENGINEERING INSTITUTE, Astrakhan (Russian Federation))" >Petrova, I Yu

    2015-01-01

    This article discusses design of the knowledge base of physical phenomena based on domain-specific ontology. Classification of various physical phenomena in the knowledge base is based on energy-information model of circuits (EIMC) suggested by the authors. This model is specially aimed at design of new operating principles of sensing elements (sensors). Such a knowledge base can be used to train intended engineers, specialists in sensors design

  6. Individual Building Extraction from TerraSAR-X Images Based on Ontological Semantic Analysis

    Directory of Open Access Journals (Sweden)

    Rong Gui

    2016-08-01

    Full Text Available Accurate building information plays a crucial role for urban planning, human settlements and environmental management. Synthetic aperture radar (SAR images, which deliver images with metric resolution, allow for analyzing and extracting detailed information on urban areas. In this paper, we consider the problem of extracting individual buildings from SAR images based on domain ontology. By analyzing a building scattering model with different orientations and structures, the building ontology model is set up to express multiple characteristics of individual buildings. Under this semantic expression framework, an object-based SAR image segmentation method is adopted to provide homogeneous image objects, and three categories of image object features are extracted. Semantic rules are implemented by organizing image object features, and the individual building objects expression based on an ontological semantic description is formed. Finally, the building primitives are used to detect buildings among the available image objects. Experiments on TerraSAR-X images of Foshan city, China, with a spatial resolution of 1.25 m × 1.25 m, have shown the total extraction rates are above 84%. The results indicate the ontological semantic method can exactly extract flat-roof and gable-roof buildings larger than 250 pixels with different orientations.

  7. 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.

  8. 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....

  9. 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.

  10. Using ontology-based semantic similarity to facilitate the article screening process for systematic reviews.

    Science.gov (United States)

    Ji, Xiaonan; Ritter, Alan; Yen, Po-Yin

    2017-05-01

    Systematic Reviews (SRs) are utilized to summarize evidence from high quality studies and are considered the preferred source of evidence-based practice (EBP). However, conducting SRs can be time and labor intensive due to the high cost of article screening. In previous studies, we demonstrated utilizing established (lexical) article relationships to facilitate the identification of relevant articles in an efficient and effective manner. Here we propose to enhance article relationships with background semantic knowledge derived from Unified Medical Language System (UMLS) concepts and ontologies. We developed a pipelined semantic concepts representation process to represent articles from an SR into an optimized and enriched semantic space of UMLS concepts. Throughout the process, we leveraged concepts and concept relations encoded in biomedical ontologies (SNOMED-CT and MeSH) within the UMLS framework to prompt concept features of each article. Article relationships (similarities) were established and represented as a semantic article network, which was readily applied to assist with the article screening process. We incorporated the concept of active learning to simulate an interactive article recommendation process, and evaluated the performance on 15 completed SRs. We used work saved over sampling at 95% recall (WSS95) as the performance measure. We compared the WSS95 performance of our ontology-based semantic approach to existing lexical feature approaches and corpus-based semantic approaches, and found that we had better WSS95 in most SRs. We also had the highest average WSS95 of 43.81% and the highest total WSS95 of 657.18%. We demonstrated using ontology-based semantics to facilitate the identification of relevant articles for SRs. Effective concepts and concept relations derived from UMLS ontologies can be utilized to establish article semantic relationships. Our approach provided a promising performance and can easily apply to any SR topics in the

  11. Ontology-Oriented Diagnostic System for Traditional Chinese Medicine Based on Relation Refinement

    Directory of Open Access Journals (Sweden)

    Peiqin Gu

    2013-01-01

    Full Text Available Although Chinese medicine treatments have become popular recently, the complicated Chinese medical knowledge has made it difficult to be applied in computer-aided diagnostics. The ability to model and use the knowledge becomes an important issue. In this paper, we define the diagnosis in Traditional Chinese Medicine (TCM as discovering the fuzzy relations between symptoms and syndromes. An Ontology-oriented Diagnosis System (ODS is created to address the knowledge-based diagnosis based on a well-defined ontology of syndromes. The ontology transforms the implicit relationships among syndromes into a machine-interpretable model. The clinical data used for feature selection is collected from a national TCM research institute in China, which serves as a training source for syndrome differentiation. The ODS analyzes the clinical cases to obtain a statistical mapping relation between each syndrome and associated symptom set, before rechecking the completeness of related symptoms via ontology refinement. Our diagnostic system provides an online web interface to interact with users, so that users can perform self-diagnosis. We tested 12 common clinical cases on the diagnosis system, and it turned out that, given the agree metric, the system achieved better diagnostic accuracy compared to nonontology method—92% of the results fit perfectly with the experts’ expectations.

  12. Ontology-oriented diagnostic system for traditional Chinese medicine based on relation refinement.

    Science.gov (United States)

    Gu, Peiqin; Chen, Huajun; Yu, Tong

    2013-01-01

    Although Chinese medicine treatments have become popular recently, the complicated Chinese medical knowledge has made it difficult to be applied in computer-aided diagnostics. The ability to model and use the knowledge becomes an important issue. In this paper, we define the diagnosis in Traditional Chinese Medicine (TCM) as discovering the fuzzy relations between symptoms and syndromes. An Ontology-oriented Diagnosis System (ODS) is created to address the knowledge-based diagnosis based on a well-defined ontology of syndromes. The ontology transforms the implicit relationships among syndromes into a machine-interpretable model. The clinical data used for feature selection is collected from a national TCM research institute in China, which serves as a training source for syndrome differentiation. The ODS analyzes the clinical cases to obtain a statistical mapping relation between each syndrome and associated symptom set, before rechecking the completeness of related symptoms via ontology refinement. Our diagnostic system provides an online web interface to interact with users, so that users can perform self-diagnosis. We tested 12 common clinical cases on the diagnosis system, and it turned out that, given the agree metric, the system achieved better diagnostic accuracy compared to nonontology method-92% of the results fit perfectly with the experts' expectations.

  13. Study on distributed generation algorithm of variable precision concept lattice based on ontology heterogeneous database

    Science.gov (United States)

    WANG, Qingrong; ZHU, Changfeng

    2017-06-01

    Integration of distributed heterogeneous data sources is the key issues under the big data applications. In this paper the strategy of variable precision is introduced to the concept lattice, and the one-to-one mapping mode of variable precision concept lattice and ontology concept lattice is constructed to produce the local ontology by constructing the variable precision concept lattice for each subsystem, and the distributed generation algorithm of variable precision concept lattice based on ontology heterogeneous database is proposed to draw support from the special relationship between concept lattice and ontology construction. Finally, based on the standard of main concept lattice of the existing heterogeneous database generated, a case study has been carried out in order to testify the feasibility and validity of this algorithm, and the differences between the main concept lattice and the standard concept lattice are compared. Analysis results show that this algorithm above-mentioned can automatically process the construction process of distributed concept lattice under the heterogeneous data sources.

  14. Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria.

    Directory of Open Access Journals (Sweden)

    Mario Fruzangohar

    Full Text Available The primary means of classifying new functions for genes and proteins relies on Gene Ontology (GO, which defines genes/proteins using a controlled vocabulary in terms of their Molecular Function, Biological Process and Cellular Component. The challenge is to present this information to researchers to compare and discover patterns in multiple datasets using visually comprehensible and user-friendly statistical reports. Importantly, while there are many GO resources available for eukaryotes, there are none suitable for simultaneous, graphical and statistical comparison between multiple datasets. In addition, none of them supports comprehensive resources for bacteria. By using Streptococcus pneumoniae as a model, we identified and collected GO resources including genes, proteins, taxonomy and GO relationships from NCBI, UniProt and GO organisations. Then, we designed database tables in PostgreSQL database server and developed a Java application to extract data from source files and loaded into database automatically. We developed a PHP web application based on Model-View-Control architecture, used a specific data structure as well as current and novel algorithms to estimate GO graphs parameters. We designed different navigation and visualization methods on the graphs and integrated these into graphical reports. This tool is particularly significant when comparing GO groups between multiple samples (including those of pathogenic bacteria from different sources simultaneously. Comparing GO protein distribution among up- or down-regulated genes from different samples can improve understanding of biological pathways, and mechanism(s of infection. It can also aid in the discovery of genes associated with specific function(s for investigation as a novel vaccine or therapeutic targets.http://turing.ersa.edu.au/BacteriaGO.

  15. Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria.

    Science.gov (United States)

    Fruzangohar, Mario; Ebrahimie, Esmaeil; Ogunniyi, Abiodun D; Mahdi, Layla K; Paton, James C; Adelson, David L

    2013-01-01

    The primary means of classifying new functions for genes and proteins relies on Gene Ontology (GO), which defines genes/proteins using a controlled vocabulary in terms of their Molecular Function, Biological Process and Cellular Component. The challenge is to present this information to researchers to compare and discover patterns in multiple datasets using visually comprehensible and user-friendly statistical reports. Importantly, while there are many GO resources available for eukaryotes, there are none suitable for simultaneous, graphical and statistical comparison between multiple datasets. In addition, none of them supports comprehensive resources for bacteria. By using Streptococcus pneumoniae as a model, we identified and collected GO resources including genes, proteins, taxonomy and GO relationships from NCBI, UniProt and GO organisations. Then, we designed database tables in PostgreSQL database server and developed a Java application to extract data from source files and loaded into database automatically. We developed a PHP web application based on Model-View-Control architecture, used a specific data structure as well as current and novel algorithms to estimate GO graphs parameters. We designed different navigation and visualization methods on the graphs and integrated these into graphical reports. This tool is particularly significant when comparing GO groups between multiple samples (including those of pathogenic bacteria) from different sources simultaneously. Comparing GO protein distribution among up- or down-regulated genes from different samples can improve understanding of biological pathways, and mechanism(s) of infection. It can also aid in the discovery of genes associated with specific function(s) for investigation as a novel vaccine or therapeutic targets. http://turing.ersa.edu.au/BacteriaGO.

  16. Ontology based molecular signatures for immune cell types via gene expression analysis

    Science.gov (United States)

    2013-01-01

    Background New technologies are focusing on characterizing cell types to better understand their heterogeneity. With large volumes of cellular data being generated, innovative methods are needed to structure the resulting data analyses. Here, we describe an ‘Ontologically BAsed Molecular Signature’ (OBAMS) method that identifies novel cellular biomarkers and infers biological functions as characteristics of particular cell types. This method finds molecular signatures for immune cell types based on mapping biological samples to the Cell Ontology (CL) and navigating the space of all possible pairwise comparisons between cell types to find genes whose expression is core to a particular cell type’s identity. Results We illustrate this ontological approach by evaluating expression data available from the Immunological Genome project (IGP) to identify unique biomarkers of mature B cell subtypes. We find that using OBAMS, candidate biomarkers can be identified at every strata of cellular identity from broad classifications to very granular. Furthermore, we show that Gene Ontology can be used to cluster cell types by shared biological processes in order to find candidate genes responsible for somatic hypermutation in germinal center B cells. Moreover, through in silico experiments based on this approach, we have identified genes sets that represent genes overexpressed in germinal center B cells and identify genes uniquely expressed in these B cells compared to other B cell types. Conclusions This work demonstrates the utility of incorporating structured ontological knowledge into biological data analysis – providing a new method for defining novel biomarkers and providing an opportunity for new biological insights. PMID:24004649

  17. 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

  18. The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection.

    Directory of Open Access Journals (Sweden)

    Chantal Hulo

    Full Text Available Viruses are genetically diverse, infect a wide range of tissues and host cells and follow unique processes for replicating themselves. All these processes were investigated and indexed in ViralZone knowledge base. To facilitate standardizing data, a simple ontology of viral life-cycle terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address unique viral replication cycle processes, and existing terminology was modified and adapted. The virus life-cycle is classically described by schematic pictures. Using this ontology, it can be represented by a combination of successive terms: "entry", "latency", "transcription", "replication" and "exit". Each of these parts is broken down into discrete steps. For example Zika virus "entry" is broken down in successive steps: "Attachment", "Apoptotic mimicry", "Viral endocytosis/ macropinocytosis", "Fusion with host endosomal membrane", "Viral factory". To demonstrate the utility of a standard ontology for virus biology, this work was completed by annotating virus data in the ViralZone, UniProtKB and Gene Ontology databases.

  19. Virtual Learning Spaces Creation Based on the Systematic Population of an Ontology

    Directory of Open Access Journals (Sweden)

    Cristiana Araújo

    2018-02-01

    Full Text Available The creation of Learning Spaces on the Web, like the exhibition rooms of virtual museums, supported by an ontology that enables a conceptual navigation over the learning objects exposed, is a hard and complex task but of uttermost importance for the success of the knowledge acquisition process. In our opinion, the creation must be systematic and reusable from case to case, based on the query of the ontology instances that describe the museum assets. We will discuss how the ontology definition drives the way SPARQL (SPARQL Protocol and RDF Query Language queries extract information from the TripleStore to be prepared for visualization. However, to enable this approach, we need to populate the ontology in an automatic way, extracting the data from the annotated documents in the institution repository. We intend to show how that process can be implemented using the Museum of the Person (MP as a case-study, describing the XML2RDF tool developed. To illustrate the complete approach proposed we will include a guided visit to the exhibition rooms of MP created according to that proposal and by our tools.

  20. Security of Heterogeneous Content in Cloud Based Library Information Systems Using an Ontology Based Approach

    Directory of Open Access Journals (Sweden)

    Mihai DOINEA

    2014-01-01

    Full Text Available As in any domain that involves the use of software, the library information systems take advantages of cloud computing. The paper highlights the main aspect of cloud based systems, describing some public solutions provided by the most important players on the market. Topics related to content security in cloud based services are tackled in order to emphasize the requirements that must be met by these types of systems. A cloud based implementation of an Information Library System is presented and some adjacent tools that are used together with it to provide digital content and metadata links are described. In a cloud based Information Library System security is approached by means of ontologies. Aspects such as content security in terms of digital rights are presented and a methodology for security optimization is proposed.

  1. User interaction with legal knowledge-based systems

    NARCIS (Netherlands)

    Dijkstra, Jacob; Breuker, J.; Leenes, R.; Winkels, R.

    2000-01-01

    This paper gives an overview of my PhD study into the persuasiveness of (legal) knowledge-based systems'. The results of three experiments show the possible problems that may arise when computerised legal decision aids are put into practice. The users in the experiments had great difficulties with

  2. Legal Bases for Dealing with Academic Dishonesty

    Science.gov (United States)

    Bricault, Dennis

    2007-01-01

    Academic dishonesty poses a threat to the goals of every educational institution. This article draws heavily from current literature and case law to provide an overview of academic dishonesty, paying particular attention to associated legal aspects, such as due process, the content and communication of policies, sanctions, prevention, and…

  3. User centered and ontology based information retrieval system for life sciences.

    Science.gov (United States)

    Sy, Mohameth-François; Ranwez, Sylvie; Montmain, Jacky; Regnault, Armelle; Crampes, Michel; Ranwez, Vincent

    2012-01-25

    Because of the increasing number of electronic resources, designing efficient tools to retrieve and exploit them is a major challenge. Some improvements have been offered by semantic Web technologies and applications based on domain ontologies. In life science, for instance, the Gene Ontology is widely exploited in genomic applications and the Medical Subject Headings is the basis of biomedical publications indexation and information retrieval process proposed by PubMed. However current search engines suffer from two main drawbacks: there is limited user interaction with the list of retrieved resources and no explanation for their adequacy to the query is provided. Users may thus be confused by the selection and have no idea on how to adapt their queries so that the results match their expectations. This paper describes an information retrieval system that relies on domain ontology to widen the set of relevant documents that is retrieved and that uses a graphical rendering of query results to favor user interactions. Semantic proximities between ontology concepts and aggregating models are used to assess documents adequacy with respect to a query. The selection of documents is displayed in a semantic map to provide graphical indications that make explicit to what extent they match the user's query; this man/machine interface favors a more interactive and iterative exploration of data corpus, by facilitating query concepts weighting and visual explanation. We illustrate the benefit of using this information retrieval system on two case studies one of which aiming at collecting human genes related to transcription factors involved in hemopoiesis pathway. The ontology based information retrieval system described in this paper (OBIRS) is freely available at: http://www.ontotoolkit.mines-ales.fr/ObirsClient/. This environment is a first step towards a user centred application in which the system enlightens relevant information to provide decision help.

  4. User centered and ontology based information retrieval system for life sciences

    Directory of Open Access Journals (Sweden)

    Sy Mohameth-François

    2012-01-01

    Full Text Available Abstract Background Because of the increasing number of electronic resources, designing efficient tools to retrieve and exploit them is a major challenge. Some improvements have been offered by semantic Web technologies and applications based on domain ontologies. In life science, for instance, the Gene Ontology is widely exploited in genomic applications and the Medical Subject Headings is the basis of biomedical publications indexation and information retrieval process proposed by PubMed. However current search engines suffer from two main drawbacks: there is limited user interaction with the list of retrieved resources and no explanation for their adequacy to the query is provided. Users may thus be confused by the selection and have no idea on how to adapt their queries so that the results match their expectations. Results This paper describes an information retrieval system that relies on domain ontology to widen the set of relevant documents that is retrieved and that uses a graphical rendering of query results to favor user interactions. Semantic proximities between ontology concepts and aggregating models are used to assess documents adequacy with respect to a query. The selection of documents is displayed in a semantic map to provide graphical indications that make explicit to what extent they match the user's query; this man/machine interface favors a more interactive and iterative exploration of data corpus, by facilitating query concepts weighting and visual explanation. We illustrate the benefit of using this information retrieval system on two case studies one of which aiming at collecting human genes related to transcription factors involved in hemopoiesis pathway. Conclusions The ontology based information retrieval system described in this paper (OBIRS is freely available at: http://www.ontotoolkit.mines-ales.fr/ObirsClient/. This environment is a first step towards a user centred application in which the system enlightens

  5. A Novel Mobile Video Community Discovery Scheme Using Ontology-Based Semantical Interest Capture

    Directory of Open Access Journals (Sweden)

    Ruiling Zhang

    2016-01-01

    Full Text Available Leveraging network virtualization technologies, the community-based video systems rely on the measurement of common interests to define and steady relationship between community members, which promotes video sharing performance and improves scalability community structure. In this paper, we propose a novel mobile Video Community discovery scheme using ontology-based semantical interest capture (VCOSI. An ontology-based semantical extension approach is proposed, which describes video content and measures video similarity according to video key word selection methods. In order to reduce the calculation load of video similarity, VCOSI designs a prefix-filtering-based estimation algorithm to decrease energy consumption of mobile nodes. VCOSI further proposes a member relationship estimate method to construct scalable and resilient node communities, which promotes video sharing capacity of video systems with the flexible and economic community maintenance. Extensive tests show how VCOSI obtains better performance results in comparison with other state-of-the-art solutions.

  6. Real-time context aware reasoning in on-board intelligent traffic systems: An Architecture for Ontology-based Reasoning using Finite State Machines

    NARCIS (Netherlands)

    Stoter, Arjan; Dalmolen, Simon; Drenth, Eduard; Cornelisse, Erik; Mulder, Wico

    2011-01-01

    In-vehicle information management is vital in intelligent traffic systems. In this paper we motivate an architecture for ontology-based context-aware reasoning for in-vehicle information management. An ontology is essential for system standardization and communication, and ontology-based reasoning

  7. A System for Ontology-Based Sharing of Expert Knowledge in Sustainability Science

    Directory of Open Access Journals (Sweden)

    Steven Kraines

    2011-01-01

    Full Text Available Work towards creation of a knowledge sharing system for sustainability science through the application of semantic data modeling is described. An ontology grounded in description logics was developed based on the ISO 15926 data model to describe three types of sustainability science conceptualizations: situational knowledge, analytic methods, and scenario frameworks. Semantic statements were then created using this ontology to describe expert knowledge expressed in research proposals and papers related to sustainability science and in scenarios for achieving sustainable societies. Semantic matching based on logic and rule-based inference was used to quantify the conceptual overlap of semantic statements, which shows the semantic similarity of topics studied by different researchers in sustainability science, similarities that might be unknown to the researchers themselves.

  8. Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations

    KAUST Repository

    Smaili, Fatima Zohra

    2018-01-31

    We propose the Onto2Vec method, an approach to learn feature vectors for biological entities based on their annotations to biomedical ontologies. Our method can be applied to a wide range of bioinformatics research problems such as similarity-based prediction of interactions between proteins, classification of interaction types using supervised learning, or clustering.

  9. 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…

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

    OpenAIRE

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

    2016-01-01

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

  11. Research of image retrieval system framework based on ontology and content

    Science.gov (United States)

    Liu, Hong

    2012-01-01

    The current most desirable image retrieval feature is retrieving images based on their semantic content. In order to improve the retrieval accuracy of content-based image retrieval systems, research focus has been shifted from designing sophisticated low-level feature extraction algorithms to reducing the 'semantic gap' between the visual features and the richness of human semantics. In this paper, we put forward a system framework of image retrieval based on content and ontology, which has the potential to fully describe the semantic content of an image, allowing the similarity between images and retrieval query to be computed accurately. In the system, we identify third major categories of techniques in narrowing down the "semantic gap": (1) using object ontology to define high-level concepts; (2) using machine learning methods to associate low-level features with query concepts; (3) using ontology reasoning to extend image retrieval. Finally, the paper does some testing experiment, whose result shows the feasibility of the system framework.

  12. Home-Explorer: Ontology-Based Physical Artifact Search and Hidden Object Detection System

    Directory of Open Access Journals (Sweden)

    Bin Guo

    2008-01-01

    Full Text Available A new system named Home-Explorer that searches and finds physical artifacts in a smart indoor environment is proposed. The view on which it is based is artifact-centered and uses sensors attached to the everyday artifacts (called smart objects in the real world. This paper makes two main contributions: First, it addresses, the robustness of the embedded sensors, which is seldom discussed in previous smart artifact research. Because sensors may sometimes be broken or fail to work under certain conditions, smart objects become hidden ones. However, current systems provide no mechanism to detect and manage objects when this problem occurs. Second, there is no common context infrastructure for building smart artifact systems, which makes it difficult for separately developed applications to interact with each other and uneasy for them to share and reuse knowledge. Unlike previous systems, Home-Explorer builds on an ontology-based knowledge infrastructure named Sixth-Sense, which makes it easy for the system to interact with other applications or agents also based on this ontology. The hidden object problem is also reflected in our ontology, which enables Home-Explorer to deal with both smart objects and hidden objects. A set of rules for deducing an object's status or location information and for locating hidden objects are described and evaluated.

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

    DEFF Research Database (Denmark)

    Iftikhar, Nadeem

    2013-01-01

    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......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...... to response time. In most cases, the big dimension modeling process is complicated since it usually requires accurate description of business semantics, multiple design revisions and comprehensive testing. In this paper, we present the design methods for modeling big dimensions, which include horizontal...

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

    Science.gov (United States)

    Djuana, E.

    2018-03-01

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

  15. Generic-distributed framework for cloud services marketplace based on unified ontology.

    Science.gov (United States)

    Hasan, Samer; Valli Kumari, V

    2017-11-01

    Cloud computing is a pattern for delivering ubiquitous and on demand computing resources based on pay-as-you-use financial model. Typically, cloud providers advertise cloud service descriptions in various formats on the Internet. On the other hand, cloud consumers use available search engines (Google and Yahoo) to explore cloud service descriptions and find the adequate service. Unfortunately, general purpose search engines are not designed to provide a small and complete set of results, which makes the process a big challenge. This paper presents a generic-distrusted framework for cloud services marketplace to automate cloud services discovery and selection process, and remove the barriers between service providers and consumers. Additionally, this work implements two instances of generic framework by adopting two different matching algorithms; namely dominant and recessive attributes algorithm borrowed from gene science and semantic similarity algorithm based on unified cloud service ontology. Finally, this paper presents unified cloud services ontology and models the real-life cloud services according to the proposed ontology. To the best of the authors' knowledge, this is the first attempt to build a cloud services marketplace where cloud providers and cloud consumers can trend cloud services as utilities. In comparison with existing work, semantic approach reduced the execution time by 20% and maintained the same values for all other parameters. On the other hand, dominant and recessive attributes approach reduced the execution time by 57% but showed lower value for recall.

  16. A new algorithm to extract hidden rules of gastric cancer data based on ontology.

    Science.gov (United States)

    Mahmoodi, Seyed Abbas; Mirzaie, Kamal; Mahmoudi, Seyed Mostafa

    2016-01-01

    Cancer is the leading cause of death in economically developed countries and the second leading cause of death in developing countries. Gastric cancers are among the most devastating and incurable forms of cancer and their treatment may be excessively complex and costly. Data mining, a technology that is used to produce analytically useful information, has been employed successfully with medical data. Although the use of traditional data mining techniques such as association rules helps to extract knowledge from large data sets, sometimes the results obtained from a data set are so large that it is a major problem. In fact, one of the disadvantages of this technique is a lot of nonsense and redundant rules due to the lack of attention to the concept and meaning of items or the samples. This paper presents a new method to discover association rules using ontology to solve the expressed problems. This paper reports a data mining based on ontology on a medical database containing clinical data on patients referring to the Imam Reza Hospital at Tabriz. The data set used in this paper is gathered from 490 random visitors to the Imam Reza Hospital at Tabriz, who had been suspicions of having gastric cancer. The proposed data mining algorithm based on ontology makes rules more intuitive, appealing and understandable, eliminates waste and useless rules, and as a minor result, significantly reduces Apriori algorithm running time. The experimental results confirm the efficiency and advantages of this algorithm.

  17. Ontology-based vector space model and fuzzy query expansion to retrieve knowledge on medical computational problem solutions.

    Science.gov (United States)

    Bratsas, Charalampos; Koutkias, Vassilis; Kaimakamis, Evangelos; Bamidis, Panagiotis; Maglaveras, Nicos

    2007-01-01

    Medical Computational Problem (MCP) solving is related to medical problems and their computerized algorithmic solutions. In this paper, an extension of an ontology-based model to fuzzy logic is presented, as a means to enhance the information retrieval (IR) procedure in semantic management of MCPs. We present herein the methodology followed for the fuzzy expansion of the ontology model, the fuzzy query expansion procedure, as well as an appropriate ontology-based Vector Space Model (VSM) that was constructed for efficient mapping of user-defined MCP search criteria and MCP acquired knowledge. The relevant fuzzy thesaurus is constructed by calculating the simultaneous occurrences of terms and the term-to-term similarities derived from the ontology that utilizes UMLS (Unified Medical Language System) concepts by using Concept Unique Identifiers (CUI), synonyms, semantic types, and broader-narrower relationships for fuzzy query expansion. The current approach constitutes a sophisticated advance for effective, semantics-based MCP-related IR.

  18. Ontology-Based Information Visualization: Toward Semantic Web Applications

    NARCIS (Netherlands)

    Fluit, Christiaan; Sabou, Marta; Harmelen, Frank van

    2006-01-01

    The Semantic Web is an extension of the current World Wide Web, based on the idea of exchanging information with explicit, formal, and machine-accessible descriptions of meaning. Providing information with such semantics will enable the construction of applications that have an increased awareness

  19. Ontology-based Semantic Search Engine for Healthcare Services

    OpenAIRE

    Jotsna Molly Rajan; M. Deepa Lakshmi

    2012-01-01

    With the development of Web Services, the retrieval of relevant services has become a challenge. The keyword-based discovery mechanism using UDDI and WSDL is insufficient due to the retrievalof a large amount of irrelevant information. Also, keywords are insufficient in expressing semantic concepts since a single concept can be referred using syntactically different terms. Hence, service capabilities need to be manually analyzed, which lead to the development of the Semantic Web for automatic...

  20. Improving the extraction of complex regulatory events from scientific text by using ontology-based inference.

    Science.gov (United States)

    Kim, Jung-Jae; Rebholz-Schuhmann, Dietrich

    2011-10-06

    The extraction of complex events from biomedical text is a challenging task and requires in-depth semantic analysis. Previous approaches associate lexical and syntactic resources with ontologies for the semantic analysis, but fall short in testing the benefits from the use of domain knowledge. We developed a system that deduces implicit events from explicitly expressed events by using inference rules that encode domain knowledge. We evaluated the system with the inference module on three tasks: First, when tested against a corpus with manually annotated events, the inference module of our system contributes 53.2% of correct extractions, but does not cause any incorrect results. Second, the system overall reproduces 33.1% of the transcription regulatory events contained in RegulonDB (up to 85.0% precision) and the inference module is required for 93.8% of the reproduced events. Third, we applied the system with minimum adaptations to the identification of cell activity regulation events, confirming that the inference improves the performance of the system also on this task. Our research shows that the inference based on domain knowledge plays a significant role in extracting complex events from text. This approach has great potential in recognizing the complex concepts of such biomedical ontologies as Gene Ontology in the literature.

  1. Improving the extraction of complex regulatory events from scientific text by using ontology-based inference

    Directory of Open Access Journals (Sweden)

    Kim Jung-jae

    2011-10-01

    Full Text Available Abstract Background The extraction of complex events from biomedical text is a challenging task and requires in-depth semantic analysis. Previous approaches associate lexical and syntactic resources with ontologies for the semantic analysis, but fall short in testing the benefits from the use of domain knowledge. Results We developed a system that deduces implicit events from explicitly expressed events by using inference rules that encode domain knowledge. We evaluated the system with the inference module on three tasks: First, when tested against a corpus with manually annotated events, the inference module of our system contributes 53.2% of correct extractions, but does not cause any incorrect results. Second, the system overall reproduces 33.1% of the transcription regulatory events contained in RegulonDB (up to 85.0% precision and the inference module is required for 93.8% of the reproduced events. Third, we applied the system with minimum adaptations to the identification of cell activity regulation events, confirming that the inference improves the performance of the system also on this task. Conclusions Our research shows that the inference based on domain knowledge plays a significant role in extracting complex events from text. This approach has great potential in recognizing the complex concepts of such biomedical ontologies as Gene Ontology in the literature.

  2. Ontology-Based High-Level Context Inference for Human Behavior Identification

    Directory of Open Access Journals (Sweden)

    Claudia Villalonga

    2016-09-01

    Full Text Available Recent years have witnessed a huge progress in the automatic identification of individual primitives of human behavior, such as activities or locations. However, the complex nature of human behavior demands more abstract contextual information for its analysis. This work presents an ontology-based method that combines low-level primitives of behavior, namely activity, locations and emotions, unprecedented to date, to intelligently derive more meaningful high-level context information. The paper contributes with a new open ontology describing both low-level and high-level context information, as well as their relationships. Furthermore, a framework building on the developed ontology and reasoning models is presented and evaluated. The proposed method proves to be robust while identifying high-level contexts even in the event of erroneously-detected low-level contexts. Despite reasonable inference times being obtained for a relevant set of users and instances, additional work is required to scale to long-term scenarios with a large number of users.

  3. Ontology-Based High-Level Context Inference for Human Behavior Identification.

    Science.gov (United States)

    Villalonga, Claudia; Razzaq, Muhammad Asif; Khan, Wajahat Ali; Pomares, Hector; Rojas, Ignacio; Lee, Sungyoung; Banos, Oresti

    2016-09-29

    Recent years have witnessed a huge progress in the automatic identification of individual primitives of human behavior, such as activities or locations. However, the complex nature of human behavior demands more abstract contextual information for its analysis. This work presents an ontology-based method that combines low-level primitives of behavior, namely activity, locations and emotions, unprecedented to date, to intelligently derive more meaningful high-level context information. The paper contributes with a new open ontology describing both low-level and high-level context information, as well as their relationships. Furthermore, a framework building on the developed ontology and reasoning models is presented and evaluated. The proposed method proves to be robust while identifying high-level contexts even in the event of erroneously-detected low-level contexts. Despite reasonable inference times being obtained for a relevant set of users and instances, additional work is required to scale to long-term scenarios with a large number of users.

  4. Ontology-Based Controlled Natural Language Editor Using CFG with Lexical Dependency

    Science.gov (United States)

    Namgoong, Hyun; Kim, Hong-Gee

    In recent years, CNL (Controlled Natural Language) has received much attention with regard to ontology-based knowledge acquisition systems. CNLs, as subsets of natural languages, can be useful for both humans and computers by eliminating ambiguity of natural languages. Our previous work, OntoPath [10], proposed to edit natural language-like narratives that are structured in RDF (Resource Description Framework) triples, using a domain-specific ontology as their language constituents. However, our previous work and other systems employing CFG for grammar definition have difficulties in enlarging the expression capacity. A newly developed editor, which we propose in this paper, permits grammar definitions through CFG-LD (Context-Free Grammar with Lexical Dependency) that includes sequential and semantic structures of the grammars. With CFG describing the sequential structure of grammar, lexical dependencies between sentence elements can be designated in the definition system. Through the defined grammars, the implemented editor guides users' narratives in more familiar expressions with a domain-specific ontology and translates the content into RDF triples.

  5. 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.

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

    Science.gov (United States)

    NIXDORF, D. R.; DRANGSHOLT, M. T.; ETTLIN, D. A.; GAUL, C.; DE LEEUW, R.; SVENSSON, P.; ZAKRZEWSKA, J. M.; DE LAAT, A.; CEUSTERS, W.

    2012-01-01

    SUMMARY Propose a new taxonomy model based on ontological principles for disorders that manifest themselves through the symptom of persistent orofacial pain and are commonly seen in clinical practice and difficult to manage. Consensus meeting of eight experts from various geographic areas representing different perspectives (orofacial pain, headache, oral medicine and ontology) as an initial step towards improving the taxonomy. Ontological principles were introduced, reviewed and applied during the consensus building process. Diagnostic criteria for persistent dento-alveolar pain disorder (PDAP) were formulated as an example to be used to model the taxonomical structure of all orofacial pain conditions. These criteria have the advantage of being (i) anatomically defined, (ii) in accordance with other classification systems for the provision of clinical care, (iii) descriptive and succinct, (iv) easy to adapt for applications in varying settings, (v) scalable and (vi) transferable for the description of pain disorders in other orofacial regions of interest. Limitations are that the criteria introduce new terminology, do not have widespread acceptance and have yet to be tested. These results were presented to the greater conference membership and were unanimously accepted. Consensus for the diagnostic criteria of PDAP was established within this working group. This is an initial first step towards developing a coherent taxonomy for orofacial pain disorders, which is needed to improve clinical research and care. PMID:21848527

  7. Ontology Repositories

    OpenAIRE

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

    2009-01-01

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

  8. 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

  9. An ontology-based comparative anatomy information system

    Science.gov (United States)

    Travillian, Ravensara S.; Diatchka, Kremena; Judge, Tejinder K.; Wilamowska, Katarzyna; Shapiro, Linda G.

    2010-01-01

    Introduction This paper describes the design, implementation, and potential use of a comparative anatomy information system (CAIS) for querying on similarities and differences between homologous anatomical structures across species, the knowledge base it operates upon, the method it uses for determining the answers to the queries, and the user interface it employs to present the results. The relevant informatics contributions of our work include (1) the development and application of the structural difference method, a formalism for symbolically representing anatomical similarities and differences across species; (2) the design of the structure of a mapping between the anatomical models of two different species and its application to information about specific structures in humans, mice, and rats; and (3) the design of the internal syntax and semantics of the query language. These contributions provide the foundation for the development of a working system that allows users to submit queries about the similarities and differences between mouse, rat, and human anatomy; delivers result sets that describe those similarities and differences in symbolic terms; and serves as a prototype for the extension of the knowledge base to any number of species. Additionally, we expanded the domain knowledge by identifying medically relevant structural questions for the human, the mouse, and the rat, and made an initial foray into the validation of the application and its content by means of user questionnaires, software testing, and other feedback. Methods The anatomical structures of the species to be compared, as well as the mappings between species, are modeled on templates from the Foundational Model of Anatomy knowledge base, and compared using graph-matching techniques. A graphical user interface allows users to issue queries that retrieve information concerning similarities and differences between structures in the species being examined. Queries from diverse information

  10. Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism.

    Science.gov (United States)

    Liu, Qingping; Wang, Jiahao; Zhu, Yan; He, Yongqun

    2017-12-21

    Rheumatism represents any disease condition marked with inflammation and pain in the joints, muscles, or connective tissues. Many traditional Chinese drugs have been used for a long time to treat rheumatism. However, a comprehensive information source for these drugs is still missing, and their anti-rheumatism mechanisms remain unclear. An ontology for anti-rheumatism traditional Chinese drugs would strongly support the representation, analysis, and understanding of these drugs. In this study, we first systematically collected reported information about 26 traditional Chinese decoction pieces drugs, including their chemical ingredients and adverse events (AEs). By mostly reusing terms from existing ontologies (e.g., TCMDPO for traditional Chinese medicines, NCBITaxon for taxonomy, ChEBI for chemical elements, and OAE for adverse events) and making semantic axioms linking different entities, we developed the Ontology of Chinese Medicine for Rheumatism (OCMR) that includes over 3000 class terms. Our OCMR analysis found that these 26 traditional Chinese decoction pieces are made from anatomic entities (e.g., root and stem) from 3 Bilateria animals and 23 Mesangiospermae plants. Anti-inflammatory and antineoplastic roles are important for anti-rheumatism drugs. Using the total of 555 unique ChEBI chemical entities identified from these drugs, our ChEBI-based classification analysis identified 18 anti-inflammatory, 33 antineoplastic chemicals, and 9 chemicals (including 3 diterpenoids and 3 triterpenoids) having both anti-inflammatory and antineoplastic roles. Furthermore, our study detected 22 diterpenoids and 23 triterpenoids, including 16 pentacyclic triterpenoids that are likely bioactive against rheumatism. Six drugs were found to be associated with 184 unique AEs, including three AEs (i.e., dizziness, nausea and vomiting, and anorexia) each associated with 5 drugs. Several chemical entities are classified as neurotoxins (e.g., diethyl phthalate) and allergens (e

  11. LEGAL

    African Journals Online (AJOL)

    This is because the discounts and rebates offered in the past to some resulted in higher prices for others. But on average, however, prices should drop slightly because the. SEPs are based on figures from last year. DISPENSING FEES. The new law on dispensing fees only comes into effect on. 2 August 2004. Until then ...

  12. Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies.

    Science.gov (United States)

    Samwald, Matthias; Miñarro Giménez, Jose Antonio; Boyce, Richard D; Freimuth, Robert R; Adlassnig, Klaus-Peter; Dumontier, Michel

    2015-02-22

    Every year, hundreds of thousands of patients experience treatment failure or adverse drug reactions (ADRs), many of which could be prevented by pharmacogenomic testing. However, the primary knowledge needed for clinical pharmacogenomics is currently dispersed over disparate data structures and captured in unstructured or semi-structured formalizations. This is a source of potential ambiguity and complexity, making it difficult to create reliable information technology systems for enabling clinical pharmacogenomics. We developed Web Ontology Language (OWL) ontologies and automated reasoning methodologies to meet the following goals: 1) provide a simple and concise formalism for representing pharmacogenomic knowledge, 2) finde errors and insufficient definitions in pharmacogenomic knowledge bases, 3) automatically assign alleles and phenotypes to patients, 4) match patients to clinically appropriate pharmacogenomic guidelines and clinical decision support messages and 5) facilitate the detection of inconsistencies and overlaps between pharmacogenomic treatment guidelines from different sources. We evaluated different reasoning systems and test our approach with a large collection of publicly available genetic profiles. Our methodology proved to be a novel and useful choice for representing, analyzing and using pharmacogenomic data. The Genomic Clinical Decision Support (Genomic CDS) ontology represents 336 SNPs with 707 variants; 665 haplotypes related to 43 genes; 22 rules related to drug-response phenotypes; and 308 clinical decision support rules. OWL reasoning identified CDS rules with overlapping target populations but differing treatment recommendations. Only a modest number of clinical decision support rules were triggered for a collection of 943 public genetic profiles. We found significant performance differences across available OWL reasoners. The ontology-based framework we developed can be used to represent, organize and reason over the growing wealth of

  13. OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia

    Science.gov (United States)

    2012-01-01

    Background The OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org), aims at providing a unified access to toxicity data, predictive models and validation procedures. Interoperability of resources is achieved using a common information model, based on the OpenTox ontologies, describing predictive algorithms, models and toxicity data. As toxicological data may come from different, heterogeneous sources, a deployed ontology, unifying the terminology and the resources, is critical for the rational and reliable organization of the data, and its automatic processing. Results The following related ontologies have been developed for OpenTox: a) Toxicological ontology – listing the toxicological endpoints; b) Organs system and Effects ontology – addressing organs, targets/examinations and effects observed in in vivo studies; c) ToxML ontology – representing semi-automatic conversion of the ToxML schema; d) OpenTox ontology– representation of OpenTox framework components: chemical compounds, datasets, types of algorithms, models and validation web services; e) ToxLink–ToxCast assays ontology and f) OpenToxipedia community knowledge resource on toxicology terminology. OpenTox components are made available through standardized REST web services, where every compound, data set, and predictive method has a unique resolvable address (URI), used to retrieve its Resource Description Framework (RDF) representation, or to initiate the associated calculations and generate new RDF-based resources. The services support the integration of toxicity and chemical data from various sources, the generation and validation of computer models for toxic effects, seamless integration of new algorithms and scientifically sound validation routines and provide a flexible framework, which allows building arbitrary number of applications, tailored to solving different problems by end users (e.g. toxicologists). Availability The OpenTox toxicological

  14. An Approach to Folksonomy-Based Ontology Maintenance for Learning Environments

    Science.gov (United States)

    Gasevic, D.; Zouaq, Amal; Torniai, Carlo; Jovanovic, J.; Hatala, Marek

    2011-01-01

    Recent research in learning technologies has demonstrated many promising contributions from the use of ontologies and semantic web technologies for the development of advanced learning environments. In spite of those benefits, ontology development and maintenance remain the key research challenges to be solved before ontology-enhanced learning…

  15. ANALYSIS OF NORMATIVE-LEGAL BASE OF REGULATION THE RUSSIAN ADVERTISING MARKET

    Directory of Open Access Journals (Sweden)

    Ekaterina F. Devochkina

    2014-01-01

    Full Text Available The article contains analysis of normative-legal base of Russian advertisingcompanies business. Also the problem of absence the legal system is consecrated.The author mentioned comparative characteristics of advertising legal system ofdifferent years.

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

    Lifescience Database Archive (English)

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

  17. Classification of high resolution remote sensing image based on geo-ontology and conditional random fields

    Science.gov (United States)

    Hong, Liang

    2013-10-01

    The availability of high spatial resolution remote sensing data provides new opportunities for urban land-cover classification. More geometric details can be observed in the high resolution remote sensing image, Also Ground objects in the high resolution remote sensing image have displayed rich texture, structure, shape and hierarchical semantic characters. More landscape elements are represented by a small group of pixels. Recently years, the an object-based remote sensing analysis methodology is widely accepted and applied in high resolution remote sensing image processing. The classification method based on Geo-ontology and conditional random fields is presented in this paper. The proposed method is made up of four blocks: (1) the hierarchical ground objects semantic framework is constructed based on geoontology; (2) segmentation by mean-shift algorithm, which image objects are generated. And the mean-shift method is to get boundary preserved and spectrally homogeneous over-segmentation regions ;(3) the relations between the hierarchical ground objects semantic and over-segmentation regions are defined based on conditional random fields framework ;(4) the hierarchical classification results are obtained based on geo-ontology and conditional random fields. Finally, high-resolution remote sensed image data -GeoEye, is used to testify the performance of the presented method. And the experimental results have shown the superiority of this method to the eCognition method both on the effectively and accuracy, which implies it is suitable for the classification of high resolution remote sensing image.

  18. G-Bean: an ontology-graph based web tool for biomedical literature retrieval.

    Science.gov (United States)

    Wang, James Z; Zhang, Yuanyuan; Dong, Liang; Li, Lin; Srimani, Pradip K; Yu, Philip S

    2014-01-01

    Currently, most people use NCBI's PubMed to search the MEDLINE database, an important bibliographical information source for life science and biomedical information. However, PubMed has some drawbacks that make it difficult to find relevant publications pertaining to users' individual intentions, especially for non-expert users. To ameliorate the disadvantages of PubMed, we developed G-Bean, a graph based biomedical search engine, to search biomedical articles in MEDLINE database more efficiently. G-Bean addresses PubMed's limitations with three innovations: (1) Parallel document index creation: a multithreaded index creation strategy is employed to generate the document index for G-Bean in parallel; (2) Ontology-graph based query expansion: an ontology graph is constructed by merging four major UMLS (Version 2013AA) vocabularies, MeSH, SNOMEDCT, CSP and AOD, to cover all concepts in National Library of Medicine (NLM) database; a Personalized PageRank algorithm is used to compute concept relevance in this ontology graph and the Term Frequency - Inverse Document Frequency (TF-IDF) weighting scheme is used to re-rank the concepts. The top 500 ranked concepts are selected for expanding the initial query to retrieve more accurate and relevant information; (3) Retrieval and re-ranking of documents based on user's search intention: after the user selects any article from the existing search results, G-Bean analyzes user's selections to determine his/her true search intention and then uses more relevant and more specific terms to retrieve additional related articles. The new articles are presented to the user in the order of their relevance to the already selected articles. Performance evaluation with 106 OHSUMED benchmark queries shows that G-Bean returns more relevant results than PubMed does when using these queries to search the MEDLINE database. PubMed could not even return any search result for some OHSUMED queries because it failed to form the appropriate Boolean

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

    Science.gov (United States)

    Fan, Hong; Zhu, Anfeng; Zhang, Weixia

    2015-12-01

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

  20. Data ontology and an information system realization for web-based management of image measurements

    Directory of Open Access Journals (Sweden)

    Dimiter eProdanov

    2011-11-01

    Full Text Available Image acquisition, processing and quantification of objects (morphometry require the integration of data inputs and outputs originating from heterogeneous sources. Management of the data exchange along this workflow in a systematic manner poses several challenges, notably the description of the heterogeneous meta data and the interoperability between the software used. The use of integrated software solutions for morphometry and management of imaging data in combination ontologies can reduce metadata data loss and greatly facilitate subsequent data analysis. This paper presents an integrated information system, called LabIS. The system has the objectives to automate (i the process of storage, annotation and querying of image measurements and (ii to provide means for data sharing with 3rd party applications consuming measurement data using open standard communication protocols. LabIS implements 3-tier architecture with a relational database back-end and an application logic middle tier realizing web-based user interface for reporting and annotation and a web service communication layer. The image processing and morphometry functionality is backed by interoperability with ImageJ, a public domain image processing software, via integrated clients. Instrumental for the latter was the construction of a data ontology representing the common measurement data model. LabIS supports user profiling and can store arbitrary types of measurements, regions of interest, calibrations and ImageJ settings. Integration of the stored measurements is facilitated by atlas mapping and ontology-based markup. The system can be used as an experimental workflow management tool allowing for description and reporting of the performed experiments. LabIS can be also used as a measurements repository that can be transparently accessed by computational environments, such as Matlab. Finally, the system can be used as a data sharing tool.

  1. Data ontology and an information system realization for web-based management of image measurements.

    Science.gov (United States)

    Prodanov, Dimiter

    2011-01-01

    Image acquisition, processing, and quantification of objects (morphometry) require the integration of data inputs and outputs originating from heterogeneous sources. Management of the data exchange along this workflow in a systematic manner poses several challenges, notably the description of the heterogeneous meta-data and the interoperability between the software used. The use of integrated software solutions for morphometry and management of imaging data in combination with ontologies can reduce meta-data loss and greatly facilitate subsequent data analysis. This paper presents an integrated information system, called LabIS. The system has the objectives to automate (i) the process of storage, annotation, and querying of image measurements and (ii) to provide means for data sharing with third party applications consuming measurement data using open standard communication protocols. LabIS implements 3-tier architecture with a relational database back-end and an application logic middle tier realizing web-based user interface for reporting and annotation and a web-service communication layer. The image processing and morphometry functionality is backed by interoperability with ImageJ, a public domain image processing software, via integrated clients. Instrumental for the latter feat was the construction of a data ontology representing the common measurement data model. LabIS supports user profiling and can store arbitrary types of measurements, regions of interest, calibrations, and ImageJ settings. Interpretation of the stored measurements is facilitated by atlas mapping and ontology-based markup. The system can be used as an experimental workflow management tool allowing for description and reporting of the performed experiments. LabIS can be also used as a measurements repository that can be transparently accessed by computational environments, such as Matlab. Finally, the system can be used as a data sharing tool.

  2. Improving the Computational Performance of Ontology-Based Classification Using Graph Databases

    Directory of Open Access Journals (Sweden)

    Thomas J. Lampoltshammer

    2015-07-01

    Full Text Available The increasing availability of very high-resolution remote sensing imagery (i.e., from satellites, airborne laser scanning, or aerial photography represents both a blessing and a curse for researchers. The manual classification of these images, or other similar geo-sensor data, is time-consuming and leads to subjective and non-deterministic results. Due to this fact, (semi- automated classification approaches are in high demand in affected research areas. Ontologies provide a proper way of automated classification for various kinds of sensor data, including remotely sensed data. However, the processing of data entities—so-called individuals—is one of the most cost-intensive computational operations within ontology reasoning. Therefore, an approach based on graph databases is proposed to overcome the issue of a high time consumption regarding the classification task. The introduced approach shifts the classification task from the classical Protégé environment and its common reasoners to the proposed graph-based approaches. For the validation, the authors tested the approach on a simulation scenario based on a real-world example. The results demonstrate a quite promising improvement of classification speed—up to 80,000 times faster than the Protégé-based approach.

  3. An ontology-based semantic configuration approach to constructing Data as a Service for enterprises

    Science.gov (United States)

    Cai, Hongming; Xie, Cheng; Jiang, Lihong; Fang, Lu; Huang, Chenxi

    2016-03-01

    To align business strategies with IT systems, enterprises should rapidly implement new applications based on existing information with complex associations to adapt to the continually changing external business environment. Thus, Data as a Service (DaaS) has become an enabling technology for enterprise through information integration and the configuration of existing distributed enterprise systems and heterogonous data sources. However, business modelling, system configuration and model alignment face challenges at the design and execution stages. To provide a comprehensive solution to facilitate data-centric application design in a highly complex and large-scale situation, a configurable ontology-based service integrated platform (COSIP) is proposed to support business modelling, system configuration and execution management. First, a meta-resource model is constructed and used to describe and encapsulate information resources by way of multi-view business modelling. Then, based on ontologies, three semantic configuration patterns, namely composite resource configuration, business scene configuration and runtime environment configuration, are designed to systematically connect business goals with executable applications. Finally, a software architecture based on model-view-controller (MVC) is provided and used to assemble components for software implementation. The result of the case study demonstrates that the proposed approach provides a flexible method of implementing data-centric applications.

  4. Ontology-based literature mining of E. coli vaccine-associated gene interaction networks.

    Science.gov (United States)

    Hur, Junguk; Özgür, Arzucan; He, Yongqun

    2017-03-14

    Pathogenic Escherichia coli infections cause various diseases in humans and many animal species. However, with extensive E. coli vaccine research, we are still unable to fully protect ourselves against E. coli infections. To more rational development of effective and safe E. coli vaccine, it is important to better understand E. coli vaccine-associated gene interaction networks. In this study, we first extended the Vaccine Ontology (VO) to semantically represent various E. coli vaccines and genes used in the vaccine development. We also normalized E. coli gene names compiled from the annotations of various E. coli strains using a pan-genome-based annotation strategy. The Interaction Network Ontology (INO) includes a hierarchy of various interaction-related keywords useful for literature mining. Using VO, INO, and normalized E. coli gene names, we applied an ontology-based SciMiner literature mining strategy to mine all PubMed abstracts and retrieve E. coli vaccine-associated E. coli gene interactions. Four centrality metrics (i.e., degree, eigenvector, closeness, and betweenness) were calculated for identifying highly ranked genes and interaction types. Using vaccine-related PubMed abstracts, our study identified 11,350 sentences that contain 88 unique INO interactions types and 1,781 unique E. coli genes. Each sentence contained at least one interaction type and two unique E. coli genes. An E. coli gene interaction network of genes and INO interaction types was created. From this big network, a sub-network consisting of 5 E. coli vaccine genes, including carA, carB, fimH, fepA, and vat, and 62 other E. coli genes, and 25 INO interaction types was identified. While many interaction types represent direct interactions between two indicated genes, our study has also shown that many of these retrieved interaction types are indirect in that the two genes participated in the specified interaction process in a required but indirect process. Our centrality analysis of

  5. My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development.

    Science.gov (United States)

    Rabattu, Pierre-Yves; Massé, Benoit; Ulliana, Federico; Rousset, Marie-Christine; Rohmer, Damien; Léon, Jean-Claude; Palombi, Olivier

    2015-01-01

    Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physically based modeling are used to assist the visualization and the simulation of virtual humans for numerous domains such as surgical simulation and learning. On the other side, the ontology-based approach applied to knowledge representation is more and more successfully adopted in the life-science domains to formalize biological entities and phenomena, thanks to a declarative approach for expressing and reasoning over symbolic information. 3D models and ontologies are two complementary ways to describe biological entities that remain largely separated. Indeed, while many ontologies providing a unified formalization of anatomy and embryology exist, they remain only descriptive and make the access to anatomical content of complex 3D embryology models and simulations difficult. In this work, we present a novel ontology describing the development of the human embryology deforming 3D models. Beyond describing how organs and structures are composed, our ontology integrates a procedural description of their 3D representations, temporal deformation and relations with respect to their developments. We also created inferences rules to express complex connections between entities. It results in a unified description of both the knowledge of the organs deformation and their 3D representations enabling to visualize dynamically the embryo deformation during the Carnegie stages. Through a simplified ontology, containing representative entities which are linked to spatial position and temporal process information, we illustrate the added-value of such a declarative approach for interactive simulation and visualization of 3D embryos. Combining ontologies and 3D models enables a declarative description of different embryological models that capture the complexity of human

  6. An ontology-driven, case-based clinical decision support model for removable partial denture design

    Science.gov (United States)

    Chen, Qingxiao; Wu, Ji; Li, Shusen; Lyu, Peijun; Wang, Yong; Li, Miao

    2016-06-01

    We present the initial work toward developing a clinical decision support model for specific design of removable partial dentures (RPDs) in dentistry. We developed an ontological paradigm to represent knowledge of a patient’s oral conditions and denture component parts. During the case-based reasoning process, a cosine similarity algorithm was applied to calculate similarity values between input patients and standard ontology cases. A group of designs from the most similar cases were output as the final results. To evaluate this model, the output designs of RPDs for 104 randomly selected patients were compared with those selected by professionals. An area under the curve of the receiver operating characteristic (AUC-ROC) was created by plotting true-positive rates against the false-positive rate at various threshold settings. The precision at position 5 of the retrieved cases was 0.67 and at the top of the curve it was 0.96, both of which are very high. The mean average of precision (MAP) was 0.61 and the normalized discounted cumulative gain (NDCG) was 0.74 both of which confirmed the efficient performance of our model. All the metrics demonstrated the efficiency of our model. This methodology merits further research development to match clinical applications for designing RPDs. This paper is organized as follows. After the introduction and description of the basis for the paper, the evaluation and results are presented in Section 2. Section 3 provides a discussion of the methodology and results. Section 4 describes the details of the ontology, similarity algorithm, and application.

  7. Conceptual querying through ontologies

    DEFF Research Database (Denmark)

    Andreasen, Troels; Bulskov, Henrik

    2009-01-01

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

  8. How substance-based ontologies for gravity can be productive: A case study

    Science.gov (United States)

    Gupta, Ayush; Elby, Andrew; Conlin, Luke D.

    2014-06-01

    Many science education researchers have argued that learners' commitment to a substance (matter-based) ontology impedes the learning of scientific concepts that scientists typically conceptualize as processes or interactions, such as force, electric current, and heat. By this account, students' tendency to classify these entities as substances or properties of substances leads to robust misconceptions, and instruction should steer novices away from substance-based reasoning. We argue that substance-based reasoning can contribute to the learning and understanding of these very same physics concepts. Our case study focuses on a group of elementary school science teachers in our professional development program. Starting from substance-based metaphors for gravity, the teachers build a sophisticated explanation for why objects of different masses fall with the same acceleration. We argue that, for conceptual, epistemological, and affective reasons, instructional interventions should focus on tapping these productive substance-based resources when they arise rather than attempting to suppress them.

  9. REGULARYFRAMWORK AND LEGAL BASE OF ELECTRONIC DOCUMENT CIRCULATION

    Directory of Open Access Journals (Sweden)

    Taisiia H. Omelchenko

    2010-08-01

    Full Text Available The general characteristic of legal base of electronic document circulation is presented in the article. It legislatively regulates the relations which connected with the information and information communication technologies. There is presented the list of the basic acts of regulation of sphere of information relations.

  10. Supporting Analogy-based Effort Estimation with the Use of Ontologies

    Directory of Open Access Journals (Sweden)

    Joanna Kowalska

    2014-06-01

    Full Text Available The paper concerns effort estimation of software development projects, in particular, at the level of product delivery stages. It proposes a new approach to model project data to support expert-supervised analogy-based effort estimation. The data is modeled using Semantic Web technologies, such as Resource Description Framework (RDF and Ontology Language for the Web (OWL. Moreover, in the paper, we define a method of supervised case-based reasoning. The method enables to search for similar projects’ tasks at different levels of abstraction. For instance, instead of searching for a task performed by a specific person, one could look for tasks performed by people with similar capabilities. The proposed method relies on ontology that defines the core concepts and relationships. However, it is possible to introduce new classes and relationships, without the need of altering the search mechanisms. Finally, we implemented a prototype tool that was used to preliminary validate the proposed approach. We observed that the proposed approach could potentially help experts in estimating non-trivial tasks that are often underestimated.

  11. A Knowledge Modeling Method for Computer Graphics Design & Production Based on Ontology

    Directory of Open Access Journals (Sweden)

    Chen Tong

    2017-01-01

    Full Text Available As one of the most critical stages of CG (Computer Graphics industry, CG design & production needs the support of professional knowledge and practice experience of multidisciplinary. With the outstanding performance in knowledge sharing, integration and reuse, knowledge modeling could increase greatly the efficiency, reduce the cost and avoid repeated error in CG design & production. However, knowledge modeling of CG design & production differs greatly from those of other fields. On the one hand, it is similar to physical product design, which involves great deal of tacit knowledge such as modeling skills, reasoning knowledge and so on. On the other hand, as film, CG design & production needs a lot of unstructured description information. The heterogeneity between physical product and film makes knowledge modeling more complicated. Thus a systematic knowledge modelling method based on Ontology is proposed to aid CG design & production in this paper. CG animation knowledge is capture and organized from viewpoint of three aspects: requirements and design and production. The knowledge are categorized into static and dynamic knowledge, and Ontology is adopted to construct a hierarchic model to organize the knowledge, so as to offer a uniform communication semantic foundations for designers from different fields. Based on animation script, the CG design task model is proposed to drive the organization and management of different knowledge involved in CG design & production. Finally, we apply this method in the knowledge modeling of naked-eye animation design and production to illustrate effectiveness of this method.

  12. Region-Based Image Retrieval Using an Object Ontology and Relevance Feedback

    Directory of Open Access Journals (Sweden)

    Kompatsiaris Ioannis

    2004-01-01

    Full Text Available An image retrieval methodology suited for search in large collections of heterogeneous images is presented. The proposed approach employs a fully unsupervised segmentation algorithm to divide images into regions and endow the indexing and retrieval system with content-based functionalities. Low-level descriptors for the color, position, size, and shape of each region are subsequently extracted. These arithmetic descriptors are automatically associated with appropriate qualitative intermediate-level descriptors, which form a simple vocabulary termed object ontology. The object ontology is used to allow the qualitative definition of the high-level concepts the user queries for (semantic objects, each represented by a keyword and their relations in a human-centered fashion. When querying for a specific semantic object (or objects, the intermediate-level descriptor values associated with both the semantic object and all image regions in the collection are initially compared, resulting in the rejection of most image regions as irrelevant. Following that, a relevance feedback mechanism, based on support vector machines and using the low-level descriptors, is invoked to rank the remaining potentially relevant image regions and produce the final query results. Experimental results and comparisons demonstrate, in practice, the effectiveness of our approach.

  13. Ontology Evaluation

    OpenAIRE

    Vrandecic, Zdenko

    2010-01-01

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

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

    Science.gov (United States)

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

    2017-07-24

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

  15. Constitutionally-Legal Policy as Base Type of Legal Policy of Russia

    Science.gov (United States)

    Anichkin, Eugene S.

    2016-01-01

    The article deals with reasons for formation, nature and specifics of the constitutionally legal policy of modern Russia. The special attention is spared to the exposure of the aim, long-term and short-term tasks, and principles of national constitutionally legal policy. The functions of constitutionally legal policy are separately considered:…

  16. Ontology-based Deep Learning for Human Behavior Prediction with Explanations in Health Social Networks.

    Science.gov (United States)

    Phan, Nhathai; Dou, Dejing; Wang, Hao; Kil, David; Piniewski, Brigitte

    2017-04-01

    Human behavior modeling is a key component in application domains such as healthcare and social behavior research. In addition to accurate prediction, having the capacity to understand the roles of human behavior determinants and to provide explanations for the predicted behaviors is also important. Having this capacity increases trust in the systems and the likelihood that the systems actually will be adopted, thus driving engagement and loyalty. However, most prediction models do not provide explanations for the behaviors they predict. In this paper, we study the research problem, human behavior prediction with explanations , for healthcare intervention systems in health social networks. We propose an ontology-based deep learning model ( ORBM + ) for human behavior prediction over undirected and nodes-attributed graphs. We first propose a bottom-up algorithm to learn the user representation from health ontologies. Then the user representation is utilized to incorporate self-motivation , social influences , and environmental events together in a human behavior prediction model, which extends a well-known deep learning method, the Restricted Boltzmann Machine. ORBM + not only predicts human behaviors accurately, but also, it generates explanations for each predicted behavior. Experiments conducted on both real and synthetic health social networks have shown the tremendous effectiveness of our approach compared with conventional methods.

  17. Semantic Mining based on graph theory and ontologies. Case Study: Cell Signaling Pathways

    Directory of Open Access Journals (Sweden)

    Carlos R. Rangel

    2016-08-01

    Full Text Available In this paper we use concepts from graph theory and cellular biology represented as ontologies, to carry out semantic mining tasks on signaling pathway networks. Specifically, the paper describes the semantic enrichment of signaling pathway networks. A cell signaling network describes the basic cellular activities and their interactions. The main contribution of this paper is in the signaling pathway research area, it proposes a new technique to analyze and understand how changes in these networks may affect the transmission and flow of information, which produce diseases such as cancer and diabetes. Our approach is based on three concepts from graph theory (modularity, clustering and centrality frequently used on social networks analysis. Our approach consists into two phases: the first uses the graph theory concepts to determine the cellular groups in the network, which we will call them communities; the second uses ontologies for the semantic enrichment of the cellular communities. The measures used from the graph theory allow us to determine the set of cells that are close (for example, in a disease, and the main cells in each community. We analyze our approach in two cases: TGF-ß and the Alzheimer Disease.

  18. Music education for the 21st century: Epistemology and ontology as bases for student aesthetic education.

    Directory of Open Access Journals (Sweden)

    José Luis Aróstegui

    2004-09-01

    Full Text Available We seek to understand why persons develop their musical preferences by identifying with a particular cultural group and social background. This identification is greatly shaped by experience in their environment. Resources employed for this identification are mostly different from those employed in schools to foster academic knowledge. We argue that there needs to be renewed attention to the epistemological and ontological bases of education to examine how we can most effectively educate for the 21st Century in a relativistic and globalized world. Our focus is on music education but with the entire curriculum near at hand, together seeking to bring about a better intellectual, sociological, and aesthetic process of education. Our interest in music stems from a perceived necessity that persons trained in the arts will have special answers to the challenges of this so-called postmodern world. We offer: (1 elements of epistemology, discussing how education and music education have traditionally been focused on propositional rather than interpretive knowledge; (2 a particular perspective on ontology, making evident the ways that individuals construct meanings, interacting with their cultural environment in the shaping of social identity; and (3 the need, today more than ever, for a music curriculum fostering aesthetic experiences that develop interpretive understanding of reality and personal self. Characteristics of postmodernism in cultural studies will be employed throughout the paper.

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

    Directory of Open Access Journals (Sweden)

    B Ritschel

    2012-10-01

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

  20. Context-aware recommender system based on ontology for recommending tourist destinations at Bandung

    Science.gov (United States)

    Rizaldy Hafid Arigi, L.; Abdurahman Baizal, Z. K.; Herdiani, Anisa

    2018-03-01

    Recommender System is software that is able to provide personalized recommendation suits users’ needs. Recommender System has been widely implemented in various domains, including tourism. One approach that can be done for more personalized recommendations is the use of contextual information. This paper proposes a context aware recommender based ontology system in the tourism domain. The system is capable of recommending tourist destinations by using user preferences of the categories of tourism and contextual information such as user locations, weather around tourist destinations and close time of destination. Based on the evaluation, the system has accuracy of of 0.94 (item recommendation precision evaluated by expert) and 0.58 (implicitly from system-end user interaction). Based on the evaluation of user satisfaction, the system provides a satisfaction level of more than 0.7 (scale 0 to 1) for speed factors for providing liked recommendations (PE), informative description of recommendations (INF) and user trust (TR).

  1. Ontological dependency

    NARCIS (Netherlands)

    Stamper, R.K.

    1996-01-01

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

  2. Using XML technology for the ontology-based semantic integration of life science databases.

    Science.gov (United States)

    Philippi, Stephan; Köhler, Jacob

    2004-06-01

    Several hundred internet accessible life science databases with constantly growing contents and varying areas of specialization are publicly available via the internet. Database integration, consequently, is a fundamental prerequisite to be able to answer complex biological questions. Due to the presence of syntactic, schematic, and semantic heterogeneities, large scale database integration at present takes considerable efforts. As there is a growing apprehension of extensible markup language (XML) as a means for data exchange in the life sciences, this article focuses on the impact of XML technology on database integration in this area. In detail, a general architecture for ontology-driven data integration based on XML technology is introduced, which overcomes some of the traditional problems in this area. As a proof of concept, a prototypical implementation of this architecture based on a native XML database and an expert system shell is described for the realization of a real world integration scenario.

  3. Automatic classification of epilepsy types using ontology-based and genetics-based machine learning.

    Science.gov (United States)

    Kassahun, Yohannes; Perrone, Roberta; De Momi, Elena; Berghöfer, Elmar; Tassi, Laura; Canevini, Maria Paola; Spreafico, Roberto; Ferrigno, Giancarlo; Kirchner, Frank

    2014-06-01

    In the presurgical analysis for drug-resistant focal epilepsies, the definition of the epileptogenic zone, which is the cortical area where ictal discharges originate, is usually carried out by using clinical, electrophysiological and neuroimaging data analysis. Clinical evaluation is based on the visual detection of symptoms during epileptic seizures. This work aims at developing a fully automatic classifier of epileptic types and their localization using ictal symptoms and machine learning methods. We present the results achieved by using two machine learning methods. The first is an ontology-based classification that can directly incorporate human knowledge, while the second is a genetics-based data mining algorithm that learns or extracts the domain knowledge from medical data in implicit form. The developed methods are tested on a clinical dataset of 129 patients. The performance of the methods is measured against the performance of seven clinicians, whose level of expertise is high/very high, in classifying two epilepsy types: temporal lobe epilepsy and extra-temporal lobe epilepsy. When comparing the performance of the algorithms with that of a single clinician, who is one of the seven clinicians, the algorithms show a slightly better performance than the clinician on three test sets generated randomly from 99 patients out of the 129 patients. The accuracy obtained for the two methods and the clinician is as follows: first test set 65.6% and 75% for the methods and 56.3% for the clinician, second test set 66.7% and 76.2% for the methods and 61.9% for the clinician, and third test set 77.8% for the methods and the clinician. When compared with the performance of the whole population of clinicians on the rest 30 patients out of the 129 patients, where the patients were selected by the clinicians themselves, the mean accuracy of the methods (60%) is slightly worse than the mean accuracy of the clinicians (61.6%). Results show that the methods perform at the

  4. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining.

    Science.gov (United States)

    Hur, Junguk; Ozgür, Arzucan; Xiang, Zuoshuang; He, Yongqun

    2012-12-20

    Fever is one of the most common adverse events of vaccines. The detailed mechanisms of fever and vaccine-associated gene interaction networks are not fully understood. In the present study, we employed a genome-wide, Centrality and Ontology-based Network Discovery using Literature data (CONDL) approach to analyse the genes and gene interaction networks associated with fever or vaccine-related fever responses. Over 170,000 fever-related articles from PubMed abstracts and titles were retrieved and analysed at the sentence level using natural language processing techniques to identify genes and vaccines (including 186 Vaccine Ontology terms) as well as their interactions. This resulted in a generic fever network consisting of 403 genes and 577 gene interactions. A vaccine-specific fever sub-network consisting of 29 genes and 28 gene interactions was extracted from articles that are related to both fever and vaccines. In addition, gene-vaccine interactions were identified. Vaccines (including 4 specific vaccine names) were found to directly interact with 26 genes. Gene set enrichment analysis was performed using the genes in the generated interaction networks. Moreover, the genes in these networks were prioritized using network centrality metrics. Making scientific discoveries and generating new hypotheses were possible by using network centrality and gene set enrichment analyses. For example, our study found that the genes in the generic fever network were more enriched in cell death and responses to wounding, and the vaccine sub-network had more gene enrichment in leukocyte activation and phosphorylation regulation. The most central genes in the vaccine-specific fever network are predicted to be highly relevant to vaccine-induced fever, whereas genes that are central only in the generic fever network are likely to be highly relevant to generic fever responses. Interestingly, no Toll-like receptors (TLRs) were found in the gene-vaccine interaction network. Since

  5. Hierarchical Role Ontology-based Assessment of Trainee’s Conceptual Knowledge

    Directory of Open Access Journals (Sweden)

    V. V. Belous

    2014-01-01

    Full Text Available We believe that this knowledge base of training system structure is based on the subject semantic network (SSN containing concepts of subject domain and relations between them. The SSN is represented as a direct graph, with tops corresponding to concepts, and arcs corresponding to relations. We consider a technique for trainee’s conceptual knowledge assessment using the cognitive maps of trainees (CMT, each of which formalizes his ideas of some SSN fragment and theoretically coincides with this fragment. Assessment of trainee’s achievement of this SSN fragment comes to comparison of SSN subgraph, corresponding to this fragment, with the direct graph, which is defined by the corresponding CMT.A number of important subject domains possess the property that concepts in them have the attribute called ‘role’, and roles of concepts can be linearly sorted. The direct graph SSN, corresponding to such ontology can be presented in a tiered form.The work concerns the assessment of trainee’s conceptual knowledge in the subject domains of this class. The work represents the SSN and CMT models used, describes the offered methods to create CMT, as well metrics for trainee’s achievement of the conceptual knowledge based on his CMT.The main results of work are the following: the model of the semantic network corresponding to hierarchical role ontology, and also a model of a trainee’s cognitive map of are offered, methods for creating the trainee’s cognitive maps are developed, metrics of trainee’s achievement of conceptual knowledge are suggested.

  6. 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...

  7. Al-Quran ontology based on knowledge themes | Ta'a | Journal of ...

    African Journals Online (AJOL)

    Islamic knowledge is gathered through the understanding the Al-Quran. It requires ontology which can capture the knowledge and present it in a machine readable structured. However, current ontology approaches is irrelevant and inaccuracy in producing true concepts of Al-Quran knowledge, because it used traditional ...

  8. DServO: A Peer-to-Peer-based Approach to Biomedical Ontology Repositories.

    Science.gov (United States)

    Mambone, Zakaria; Savadogo, Mahamadi; Some, Borlli Michel Jonas; Diallo, Gayo

    2015-01-01

    We present in this poster an extension of the ServO ontology server system, which adopts a decentralized Peer-To-Peer approach for managing multiple heterogeneous knowledge organization systems. It relies on the use of the JXTA protocol coupled with information retrieval techniques to provide a decentralized infrastructure for managing multiples instances of Ontology Repositories.

  9. An Ontology-based Context-aware System for Smart Homes: E-care@home.

    Science.gov (United States)

    Alirezaie, Marjan; Renoux, Jennifer; Köckemann, Uwe; Kristoffersson, Annica; Karlsson, Lars; Blomqvist, Eva; Tsiftes, Nicolas; Voigt, Thiemo; Loutfi, Amy

    2017-07-06

    Smart home environments have a significant potential to provide for long-term monitoring of users with special needs in order to promote the possibility to age at home. Such environments are typically equipped with a number of heterogeneous sensors that monitor both health and environmental parameters. This paper presents a framework called E-care@home, consisting of an IoT infrastructure, which provides information with an unambiguous, shared meaning across IoT devices, end-users, relatives, health and care professionals and organizations. We focus on integrating measurements gathered from heterogeneous sources by using ontologies in order to enable semantic interpretation of events and context awareness. Activities are deduced using an incremental answer set solver for stream reasoning. The paper demonstrates the proposed framework using an instantiation of a smart environment that is able to perform context recognition based on the activities and the events occurring in the home.

  10. 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.

  11. Improvements to the Ontology-based Metadata Portal for Unified Semantics (OlyMPUS)

    Science.gov (United States)

    Linsinbigler, M. A.; Gleason, J. L.; Huffer, E.

    2016-12-01

    The Ontology-based Metadata Portal for Unified Semantics (OlyMPUS), funded by the NASA Earth Science Technology Office Advanced Information Systems Technology program, is an end-to-end system designed to support Earth Science data consumers and data providers, enabling the latter to register data sets and provision them with the semantically rich metadata that drives the Ontology-Driven Interactive Search Environment for Earth Sciences (ODISEES). OlyMPUS complements the ODISEES' data discovery system with an intelligent tool to enable data producers to auto-generate semantically enhanced metadata and upload it to the metadata repository that drives ODISEES. Like ODISEES, the OlyMPUS metadata provisioning tool leverages robust semantics, a NoSQL database and query engine, an automated reasoning engine that performs first- and second-order deductive inferencing, and uses a controlled vocabulary to support data interoperability and automated analytics. The ODISEES data discovery portal leverages this metadata to provide a seamless data discovery and access experience for data consumers who are interested in comparing and contrasting the multiple Earth science data products available across NASA data centers. Olympus will support scientists' services and tools for performing complex analyses and identifying correlations and non-obvious relationships across all types of Earth System phenomena using the full spectrum of NASA Earth Science data available. By providing an intelligent discovery portal that supplies users - both human users and machines - with detailed information about data products, their contents and their structure, ODISEES will reduce the level of effort required to identify and prepare large volumes of data for analysis. This poster will explain how OlyMPUS leverages deductive reasoning and other technologies to create an integrated environment for generating and exploiting semantically rich metadata.

  12. Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph.

    Science.gov (United States)

    Richards, Adam J; Muller, Brian; Shotwell, Matthew; Cowart, L Ashley; Rohrer, Bäerbel; Lu, Xinghua

    2010-06-15

    The results of initial analyses for many high-throughput technologies commonly take the form of gene or protein sets, and one of the ensuing tasks is to evaluate the functional coherence of these sets. The study of gene set function most commonly makes use of controlled vocabulary in the form of ontology annotations. For a given gene set, the statistical significance of observing these annotations or 'enrichment' may be tested using a number of methods. Instead of testing for significance of individual terms, this study is concerned with the task of assessing the global functional coherence of gene sets, for which novel metrics and statistical methods have been devised. The metrics of this study are based on the topological properties of graphs comprised of genes and their Gene Ontology annotations. A novel aspect of these methods is that both the enrichment of annotations and the relationships among annotations are considered when determining the significance of functional coherence. We applied our methods to perform analyses on an existing database and on microarray experimental results. Here, we demonstrated that our approach is highly discriminative in terms of differentiating coherent gene sets from random ones and that it provides biologically sensible evaluations in microarray analysis. We further used examples to show the utility of graph visualization as a tool for studying the functional coherence of gene sets. The implementation is provided as a freely accessible web application at: http://projects.dbbe.musc.edu/gosteiner. Additionally, the source code written in the Python programming language, is available under the General Public License of the Free Software Foundation. Supplementary data are available at Bioinformatics online.

  13. THE LEGAL ARRANGEMENT OF WAGE PROTECTION BASED ON THE PRINCIPLE OF LEGAL CERTAINTY

    Directory of Open Access Journals (Sweden)

    Yetniwati

    2016-05-01

    Full Text Available The wage protection in Indonesian positive law is still not provide legal certainty for the weaker party in the aspect of social economic. In every anniversary of May Day, labor union always demanded to abolish the wage cost, which the Government Regulation No. 78 Year 2015 leanihg to the interests of investors. The principle of legal certainty in the norm of wage protection needs to be realized with respect to: the concept of wage protection, lack of certainty purpose of law, established by the competent authorities, accepted by society, legal materials in accordance with the legal hierarchy, the company's obligation to make books wages, and avoid multiple interpretations in legal norms.

  14. 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.

  15. Legal Issues of A Surrogacy Contract Based on Iranian Acts

    Directory of Open Access Journals (Sweden)

    Amir Pirouz

    2011-06-01

    Full Text Available Assistive technologies have always opened new horizons in human's life, posed solutions to problemsand brought relief and prosperity for human beings. Iranian judicial authorities have recently recognizedthe importance of medical technologies. Accordingly, Iranian legal system has recognized surrogacy anda surrogacy contract seems unavoidable for surrogacy to be legally valid, socially acceptable andreligiously legitimate. As a legal defense of including a typical surrogacy contract in contract law, thisreview studies the four building blocks of a valid contract: the intention and consent of parties, theirlegal capacity, the subject of the contract and its legitimacy. Discussing related Iranian Acts concerningcontracts and responsibilities of parties, the authors of the present article deal with main commitmentsand responsibilities of the parties to a typical surrogacy contract: infertile couples, surrogate, fertilityclinic or medical institute, and surrogate's husband. The authors conclude that a surrogacy contract isaccepted based on article 10 of Iranian Civil Act 1928, pose some suggestions to be included in such acontract, and emphasize that a specific Act concerning surrogacy should be approved to cover rights andlegal needs of all parties to a surrogacy contract.

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

    Science.gov (United States)

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

    2014-01-01

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

  17. Ontology-based knowledge representation for resolution of semantic heterogeneity in GIS

    Science.gov (United States)

    Liu, Ying; Xiao, Han; Wang, Limin; Han, Jialing

    2017-07-01

    Lack of semantic interoperability in geographical information systems has been identified as the main obstacle for data sharing and database integration. The new method should be found to overcome the problems of semantic heterogeneity. Ontologies are considered to be one approach to support geographic information sharing. This paper presents an ontology-driven integration approach to help in detecting and possibly resolving semantic conflicts. Its originality is that each data source participating in the integration process contains an ontology that defines the meaning of its own data. This approach ensures the automation of the integration through regulation of semantic integration algorithm. Finally, land classification in field GIS is described as the example.

  18. A Web-Based Data-Querying Tool Based on Ontology-Driven Methodology and Flowchart-Based Model

    Science.gov (United States)

    Ping, Xiao-Ou; Chung, Yufang; Liang, Ja-Der; Yang, Pei-Ming; Huang, Guan-Tarn; Lai, Feipei

    2013-01-01

    Background Because of the increased adoption rate of electronic medical record (EMR) systems, more health care records have been increasingly accumulating in clinical data repositories. Therefore, querying the data stored in these repositories is crucial for retrieving the knowledge from such large volumes of clinical data. Objective The aim of this study is to develop a Web-based approach for enriching the capabilities of the data-querying system along the three following considerations: (1) the interface design used for query formulation, (2) the representation of query results, and (3) the models used for formulating query criteria. Methods The Guideline Interchange Format version 3.5 (GLIF3.5), an ontology-driven clinical guideline representation language, was used for formulating the query tasks based on the GLIF3.5 flowchart in the Protégé environment. The flowchart-based data-querying model (FBDQM) query execution engine was developed and implemented for executing queries and presenting the results through a visual and graphical interface. To examine a broad variety of patient data, the clinical data generator was implemented to automatically generate the clinical data in the repository, and the generated data, thereby, were employed to evaluate the system. The accuracy and time performance of the system for three medical query tasks relevant to liver cancer were evaluated based on the clinical data generator in the experiments with varying numbers of patients. Results In this study, a prototype system was developed to test the feasibility of applying a methodology for building a query execution engine using FBDQMs by formulating query tasks using the existing GLIF. The FBDQM-based query execution engine was used to successfully retrieve the clinical data based on the query tasks formatted using the GLIF3.5 in the experiments with varying numbers of patients. The accuracy of the three queries (ie, “degree of liver damage,” “degree of liver damage

  19. CREATION OF IT-ORIENTED ONTOLOGICAL FRAMEWORK FOR THE PURPOSE OF MAKING EDUCATIONAL PROGRAMS ON THE BASE OF COMPETENCIES

    Directory of Open Access Journals (Sweden)

    G. M. Korotenko

    2017-08-01

    Full Text Available Purpose. Taking into account the expansion of computing application scopes there is a need to identify the links and features of the constantly emerging professional competencies of the new sections of computing knowledge to improve the process of forming new curricula. Methodology. Authors propose the new approach aimed to build specialized knowledge bases generated using artificial intelligence technology and focused on the use of multiple heterogeneous resources or data sources on specific educational topics is proposed. As a tool, ensuring the formation of the base ontology the Protégé 4.2 ontology editor is used. As one of the modules of the developed system of semantic analysis, which provides access to ontology and the possibility of its processing, the Apache Jena Java framework should be used, which forms the software environment for working with data in RDF, RDFS and OWL formats, and also supports the ability to form queries to Ontologies in the SPARQL language. The peculiarity of this approach is the binding of information resources of the three-platform presentation of the disciplinary structure in the context of identifying the links of professional competencies. Findings. The model and structure of the IT-oriented ontological framework designed to ensure the components convergence of the university three-platform information and communication environment are developed. The structure of the knowledge base ontology-basis, describing the main essence of the educational standards of the "Information Technologies" branch is formed. Originality. Within the framework of design and formation of the knowledge sector disciplinary structure "Information Technologies" in the context of the competence approach to education, the architecture of the competence descriptors of semantic analysis system is proposed. It implements the algorithm for integrating the ontological and product models of knowledge representation about the subject domain

  20. OntoFire: an ontology-based geo-portal for wildfires

    Directory of Open Access Journals (Sweden)

    K. Kalabokidis

    2011-12-01

    Full Text Available With the proliferation of the geospatial technologies on the Internet, the role of geo-portals (i.e. gateways to Spatial Data Infrastructures in the area of wildfires management emerges. However, keyword-based techniques often frustrate users when looking for data of interest in geo-portal environments, while little attention has been paid to shift from the conventional keyword-based to navigation-based mechanisms. The presented OntoFire system is an ontology-based geo-portal about wildfires. Through the proposed navigation mechanisms, the relationships between the data can be discovered, which would otherwise not be possible when using conventional querying techniques alone. End users can use the browsing interface to find resources of interest by using the navigation mechanisms provided. Data providers can use the publishing interface to submit new metadata, modify metadata or removing metadata in/from the catalogue. The proposed approach can improve the discovery of valuable information that is necessary to set priorities for disaster mitigation and prevention strategies. OntoFire aspires to be a focal point of integration and management of a very large amount of information, contributing in this way to the dissemination of knowledge and to the preparedness of the operational stakeholders.

  1. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network.

    Science.gov (United States)

    Hur, Junguk; Xiang, Zuoshuang; Feldman, Eva L; He, Yongqun

    2011-08-26

    Vaccine literature indexing is poorly performed in PubMed due to limited hierarchy of Medical Subject Headings (MeSH) annotation in the vaccine field. Vaccine Ontology (VO) is a community-based biomedical ontology that represents various vaccines and their relations. SciMiner is an in-house literature mining system that supports literature indexing and gene name tagging. We hypothesize that application of VO in SciMiner will aid vaccine literature indexing and mining of vaccine-gene interaction networks. As a test case, we have examined vaccines for Brucella, the causative agent of brucellosis in humans and animals. The VO-based SciMiner (VO-SciMiner) was developed to incorporate a total of 67 Brucella vaccine terms. A set of rules for term expansion of VO terms were learned from training data, consisting of 90 biomedical articles related to Brucella vaccine terms. VO-SciMiner demonstrated high recall (91%) and precision (99%) from testing a separate set of 100 manually selected biomedical articles. VO-SciMiner indexing exhibited superior performance in retrieving Brucella vaccine-related papers over that obtained with MeSH-based PubMed literature search. For example, a VO-SciMiner search of "live attenuated Brucella vaccine" returned 922 hits as of April 20, 2011, while a PubMed search of the same query resulted in only 74 hits. Using the abstracts of 14,947 Brucella-related papers, VO-SciMiner identified 140 Brucella genes associated with Brucella vaccines. These genes included known protective antigens, virulence factors, and genes closely related to Brucella vaccines. These VO-interacting Brucella genes were significantly over-represented in biological functional categories, including metabolite transport and metabolism, replication and repair, cell wall biogenesis, intracellular trafficking and secretion, posttranslational modification, and chaperones. Furthermore, a comprehensive interaction network of Brucella vaccines and genes were identified. The asserted

  2. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network

    Science.gov (United States)

    2011-01-01

    Background Vaccine literature indexing is poorly performed in PubMed due to limited hierarchy of Medical Subject Headings (MeSH) annotation in the vaccine field. Vaccine Ontology (VO) is a community-based biomedical ontology that represents various vaccines and their relations. SciMiner is an in-house literature mining system that supports literature indexing and gene name tagging. We hypothesize that application of VO in SciMiner will aid vaccine literature indexing and mining of vaccine-gene interaction networks. As a test case, we have examined vaccines for Brucella, the causative agent of brucellosis in humans and animals. Results The VO-based SciMiner (VO-SciMiner) was developed to incorporate a total of 67 Brucella vaccine terms. A set of rules for term expansion of VO terms were learned from training data, consisting of 90 biomedical articles related to Brucella vaccine terms. VO-SciMiner demonstrated high recall (91%) and precision (99%) from testing a separate set of 100 manually selected biomedical articles. VO-SciMiner indexing exhibited superior performance in retrieving Brucella vaccine-related papers over that obtained with MeSH-based PubMed literature search. For example, a VO-SciMiner search of "live attenuated Brucella vaccine" returned 922 hits as of April 20, 2011, while a PubMed search of the same query resulted in only 74 hits. Using the abstracts of 14,947 Brucella-related papers, VO-SciMiner identified 140 Brucella genes associated with Brucella vaccines. These genes included known protective antigens, virulence factors, and genes closely related to Brucella vaccines. These VO-interacting Brucella genes were significantly over-represented in biological functional categories, including metabolite transport and metabolism, replication and repair, cell wall biogenesis, intracellular trafficking and secretion, posttranslational modification, and chaperones. Furthermore, a comprehensive interaction network of Brucella vaccines and genes were

  3. An Ontology-Based Architecture for Adaptive Work-Centered User Interface Technology

    National Research Council Canada - National Science Library

    Aragones, Amy; Bruno, Jeanette; Crapo, Andrew; Garbiras, Marc

    2005-01-01

    .... The first concept is to use an ontology modeling approach to characterize a work domain in terms of "work-centered" activities as well as the computation mechanisms that achieve an implementation...

  4. A generic organ based ontology system, applied to vertebrate heart anatomy, development and physiology

    Directory of Open Access Journals (Sweden)

    Bertens Laura M.F.

    2011-03-01

    Full Text Available We present a novel approach to modelling biological information using ontologies. The system interlinks three ontologies, comprising anatomical, developmental and taxonomical information, and includes instances of structures for different species. The framework is constructed for comparative analyses in the field of evolutionary development. We have applied the approach to the vertebrate heart and present four case studies of the functionality of the system, focusing on cross-species comparisons, developmental studies, physiological studies and 3D visualisation.

  5. Legal reality of Russia: constants and variables

    Directory of Open Access Journals (Sweden)

    Andrey Valeryevich Skorobogatov

    2015-06-01

    Full Text Available Objective to develop the sciencebased knowledge about essential and substantial aspects of the current legal reality of Russia in the context of postclassical paradigm. Methods the methodological basis of this research is the synthesis of classical and postclassical paradigms that determine the choice of specific methods of research formallegal comparative legal modeling method hermeneutic discursive methods. Results basing on the postclassical methodology it is proved that the legal reality of Russia consists of three levels legislation law enforcement and legal behavior. The determinant level of legal reality is legal behavior that is aimed at observing the unwritten rules. The legal reality of Russia is characterized by a transgressive state of the modern Russian society expressed in broad application of nonlegislative nonlegal practices low level of legal culture legal nihilism and legal infantilism. Scientific novelty the article for the first time analyzes the ontological and phenomenological essence of the legal reality in Russia and determines its transgressive nature at the present stage of development. Practical value the main provisions and conclusions of the article can be used in scientific and pedagogical activity when considering questions about the nature and content of legal development. nbsp

  6. An ontology-based nurse call management system (oNCS with probabilistic priority assessment

    Directory of Open Access Journals (Sweden)

    Verhoeve Piet

    2011-02-01

    Full Text Available Abstract Background The current, place-oriented nurse call systems are very static. A patient can only make calls with a button which is fixed to a wall of a room. Moreover, the system does not take into account various factors specific to a situation. In the future, there will be an evolution to a mobile button for each patient so that they can walk around freely and still make calls. The system would become person-oriented and the available context information should be taken into account to assign the correct nurse to a call. The aim of this research is (1 the design of a software platform that supports the transition to mobile and wireless nurse call buttons in hospitals and residential care and (2 the design of a sophisticated nurse call algorithm. This algorithm dynamically adapts to the situation at hand by taking the profile information of staff members and patients into account. Additionally, the priority of a call probabilistically depends on the risk factors, assigned to a patient. Methods The ontology-based Nurse Call System (oNCS was developed as an extension of a Context-Aware Service Platform. An ontology is used to manage the profile information. Rules implement the novel nurse call algorithm that takes all this information into account. Probabilistic reasoning algorithms are designed to determine the priority of a call based on the risk factors of the patient. Results The oNCS system is evaluated through a prototype implementation and simulations, based on a detailed dataset obtained from Ghent University Hospital. The arrival times of nurses at the location of a call, the workload distribution of calls amongst nurses and the assignment of priorities to calls are compared for the oNCS system and the current, place-oriented nurse call system. Additionally, the performance of the system is discussed. Conclusions The execution time of the nurse call algorithm is on average 50.333 ms. Moreover, the oNCS system significantly improves

  7. An ontology-based nurse call management system (oNCS) with probabilistic priority assessment.

    Science.gov (United States)

    Ongenae, Femke; Myny, Dries; Dhaene, Tom; Defloor, Tom; Van Goubergen, Dirk; Verhoeve, Piet; Decruyenaere, Johan; De Turck, Filip

    2011-02-04

    The current, place-oriented nurse call systems are very static. A patient can only make calls with a button which is fixed to a wall of a room. Moreover, the system does not take into account various factors specific to a situation. In the future, there will be an evolution to a mobile button for each patient so that they can walk around freely and still make calls. The system would become person-oriented and the available context information should be taken into account to assign the correct nurse to a call.The aim of this research is (1) the design of a software platform that supports the transition to mobile and wireless nurse call buttons in hospitals and residential care and (2) the design of a sophisticated nurse call algorithm. This algorithm dynamically adapts to the situation at hand by taking the profile information of staff members and patients into account. Additionally, the priority of a call probabilistically depends on the risk factors, assigned to a patient. The ontology-based Nurse Call System (oNCS) was developed as an extension of a Context-Aware Service Platform. An ontology is used to manage the profile information. Rules implement the novel nurse call algorithm that takes all this information into account. Probabilistic reasoning algorithms are designed to determine the priority of a call based on the risk factors of the patient. The oNCS system is evaluated through a prototype implementation and simulations, based on a detailed dataset obtained from Ghent University Hospital. The arrival times of nurses at the location of a call, the workload distribution of calls amongst nurses and the assignment of priorities to calls are compared for the oNCS system and the current, place-oriented nurse call system. Additionally, the performance of the system is discussed. The execution time of the nurse call algorithm is on average 50.333 ms. Moreover, the oNCS system significantly improves the assignment of nurses to calls. Calls generally have a nurse

  8. Transparent mediation-based access to multiple yeast data sources using an ontology driven interface.

    Science.gov (United States)

    Briache, Abdelaali; Marrakchi, Kamar; Kerzazi, Amine; Navas-Delgado, Ismael; Rossi Hassani, Badr D; Lairini, Khalid; Aldana-Montes, José F

    2012-01-25

    Saccharomyces cerevisiae is recognized as a model system representing a simple eukaryote whose genome can be easily manipulated. Information solicited by scientists on its biological entities (Proteins, Genes, RNAs...) is scattered within several data sources like SGD, Yeastract, CYGD-MIPS, BioGrid, PhosphoGrid, etc. Because of the heterogeneity of these sources, querying them separately and then manually combining the returned results is a complex and time-consuming task for biologists most of whom are not bioinformatics expert. It also reduces and limits the use that can be made on the available data. To provide transparent and simultaneous access to yeast sources, we have developed YeastMed: an XML and mediator-based system. In this paper, we present our approach in developing this system which takes advantage of SB-KOM to perform the query transformation needed and a set of Data Services to reach the integrated data sources. The system is composed of a set of modules that depend heavily on XML and Semantic Web technologies. User queries are expressed in terms of a domain ontology through a simple form-based web interface. YeastMed is the first mediation-based system specific for integrating yeast data sources. It was conceived mainly to help biologists to find simultaneously relevant data from multiple data sources. It has a biologist-friendly interface easy to use. The system is available at http://www.khaos.uma.es/yeastmed/.

  9. Protein-Protein Interactions Prediction Based on Iterative Clique Extension with Gene Ontology Filtering

    Directory of Open Access Journals (Sweden)

    Lei Yang

    2014-01-01

    Full Text Available Cliques (maximal complete subnets in protein-protein interaction (PPI network are an important resource used to analyze protein complexes and functional modules. Clique-based methods of predicting PPI complement the data defection from biological experiments. However, clique-based predicting methods only depend on the topology of network. The false-positive and false-negative interactions in a network usually interfere with prediction. Therefore, we propose a method combining clique-based method of prediction and gene ontology (GO annotations to overcome the shortcoming and improve the accuracy of predictions. According to different GO correcting rules, we generate two predicted interaction sets which guarantee the quality and quantity of predicted protein interactions. The proposed method is applied to the PPI network from the Database of Interacting Proteins (DIP and most of the predicted interactions are verified by another biological database, BioGRID. The predicted protein interactions are appended to the original protein network, which leads to clique extension and shows the significance of biological meaning.

  10. Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach.

    Science.gov (United States)

    Peng, Jiajie; Zhang, Xuanshuo; Hui, Weiwei; Lu, Junya; Li, Qianqian; Liu, Shuhui; Shang, Xuequn

    2018-03-19

    Gene Ontology (GO) is one of the most popular bioinformatics resources. In the past decade, Gene Ontology-based gene semantic similarity has been effectively used to model gene-to-gene interactions in multiple research areas. However, most existing semantic similarity approaches rely only on GO annotations and structure, or incorporate only local interactions in the co-functional network. This may lead to inaccurate GO-based similarity resulting from the incomplete GO topology structure and gene annotations. We present NETSIM2, a new network-based method that allows researchers to measure GO-based gene functional similarities by considering the global structure of the co-functional network with a random walk with restart (RWR)-based method, and by selecting the significant term pairs to decrease the noise information. Based on the EC number (Enzyme Commission)-based groups of yeast and Arabidopsis, evaluation test shows that NETSIM2 can enhance the accuracy of Gene Ontology-based gene functional similarity. Using NETSIM2 as an example, we found that the accuracy of semantic similarities can be significantly improved after effectively incorporating the global gene-to-gene interactions in the co-functional network, especially on the species that gene annotations in GO are far from complete.

  11. A Legal Negotiatiton Support System Based on A Diagram

    Science.gov (United States)

    Nitta, Katsumi; Shibasaki, Masato; Yasumura, Yoshiaki; Hasegawa, Ryuzo; Fujita, Hiroshi; Koshimura, Miyuki; Inoue, Katsumi; Shirai, Yasuyuki; Komatsu, Hiroshi

    We present an overview of a legal negotiation support system, ANS (Argumentation based Negotiation support System). ANS consists of a user interface, three inference engines, a database of old cases, and two decision support modules. The ANS users negotiates or disputes with others via a computer network. The negotiation status is managed in the form of the negotiation diagram. The negotiation diagram is an extension of Toulmin’s argument diagram, and it contains all arguments insisted by participants. The negotiation protocols are defined as operations to the negotiation diagram. By exchanging counter arguments each other, the negotiation diagram grows up. Nonmonotonic reasoning using rule priorities are applied to the negotiation diagram.

  12. 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...

  13. KnowBaSICS-M: an ontology-based system for semantic management of medical problems and computerised algorithmic solutions.

    Science.gov (United States)

    Bratsas, Charalampos; Koutkias, Vassilis; Kaimakamis, Evangelos; Bamidis, Panagiotis D; Pangalos, George I; Maglaveras, Nicos

    2007-10-01

    In this paper, an ontology-based system (KnowBaSICS-M) is presented for the semantic management of Medical Computational Problems (MCPs), i.e., medical problems and computerised algorithmic solutions. The system provides an open environment, which: (1) allows clinicians and researchers to retrieve potential algorithmic solutions pertinent to a medical problem and (2) enables incorporation of new MCPs into its underlying Knowledge Base (KB). KnowBaSICS-M is a modular system for MCP acquisition and discovery that relies on an innovative ontology-based model incorporating concepts from the Unified Medical Language System (UMLS). Information retrieval (IR) is based on an ontology-based Vector Space Model (VSM) that estimates the similarity among user-defined MCP search criteria and registered MCP solutions in the KB. The results of a preliminary evaluation and specific examples of use are presented to illustrate the benefits of the system. KnowBaSICS-M constitutes an approach towards the construction of an integrated and manageable MCP repository for the biomedical research community.

  14. The OntoREA Accounting Model: Ontology-based Modeling of the Accounting Domain

    Directory of Open Access Journals (Sweden)

    Christian Fischer-Pauzenberger

    2017-07-01

    Full Text Available McCarthy developed a framework for modeling the economic rationale of different business transactions along the enterprise value chain described in his seminal article “The REA Accounting Model – A Generalized Framework for Accounting Systems in a Shared Data Environment” Originally, the REA accounting model was specified in the entity-relationship (ER language. Later on other languages – especially in form of generic data models and UML class models (UML language – were used. Recently, the OntoUML language was developed by Guizzardi and used by Gailly et al. for a metaphysical reengineering of the REA enterprise ontology. Although the REA accounting model originally addressed the accounting domain, it most successfuly is applied as a reference framework for the conceptual modeling of enterprise systems. The primary research objective of this article is to anchor the REA-based models more deeply in the accounting domain. In order to achieve this objective, essential primitives of the REA model are identified and conceptualized in the OntoUML language within the Asset Liability Equity (ALE context of the traditional ALE accounting domain.

  15. QuickGO: a user tutorial for the web-based Gene Ontology browser.

    Science.gov (United States)

    Huntley, Rachael P; Binns, David; Dimmer, Emily; Barrell, Daniel; O'Donovan, Claire; Apweiler, Rolf

    2009-01-01

    The Gene Ontology (GO) has proven to be a valuable resource for functional annotation of gene products. At well over 27 000 terms, the descriptiveness of GO has increased rapidly in line with the biological data it represents. Therefore, it is vital to be able to easily and quickly mine the functional information that has been made available through these GO terms being associated with gene products. QuickGO is a fast, web-based tool for browsing the GO and all associated GO annotations provided by the GOA group. After undergoing a redevelopment, QuickGO is now able to offer many more features beyond simple browsing. Users have responded well to the new tool and given very positive feedback about its usefulness. This tutorial will demonstrate how some of these features could be useful to the researcher wanting to discover more about their dataset, particular areas of biology or to find new ways of directing their research.Database URL:http://www.ebi.ac.uk/QuickGO.

  16. Ontology-Based User Profiling for Personalized Acces to Information within Collaborative Learning System

    Directory of Open Access Journals (Sweden)

    Mohammed Amine Alimam

    2014-06-01

    Full Text Available The use of modern educational technology methods has become an important area of research in order to support learning as well as collaboration. This is especially evident with the rise of internet and web 2.0 platforms that have transformed users’ role from mere content consumers to fully content consumers-producers. Furthermore, people engaged in collaborative learning capitalize on one another’s resources and skills, unlike individual learning. This paper proceeds with a categorization of the main tools and functions that characterize the personalization learning aspect, in order to discuss their trade-offs with collaborative learning systems. It proposes a framework of a personalized information research (IR within a collaborative learning system, incorporating the characterization of the research type carried by the query, as well as modeling and constructing semantic users’ profiles. We use the context of the user query into a prediction mechanism of the search type, based on a previous identification of users’ levels and interests. The paper is concluded by presenting experiment results, revealing that the use of the subject ontology extension approach satisfyingly contributes to improvement in the accuracy of system recommendations.

  17. An Ontology-Based Reasoning Framework for Querying Satellite Images for Disaster Monitoring

    Directory of Open Access Journals (Sweden)

    Marjan Alirezaie

    2017-11-01

    Full Text Available This paper presents a framework in which satellite images are classified and augmented with additional semantic information to enable queries about what can be found on the map at a particular location, but also about paths that can be taken. This is achieved by a reasoning framework based on qualitative spatial reasoning that is able to find answers to high level queries that may vary on the current situation. This framework called SemCityMap, provides the full pipeline from enriching the raw image data with rudimentary labels to the integration of a knowledge representation and reasoning methods to user interfaces for high level querying. To illustrate the utility of SemCityMap in a disaster scenario, we use an urban environment—central Stockholm—in combination with a flood simulation. We show that the system provides useful answers to high-level queries also with respect to the current flood status. Examples of such queries concern path planning for vehicles or retrieval of safe regions such as “find all regions close to schools and far from the flooded area”. The particular advantage of our approach lies in the fact that ontological information and reasoning is explicitly integrated so that queries can be formulated in a natural way using concepts on appropriate level of abstraction, including additional constraints.

  18. Applying of an Ontology based Modeling Approach to Cultural Heritage Systems

    Directory of Open Access Journals (Sweden)

    POPOVICI, D.-M.

    2011-08-01

    Full Text Available Any virtual environment (VE built in a classical way is dedicated to a very specific domain. Its modification or even adaptation to another domain requires an expensive human intervention measured in time and money. This way, the product, that means the VE, returns at the first phases of the development process. In a previous work we proposed an approach that combines domain ontologies and conceptual modeling to construct more accurate VEs. Our method is based on the description of the domain knowledge in a standard format and the assisted creation (using these pieces of knowledge of the VE. This permits the explanation within the virtual reality (VR simulation of the semantic of the whole context and of each object. This knowledge may be then transferred to the public users. In this paper we prove the effectiveness of our method on the construction process of an VE that simulates the organization of a Greek-Roman colony situated on the Black Sea coast and the economic and social activities of its people.

  19. 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.

  20. Semantic similarity measurement between gene ontology terms based on exclusively inherited shared information.

    Science.gov (United States)

    Zhang, Shu-Bo; Lai, Jian-Huang

    2015-03-01

    Quantifying the semantic similarities between pairs of terms in the Gene Ontology (GO) structure can help to explore the functional relationships between biological entities. A common approach to this problem is to measure the information they have in common based on the information content of their common ancestors. However, many studies have their limitations in measuring the information two GO terms share. This study presented a new measurement, exclusively inherited shared information (EISI) that captured the information shared by two terms based on an intuitive observation on the multiple inheritance relationships among the terms in the GO graph. EISI was derived from the information content of the exclusively inherited common ancestors (EICAs), which were screened from the common ancestors according to the attribute of their direct children. The effectiveness of EISI was evaluated against some state-of-the-art measurements on both artificial and real datasets, it produced more relevant results with experts' scores on the artificial dataset, and supported the prior knowledge of gene function in pathways on the Saccharomyces genome database (SGD). The promising features of EISI are the following: (1) it provides a more effective way to characterize the semantic relationship between two GO terms by taking into account multiple common ancestors related, and (2) can quickly detect all EICAs with time complexity of O(n), which is much more efficient than other methods based on disjunctive common ancestors. It is a promising alternative to multiple inheritance based methods for practical applications on large-scale dataset. The algorithm EISI was implemented in Matlab and is freely available from http://treaton.evai.pl/EISI/. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Developing and Utilizing Ontology of Golf Based on the Open Travel Alliance Golf Messages

    Science.gov (United States)

    Cieślik, Agnieszka; Ganzha, Maria; Paprzycki, Marcin

    While the vision of the Semantic Web is an extremely appealing one, its success depends not only on development of new ontologies that represent various aspects of the world. Pragmatic view suggests that such activities have to go hand-in-hand with facilitating support for existing domain-specific real-world standards. One of such interesting standards that is systematically gaining popularity in the travel industry, is the Open Travel Alliance (OTA) messaging. Specifically, the OTA standardizes the way that businesses in the travel industry can communicate with each other. The aim of this chapter is to outline our efforts leading toward (re)engineering an ontology of golf (understood as a leisurely activity) anchored in the OTA golf messaging specification. Furthermore we discuss how such ontology could be used in a Travel Support System. Here, in addition to general scenarios, details concerning implementation of needed translators are presented.

  2. OntoStudyEdit: a new approach for ontology-based representation and management of metadata in clinical and epidemiological research.

    Science.gov (United States)

    Uciteli, Alexandr; Herre, Heinrich

    2015-01-01

    The specification of metadata in clinical and epidemiological study projects absorbs significant expense. The validity and quality of the collected data depend heavily on the precise and semantical correct representation of their metadata. In various research organizations, which are planning and coordinating studies, the required metadata are specified differently, depending on many conditions, e.g., on the used study management software. The latter does not always meet the needs of a particular research organization, e.g., with respect to the relevant metadata attributes and structuring possibilities. The objective of the research, set forth in this paper, is the development of a new approach for ontology-based representation and management of metadata. The basic features of this approach are demonstrated by the software tool OntoStudyEdit (OSE). The OSE is designed and developed according to the three ontology method. This method for developing software is based on the interactions of three different kinds of ontologies: a task ontology, a domain ontology and a top-level ontology. The OSE can be easily adapted to different requirements, and it supports an ontologically founded representation and efficient management of metadata. The metadata specifications can by imported from various sources; they can be edited with the OSE, and they can be exported in/to several formats, which are used, e.g., by different study management software. Advantages of this approach are the adaptability of the OSE by integrating suitable domain ontologies, the ontological specification of mappings between the import/export formats and the DO, the specification of the study metadata in a uniform manner and its reuse in different research projects, and an intuitive data entry for non-expert users.

  3. Reputation-based ontology alignment for autonomy and interoperability in distributed access control

    NARCIS (Netherlands)

    Trivellato, Daniel; Spiessens, Fred; Zannone, Nicola; Etalle, Sandro

    2009-01-01

    Vocabulary alignment is a main challenge in distributedaccess control as peers should understand each other’spolicies unambiguously. Ontologies enable mutual understanding among peers by providing a precise semantics to concepts and relationships in a domain. However, due to the distributed nature

  4. Extraction of Graph Information Based on Image Contents and the Use of Ontology

    Science.gov (United States)

    Kanjanawattana, Sarunya; Kimura, Masaomi

    2016-01-01

    A graph is an effective form of data representation used to summarize complex information. Explicit information such as the relationship between the X- and Y-axes can be easily extracted from a graph by applying human intelligence. However, implicit knowledge such as information obtained from other related concepts in an ontology also resides in…

  5. Multi-source and ontology-based retrieval engine for maize mutant phenotypes.

    Science.gov (United States)

    Green, Jason M; Harnsomburana, Jaturon; Schaeffer, Mary L; Lawrence, Carolyn J; Shyu, Chi-Ren

    2011-01-01

    Model Organism Databases, including the various plant genome databases, collect and enable access to massive amounts of heterogeneous information, including sequence data, gene product information, images of mutant phenotypes, etc, as well as textual descriptions of many of these entities. While a variety of basic browsing and search capabilities are available to allow researchers to query and peruse the names and attributes of phenotypic data, next-generation search mechanisms that allow querying and ranking of text descriptions are much less common. In addition, the plant community needs an innovative way to leverage the existing links in these databases to search groups of text descriptions simultaneously. Furthermore, though much time and effort have been afforded to the development of plant-related ontologies, the knowledge embedded in these ontologies remains largely unused in available plant search mechanisms. Addressing these issues, we have developed a unique search engine for mutant phenotypes from MaizeGDB. This advanced search mechanism integrates various text description sources in MaizeGDB to aid a user in retrieving desired mutant phenotype information. Currently, descriptions of mutant phenotypes, loci and gene products are utilized collectively for each search, though expansion of the search mechanism to include other sources is straightforward. The retrieval engine, to our knowledge, is the first engine to exploit the content and structure of available domain ontologies, currently the Plant and Gene Ontologies, to expand and enrich retrieval results in major plant genomic databases. Database URL: http:www.PhenomicsWorld.org/QBTA.php.

  6. Evaluating the significance of protein functional similarity based on gene ontology.

    Science.gov (United States)

    Konopka, Bogumil M; Golda, Tomasz; Kotulska, Malgorzata

    2014-11-01

    Gene ontology is among the most successful ontologies in the biomedical domain. It is used to describe, unambiguously, protein molecular functions, cellular localizations, and processes in which proteins participate. The hierarchical structure of gene ontology allows quantifying protein functional similarity by application of algorithms that calculate semantic similarities. The scores, however, are meaningless without a given context. Here, we propose how to evaluate the significance of protein function semantic similarity scores by comparing them to reference distributions calculated for randomly chosen proteins. In the study, thresholds for significant functional semantic similarity, in four representative annotation corpuses, were estimated. We also show that the score significance is influenced by the number and specificity of gene ontology terms that are annotated to compared proteins. While proteins with a greater number of terms tend to yield higher similarity scores, proteins with more specific terms produce lower scores. The estimated significance thresholds were validated using protein sequence-function and structure-function relationships. Taking into account the term number and term specificity improves the distinction between significant and insignificant semantic similarity comparisons.

  7. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes

    Directory of Open Access Journals (Sweden)

    Saber Jelokhani-Niaraki

    2015-03-01

    Full Text Available During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.

  8. Ontology-based concept map learning path reasoning system using SWRL rules

    Energy Technology Data Exchange (ETDEWEB)

    Chu, K.-K.; Lee, C.-I. [National Univ. of Tainan, Taiwan (China). Dept. of Computer Science and Information Learning Technology

    2010-08-13

    Concept maps are graphical representations of knowledge. Concept mapping may reduce students' cognitive load and extend simple memory function. The purpose of this study was on the diagnosis of students' concept map learning abilities and the provision of personally constructive advice dependant on their learning path and progress. Ontology is a useful method with which to represent and store concept map information. Semantic web rule language (SWRL) rules are easy to understand and to use as specific reasoning services. This paper discussed the selection of grade 7 lakes and rivers curriculum for which to devise a concept map learning path reasoning service. The paper defined a concept map e-learning ontology and two SWRL semantic rules, and collected users' concept map learning path data to infer implicit knowledge and to recommend the next learning path for users. It was concluded that the designs devised in this study were feasible and advanced and the ontology kept the domain knowledge preserved. SWRL rules identified an abstraction model for inferred properties. Since they were separate systems, they did not interfere with each other, while ontology or SWRL rules were maintained, ensuring persistent system extensibility and robustness. 15 refs., 1 tab., 8 figs.

  9. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes.

    Science.gov (United States)

    Jelokhani-Niaraki, Saber; Tahmoorespur, Mojtaba; Minuchehr, Zarrin; Nassiri, Mohammad Reza

    2015-03-01

    During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.

  10. An Ontology-Based GIS for Genomic Data Management of Rumen Microbes

    Science.gov (United States)

    Jelokhani-Niaraki, Saber; Minuchehr, Zarrin; Nassiri, Mohammad Reza

    2015-01-01

    During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data. PMID:25873847

  11. Towards Cache-Enabled, Order-Aware, Ontology-Based Stream Reasoning Framework

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Rui; Praggastis, Brenda L.; Smith, William P.; McGuinness, Deborah L.

    2016-08-16

    While streaming data have become increasingly more popular in business and research communities, semantic models and processing software for streaming data have not kept pace. Traditional semantic solutions have not addressed transient data streams. Semantic web languages (e.g., RDF, OWL) have typically addressed static data settings and linked data approaches have predominantly addressed static or growing data repositories. Streaming data settings have some fundamental differences; in particular, data are consumed on the fly and data may expire. Stream reasoning, a combination of stream processing and semantic reasoning, has emerged with the vision of providing "smart" processing of streaming data. C-SPARQL is a prominent stream reasoning system that handles semantic (RDF) data streams. Many stream reasoning systems including C-SPARQL use a sliding window and use data arrival time to evict data. For data streams that include expiration times, a simple arrival time scheme is inadequate if the window size does not match the expiration period. In this paper, we propose a cache-enabled, order-aware, ontology-based stream reasoning framework. This framework consumes RDF streams with expiration timestamps assigned by the streaming source. Our framework utilizes both arrival and expiration timestamps in its cache eviction policies. In addition, we introduce the notion of "semantic importance" which aims to address the relevance of data to the expected reasoning, thus enabling the eviction algorithms to be more context- and reasoning-aware when choosing what data to maintain for question answering. We evaluate this framework by implementing three different prototypes and utilizing five metrics. The trade-offs of deploying the proposed framework are also discussed.

  12. 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.

  13. 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.

  14. 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.

  15. Sample evaluation of ontology-matching systems

    NARCIS (Netherlands)

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

    2007-01-01

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

  16. 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.

  17. 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.

  18. SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data

    Science.gov (United States)

    Pang, Chao; Sollie, Annet; Sijtsma, Anna; Hendriksen, Dennis; Charbon, Bart; de Haan, Mark; de Boer, Tommy; Kelpin, Fleur; Jetten, Jonathan; van der Velde, Joeri K.; Smidt, Nynke; Sijmons, Rolf; Hillege, Hans; Swertz, Morris A.

    2015-01-01

    There is an urgent need to standardize the semantics of biomedical data values, such as phenotypes, to enable comparative and integrative analyses. However, it is unlikely that all studies will use the same data collection protocols. As a result, retrospective standardization is often required, which involves matching of original (unstructured or locally coded) data to widely used coding or ontology systems such as SNOMED CT (clinical terms), ICD-10 (International Classification of Disease) and HPO (Human Phenotype Ontology). This data curation process is usually a time-consuming process performed by a human expert. To help mechanize this process, we have developed SORTA, a computer-aided system for rapidly encoding free text or locally coded values to a formal coding system or ontology. SORTA matches original data values (uploaded in semicolon delimited format) to a target coding system (uploaded in Excel spreadsheet, OWL ontology web language or OBO open biomedical ontologies format). It then semi- automatically shortlists candidate codes for each data value using Lucene and n-gram based matching algorithms, and can also learn from matches chosen by human experts. We evaluated SORTA’s applicability in two use cases. For the LifeLines biobank, we used SORTA to recode 90 000 free text values (including 5211 unique values) about physical exercise to MET (Metabolic Equivalent of Task) codes. For the CINEAS clinical symptom coding system, we used SORTA to map to HPO, enriching HPO when necessary (315 terms matched so far). Out of the shortlists at rank 1, we found a precision/recall of 0.97/0.98 in LifeLines and of 0.58/0.45 in CINEAS. More importantly, users found the tool both a major time saver and a quality improvement because SORTA reduced the chances of human mistakes. Thus, SORTA can dramatically ease data (re)coding tasks and we believe it will prove useful for many more projects. Database URL: http://molgenis.org/sorta or as an open source download from

  19. DOSim: An R package for similarity between diseases based on Disease Ontology

    Science.gov (United States)

    2011-01-01

    Background The construction of the Disease Ontology (DO) has helped promote the investigation of diseases and disease risk factors. DO enables researchers to analyse disease similarity by adopting semantic similarity measures, and has expanded our understanding of the relationships between different diseases and to classify them. Simultaneously, similarities between genes can also be analysed by their associations with similar diseases. As a result, disease heterogeneity is better understood and insights into the molecular pathogenesis of similar diseases have been gained. However, bioinformatics tools that provide easy and straight forward ways to use DO to study disease and gene similarity simultaneously are required. Results We have developed an R-based software package (DOSim) to compute the similarity between diseases and to measure the similarity between human genes in terms of diseases. DOSim incorporates a DO-based enrichment analysis function that can be used to explore the disease feature of an independent gene set. A multilayered enrichment analysis (GO and KEGG annotation) annotation function that helps users explore the biological meaning implied in a newly detected gene module is also part of the DOSim package. We used the disease similarity application to demonstrate the relationship between 128 different DO cancer terms. The hierarchical clustering of these 128 different cancers showed modular characteristics. In another case study, we used the gene similarity application on 361 obesity-related genes. The results revealed the complex pathogenesis of obesity. In addition, the gene module detection and gene module multilayered annotation functions in DOSim when applied on these 361 obesity-related genes helped extend our understanding of the complex pathogenesis of obesity risk phenotypes and the heterogeneity of obesity-related diseases. Conclusions DOSim can be used to detect disease-driven gene modules, and to annotate the modules for functions and

  20. NeuroLOG: sharing neuroimaging data using an ontology-based federated approach.

    Science.gov (United States)

    Gibaud, Bernard; Kassel, Gilles; Dojat, Michel; Batrancourt, Bénédicte; Michel, Franck; Gaignard, Alban; Montagnat, Johan

    2011-01-01

    This paper describes the design of the NeuroLOG middleware data management layer, which provides a platform to share heterogeneous and distributed neuroimaging data using a federated approach. The semantics of shared information is captured through a multi-layer application ontology and a derived Federated Schema used to align the heterogeneous database schemata from different legacy repositories. The system also provides a facility to translate the relational data into a semantic representation that can be queried using a semantic search engine thus enabling the exploitation of knowledge embedded in the ontology. This work shows the relevance of the distributed approach for neurosciences data management. Although more complex than a centralized approach, it is also more realistic when considering the federation of large data sets, and open strong perspectives to implement multi-centric neurosciences studies.

  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. Towards an Ontology for the Global Geodynamics Project: Automated Extraction of Resource Descriptions from an XML-Based Data Model

    Science.gov (United States)

    Lumb, L. I.; Aldridge, K. D.

    2005-12-01

    Using the Earth Science Markup Language (ESML), an XML-based data model for the Global Geodynamics Project (GGP) was recently introduced [Lumb & Aldridge, Proc. HPCS 2005, Kotsireas & Stacey, eds., IEEE, 2005, 216-222]. This data model possesses several key attributes -i.e., it: makes use of XML schema; supports semi-structured ASCII format files; includes Earth Science affinities; and is on track for compliance with emerging Grid computing standards (e.g., the Global Grid Forum's Data Format Description Language, DFDL). Favorable attributes notwithstanding, metadata (i.e., data about data) was identified [Lumb & Aldridge, 2005] as a key challenge for progress in enabling the GGP for Grid computing. Even in projects of small-to-medium scale like the GGP, the manual introduction of metadata has the potential to be the rate-determining metric for progress. Fortunately, an automated approach for metadata introduction has recently emerged. Based on Gleaning Resource Descriptions from Dialects of Languages (GRDDL, http://www.w3.org/2004/01/rdxh/spec), this bottom-up approach allows for the extraction of Resource Description Format (RDF) representations from the XML-based data model (i.e., the ESML representation of GGP data) subject to rules of transformation articulated via eXtensible Stylesheet Language Transformations (XSLT). In addition to introducing relationships into the GGP data model, and thereby addressing the metadata requirement, the syntax and semantics of RDF comprise a requisite for a GGP ontology - i.e., ``the common words and concepts (the meaning) used to describe and represent an area of knowledge'' [Daconta et al., The Semantic Web, Wiley, 2003]. After briefly reviewing the XML-based model for the GGP, attention focuses on the automated extraction of an RDF representation via GRDDL with XSLT-delineated templates. This bottom-up approach, in tandem with a top-down approach based on the Protege integrated development environment for ontologies (http

  3. Ontological Surprises

    DEFF Research Database (Denmark)

    Leahu, Lucian

    2016-01-01

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

  4. 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.

  5. Large-scale computer networks and the future of legal knowledge-based systems

    NARCIS (Netherlands)

    Leenes, R.E.; Svensson, Jorgen S.; Hage, J.C.; Bench-Capon, T.J.M.; Cohen, M.J.; van den Herik, H.J.

    1995-01-01

    In this paper we investigate the relation between legal knowledge-based systems and large-scale computer networks such as the Internet. On the one hand, researchers of legal knowledge-based systems have claimed huge possibilities, but despite the efforts over the last twenty years, the number of

  6. Ontology-based Medical Decision Support System to Enhance Chronic Patients' Lifestyle within E-care Telemonitoring Platform.

    Science.gov (United States)

    Benmimoune, Lamine; Hajjam, Amir; Ghodous, Parisa; Andres, Emmanuel; Talha, Samy; Hajjam, Mohamed

    2015-01-01

    The aim of this paper is to describe an original approach which consists of designing ontology based Medical Decision Support System (MDSS) to enhance the patients' lifestyle. This system is composed of two main parts: data collector which collects relevant lifestyle-related patent data by prompting the only significant questions in connection with the patient's medical background, and advices provider which provides personalized lifestyle advices to the patients regarding their lifestyle changes. The proposed MDSS is integrated within E-care home health monitoring platform in order to: (i) improve the patient's healthy lifestyle; (ii) educate the patients towards their disease; (iii) increase the early detection of risky situation.

  7. Innovative Bayesian and Parsimony Phylogeny of Dung Beetles (Coleoptera, Scarabaeidae, Scarabaeinae) Enhanced by Ontology-Based Partitioning of Morphological Characters

    Science.gov (United States)

    Tarasov, Sergei; Génier, François

    2015-01-01

    Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characters located on different body regions evolve at different rates and that partitioning of the data matrix using anatomy ontology is reasonable; however, trees from the parsimony and all the Bayesian analyses were quite consistent. The hypothesized phylogeny reveals many novel clades and provides additional support for some clades recovered in previous analyses. Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described. Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a

  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. Framing a Knowledge Base for a Legal Expert System Dealing with Indeterminate Concepts

    Directory of Open Access Journals (Sweden)

    Michał Araszkiewicz

    2015-01-01

    Full Text Available Despite decades of development of formal tools for modelling legal knowledge and reasoning, the creation of a fully fledged legal decision support system remains challenging. Among those challenges, such system requires an enormous amount of commonsense knowledge to derive legal expertise. This paper describes the development of a negotiation decision support system (the Parenting Plan Support System or PPSS to support parents in drafting an agreement (the parenting plan for the exercise of parental custody of minor children after a divorce is granted. The main objective here is to discuss problems of framing an intuitively appealing and computationally efficient knowledge base that can adequately represent the indeterminate legal concept of the well-being of the child in the context of continental legal culture and of Polish law in particular. In addition to commonsense reasoning, interpretation of such a concept demands both legal expertise and significant professional knowledge from other domains.

  10. Building a drug ontology based on RxNorm and other sources.

    Science.gov (United States)

    Hanna, Josh; Joseph, Eric; Brochhausen, Mathias; Hogan, William R

    2013-12-18

    We built the Drug Ontology (DrOn) because we required correct and consistent drug information in a format for use in semantic web applications, and no existing resource met this requirement or could be altered to meet it. One of the obstacles we faced when creating DrOn was the difficulty in reusing drug information from existing sources. The primary external source we have used at this stage in DrOn's development is RxNorm, a standard drug terminology curated by the National Library of Medicine (NLM). To build DrOn, we (1) mined data from historical releases of RxNorm and (2) mapped many RxNorm entities to Chemical Entities of Biological Interest (ChEBI) classes, pulling relevant information from ChEBI while doing so. We built DrOn in a modular fashion to facilitate simpler extension and development of the ontology and to allow reasoning and construction to scale. Classes derived from each source are serialized in separate modules. For example, the classes in DrOn that are programmatically derived from RxNorm are stored in a separate module and subsumed by classes in a manually-curated, realist, upper-level module of DrOn with terms such as 'clinical drug role', 'tablet', 'capsule', etc. DrOn is a modular, extensible ontology of drug products, their ingredients, and their biological activity that avoids many of the fundamental flaws found in other, similar artifacts and meets the requirements of our comparative-effectiveness research use-case.

  11. Building a drug ontology based on RxNorm and other sources

    OpenAIRE

    Hanna, Josh; Joseph, Eric; Brochhausen, Mathias; Hogan, William R

    2013-01-01

    Background We built the Drug Ontology (DrOn) because we required correct and consistent drug information in a format for use in semantic web applications, and no existing resource met this requirement or could be altered to meet it. One of the obstacles we faced when creating DrOn was the difficulty in reusing drug information from existing sources. The primary external source we have used at this stage in DrOn’s development is RxNorm, a standard drug terminology curated by the National Libra...

  12. Ontology-Based Quality Attributes Prediction in Component-Based Development

    OpenAIRE

    Chengpu Li; Rob Pooley; Xiaodong Liu

    2010-01-01

    Despite the success that Component-Based Development (CBD) has achieved so far, componentmismatch remains as a big obstacle for wider and smoother component reuse. Mismatch refers that theselected component does not satisfy the functional requirements, or that it fails the user’s expectation interms of the Quality Attributes (QAs) of the component-based system. This allows us the potential topredict the quality attributes of a software system by analysing the result of component retrieval. In...

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

    Directory of Open Access Journals (Sweden)

    Akram Fathian Dastgerdi

    2012-03-01

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

  14. Legal Office Procedures: Task Analyses. Competency-Based Education. Review Draft.

    Science.gov (United States)

    Virginia Polytechnic Inst. and State Univ., Blacksburg.

    This task analysis guide is intended to help teachers and administrators develop instructional materials and implement competency-based education in a course on legal office procedures. Section 1 contains a validated task inventory for legal office procedures. For each task, applicable information pertaining to performance and enabling objectives,…

  15. An ontology-based search engine for protein-protein interactions.

    Science.gov (United States)

    Park, Byungkyu; Han, Kyungsook

    2010-01-18

    Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology.

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

    Directory of Open Access Journals (Sweden)

    Alexander Willner

    2015-12-01

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

  17. Handling Real-World Context Awareness, Uncertainty and Vagueness in Real-Time Human Activity Tracking and Recognition with a Fuzzy Ontology-Based Hybrid Method

    Science.gov (United States)

    Díaz-Rodríguez, Natalia; Cadahía, Olmo León; Cuéllar, Manuel Pegalajar; Lilius, Johan; Calvo-Flores, Miguel Delgado

    2014-01-01

    Human activity recognition is a key task in ambient intelligence applications to achieve proper ambient assisted living. There has been remarkable progress in this domain, but some challenges still remain to obtain robust methods. Our goal in this work is to provide a system that allows the modeling and recognition of a set of complex activities in real life scenarios involving interaction with the environment. The proposed framework is a hybrid model that comprises two main modules: a low level sub-activity recognizer, based on data-driven methods, and a high-level activity recognizer, implemented with a fuzzy ontology to include the semantic interpretation of actions performed by users. The fuzzy ontology is fed by the sub-activities recognized by the low level data-driven component and provides fuzzy ontological reasoning to recognize both the activities and their influence in the environment with semantics. An additional benefit of the approach is the ability to handle vagueness and uncertainty in the knowledge-based module, which substantially outperforms the treatment of incomplete and/or imprecise data with respect to classic crisp ontologies. We validate these advantages with the public CAD-120 dataset (Cornell Activity Dataset), achieving an accuracy of 90.1% and 91.07% for low-level and high-level activities, respectively. This entails an improvement over fully data-driven or ontology-based approaches. PMID:25268914

  18. Handling Real-World Context Awareness, Uncertainty and Vagueness in Real-Time Human Activity Tracking and Recognition with a Fuzzy Ontology-Based Hybrid Method

    Directory of Open Access Journals (Sweden)

    Natalia Díaz-Rodríguez

    2014-09-01

    Full Text Available Human activity recognition is a key task in ambient intelligence applications to achieve proper ambient assisted living. There has been remarkable progress in this domain, but some challenges still remain to obtain robust methods. Our goal in this work is to provide a system that allows the modeling and recognition of a set of complex activities in real life scenarios involving interaction with the environment. The proposed framework is a hybrid model that comprises two main modules: a low level sub-activity recognizer, based on data-driven methods, and a high-level activity recognizer, implemented with a fuzzy ontology to include the semantic interpretation of actions performed by users. The fuzzy ontology is fed by the sub-activities recognized by the low level data-driven component and provides fuzzy ontological reasoning to recognize both the activities and their influence in the environment with semantics. An additional benefit of the approach is the ability to handle vagueness and uncertainty in the knowledge-based module, which substantially outperforms the treatment of incomplete and/or imprecise data with respect to classic crisp ontologies. We validate these advantages with the public CAD-120 dataset (Cornell Activity Dataset, achieving an accuracy of 90.1% and 91.07% for low-level and high-level activities, respectively. This entails an improvement over fully data-driven or ontology-based approaches.

  19. Ontological View-Driven Semantic Integration in Collaborative Networks

    Science.gov (United States)

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

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

  20. Ontologies as integrative tools for plant science.

    Science.gov (United States)

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

    2012-08-01

    Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education. Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.

  1. 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.

  2. Grid workflow validation using ontology-based tacit knowledge: A case study for quantitative remote sensing applications

    Science.gov (United States)

    Liu, Jia; Liu, Longli; Xue, Yong; Dong, Jing; Hu, Yingcui; Hill, Richard; Guang, Jie; Li, Chi

    2017-01-01

    Workflow for remote sensing quantitative retrieval is the ;bridge; between Grid services and Grid-enabled application of remote sensing quantitative retrieval. Workflow averts low-level implementation details of the Grid and hence enables users to focus on higher levels of application. The workflow for remote sensing quantitative retrieval plays an important role in remote sensing Grid and Cloud computing services, which can support the modelling, construction and implementation of large-scale complicated applications of remote sensing science. The validation of workflow is important in order to support the large-scale sophisticated scientific computation processes with enhanced performance and to minimize potential waste of time and resources. To research the semantic correctness of user-defined workflows, in this paper, we propose a workflow validation method based on tacit knowledge research in the remote sensing domain. We first discuss the remote sensing model and metadata. Through detailed analysis, we then discuss the method of extracting the domain tacit knowledge and expressing the knowledge with ontology. Additionally, we construct the domain ontology with Protégé. Through our experimental study, we verify the validity of this method in two ways, namely data source consistency error validation and parameters matching error validation.

  3. Sentiment analysis of Chinese microblogging based on sentiment ontology: a case study of `7.23 Wenzhou Train Collision'

    Science.gov (United States)

    Shi, Wei; Wang, Hongwei; He, Shaoyi

    2013-12-01

    Sentiment analysis of microblogging texts can facilitate both organisations' public opinion monitoring and governments' response strategies development. Nevertheless, most of the existing analysis methods are conducted on Twitter, lacking of sentiment analysis of Chinese microblogging (Weibo), and they generally rely on a large number of manually annotated training or machine learning to perform sentiment classification, yielding with difficulties in application. This paper addresses these problems and employs a sentiment ontology model to examine sentiment analysis of Chinese microblogging. We conduct a sentiment analysis of all public microblogging posts about '7.23 Wenzhou Train Collision' broadcasted by Sina microblogging users between 23 July and 1 August 2011. For every day in this time period, we first extract eight dimensions of sentiment (expect, joy, love, surprise, anxiety, sorrow, angry, and hate), and then build fuzzy sentiment ontology based on HowNet and semantic similarity for sentiment analysis; we also establish computing methods of influence and sentiment of microblogging texts; and we finally explore the change of public sentiment after '7.23 Wenzhou Train Collision'. The results show that the established sentiment analysis method has excellent application, and the change of different emotional values can reflect the success or failure of guiding the public opinion by the government.

  4. CD-KES: An Ontology Based Knowledge Education System for Patients with Chronic Diseases and Its Constructing Approach.

    Science.gov (United States)

    Wu, Chengkai; Gou, Ling; Wang, Yu; Shang, Yong; Tian, Yu; Li, Jing-Song

    2017-01-01

    Patients' participation plays a crucial role in the management of chronic diseases. Educating patients about their diseases allows patients to self-regulate their daily health conditions more reasonably and effectively. This study focuses on an informative way to develop daily education and guidance among patients. We provide a systematic approach to establish, process, and present the knowledge map of chronic diseases. An ontology technique is used to model clinical knowledge and rules. Rule-based inference service is constructed based on the RETE reasoning algorithm. Several considerations in semantic visualization and interaction are listed as recommendations. A prototype of Chronic Disease Knowledge Education System (CD-KES) based on this approach has been built for diabetes mellitus. With the prototype, comparative evaluations for system performances in knowledge querying and browsing are taken. The results shows the system can help patients to more easily understand medical knowledge and avoid potential negative consequences.

  5. Legal and methodological bases of comprehensive forensic enquiry of pornography

    Directory of Open Access Journals (Sweden)

    Berdnikov D.V.

    2016-03-01

    Full Text Available The article gives an analysis of the legal definition of pornography. The author identified descriptive and target criteria groups which are required for the analysis and analyses the content of descriptive criteria of pornography and the way how they should be documented. Fixing attention to the anatomical and physiological characteristics of the sexual relations is determine as necessary target criterion. It is noted that the term "pornography" is a legal and cannot be subject of expertise. That is why author underlined some methodological basis of complex psycho-linguistic and psycho-art expertise. The article presents general issue depends on expert conclusion and studies cases where the research is necessary to involve doctors, as well as criteria for expert's opinion. Besides that, author defined subject, object and main tasks of psychological studies of pornographic information.

  6. Culto: AN Ontology-Based Annotation Tool for Data Curation in Cultural Heritage

    Science.gov (United States)

    Garozzo, R.; Murabito, F.; Santagati, C.; Pino, C.; Spampinato, C.

    2017-08-01

    This paper proposes CulTO, a software tool relying on a computational ontology for Cultural Heritage domain modelling, with a specific focus on religious historical buildings, for supporting cultural heritage experts in their investigations. It is specifically thought to support annotation, automatic indexing, classification and curation of photographic data and text documents of historical buildings. CULTO also serves as a useful tool for Historical Building Information Modeling (H-BIM) by enabling semantic 3D data modeling and further enrichment with non-geometrical information of historical buildings through the inclusion of new concepts about historical documents, images, decay or deformation evidence as well as decorative elements into BIM platforms. CulTO is the result of a joint research effort between the Laboratory of Surveying and Architectural Photogrammetry "Luigi Andreozzi" and the PeRCeiVe Lab (Pattern Recognition and Computer Vision Lab) of the University of Catania,

  7. Research on Ontology Modeling of Steel Manufacturing Process Based on Big Data Analysis

    Directory of Open Access Journals (Sweden)

    Bao Qing

    2016-01-01

    Full Text Available As an important method that steel industries ride the Indutrie 4.0 wave, knowledge management is expected to be versatile, effective and intelligent. Mechanism modeling difficulties, numerous influencing factors and complex industrial chains hinder the development of knowledge and information integration. Using data potentials, big data analysis can be an effective way to deal with knowledge acquisition as it solves the inaccuracy and imperfection mechanism modeling may lead to. This paper proposes a big data knowledge management system(BDAKMS adhering to data driven, intelligent analysis, service publication, dynamic update principle which can effectively extracts knowledge from mass data. Then, ontology modeling gives the knowledge unified descriptions as well as inference details combined with semantic web techniques.

  8. Simple Ontology of Manipulation Actions based on Hand-Object Relations

    DEFF Research Database (Denmark)

    Wörgötter, Florentin; Aksoy, E. E.; Krüger, Norbert

    2013-01-01

    and time. For this we use as temporal anchor points those moments where two objects (or hand and object) touch or un-touch each other during a manipulation. We show that by this one can define a relatively small tree-like manipulation ontology. We find less than 30 fundamental manipulations. The temporal......Humans can perform a multitude of different actions with their hands (manipulations). In spite of this, so far there have been only a few attempts to represent manipulation types trying to understand the underlying principles. Here we first discuss how manipulation actions are structured in space...... anchors also provide us with information about when to pay attention to additional important information, for example when to consider trajectory shapes and relative poses between objects. As a consequence a highly condensed representation emerges by which different manipulations can be recognized...

  9. A hybrid fuzzy-ontology based intelligent system to determine level of severity and treatment recommendation for Benign Prostatic Hyperplasia.

    Science.gov (United States)

    Torshizi, Abolfazl Doostparast; Zarandi, Mohammad Hossein Fazel; Torshizi, Ghazaleh Doostparast; Eghbali, Kamyar

    2014-01-01

    This paper deals with application of fuzzy intelligent systems in diagnosing severity level and recommending appropriate therapies for patients having Benign Prostatic Hyperplasia. Such an intelligent system can have remarkable impacts on correct diagnosis of the disease and reducing risk of mortality. This system captures various factors from the patients using two modules. The first module determines severity level of the Benign Prostatic Hyperplasia and the second module, which is a decision making unit, obtains output of the first module accompanied by some external knowledge and makes an appropriate treatment decision based on its ontology model and a fuzzy type-1 system. In order to validate efficiency and accuracy of the developed system, a case study is conducted by 44 participants. Then the results are compared with the recommendations of a panel of experts on the experimental data. Then precision and accuracy of the results were investigated based on a statistical analysis. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  10. Gene-ontology enrichment analysis in two independent family-based samples highlights biologically plausible processes for autism spectrum disorders.

    LENUS (Irish Health Repository)

    Anney, Richard J L

    2012-02-01

    Recent genome-wide association studies (GWAS) have implicated a range of genes from discrete biological pathways in the aetiology of autism. However, despite the strong influence of genetic factors, association studies have yet to identify statistically robust, replicated major effect genes or SNPs. We apply the principle of the SNP ratio test methodology described by O\\'Dushlaine et al to over 2100 families from the Autism Genome Project (AGP). Using a two-stage design we examine association enrichment in 5955 unique gene-ontology classifications across four groupings based on two phenotypic and two ancestral classifications. Based on estimates from simulation we identify excess of association enrichment across all analyses. We observe enrichment in association for sets of genes involved in diverse biological processes, including pyruvate metabolism, transcription factor activation, cell-signalling and cell-cycle regulation. Both genes and processes that show enrichment have previously been examined in autistic disorders and offer biologically plausibility to these findings.

  11. 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

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

    Science.gov (United States)

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

    2009-04-01

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

  13. A New Browser-based, Ontology-driven Tool for Generating Standardized, Deep Descriptions of Geoscience Models

    Science.gov (United States)

    Peckham, S. D.; Kelbert, A.; Rudan, S.; Stoica, M.

    2016-12-01

    Standardized metadata for models is the key to reliable and greatly simplified coupling in model coupling frameworks like CSDMS (Community Surface Dynamics Modeling System). This model metadata also helps model users to understand the important details that underpin computational models and to compare the capabilities of different models. These details include simplifying assumptions on the physics, governing equations and the numerical methods used to solve them, discretization of space (the grid) and time (the time-stepping scheme), state variables (input or output), model configuration parameters. This kind of metadata provides a "deep description" of a computational model that goes well beyond other types of metadata (e.g. author, purpose, scientific domain, programming language, digital rights, provenance, execution) and captures the science that underpins a model. While having this kind of standardized metadata for each model in a repository opens up a wide range of exciting possibilities, it is difficult to collect this information and a carefully conceived "data model" or schema is needed to store it. Automated harvesting and scraping methods can provide some useful information, but they often result in metadata that is inaccurate or incomplete, and this is not sufficient to enable the desired capabilities. In order to address this problem, we have developed a browser-based tool called the MCM Tool (Model Component Metadata) which runs on notebooks, tablets and smart phones. This tool was partially inspired by the TurboTax software, which greatly simplifies the necessary task of preparing tax documents. It allows a model developer or advanced user to provide a standardized, deep description of a computational geoscience model, including hydrologic models. Under the hood, the tool uses a new ontology for models built on the CSDMS Standard Names, expressed as a collection of RDF files (Resource Description Framework). This ontology is based on core concepts

  14. Desain Sistem Semantic Data Warehouse dengan Metode Ontology dan Rule Based untuk Mengolah Data Akademik Universitas XYZ di Bali

    Directory of Open Access Journals (Sweden)

    Made Pradnyana Ambara

    2016-06-01

    Full Text Available Data warehouse pada umumnya yang sering dikenal data warehouse tradisional mempunyai beberapa kelemahan yang mengakibatkan kualitas data yang dihasilkan tidak spesifik dan efektif. Sistem semantic data warehouse merupakan solusi untuk menangani permasalahan pada data warehouse tradisional dengan kelebihan antara lain: manajeman kualitas data yang spesifik dengan format data seragam untuk mendukung laporan OLAP yang baik, dan performance pencarian informasi yang lebih efektif dengan kata kunci bahasa alami. Pemodelan sistem semantic data warehouse menggunakan metode ontology menghasilkan model resource description framework schema (RDFS logic yang akan ditransformasikan menjadi snowflake schema. Laporan akademik yang dibutuhkan dihasilkan melalui metode nine step Kimball dan pencarian semantic menggunakan metode rule based. Pengujian dilakukan menggunakan dua metode uji yaitu pengujian dengan black box testing dan angket kuesioner cheklist. Dari hasil penelitian ini dapat disimpulkan bahwa sistem semantic data warehouse dapat membantu proses pengolahan data akademik yang menghasilkan laporan yang berkualitas untuk mendukung proses pengambilan keputusan.

  15. Evaluation Results of an Ontology-based Design Model of Virtual Environments for Upper Limb Motor Rehabilitation of Stroke Patients.

    Science.gov (United States)

    Ramírez-Fernández, Cristina; Morán, Alberto L; García-Canseco, Eloísa; Gómez-Montalvo, Jorge R

    2017-03-23

    1) To enhance the content of an ontology for designing virtual environments (VEs) for upper limb motor rehabilitation of stroke patients according to the suggestions and comments of rehabilitation specialists and software developers, 2) to characterize the perceived importance level of the ontology, 3) to determine the perceived usefulness of the ontology, and 4) to identify the safety characteristics of the ontology for VEs design according to the rehabilitation specialists. Using two semi-structured Web questionnaires, we asked six rehabilitation specialists and six software developers to provide us with their perception regarding the level of importance and the usability of the ontology. From their responses we have identified themes related to perceived and required safety characteristics of the ontology. Significant differences in the importance level were obtained for the Stroke Disability, VE Configuration, Outcome Measures, and Safety Calibration classes, which were perceived as highly important by rehabilitation specialists. Regarding usability, the ontology was perceived by both groups with high usefulness, ease of use, learnability and intention of use. Concerning the thematic analysis of recommendations, eight topics for safety characteristics of the ontology were identified: adjustment of therapy strategies; selection and delimitation of movements; selection and proper calibration of the interaction device; proper selection of measuring instruments; gradual modification of the difficulty of the exercise; adaptability and variability of therapy exercises; feedback according to the capabilities of the patient; and real-time support for exercise training. The rehabilitation specialists and software developers confirmed the importance of the information contained in the ontology regarding motor rehabilitation of the upper limb. Their recommendations highlight the safety features and the advantages of the ontology as a guide for the effective design of VEs.

  16. WaterOnto: Ontology of Context-Aware Grid-Based Riverine Water Management System

    Directory of Open Access Journals (Sweden)

    Muhammad Hussain Mughal

    2017-06-01

    Full Text Available The management of riverine water always remains a big challenge, because the volatility of water flow creates hurdles to determine the exact time and quantity of water flowing in rivers and available for daily use. The volatile water caused by various water sources and irregular flow pattern generates different kinds of challenges for management. Distribution of flow of water in irrigation network affects the relevant community in either way. In the monsoon seasons, river belt community high risk of flood, while far living community suffering drought. Contemplating this situation, we have developed an ontology for context-aware information representation of riverine water management system abetting the visualization and proactive planning for the complex real-time situation. The purpose of this WaterOnto is to improve river water management and enable for efficient use of this precious natural resource. This would also be helpful to save the extra water being discharged in sea & non-irrigational areas, and magnitude and location of water leakage. We conceptualized stakeholder and relevant entities. We developed a taxonomy of irrigation system concepts in machine process able structure. Being woven these hierarchies together we developed a detailed conceptualization of river flow that helps us to manage the flow of water and enable to extract danger situation.

  17. LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies.

    Science.gov (United States)

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

    2009-10-26

    The Lexical Grid (LexGrid) project is an on-going community-driven initiative coordinated by the Mayo Clinic Division of Biomedical Statistics and Informatics (BSI). It provides a common terminology model to represent multiple vocabulary and ontology sources as well as a scalable and robust API for accessing such information. While successfully used and adopted in the biomedical and clinical community, an important requirement is to align the existing LexGrid model with emerging Semantic Web standards and specifications. This paper introduces the LexRDF model, which maps the LexGrid model elements to corresponding constructs in W3C specifications such as RDF, OWL, and SKOS. Our mapping specification successfully used W3C standards to represent most of the existing LexGrid components, and those that did not map point out issues in the existing specifications that the W3C may want to consider in future work. With LexRDF, the terminological information represented in LexGrid can be translated to RDF triples, and therefore allowing LexGrid to leverage standard tools and technologies such as SPARQL and RDF triple stores.

  18. A new measure for functional similarity of gene products based on Gene Ontology

    Directory of Open Access Journals (Sweden)

    Lengauer Thomas

    2006-06-01

    Full Text Available Abstract Background Gene Ontology (GO is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. Results We present a new method for comparing sets of GO terms and for assessing the functional similarity of gene products. The method relies on two semantic similarity measures; simRel and funSim. One measure (simRel is applied in the comparison of the biological processes found in different groups of organisms. The other measure (funSim is used to find functionally related gene products within the same or between different genomes. Results indicate that the method, in addition to being in good agreement with established sequence similarity approaches, also provides a means for the identification of functionally related proteins independent of evolutionary relationships. The method is also applied to estimating functional similarity between all proteins in Saccharomyces cerevisiae and to visualizing the molecular function space of yeast in a map of the functional space. A similar approach is used to visualize the functional relationships between protein families. Conclusion The approach enables the comparison of the underlying molecular biology of different taxonomic groups and provides a new comparative genomics tool identifying functionally related gene products independent of homology. The proposed map of the functional space provides a new global view on the functional relationships between gene products or protein families.

  19. Versioning System for Distributed Ontology Development

    Science.gov (United States)

    2016-03-15

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

  20. 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.

  1. The foundational ontology library ROMULUS

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-09-01

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

  2. 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).

  3. Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research.

    Science.gov (United States)

    He, Yongqun

    2016-06-01

    Compared with controlled terminologies ( e.g. , MedDRA, CTCAE, and WHO-ART), the community-based Ontology of AEs (OAE) has many advantages in adverse event (AE) classifications. The OAE-derived Ontology of Vaccine AEs (OVAE) and Ontology of Drug Neuropathy AEs (ODNAE) serve as AE knowledge bases and support data integration and analysis. The Immune Response Gene Network Theory explains molecular mechanisms of vaccine-related AEs. The OneNet Theory of Life treats the whole process of a life of an organism as a single complex and dynamic network ( i.e. , OneNet). A new "OneNet effectiveness" tenet is proposed here to expand the OneNet theory. Derived from the OneNet theory, the author hypothesizes that one human uses one single genotype-rooted mechanism to respond to different vaccinations and drug treatments, and experimentally identified mechanisms are manifestations of the OneNet blueprint mechanism under specific conditions. The theories and ontologies interact together as semantic frameworks to support integrative pharmacovigilance research.

  4. Validating an ontology-based algorithm to identify patients with type 2 diabetes mellitus in electronic health records.

    Science.gov (United States)

    Rahimi, Alireza; Liaw, Siaw-Teng; Taggart, Jane; Ray, Pradeep; Yu, Hairong

    2014-10-01

    Improving healthcare for people with chronic conditions requires clinical information systems that support integrated care and information exchange, emphasizing a semantic approach to support multiple and disparate Electronic Health Records (EHRs). Using a literature review, the Australian National Guidelines for Type 2 Diabetes Mellitus (T2DM), SNOMED-CT-AU and input from health professionals, we developed a Diabetes Mellitus Ontology (DMO) to diagnose and manage patients with diabetes. This paper describes the manual validation of the DMO-based approach using real world EHR data from a general practice (n=908 active patients) participating in the electronic Practice Based Research Network (ePBRN). The DMO-based algorithm to query, using Semantic Protocol and RDF Query Language (SPARQL), the structured fields in the ePBRN data repository were iteratively tested and refined. The accuracy of the final DMO-based algorithm was validated with a manual audit of the general practice EHR. Contingency tables were prepared and Sensitivity and Specificity (accuracy) of the algorithm to diagnose T2DM measured, using the T2DM cases found by manual EHR audit as the gold standard. Accuracy was determined with three attributes - reason for visit (RFV), medication (Rx) and pathology (path) - singly and in combination. The Sensitivity and Specificity of the algorithm were 100% and 99.88% with RFV; 96.55% and 98.97% with Rx; and 15.6% and 98.92% with Path. This suggests that Rx and Path data were not as complete or correct as the RFV for this general practice, which kept its RFV information complete and current for diabetes. However, the completeness is good enough for this purpose as confirmed by the very small relative deterioration of the accuracy (Sensitivity and Specificity of 97.67% and 99.18%) when calculated for the combination of RFV, Rx and Path. The manual EHR audit suggested that the accuracy of the algorithm was influenced by data quality such as incorrect data due to

  5. Construction of Fuzzy Ontologies from Fuzzy UML Models

    Directory of Open Access Journals (Sweden)

    Fu Zhang

    2013-05-01

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

  6. A longitudinal simulation-based ethical-legal curriculum for otolaryngology residents.

    Science.gov (United States)

    Fanous, Amanda; Rappaport, Jamie; Young, Meredith; Park, Yoon Soo; Manoukian, John; Nguyen, Lily H P

    2017-11-01

    To develop, implement, and evaluate a longitudinal, simulation-based ethics and legal curriculum designed specifically for otolaryngology residents. Otolaryngology residents were recruited to participate in a yearly half-day ethical-legal module, the curriculum of which spanned 4 years. Each module included: three simulated scenarios, small-group multisource feedback, and large-group debriefings. Scenarios involved encounters with standardized patients. Residents' ethical-legal knowledge was assessed pre- and postmodule with multiple-choice questions, and ethical reasoning was assessed by a variety of evaluators during the simulated scenario using a locally developed assessment tool. Participants completed an exit survey at the end of each module. Eighteen residents completed four modules from the academic years of 2008 to 2009 to 2011 to 2012. The first year was considered a pilot module, and data were collected for the following 3 years. Knowledge of legal issues improved significantly among residents (mean at pre = 3.40 and post = 4.60, P simulation-based ethical-legal curriculum tailored to otolaryngology-head and neck surgery residents. This educational program resulted in a both objective and subjective improvement in legal and ethics knowledge and skills. NA. Laryngoscope, 127:2501-2509, 2017. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  7. Ethico-legal aspects of hospital-based blood transfusion practice ...

    African Journals Online (AJOL)

    McRoy

    2014-12-31

    Dec 31, 2014 ... the ethical and legal issues related to hospital-based blood transfusion practice for medical practitioner. Methods: Relevant articles .... A review of the ethical responsibilities of medical practitioners in hospital-based blood ... individuals, governments, faith-based and non- governmental organizations (NGO).

  8. Logical development of the cell ontology.

    Science.gov (United States)

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

    2011-01-05

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

  9. Logical Development of the Cell Ontology

    Directory of Open Access Journals (Sweden)

    Blake Judith A

    2011-01-01

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

  10. Tackling the challenges of matching biomedical ontologies.

    Science.gov (United States)

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

    2018-01-15

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

  11. Markov Chain Ontology Analysis (MCOA

    Directory of Open Access Journals (Sweden)

    Frost H

    2012-02-01

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

  12. 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.

  13. 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.

  14. 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

  15. 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...

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

    Science.gov (United States)

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

    2013-01-01

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

  17. PPI-IRO: A two-stage method for protein-protein interaction extraction based on interaction relation ontology

    KAUST Repository

    Li, Chuanxi

    2014-01-01

    Mining Protein-Protein Interactions (PPIs) from the fast-growing biomedical literature resources has been proven as an effective approach for the identifi cation of biological regulatory networks. This paper presents a novel method based on the idea of Interaction Relation Ontology (IRO), which specifi es and organises words of various proteins interaction relationships. Our method is a two-stage PPI extraction method. At fi rst, IRO is applied in a binary classifi er to determine whether sentences contain a relation or not. Then, IRO is taken to guide PPI extraction by building sentence dependency parse tree. Comprehensive and quantitative evaluations and detailed analyses are used to demonstrate the signifi cant performance of IRO on relation sentences classifi cation and PPI extraction. Our PPI extraction method yielded a recall of around 80% and 90% and an F1 of around 54% and 66% on corpora of AIMed and Bioinfer, respectively, which are superior to most existing extraction methods. Copyright © 2014 Inderscience Enterprises Ltd.

  18. Machine learning versus knowledge based classification of legal texts

    NARCIS (Netherlands)

    de Maat, E.; Krabben, K.; Winkels, R.

    2010-01-01

    This paper presents results of an experiment in which we used machine learning (ML) techniques to classify sentences in Dutch legislation. These results are compared to the results of a pattern-based classifier. Overall, the ML classifier performs as accurate (>90%) as the pattern based one, but

  19. 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.

  20. Gene Ontology annotations and resources.

    Science.gov (United States)

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

    2013-01-01

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

  1. 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

  2. Anytime classification by ontology approximation

    NARCIS (Netherlands)

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

    2007-01-01

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

  3. 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.

  4. 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.

  5. An ontology for sensor networks

    Science.gov (United States)

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

    2010-05-01

    ontologies can be easily attached when instantiating the ontology for any particular sensors in a domain. After a review of previous work on the specification of sensors, the group is developing the ontology in conjunction with use case development. Part of the difficulty of such work is that relevant concepts from for example OGC standards and other ontologies must be identified and aligned and also placed in a consistent and logically correct way into the ontology. In terms of alignment with OGC's SWE, the ontology is intended to be able to model concepts from SensorML and O&M. Similar to SensorML and O&M, the ontology is based around concepts of systems, processes, and observations. It supports the description of the physical and processing structure of sensors. Sensors are not constrained to physical sensing devices: rather a sensor is anything that can estimate or calculate the value of a phenomenon, so a device or computational process or combination could play the role of a sensor. The representation of a sensor in the ontology links together what is measured (the domain phenomena), the sensor's physical and other properties and its functions and processing. Parts of the ontology are well aligned with SensorML and O&M, but parts are not, and the group is working to understand how differences from (and alignment with) the OGC standards affect the application of the ontology.

  6. [Classification of cell-based medicinal products and legal implications: An overview and an update].

    Science.gov (United States)

    Scherer, Jürgen; Flory, Egbert

    2015-11-01

    In general, cell-based medicinal products do not represent a uniform class of medicinal products, but instead comprise medicinal products with diverse regulatory classification as advanced-therapy medicinal products (ATMP), medicinal products (MP), tissue preparations, or blood products. Due to the legal and scientific consequences of the development and approval of MPs, classification should be clarified as early as possible. This paper describes the legal situation in Germany and highlights specific criteria and concepts for classification, with a focus on, but not limited to, ATMPs and non-ATMPs. Depending on the stage of product development and the specific application submitted to a competent authority, legally binding classification is done by the German Länder Authorities, Paul-Ehrlich-Institut, or European Medicines Agency. On request by the applicants, the Committee for Advanced Therapies may issue scientific recommendations for classification.

  7. The use of legal knowledge-based systems in public administration: what can go wrong?

    NARCIS (Netherlands)

    de Bruin, Hugo; Prakken, Henry; Svensson, Jorgen S.; Bench-Capon, Trevor J.M.; Daskalopulu, Aspassia; Winkels, Radboud

    2002-01-01

    In recent years, practical applications of legal knowledge-based systems have become increasingly common. This raises the issue of their functioning in practice and their actual influence on the quality of decisions. In this paper we investigate to what extent incorrect decisions may be caused by

  8. Legal Aspects of a Location-Based Mobile Advertising Platform

    DEFF Research Database (Denmark)

    Cleff, Evelyne Beatrix; Gidofalvi, Gyozo

    2008-01-01

    Recent advances in communication and information technology, such as the increasing accuracy of GPS technology and the miniaturization of wireless communication devices pave the road for Location-Based Services. Among these services, mobile advertising is predicted to represent a high yield revenue...... stream. In this article the possibilities of using a location-aware mobile messenger for the purpose of mobile advertising will be introduced. However, mobile advertising may become an extremely intrusive practice if the user's privacy is not taken in account. The objective of this article is therefore...

  9. An Ontology-Based Approach for Knowledge Lifecycle Management within Aircraft Lifecycle Phases

    NARCIS (Netherlands)

    Verhagen, W.J.C.

    2013-01-01

    In the aerospace domain, manufacturers and operators constantly seek to improve their products and processes. Increasingly, knowledge-based applications are developed to support or automate knowledge-intensive engineering tasks, saving time and money. However, engineering knowledge changes over

  10. Reflections from the Jury Box: Improving Evidence Based Practice through a Comparison with Our Legal System

    Directory of Open Access Journals (Sweden)

    Valerie Coppenrath

    2017-08-01

    Full Text Available Background: An experience serving jury duty prompted reflection on the parallels between evidenced based medicine and our legal system. Findings: The steps of the legal system can be tied to each step of the practice of evidenced based medicine. Implications: Patients should be included in evidence based decisions. Pharmacists can act as resources for other providers practicing evidenced based medicine. Educators can use this analogy to teach evidence based medicine. Conflict of Interest We declare no conflicts of interest or financial interests that the authors or members of their immediate families have in any product or service discussed in the manuscript, including grants (pending or received, employment, gifts, stock holdings or options, honoraria, consultancies, expert testimony, patents and royalties.   Type: Commentary

  11. MIMU-Wear: ontology-based sensor selection for real-world wearable activity recognition

    NARCIS (Netherlands)

    Villalonga, Claudia; Pomares, Hector; Rojas, Ignacio; Banos Legran, Oresti

    2017-01-01

    An enormous effort has been made during the recent years towards the recognition of human activity based on wearable sensors. Despite the wide variety of proposed systems, most existing solutions have in common to solely operate on predefined settings and constrained sensor setups. Real-world

  12. CogSkillnet: An Ontology-Based Representation of Cognitive Skills

    Science.gov (United States)

    Askar, Petek; Altun, Arif

    2009-01-01

    A number of studies emphasized the need to capture learners' interaction patterns in order to personalize their learning process as they study through learning objects. In education context, learning materials are designed based on pre-determined expectations and learners are evaluated to what extent they master these expectations. Representation…

  13. Creating a Structured Adverse Outcome Pathway Knowledgebase via Ontology-Based Annotations

    Science.gov (United States)

    The Adverse Outcome Pathway (AOP) framework is increasingly used to integrate data based on traditional and emerging toxicity testing paradigms. As the number of AOP descriptions has increased, so has the need to define the AOP in computable terms. Herein, we present a comprehens...

  14. Ontology-Driven Instant Messaging-Based Dialogue System for Device Control

    KAUST Repository

    Noguera-Arnaldos, José Ángel

    2015-10-14

    The im4Things platform aims to develop a communication interface for devices in the Internet of the Things (IoT) through intelligent dialogue based on written natural language over instant messaging services. This type of communication can be established in different ways such as order sending and, status querying. Also, the devices themselves are responsible for alerting users when a change has been produced in the device’s sensors. The system has been validated and it has obtained promising results.

  15. An Ontology-Based Autonomic System for Improving Data Warehouses by Cache Allocation Management

    OpenAIRE

    Nicolicin-Georgescu, Vlad; Benatier, Vincent; Lehn, Rémi; Briand, Henri

    2009-01-01

    International audience; With the increase in the amount and complexity of information, data warehouse performance has become a constant issue, especially for decision support systems. As a consequence, decision experts are faced with the management of all this information, and thus realize that special techniques are required to keep good performances. This paper proposes an approach to data warehouse systems improvement based on Autonomic Computing. The idea is that by rendering certain task...

  16. An ontology-based approach to patient follow-up assessment for continuous and personalized chronic disease management.

    Science.gov (United States)

    Zhang, Yi-Fan; Gou, Ling; Zhou, Tian-Shu; Lin, De-Nan; Zheng, Jing; Li, Ye; Li, Jing-Song

    2017-08-01

    Chronic diseases are complex and persistent clinical conditions that require close collaboration among patients and health care providers in the implementation of long-term and integrated care programs. However, current solutions focus partially on intensive interventions at hospitals rather than on continuous and personalized chronic disease management. This study aims to fill this gap by providing computerized clinical decision support during follow-up assessments of chronically ill patients at home. We proposed an ontology-based framework to integrate patient data, medical domain knowledge, and patient assessment criteria for chronic disease patient follow-up assessments. A clinical decision support system was developed to implement this framework for automatic selection and adaptation of standard assessment protocols to suit patient personal conditions. We evaluated our method in the case study of type 2 diabetic patient follow-up assessments. The proposed framework was instantiated using real data from 115,477 follow-up assessment records of 36,162 type 2 diabetic patients. Standard evaluation criteria were automatically selected and adapted to the particularities of each patient. Assessment results were generated as a general typing of patient overall condition and detailed scoring for each criterion, providing important indicators to the case manager about possible inappropriate judgments, in addition to raising patient awareness of their disease control outcomes. Using historical data as the gold standard, our system achieved a rate of accuracy of 99.93% and completeness of 95.00%. This study contributes to improving the accessibility, efficiency and quality of current patient follow-up services. It also provides a generic approach to knowledge sharing and reuse for patient-centered chronic disease management. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Formal ontologies in biomedical knowledge representation.

    Science.gov (United States)

    Schulz, S; Jansen, L

    2013-01-01

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

  18. A Corpus-Based Discourse Information Analysis of Chinese EFL Learners' Autonomy in Legal Case Brief Writing

    Science.gov (United States)

    Chen, Jinshi

    2017-01-01

    Legal case brief writing is pedagogically important yet insufficiently discussed for Chinese EFL learners majoring in law. Based on process genre approach and discourse information theory (DIT), the present study designs a corpus-based analytical model for Chinese EFL learners' autonomy in legal case brief writing and explores the process of case…

  19. Algorithms to analyze the quality test parameter values of seafood in the proposed ontology based seafood quality analyzer and miner (ONTO SQAM model

    Directory of Open Access Journals (Sweden)

    Vinu Sherimon

    2017-07-01

    Full Text Available Ensuring the quality of food, particularly seafood has increasingly become an important issue nowadays. Quality Management Systems empower any organization to identify, measure, control and improve the quality of the products manufactured that will eventually lead to improved business performance. With the advent of new technologies, now intelligent systems are being developed. To ensure the quality of seafood, an ontology based seafood quality analyzer and miner (ONTO SQAM model is proposed. The knowledge is represented using ontology. The domain concepts are defined using ontology. This paper presents the initial part of the proposed model – the analysis of quality test parameter values. Two algorithms are proposed to do the analysis – Comparison Algorithm and Data Store Updater algorithm. The algorithms ensure that the values of various quality tests are in the acceptable range. The real data sets taken from different seafood companies in Kerala, India, and validated by the Marine Product Export Development Authority of India (MPEDA are used for the experiments. The performance of the algorithms is evaluated using standard performance metrics such as precision, recall, and accuracy. The results obtained show that all the three measures achieved good results.

  20. Blockchain-based framework for ontology-oriented robots’ coalition formation in cyberphysical systems

    Directory of Open Access Journals (Sweden)

    Teslya Nikolay

    2018-01-01

    Full Text Available The creation and functioning of intelligent robots coalition is impossible without the organization of an information interaction environment between them. To solve this problem, it is proposed to use the concept of cyberphysical framework, which involves the unification of physical and cyber (virtual environments. Intelligent robots can interact with each of the environments. The paper proposes methodology of the cyber physical smart space creation for the intelligent robots’ coalition formation and functioning, based on the concept of the “blackboard” with the support of smart contracts over the blockchain technology. It provides a new approach to the distribution of sensory, computational, information-control and service tasks between intelligent robots, embedded devices, fixed service equipment, cloud computing and information resources.

  1. 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

  2. Logical Characterisation of Ontology Construction using Fuzzy Description Logics

    DEFF Research Database (Denmark)

    Badie, Farshad; Götzsche, Hans

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

  3. Constructive Ontology Engineering

    Science.gov (United States)

    Sousan, William L.

    2010-01-01

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

  4. Ontologies vs. Classification Systems

    DEFF Research Database (Denmark)

    Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

    2009-01-01

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

  5. Semantic similarity in biomedical ontologies.

    Directory of Open Access Journals (Sweden)

    Catia Pesquita

    2009-07-01

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

  6. Semantic similarity in biomedical ontologies.

    Science.gov (United States)

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

    2009-07-01

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

  7. Learning and Sharing Technology in Informal Contexts. A Multiagent-Based Ontological Approach

    Directory of Open Access Journals (Sweden)

    Dino Borri

    2014-05-01

    Full Text Available An increasing debate is growing today, in both academic and research-in-action contexts, about the roles of new and traditional technologies in raising knowledge of agents involved, as well as in boosting an effective development of communities. The last century has been largely dominated by capital-intensive technologies, impacting large and populated areas. From the late 1990s up to the present days, due to social, financial, environmental concerns, new low-impact, local-born, little to medium-scale experiences have been challenging large technologies, with interesting results. The importance of such experiences seems to lay on the abilities and knowledge of local populations, which are quite difficult to emerge as formal methodologies and attain recognizable levels of generalization and sharing. Yet the effectiveness of local-based technologies is being increasingly documented, often succeeding in cases where more formal technologies had previously failed. The EU-funded ANTINOMOS project has largely dealt with local-community knowledge enhancing and managing in the water sector management, aiming at creating a real learning environment for the sharing and the active generation of knowledge through mutual synergies. In this paper, the above subject is discussed and carried out with a cross-disciplinary, cross-scale, multi-agent approach, considering the different forms of local knowledge and language involved.

  8. Assessing Performance of Three BIM-Based Views of Buildings for Communication and Management of Vertically Stratified Legal Interests

    Directory of Open Access Journals (Sweden)

    Behnam Atazadeh

    2017-07-01

    Full Text Available Multistorey buildings typically include stratified legal interests which provide entitlements to a community of owners to lawfully possess private properties and use communal and public properties. The spatial arrangements of these legal interests are often defined by multiplexing cognitively outlined spaces and physical elements of a building. In order to support 3D digital management and communication of legal arrangements of properties, a number of spatial data models have been recently developed in Geographic Information Systems (GIS and Building Information Modelling (BIM domains. While some data models, such as CityGML, IndoorGML or IFC, provide a merely physical representation of the built environment, others, e.g., LADM, mainly rely on legal data elements to support a purely legal view of multistorey buildings. More recently, spatial data models integrating legal and physical notions of multistorey buildings have been proposed to overcome issues associated with purely legal models and purely physical ones. In previous investigations, it has been found that the 3D digital data environment of BIM has the flexibility to utilize either only physical elements or only legal spaces, or an integrated view of both legal spaces and physical elements to represent spatial arrangements of stratified legal interests. In this article, the performance of these three distinct BIM-based representations of legal interests defined inside multistorey buildings is assessed in the context of the Victorian jurisdiction of Australia. The assessment metrics are a number of objects and geometry batches, visualization speed in terms of frame rate, query time, modelling legal boundaries, and visual communication of legal boundaries.

  9. 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...

  10. Mapping between the OBO and OWL ontology languages.

    Science.gov (United States)

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

    2011-03-07

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

  11. 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 ...

  12. 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.

  13. 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

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

    Directory of Open Access Journals (Sweden)

    Robert Hoehndorf

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

  15. 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

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

    Science.gov (United States)

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

    2006-01-01

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

  17. GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions

    OpenAIRE

    Doherty, Jason M; Carmichael, Lynn K; Mills, Jason C

    2006-01-01

    Abstract Background The ever-expanding population of gene expression profiles (EPs) from specified cells and tissues under a variety of experimental conditions is an important but difficult resource for investigators to utilize effectively. Software tools have been recently developed to use the distribution of gene ontology (GO) terms associated with the genes in an EP to identify specific biological functions or processes that are over- or under-represented in that EP relative to other EPs. ...

  18. Ontology-based demand-side flexibility management in smart grids using a multi-agent system

    OpenAIRE

    Hippolyte, Jean-Laurent; Howell, Shaun; Sleiman, Hassan; Vinyals, Meritxell; Yuce, Baris; Vanhée, Loïs; Mourshed, Monjur

    2016-01-01

    Power distribution network management must integrate with demand side management, alongside distributed energy resources, in order to meet sustainability, resilience, and economic challenges through a smart grid approach. This paper presents an implementation of the Universal Smart Energy Framework (USEF) through a multi-agent system and a novel semantic web ontology, which aligns and enriches relevant existing standards. USEF provides a common specification of the market processes and inform...

  19. "Legal highs" on the net-Evaluation of UK-based Websites, products and product information.

    Science.gov (United States)

    Schmidt, Martin M; Sharma, Akhilesh; Schifano, Fabrizio; Feinmann, Charlotte

    2011-03-20

    A vast array of substances are marketed as "legal highs" in the UK. These products are mainly marketed online and are packaged and produced to mimic illicit drugs. Little is known about the full range of products available at present and no studies have evaluated the product information provided to consumers. AIMS & HYPOTHESIS: To describe the available legal high products marketed by UK-based Internet retailers and evaluate the product information provided to consumers. Websites were identified using the terms "buy legal highs+UK" and two search engines. The first 100 hits and a random sample of 5% of the remaining results were screened. Websites based in the UK were included and all products were entered on a database. Information on product name, list price, claimed effects, side effects, contraindications and interactions was extracted. A descriptive analysis was conducted using SPSS v14. 115 Websites met the inclusion criteria but due to duplicate listings this was reduced to 39 unique Websites. 1308 products were found and evaluated. The average product price was 9.69 British pounds. Products took the form of pills (46.6%), smoking material (29.7%) and single plant material/extract (18.1%). Most products claimed to be stimulants (41.7%), sedatives (32.3%), or hallucinogens (12.9%). 40.1% of products failed to list ingredients, 91.9% failed to list side effects, 81.9% failed to list contraindications and 86.3% failed to list drug interactions. Top 5 products (with active ingredients in brackets) by frequency were Salvia divinorum (Salivinorin A), Kratom (Mitragynine), Hawaiian Baby Woodrose Seeds (Lysergic Acid Amide), Fly Agaric (Ibotenic Acid, Muscimol) and Genie (JWH018, CP47497). Products marketed as "legal highs" are easily available from UK-based Internet retailers and are reasonably affordable. Safety information provided to consumers is poor. Uninformed users risk serious adverse effects. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Lin Yu

    2011-10-01

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

  1. 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

  2. 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

  3. Appreciating ontological struggles

    DEFF Research Database (Denmark)

    Danholt, Peter

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

  4. 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....

  5. Ontologies, Agents and the Grid: An Overview

    OpenAIRE

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

    2009-01-01

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

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

    Science.gov (United States)

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

    2018-02-06

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

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

    Science.gov (United States)

    Cui, Wei; Li, Deren

    2005-10-01

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

  8. The design ontology

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  9. An RM-ODP Based Ontology and a CAD Tool for Modeling Hierarchical Systems in Enterprise Architecture

    OpenAIRE

    Lê, Lam Son; Wegmann, Alain

    2005-01-01

    Enterprise Architecture (EA) requires modeling enterprises across multiple levels (from markets down to IT systems) i.e. modeling hierarchical systems. Our goal is to build a Computer Aided Design (CAD) tool for EA. To be able to build this CAD tool, we need an ontology that can be used to describe hierarchical systems. The Reference Model of Open Distributed Processing (RM-ODP) was originally defined for describing IT systems and their environment. RM-ODP can also be suited to general, hier...

  10. Ontology Maintenance using Textual Analysis

    Directory of Open Access Journals (Sweden)

    Yassine Gargouri

    2003-10-01

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

  11. The Evidence-base for Using Ontologies and Semantic Integration Methodologies to Support Integrated Chronic Disease Management in Primary and Ambulatory Care: Realist Review. Contribution of the IMIA Primary Health Care Informatics WG.

    Science.gov (United States)

    Liyanage, H; Liaw, S-T; Kuziemsky, C; Terry, A L; Jones, S; Soler, J K; de Lusignan, S

    2013-01-01

    Most chronic diseases are managed in primary and ambulatory care. The chronic care model (CCM) suggests a wide range of community, technological, team and patient factors contribute to effective chronic disease management. Ontologies have the capability to enable formalised linkage of heterogeneous data sources as might be found across the elements of the CCM. To describe the evidence base for using ontologies and other semantic integration methods to support chronic disease management. We reviewed the evidence-base for the use of ontologies and other semantic integration methods within and across the elements of the CCM. We report them using a realist review describing the context in which the mechanism was applied, and any outcome measures. Most evidence was descriptive with an almost complete absence of empirical research and important gaps in the evidence-base. We found some use of ontologies and semantic integration methods for community support of the medical home and for care in the community. Ubiquitous information technology (IT) and other IT tools were deployed to support self-management support, use of shared registries, health behavioural models and knowledge discovery tools to improve delivery system design. Data quality issues restricted the use of clinical data; however there was an increased use of interoperable data and health system integration. Ontologies and semantic integration methods are emergent with limited evidence-base for their implementation. However, they have the potential to integrate the disparate community wide data sources to provide the information necessary for effective chronic disease management.

  12. Using AberOWL for fast and scalable reasoning over BioPortal ontologies

    KAUST Repository

    Slater, Luke

    2016-08-08

    Background: Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repositories, as well as most other tools utilizing ontologies, either provide access to ontologies without use of automated reasoning, or limit the number of ontologies for which automated reasoning-based access is provided. Methods: We apply the AberOWL infrastructure to provide automated reasoning-based access to all accessible and consistent ontologies in BioPortal (368 ontologies). We perform an extensive performance evaluation to determine query times, both for queries of different complexity and for queries that are performed in parallel over the ontologies. Results and conclusions: We demonstrate that, with the exception of a few ontologies, even complex and parallel queries can now be answered in milliseconds, therefore allowing automated reasoning to be used on a large scale, to run in parallel, and with rapid response times.

  13. An ontology-based, mobile-optimized system for pharmacogenomic decision support at the point-of-care.

    Directory of Open Access Journals (Sweden)

    Jose Antonio Miñarro-Giménez

    Full Text Available The development of genotyping and genetic sequencing techniques and their evolution towards low costs and quick turnaround have encouraged a wide range of applications. One of the most promising applications is pharmacogenomics, where genetic profiles are used to predict the most suitable drugs and drug dosages for the individual patient. This approach aims to ensure appropriate medical treatment and avoid, or properly manage, undesired side effects.We developed the Medicine Safety Code (MSC service, a novel pharmacogenomics decision support system, to provide physicians and patients with the ability to represent pharmacogenomic data in computable form and to provide pharmacogenomic guidance at the point-of-care. Pharmacogenomic data of individual patients are encoded as Quick Response (QR codes and can be decoded and interpreted with common mobile devices without requiring a centralized repository for storing genetic patient data. In this paper, we present the first fully functional release of this system and describe its architecture, which utilizes Web Ontology Language 2 (OWL 2 ontologies to formalize pharmacogenomic knowledge and to provide clinical decision support functionalities.The MSC system provides a novel approach for enabling the implementation of personalized medicine in clinical routine.

  14. An Ontology-Based Approach to Enable Knowledge Representation and Reasoning in Worker–Cobot Agile Manufacturing

    Directory of Open Access Journals (Sweden)

    Ahmed R. Sadik

    2017-11-01

    accomplish the cooperative manufacturing concept, a proper approach is required to describe the shared environment between the worker and the cobot. The cooperative manufacturing shared environment includes the cobot, the co-worker, and other production components such as the product itself. Furthermore, the whole cooperative manufacturing system components need to communicate and share their knowledge, to reason and process the shared information, which eventually gives the control solution the capability of obtaining collective manufacturing decisions. Putting into consideration that the control solution should also provide a natural language which is human readable and in the same time can be understood by the machine (i.e., the cobot. Accordingly, a distributed control solution which combines an ontology-based Multi-Agent System (MAS and a Business Rule Management System (BRMS is proposed, in order to solve the mentioned challenges in the cooperative manufacturing, which are: manufacturing knowledge representation, sharing, and reasoning.

  15. The unexpected high practical value of medical ontologies.

    Science.gov (United States)

    Pinciroli, Francesco; Pisanelli, Domenico M

    2006-01-01

    Ontology is no longer a mere research topic, but its relevance has been recognized in several practical fields. Current applications areas include natural language translation, e-commerce, geographic information systems, legal information systems and biology and medicine. It is the backbone of solid and effective applications in health care and can help to build more powerful and more interoperable medical information systems. The design and implementation of ontologies in medicine is mainly focused on the re-organization of medical terminologies. This is obviously a difficult task and requires a deep analysis of the structure and the concepts of such terminologies, in order to define domain ontologies able to provide both flexibility and consistency to medical information systems. The aim of this special issue of Computers in Biology and Medicine is to report the current evolution of research in biomedical ontologies, presenting both papers devoted to methodological issues and works with a more applicative emphasis.

  16. 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.

  17. Inferring gene ontologies from pairwise similarity data

    Science.gov (United States)

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

    2014-01-01

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

  18. Ontology-based systematical representation and drug class effect analysis of package insert-reported adverse events associated with cardiovascular drugs used in China.

    Science.gov (United States)

    Wang, Liwei; Li, Mei; Xie, Jiangan; Cao, Yuying; Liu, Hongfang; He, Yongqun

    2017-10-23

    With increased usage of cardiovascular drugs (CVDs) for treating cardiovascular diseases, it is important to analyze CVD-associated adverse events (AEs). In this study, we systematically collected package insert-reported AEs associated with CVDs used in China, and developed and analyzed an Ontology of Cardiovascular Drug AEs (OCVDAE). Extending the Ontology of AEs (OAE) and NDF-RT, OCVDAE includes 194 CVDs, CVD ingredients, mechanisms of actions (MoAs), and CVD-associated 736 AEs. An AE-specific drug class effect is defined to exist when all the drugs (drug chemical ingredients or drug products) in a drug class are associated with an AE, which is formulated as a new proportional class level ratio ("PCR") = 1. Our PCR-based heatmap analysis identified many class level drug effects on different AE classes such as behavioral and neurological AE and digestive system AE. Additional drug-AE correlation tests (i.e., class-level PRR, Chi-squared, and minimal case reports) were also modified and applied to further detect statistically significant drug class effects. Two drug ingredient classes and three CVD MoA classes were found to have statistically significant class effects on 13 AEs. For example, the CVD Active Transporter Interactions class (including reserpine, indapamide, digoxin, and deslanoside) has statistically significant class effect on anorexia and diarrhea AEs.

  19. The system evaluation for report writing skills of summary by HGA-SVM with Ontology: Medical case study in problem based learning

    Science.gov (United States)

    Yenaeng, Sasikanchana; Saelee, Somkid; Samai, Wirachai

    2018-01-01

    The system evaluation for report writing skills of summary by Hybrid Genetic Algorithm-Support Vector Machines (HGA-SVM) with Ontology of Medical Case Study in Problem Based Learning (PBL) is a system was developed as a guideline of scoring for the facilitators or medical teacher. The essay answers come from medical student of medical education courses in the nervous system motion and Behavior I and II subject, a third year medical student 20 groups of 9-10 people, the Faculty of Medicine in Prince of Songkla University (PSU). The audit committee have the opinion that the ratings of individual facilitators are inadequate, this system to solve such problems. In this paper proposes a development of the system evaluation for report writing skills of summary by HGA-SVM with Ontology of medical case study in PBL which the mean scores of machine learning score and humans (facilitators) score were not different at the significantly level .05 all 3 essay parts contain problem essay part, hypothesis essay part and learning objective essay part. The result show that, the average score all 3 essay parts that were not significantly different from the rate at the level of significance .05.

  20. Logical Characterisation of Ontology Construction using Fuzzy Description Logics

    DEFF Research Database (Denmark)

    Badie, Farshad; Götzsche, Hans

    Ontologies based on Description Logics (DLs) have proved to be effective in formally sharing knowledge across semantic technologies, e.g. Semantic Web, Natural Language Processing, Text Analytics, Business intelligence. Our main goal is analysing ontology construction considering vagueness. We have......, employs Description Logics in characterising and analysing fuzzy statements. And finally, provides a conceptual framework describing fuzzy concept learning in ontologies using the Inductive Logic Programming....

  1. Self-Supervised Chinese Ontology Learning from Online Encyclopedias

    OpenAIRE

    Hu, Fanghuai; Shao, Zhiqing; Ruan, Tong

    2014-01-01

    Constructing ontology manually is a time-consuming, error-prone, and tedious task. We present SSCO, a self-supervised learning based chinese ontology, which contains about 255 thousand concepts, 5 million entities, and 40 million facts. We explore the three largest online Chinese encyclopedias for ontology learning and describe how to transfer the structured knowledge in encyclopedias, including article titles, category labels, redirection pages, taxonomy systems, and InfoBox modules, into on...

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    Liang Chen

    2016-10-01

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

  4. A fuzzy ontology and its application to news summarization.

    Science.gov (United States)

    Lee, Chang-Shing; Jian, Zhi-Wei; Huang, Lin-Kai

    2005-10-01

    In this paper, a fuzzy ontology and its application to news summarization are presented. The fuzzy ontology with fuzzy concepts is an extension of the domain ontology with crisp concepts. It is more suitable to describe the domain knowledge than domain ontology for solving the uncertainty reasoning problems. First, the domain ontology with various events of news is predefined by domain experts. The document preprocessing mechanism will generate the meaningful terms based on the news corpus and the Chinese news dictionary defined by the domain expert. Then, the meaningful terms will be classified according to the events of the news by the term classifier. The fuzzy inference mechanism will generate the membership degrees for each fuzzy concept of the fuzzy ontology. Every fuzzy concept has a set of membership degrees associated with various events of the domain ontology. In addition, a news agent based on the fuzzy ontology is also developed for news summarization. The news agent contains five modules, including a retrieval agent, a document preprocessing mechanism, a sentence path extractor, a sentence generator, and a sentence filter to perform news summarization. Furthermore, we construct an experimental website to test the proposed approach. The experimental results show that the news agent based on the fuzzy ontology can effectively operate for news summarization.

  5. Exact Score Distribution Computation for Similarity Searches in Ontologies

    Science.gov (United States)

    Schulz, Marcel H.; Köhler, Sebastian; Bauer, Sebastian; Vingron, Martin; Robinson, Peter N.

    Semantic similarity searches in ontologies are an important component of many bioinformatic algorithms, e.g., protein function prediction with the Gene Ontology. In this paper we consider the exact computation of score distributions for similarity searches in ontologies, and introduce a simple null hypothesis which can be used to compute a P-value for the statistical significance of similarity scores. We concentrate on measures based on Resnik’s definition of ontological similarity. A new algorithm is proposed that collapses subgraphs of the ontology graph and thereby allows fast score distribution computation. The new algorithm is several orders of magnitude faster than the naive approach, as we demonstrate by computing score distributions for similarity searches in the Human Phenotype Ontology.

  6. 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

  7. An Ontology-Based Context Model for Wireless Sensor Network (WSN Management in the Internet of Things

    Directory of Open Access Journals (Sweden)

    Adnan Al-Anbuky

    2013-09-01

    Full Text Available Wireless sensor networks (WSNs are an enabling technology of context-aware systems. The Internet of Things (IoT, which has attracted much attention in recent years, is an emerging paradigm where everyday objects and spaces are made context-aware and interconnected through heterogeneous networks on a global scale. However, the IoT system can suffer from poor performances when its underlying networks are not optimized. In this paper, an ontology model for representing and facilitating context sharing between network entities in WSNs is proposed for the first time. The context model aims to enable optimal context-aware management of WSNs in IoT, which will also harness the rich context knowledge of IoT systems.

  8. 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

  9. 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...

  10. 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 ...

  11. Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid method.

    Directory of Open Access Journals (Sweden)

    Xiaomei Wu

    Full Text Available BACKGROUND: Explicit comparisons based on the semantic similarity of Gene Ontology terms provide a quantitative way to measure the functional similarity between gene products and are widely applied in large-scale genomic research via integration with other models. Previously, we presented an edge-based method, Relative Specificity Similarity (RSS, which takes the global position of relevant terms into account. However, edge-based semantic similarity metrics are sensitive to the intrinsic structure of GO and simply consider terms at the same level in the ontology to be equally specific nodes, revealing the weaknesses that could be complemented using information content (IC. RESULTS AND CONCLUSIONS: Here, we used the IC-based nodes to improve RSS and proposed a new method, Hybrid Relative Specificity Similarity (HRSS. HRSS outperformed other methods in distinguishing true protein-protein interactions from false. HRSS values were divided into four different levels of confidence for protein interactions. In addition, HRSS was statistically the best at obtaining the highest average functional similarity among human-mouse orthologs. Both HRSS and the groupwise measure, simGIC, are superior in correlation with sequence and Pfam similarities. Because different measures are best suited for different circumstances, we compared two pairwise strategies, the maximum and the best-match average, in the evaluation. The former was more effective at inferring physical protein-protein interactions, and the latter at estimating the functional conservation of orthologs and analyzing the CESSM datasets. In conclusion, HRSS can be applied to different biological problems by quantifying the functional similarity between gene products. The algorithm HRSS was implemented in the C programming language, which is freely available from http://cmb.bnu.edu.cn/hrss.

  12. 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....

  13. Reviem Of Legal Relevance Program School No Political Party Based On The Proportionality And Evidence And Justifiability Controls Applied By The Brazilian Supreme Court

    OpenAIRE

    Baggenstoss, Grazielly Alessandra

    2016-01-01

    This research examines the legal context of bringing the School No Political Party Program, which aims to include legal provisions in the Law of Guidelines and Bases of National Education. Therefore, the problem of research is if the mentioned project has legal relevance to the Brazilian legal system , as well as the current pedagogical context. Thus, with deductive method, the question is examined from the proportionality test of Robert Alexy and Evidence and Justifiability Controls, applied...

  14. Ontology Learning for Chinese Information Organization and Knowledge Discovery in Ethnology and Anthropology

    Directory of Open Access Journals (Sweden)

    Jing Kong

    2007-09-01

    Full Text Available This paper presents an ontology learning architecture that reflects the interaction between ontology learning and other applications such as ontology-engineering tools and information systems. Based on this architecture, we have developed a prototype system CHOL: a Chinese ontology learning tool. CHOL learns domain ontology from Chinese domain specific texts. On the one hand, it supports a semi-automatic domain ontology acquisition and dynamic maintenance, and on the other hand, it supports an auto-indexing and auto-classification of Chinese scholarly literature. CHOL has been applied in ethnology and anthropology for Chinese information organization and knowledge discovery.

  15. Marine Planning and Service Platform: specific ontology based semantic search engine serving data management and sustainable development

    Science.gov (United States)

    Manzella, Giuseppe M. R.; Bartolini, Andrea; Bustaffa, Franco; D'Angelo, Paolo; De Mattei, Maurizio; Frontini, Francesca; Maltese, Maurizio; Medone, Daniele; Monachini, Monica; Novellino, Antonio; Spada, Andrea

    2016-04-01

    The MAPS (Marine Planning and Service Platform) project is aiming at building a computer platform supporting a Marine Information and Knowledge System. One of the main objective of the project is to develop a repository that should gather, classify and structure marine scientific literature and data thus guaranteeing their accessibility to researchers and institutions by means of standard protocols. In oceanography the cost related to data collection is very high and the new paradigm is based on the concept to collect once and re-use many times (for re-analysis, marine environment assessment, studies on trends, etc). This concept requires the access to quality controlled data and to information that is provided in reports (grey literature) and/or in relevant scientific literature. Hence, creation of new technology is needed by integrating several disciplines such as data management, information systems, knowledge management. In one of the most important EC projects on data management, namely SeaDataNet (www.seadatanet.org), an initial example of knowledge management is provided through the Common Data Index, that is providing links to data and (eventually) to papers. There are efforts to develop search engines to find author's contributions to scientific literature or publications. This implies the use of persistent identifiers (such as DOI), as is done in ORCID. However very few efforts are dedicated to link publications to the data cited or used or that can be of importance for the published studies. This is the objective of MAPS. Full-text technologies are often unsuccessful since they assume the presence of specific keywords in the text; in order to fix this problem, the MAPS project suggests to use different semantic technologies for retrieving the text and data and thus getting much more complying results. The main parts of our design of the search engine are: • Syntactic parser - This module is responsible for the extraction of "rich words" from the text

  16. 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.

  17. GFVO: the Genomic Feature and Variation Ontology

    KAUST Repository

    Baran, Joachim

    2015-05-05

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

  18. GFVO: the Genomic Feature and Variation Ontology

    Directory of Open Access Journals (Sweden)

    Joachim Baran

    2015-05-01

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

  19. Taking Critical Ontology Seriously

    DEFF Research Database (Denmark)

    Wigger, Angela; Horn, Laura

    2017-01-01

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

  20. 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…

  1. OWL Web Ontology Language

    NARCIS (Netherlands)

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

    2004-01-01

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

  2. 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.

  3. 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.

  4. Evaluating the Good Ontology Design Guideline (GoodOD with the ontology quality requirements and evaluation method and metrics (OQuaRE.

    Directory of Open Access Journals (Sweden)

    Astrid Duque-Ramos

    Full Text Available OBJECTIVE: To (1 evaluate the GoodOD guideline for ontology development by applying the OQuaRE evaluation method and metrics to the ontology artefacts that were produced by students in a randomized controlled trial, and (2 informally compare the OQuaRE evaluation method with gold standard and competency questions based evaluation methods, respectively. BACKGROUND: In the last decades many methods for ontology construction and ontology evaluation have been proposed. However, none of them has become a standard and there is no empirical evidence of comparative evaluation of such methods. This paper brings together GoodOD and OQuaRE. GoodOD is a guideline for developing robust ontologies. It was previously evaluated in a randomized controlled trial employing metrics based on gold standard ontologies and competency questions as outcome parameters. OQuaRE is a method for ontology quality evaluation which adapts the SQuaRE standard for software product quality to ontologies and has been successfully used for evaluating the quality of ontologies. METHODS: In this paper, we evaluate the effect of training in ontology construction based on the GoodOD guideline within the OQuaRE quality evaluation framework and compare the results with those obtained for the previous studies based on the same data. RESULTS: Our results show a significant effect of the GoodOD training over developed ontologies by topics: (a a highly significant effect was detected in three topics from the analysis of the ontologies of untrained and trained students; (b both positive and negative training effects with respect to the gold standard were found for five topics. CONCLUSION: The GoodOD guideline had a significant effect over the quality of the ontologies developed. Our results show that GoodOD ontologies can be effectively evaluated using OQuaRE and that OQuaRE is able to provide additional useful information about the quality of the GoodOD ontologies.

  5. Evaluating the Good Ontology Design Guideline (GoodOD) with the ontology quality requirements and evaluation method and metrics (OQuaRE).

    Science.gov (United States)

    Duque-Ramos, Astrid; Boeker, Martin; Jansen, Ludger; Schulz, Stefan; Iniesta, Miguela; Fernández-Breis, Jesualdo Tomás

    2014-01-01

    To (1) evaluate the GoodOD guideline for ontology development by applying the OQuaRE evaluation method and metrics to the ontology artefacts that were produced by students in a randomized controlled trial, and (2) informally compare the OQuaRE evaluation method with gold standard and competency questions based evaluation methods, respectively. In the last decades many methods for ontology construction and ontology evaluation have been proposed. However, none of them has become a standard and there is no empirical evidence of comparative evaluation of such methods. This paper brings together GoodOD and OQuaRE. GoodOD is a guideline for developing robust ontologies. It was previously evaluated in a randomized controlled trial employing metrics based on gold standard ontologies and competency questions as outcome parameters. OQuaRE is a method for ontology quality evaluation which adapts the SQuaRE standard for software product quality to ontologies and has been successfully used for evaluating the quality of ontologies. In this paper, we evaluate the effect of training in ontology construction based on the GoodOD guideline within the OQuaRE quality evaluation framework and compare the results with those obtained for the previous studies based on the same data. Our results show a significant effect of the GoodOD training over developed ontologies by topics: (a) a highly significant effect was detected in three topics from the analysis of the ontologies of untrained and trained students; (b) both positive and negative training effects with respect to the gold standard were found for five topics. The GoodOD guideline had a significant effect over the quality of the ontologies developed. Our results show that GoodOD ontologies can be effectively evaluated using OQuaRE and that OQuaRE is able to provide additional useful information about the quality of the GoodOD ontologies.

  6. A case study in ontology library construction

    NARCIS (Netherlands)

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

    1995-01-01

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

  7. An Architectural Approach for Building Medical Ontologies

    Directory of Open Access Journals (Sweden)

    Mircea Adrian FOCŞA

    2016-07-01

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

  8. Construction of Formal Ontology on Computer

    Directory of Open Access Journals (Sweden)

    Yelda FIRAT

    2013-01-01

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

  9. 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

  10. Application of Pareto optimization method for ontology matching in nuclear reactor domain

    International Nuclear Information System (INIS)

    Meenachi, N. Madurai; Baba, M. Sai

    2017-01-01

    This article describes the need for ontology matching and describes the methods to achieve the same. Efforts are put in the implementation of the semantic web based knowledge management system for nuclear domain which necessitated use of the methods for development of ontology matching. In order to exchange information in a distributed environment, ontology mapping has been used. The constraints in matching the ontology are also discussed. Pareto based ontology matching algorithm is used to find the similarity between two ontologies in the nuclear reactor domain. Algorithms like Jaro Winkler distance, Needleman Wunsch algorithm, Bigram, Kull Back and Cosine divergence are employed to demonstrate ontology matching. A case study was carried out to analysis the ontology matching in diversity in the nuclear reactor domain and same was illustrated.

  11. Application of Pareto optimization method for ontology matching in nuclear reactor domain

    Energy Technology Data Exchange (ETDEWEB)

    Meenachi, N. Madurai [Indira Gandhi Centre for Atomic Research, HBNI, Tamil Nadu (India). Planning and Human Resource Management Div.; Baba, M. Sai [Indira Gandhi Centre for Atomic Research, HBNI, Tamil Nadu (India). Resources Management Group

    2017-12-15

    This article describes the need for ontology matching and describes the methods to achieve the same. Efforts are put in the implementation of the semantic web based knowledge management system for nuclear domain which necessitated use of the methods for development of ontology matching. In order to exchange information in a distributed environment, ontology mapping has been used. The constraints in matching the ontology are also discussed. Pareto based ontology matching algorithm is used to find the similarity between two ontologies in the nuclear reactor domain. Algorithms like Jaro Winkler distance, Needleman Wunsch algorithm, Bigram, Kull Back and Cosine divergence are employed to demonstrate ontology matching. A case study was carried out to analysis the ontology matching in diversity in the nuclear reactor domain and same was illustrated.

  12. 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.

  13. Reconciliation of ontology and terminology to cope with linguistics.

    Science.gov (United States)

    Baud, Robert H; Ceusters, Werner; Ruch, Patrick; Rassinoux, Anne-Marie; Lovis, Christian; Geissbühler, Antoine

    2007-01-01

    To discuss the relationships between ontologies, terminologies and language in the context of Natural Language Processing (NLP) applications in order to show the negative consequences of confusing them. The viewpoints of the terminologist and (computational) linguist are developed separately, and then compared, leading to the presentation of reconciliation among these points of view, with consideration of the role of the ontologist. In order to encourage appropriate usage of terminologies, guidelines are presented advocating the simultaneous publication of pragmatic vocabularies supported by terminological material based on adequate ontological analysis. Ontologies, terminologies and natural languages each have their own purpose. Ontologies support machine understanding, natural languages support human communication, and terminologies should form the bridge between them. Therefore, future terminology standards should be based on sound ontology and do justice to the diversities in natural languages. Moreover, they should support local vocabularies, in order to be easily adaptable to local needs and practices.

  14. The Bald and Golden Eagle Protection Act, species-based legal ...

    African Journals Online (AJOL)

    The Bald and Golden Eagle Protection Act of 1940 bestows legal protection on two North American eagle species in the United States of America. The Act was originally aimed at the legal protection of only one species: the Bald Eagle Haliaeetus leucocephalus, the national symbol of the USA. Later the Act was amended to ...

  15. Legal, ethical, and methodological considerations in the Internet-based study of child pornography offenders.

    Science.gov (United States)

    Ray, James V; Kimonis, Eva R; Donoghue, Christine

    2010-01-01

    With its ever-growing penetration of remote regions of the world, the Internet provides great opportunity for conducting research. Beyond clear advantages such as increased cost-effectiveness and efficiency in collecting large samples, Internet-based research has proven particularly useful in reaching hidden or marginalized populations who engage in illegal or deviant behaviors. However, this new medium for research raises important and complex legal, ethical, and methodological/technological issues that researchers must address, particularly when studying undetected criminal behaviors. The current paper chronicles various issues that were encountered in the implementation of an active Internet-based pilot research study of child pornography (CP) users. Moreover, this study was undertaken to address a critical gap in the existing research on CP offending, which has to date primarily focused on incarcerated or convicted samples. The Internet provides the optimal medium for studying community populations of CP users, given that it has become the primary market for CP distribution. This paper is designed to serve as a guide for researchers interested in conducting Internet-based research studies on criminal and sexually deviant populations, particularly CP offenders. Several recommendations are offered based on our own experiences in the implementation of this study. Copyright 2009 John Wiley & Sons, Ltd.

  16. 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

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

    Science.gov (United States)

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

    2012-01-01

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

  18. Insider Threat Indicator Ontology

    Science.gov (United States)

    2016-05-25

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

  19. Semi-automated ontology generation and evolution

    Science.gov (United States)

    Stirtzinger, Anthony P.; Anken, Craig S.

    2009-05-01

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

  20. Kant and the romantic ontology

    Directory of Open Access Journals (Sweden)

    Prole Dragan

    2015-01-01

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

  1. An ontology design pattern for surface water features

    Science.gov (United States)

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

    2014-01-01

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

  2. Ontology alignment architecture for semantic sensor Web integration.

    Science.gov (United States)

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

    2013-09-18

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

  3. Ontology Alignment Architecture for Semantic Sensor Web Integration

    Directory of Open Access Journals (Sweden)

    Bernardo Alarcos

    2013-09-01

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

  4. Modelling the cybersecurity environment using morphological ontology design engineering

    CSIR Research Space (South Africa)

    Jansen van Vuuren, JC

    2015-03-01

    Full Text Available ). This methodology is based on the combination of three different research methods, i.e. design science, general morphological analysis, and ontology based representation. General morphological analysis offers a solution for extracting meaningful information from...

  5. Keeping Kids Safe from a Design Perspective: Ethical and Legal Guidelines for Designing a Video-Based App for Children

    Science.gov (United States)

    Zydney, Janet Mannheimer; Hooper, Simon

    2015-01-01

    Educators can use video to gain invaluable information about their students. A concern is that collecting videos online can create an increased security risk for children. The purpose of this article is to provide ethical and legal guidelines for designing video-based apps for mobile devices and the web. By reviewing the literature, law, and code…

  6. Performance-Based Budgeting in South-Eastern Europe: A Legal and Economic Perspective

    Directory of Open Access Journals (Sweden)

    Aleksandra Maksimovska Veljanovski

    2014-07-01

    Full Text Available During the 2008–2013 period, a wave of fresh ideas for introducing performance-based budgeting (PBB occurred in the region of South-Eastern Europe. Based on a theoretical framework and empirical assessment using novel methodology, this study examines the preconditions and assesses the capacities for introducing PBB in South-Eastern European (SEE countries. Generally, SEE countries have demonstrated moderate progress in implementing elements of performance budgeting. All of them follow a similar approach to embarking on these reforms, but with a different policy attention to certain aspects. On the other hand, SEE countries with limited progress demonstrate strong political commitment to kick-start this area by investing in the development of budget administration skills. The study conveys a balanced mix of political, legal, administrative and economic analysis of the core elements of PBB. The novel idea of introducing a simpler model of PBB in SEE is examined. To the best of our knowledge, this is the first systematic attempt to provide a comprehensive analysis of the institutional arrangements and prospects for adopting PBB in the region of South-Eastern Europe.

  7. Nursing theories as nursing ontologies.

    Science.gov (United States)

    Flaming, Don

    2004-10-01

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

  8. Semantic Similarity in Biomedical Ontologies

    OpenAIRE

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

    2009-01-01

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

  9. A Model-Based Framework for Legal Policy Simulation and Compliance Checking

    OpenAIRE

    Soltana, Ghanem

    2017-01-01

    Information systems implementing requirements from laws and regulations, such as taxes and social benefits, need to be thoroughly verified to demonstrate their compliance. Several Verification and Validation (V&V) techniques, such as reliability testing, and modeling and simulation, can be used for assessing that such systems meet their legal. Typically, one has to model the expected (legal) behavior of the system in a form that can be executed (simulated), subject the resulting models and th...

  10. Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies.

    Science.gov (United States)

    Lamy, Jean-Baptiste

    2017-07-01

    Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies. From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated "role-filler" constraints. We also propose an algorithm for performing local closed world reasoning in simple situations. We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning. Owlready has been successfully

  11. Ontology-based image navigation: exploring 3.0-T MR neurography of the brachial plexus using AIM and RadLex.

    Science.gov (United States)

    Wang, Kenneth C; Salunkhe, Aditya R; Morrison, James J; Lee, Pearlene P; Mejino, José L V; Detwiler, Landon T; Brinkley, James F; Siegel, Eliot L; Rubin, Daniel L; Carrino, John A

    2015-01-01

    Disorders of the peripheral nervous system have traditionally been evaluated using clinical history, physical examination, and electrodiagnostic testing. In selected cases, imaging modalities such as magnetic resonance (MR) neurography may help further localize or characterize abnormalities associated with peripheral neuropathies, and the clinical importance of such techniques is increasing. However, MR image interpretation with respect to peripheral nerve anatomy and disease often presents a diagnostic challenge because the relevant knowledge base remains relatively specialized. Using the radiology knowledge resource RadLex®, a series of RadLex queries, the Annotation and Image Markup standard for image annotation, and a Web services-based software architecture, the authors developed an application that allows ontology-assisted image navigation. The application provides an image browsing interface, allowing users to visually inspect the imaging appearance of anatomic structures. By interacting directly with the images, users can access additional structure-related information that is derived from RadLex (eg, muscle innervation, muscle attachment sites). These data also serve as conceptual links to navigate from one portion of the imaging atlas to another. With 3.0-T MR neurography of the brachial plexus as the initial area of interest, the resulting application provides support to radiologists in the image interpretation process by allowing efficient exploration of the MR imaging appearance of relevant nerve segments, muscles, bone structures, vascular landmarks, anatomic spaces, and entrapment sites, and the investigation of neuromuscular relationships. RSNA, 2015

  12. The Reform of the Procedural Religious Court Law Based on Islamic Law in Indonesian Legal System

    Directory of Open Access Journals (Sweden)

    Abdullah Gofar

    2017-07-01

    Full Text Available The history of the development of religious courts and the inner atmosphere struggle of Muslims in Indonesia which faced the state’s political force in the New Order era has brought forth the religious procedural law. Article 54 of The 1989 Law No.7 stated that "the applicable law in the Religious Courts are applicable procedural law in the General Court, except those specifically regulated in this law." Philosophically, the Western law both civil substantive law (Burgerlijke Wetboek and formal law/civil procedure (HIR and Rbg, prepared using the approach of individualism, secular, the optical properties of the nature legal dispute was seen as objects (Zaak which is sheer material. While the substantive law in religious courts is the law derived from Islamic law that stem from philosophical values of Islam. So, the presence of the Religious Courts in the scope of judicial in Indonesia still raises problems, including: Why is the western law of civil procedure which promote the value of materialism and formal correctness adopted into religious procedural law, whereas the philosophical orientation is not aligned with the substantive law based on Islamic law, and what are the efforts to reform the reformulation of procedural law of religious courts.

  13. Legal requirements for human-health based appeals of wind energy projects in ontario.

    Science.gov (United States)

    Engel, Albert M

    2014-01-01

    In 2009, the government of the province of Ontario, Canada passed new legislation to promote the development of renewable energy facilities, including wind energy facilities in the province. Throughout the legislative process, concerns were raised with respect to the effect of wind energy facilities on human health. Ultimately, the government established setbacks and sound level limits for wind energy facilities and provided Ontario residents with the right to appeal the approval of a wind energy facility on the ground that engaging in the facility in accordance with its approval will cause serious harm to human health. The first approval of a wind facility under the new legislation was issued in 2010 and since then, Ontario's Environmental Review Tribunal as well as Ontario's courts has been considering evidence proffered by appellants seeking revocation of approvals on the basis of serious harm to human health. To date, the evidence has been insufficient to support the revocation of a wind facility approval. This article reviews the legal basis for the dismissal of human-health based appeals.

  14. Ontology authoring with Forza

    CSIR Research Space (South Africa)

    Keet, CM

    2014-11-01

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

  15. An effective method of large scale ontology matching.

    Science.gov (United States)

    Diallo, Gayo

    2014-01-01

    We are currently facing a proliferation of heterogeneous biomedical data sources accessible through various knowledge-based applications. These data are annotated by increasingly extensive and widely disseminated knowledge organisation systems ranging from simple terminologies and structured vocabularies to formal ontologies. In order to solve the interoperability issue, which arises due to the heterogeneity of these ontologies, an alignment task is usually performed. However, while significant effort has been made to provide tools that automatically align small ontologies containing hundreds or thousands of entities, little attention has been paid to the matching of large sized ontologies in the life sciences domain. We have designed and implemented ServOMap, an effective method for large scale ontology matching. It is a fast and efficient high precision system able to perform matching of input ontologies containing hundreds of thousands of entities. The system, which was included in the 2012 and 2013 editions of the Ontology Alignment Evaluation Initiative campaign, performed very well. It was ranked among the top systems for the large ontologies matching. We proposed an approach for large scale ontology matching relying on Information Retrieval (IR) techniques and the combination of lexical and machine learning contextual similarity computing for the generation of candidate mappings. It is particularly adapted to the life sciences domain as many of the ontologies in this domain benefit from synonym terms taken from the Unified Medical Language System and that can be used by our IR strategy. The ServOMap system we implemented is able to deal with hundreds of thousands entities with an efficient computation time.

  16. 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...

  17. 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

  18. The Ontology for Biomedical Investigations.

    Directory of Open Access Journals (Sweden)

    Anita Bandrowski

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

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

    Directory of Open Access Journals (Sweden)

    Shaker El-Sappagh

    2016-07-01

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

  20. Self-supervised Chinese ontology learning from online encyclopedias.

    Science.gov (United States)

    Hu, Fanghuai; Shao, Zhiqing; Ruan, Tong

    2014-01-01

    Constructing ontology manually is a time-consuming, error-prone, and tedious task. We present SSCO, a self-supervised learning based chinese ontology, which contains about 255 thousand concepts, 5 million entities, and 40 million facts. We explore the three largest online Chinese encyclopedias for ontology learning and describe how to transfer the structured knowledge in encyclopedias, including article titles, category labels, redirection pages, taxonomy systems, and InfoBox modules, into ontological form. In order to avoid the errors in encyclopedias and enrich the learnt ontology, we also apply some machine learning based methods. First, we proof that the self-supervised machine learning method is practicable in Chinese relation extraction (at least for synonymy and hyponymy) statistically and experimentally and train some self-supervised models (SVMs and CRFs) for synonymy extraction, concept-subconcept relation extraction, and concept-instance relation extraction; the advantages of our methods are that all training examples are automatically generated from the structural information of encyclopedias and a few general heuristic rules. Finally, we evaluate SSCO in two aspects, scale and precision; manual evaluation results show that the ontology has excellent precision, and high coverage is concluded by comparing SSCO with other famous ontologies and knowledge bases; the experiment results also indicate that the self-supervised models obviously enrich SSCO.

  1. Development of an Ontology for Periodontitis.

    Science.gov (United States)

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

    2015-01-01

    . PeriO defines more specific concepts than GO-BP, and thus can be added as descendants of GO-BP leaf nodes. PeriO defines causal relationships between the process concepts, which are not shown in GO-BP. The difference can be explained by the goal of conceptualization: PeriO focuses on mechanisms of the pathogenic progress, while GO-BP focuses on cataloguing all of the biological processes observed in experiments. The goal of conceptualization in PeriO may reflect the domain knowledge where a consequence in the causal relationships is a primary interest. We believe the peculiarities can be shared among other diseases when comparing processes in disease against GO-BP. This is the first open biomedical ontology of periodontitis capable of providing a foundation for an ontology-based model of aspects of molecular biology and pathological processes related to periodontitis, as well as its relations with systemic diseases. PeriO is available at http://bio-omix.tmd.ac.jp/periodontitis/.

  2. Ontologies and tag-statistics

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  3. 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

  4. Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

    Science.gov (United States)

    Walls, Ramona L; Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Morrison, Norman; Ó Tuama, Éamonn; Schildhauer, Mark; Smith, Barry; Stucky, Brian J; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

    2014-01-01

    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.

  5. Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

    Directory of Open Access Journals (Sweden)

    Ramona L Walls

    Full Text Available The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques, as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1 individual organisms, including voucher specimens from ecological studies and museum specimens, 2 bulk or environmental samples (e.g., gut contents, soil, water that include DNA, other molecules, and potentially many organisms, especially microbes, and 3 survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and

  6. Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

    Science.gov (United States)

    Baskauf, Steve; Blum, Stanley; Bowers, Shawn; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Tuama, Éamonn Ó.; Schildhauer, Mark; Smith, Barry; Stucky, Brian J.; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

    2014-01-01

    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers

  7. 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.…

  8. 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

  9. Stability Analysis of Learning Algorithms for Ontology Similarity Computation

    Directory of Open Access Journals (Sweden)

    Wei Gao

    2013-01-01

    Full Text Available Ontology, as a useful tool, is widely applied in lots of areas such as social science, computer science, and medical science. Ontology concept similarity calculation is the key part of the algorithms in these applications. A recent approach is to make use of similarity between vertices on ontology graphs. It is, instead of pairwise computations, based on a function that maps the vertex set of an ontology graph to real numbers. In order to obtain this, the ranking learning problem plays an important and essential role, especially k-partite ranking algorithm, which is suitable for solving some ontology problems. A ranking function is usually used to map the vertices of an ontology graph to numbers and assign ranks of the vertices through their scores. Through studying a training sample, such a function can be learned. It contains a subset of vertices of the ontology graph. A good ranking function means small ranking mistakes and good stability. For ranking algorithms, which are in a well-stable state, we study generalization bounds via some concepts of algorithmic stability. We also find that kernel-based ranking algorithms stated as regularization schemes in reproducing kernel Hilbert spaces satisfy stability conditions and have great generalization abilities.

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

    Science.gov (United States)

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

    2014-01-01

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

  11. Legal Hybrids

    DEFF Research Database (Denmark)

    Herrmann, Janne Rothmar

    2009-01-01

    The article discusses the inadequacy of traditional theory on legal personhood in relation to embryos and foetuses. To challenge the somewhat binary view of legal personhood according to which the ‘born alive' criterion is paramount the article demonstrates that the number of legal categories in ...... in which embryos and foetuses are placed are much more complex. These categories are identified using Danish legislation as an example and on that basis the article extracts and identifies the different parameters that play a part in the legal categorisation of the human conceptus....

  12. Legal Hybrids

    DEFF Research Database (Denmark)

    Herrmann, Janne Rothmar

    2009-01-01

    The article discusses the inadequacy of traditional theory on legal personhood in relation to embryos and foetuses. To challenge the somewhat binary view of legal personhood according to which the ‘born alive' criterion is paramount the article demonstrates that the number of legal categories...... in which embryos and foetuses are placed are much more complex. These categories are identified using Danish legislation as an example and on that basis the article extracts and identifies the different parameters that play a part in the legal categorisation of the human conceptus....

  13. Ulysses arrangements in psychiatric treatment: towards proposals for their use based on 'sharing' legal capacity.

    Science.gov (United States)

    Bielby, Phil

    2014-06-01

    A 'Ulysses arrangement' (UA) is an agreement where a patient may arrange for psychiatric treatment or non-treatment to occur at a later stage when she expects to change her mind. In this article, I focus on 'competence-insensitive' UAs, which raise the question of the permissibility of overriding the patient's subsequent decisionally competent change of mind on the authority of the patient's own prior agreement. In "The Ethical Justification for Ulysses Arrangements", I consider sceptical and supportive arguments concerning competence-insensitive UAs, and argue that there are compelling reasons to give such UAs serious consideration. In "Decisional Competence and Legal Capacity in UAs", I examine the nature of decisional competence and legal capacity as they arise in UAs, an issue neglected by previous research. Using the distinctions which emerge, I then identify the legal structure of a competence-insensitive UA in terms of the types of legal capacity it embodies and go on to explain how types of legal capacity might be shared between the patient and a trusted other to offer support to the patient in the creation and implementation of a competence-insensitive UA. This is significant because it suggests possibilities for building patient support mechanisms into models of legal UAs, which has not addressed in the literature to date. Drawing on this, in "Using Insights from the Competence/Capacity Distinction to Enhance Patient Support in UAs", I offer two possible models to operationalize competence-insensitive UAs in law that allow for varying degrees of patient support through the involvement of a trusted other. Finally, I outline some potential obstacles implementing these models would face and highlight areas for further research.

  14. Legal Education Beyond Dogmatism: A Case Study Based on Nussbaum Humanist Perspective

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo Paletta Guedes

    2016-12-01

    Full Text Available This article begins with a critical account of Brazilian legal education, devoted to official language and lack of reflexiveness. Any attempt to innovate deserves to be researched. The focus of the study is the discipline “Legal Institutions” taught at the UFJF, which adopts innovative pedagogical methods, especially movies and online platform. Using Martha Nussbaum concept of “cultivating humanity”, empirical-qualitative research was implemented, investigating if this method developed in the students the capacities Nussbaum describes. The data and the qualitative analysis indicate that those innovations have been successful in developing those capacities

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

    OpenAIRE

    Liang Chen; Yang Gong

    2016-01-01

    Purpose: The current development of patient safety reporting systems is criticized for loss of information and low data quality due to the lack of a uniformed domain knowledge base and text processing functionality. To improve patient safety reporting, the present paper suggests an ontological representation of patient safety knowledge. Design/methodology/approach: We propose a framework for constructing an ontological knowledge base of patient safety. The present paper describes our desig...

  16. Ontologies, taxonomies and thesauri in systems science and systematics

    CERN Document Server

    Currás, Emilia

    2010-01-01

    The originality of this book, which deals with such a new subject matter, lies in the application of methods and concepts never used before - such as ontologies and taxonomies, as well as thesauri - to the ordering of knowledge based on primary information. Chapters in the book also examine the study of ontologies, taxonomies and thesauri from the perspective of systematics and general systems theory. Ontologies, Taxonomies and Thesauri in Systems Science and Systematics will be extremely useful to those operating within the network of related fields, which includes documentation and informati

  17. OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

    Science.gov (United States)

    Huang, Jingshan; Gutierrez, Fernando; Strachan, Harrison J; Dou, Dejing; Huang, Weili; Smith, Barry; Blake, Judith A; Eilbeck, Karen; Natale, Darren A; Lin, Yu; Wu, Bin; Silva, Nisansa de; Wang, Xiaowei; Liu, Zixing; Borchert, Glen M; Tan, Ming; Ruttenberg, Alan

    2016-01-01

    As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs regulate specific target genes. It is therefore critical to identify, analyze, and cross-reference miRNA-target interactions to better explore and delineate miRNA functions. Semantic technologies can help in this regard. We previously developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), whose goal was to serve as a foundation for semantic annotation, data integration, and semantic search in the miRNA field. In this paper we describe our continuing effort to develop the OMIT, and demonstrate its use within a semantic search system, OmniSearch, designed to facilitate knowledge capture of miRNA-target interaction data. Important changes in the current version OMIT are summarized as: (1) following a modularized ontology design (with 2559 terms imported from the NCRO ontology); (2) encoding all 1884 human miRNAs (vs. 300 in previous versions); and (3) setting up a GitHub project site along with an issue tracker for more effective community collaboration on the ontology development. The OMIT ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/omit.owl. The OmniSearch system is also free and open to all users, accessible at: http://omnisearch.soc.southalabama.edu/index.php/Software.

  18. OLSVis: an animated, interactive visual browser for bio-ontologies

    Directory of Open Access Journals (Sweden)

    Vercruysse Steven

    2012-07-01

    Full Text Available Abstract Background More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS. Although OLS provides ample possibility for querying and browsing terms, the visualization of parts of the ontology graphs is rather limited and inflexible. Results We created the OLSVis web application, a visualiser for browsing all ontologies available in the OLS database. OLSVis shows customisable subgraphs of the OLS ontologies. Subgraphs are animated via a real-time force-based layout algorithm which is fully interactive: each time the user makes a change, e.g. browsing to a new term, hiding, adding, or dragging terms, the algorithm performs smooth and only essential reorganisations of the graph. This assures an optimal viewing experience, because subsequent screen layouts are not grossly altered, and users can easily navigate through the graph. URL: http://ols.wordvis.com Conclusions The OLSVis web application provides a user-friendly tool to visualise ontologies from the OLS repository. It broadens the possibilities to investigate and select ontology subgraphs through a smooth visualisation method.

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

    Science.gov (United States)

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

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

  20. 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

  1. Setting the legal standard of care for treatment and evidence-based medicine: a case study of antenatal corticosteroids.

    Science.gov (United States)

    McMurtrie, Lachlan

    2006-11-01

    This article argues that liability for negligent medical treatment should be predicated upon a standard of care reflecting what is medically and scientifically reasonable. Legal science (jurisprudence) and medical science (evidence-based medicine) should be reconciled to improve patient care and outcomes. The use of antenatal corticosteroids in obstetrics during the 1990s illustrates how most jurisprudence for setting the standard of care for treatment is ill equipped to meet the fundamental aims of tort law. The proliferation of evidence-based medical practice provides a unique opportunity for the law to encourage best medical practice when setting the standard of care for treatment. It is argued that, eventually, the law should recognise clinical practice guidelines as the prima facie standard of care for treatment. This will provide legal certainty, appropriate medical practitioner accountability, and ultimately improve patient care and outcomes.

  2. 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.

  3. Gender-Based Pay Disparities in Intercollegiate Coaching: The Legal Issues.

    Science.gov (United States)

    Gaal, John; Glazier, Michael S.; Evans, Thomas S.

    2002-01-01

    Explores the legal issues surrounding pay disparities between men and women in intercollegiate coaching, including how courts have treated disparate wage claims under the Equal Pay Act, Title VII of the Civil Rights Act of 1964, and Title IX, and the defenses used by institutions. Offers suggestions for defending claims and a detailed review of…

  4. Discrimination of legal entities: Phenomenological characteristics and legal protection

    Directory of Open Access Journals (Sweden)

    Petrušić Nevena

    2017-01-01

    Full Text Available Their social nature encourages people to associate and jointly achieve the goals that they would not be able to achieve individually. Legal entities are created as one of the legal modalities of that association, as separate entities that have their own legal personality independent of the subjectivity of their members. Legal entities are holders of some human rights, depending on the nature of the right, including the right to non-discrimination. All mechanisms envisaged for legal protection against discrimination in the national legislation are available to legal persons. On the other hand, the situation is quite different in terms of access to international forums competent to deal with cases of discrimination. Legal entities do not have access to some international forums, while they may have access to others under the same conditions prescribed for natural persons. Legal entities may be exposed to various forms of direct and indirect discrimination both in the private and in the public sphere of social relations. Phenomenological characteristics of discrimination against legal persons are not substantially different from discrimination against individuals. There are no significant differences regarding the application of discrimination test in cases of discrimination of legal entities as compared to the use of this test in cases involving discrimination of natural persons or groups of persons. Legal entities may be discriminated against on the basis of characteristics of their legal personality, such as those which are objective elements of the legal entity and part of its legal identity. Discrimination of legal entities may be based on personal characteristics of its members (i.e. people who make a personal essence of a legal entity because their characteristics can be 'transferred' to the legal entity and become part of its identity. Legal entities should also be protected from this special form of transferred (associative discrimination.

  5. Ontology in association rules.

    Science.gov (United States)

    Ferraz, Inhaúma Neves; Garcia, Ana Cristina Bicharra

    2013-01-01

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

  6. Automated compound classification using a chemical ontology

    Directory of Open Access Journals (Sweden)

    Bobach Claudia

    2012-12-01

    Full Text Available Abstract Background Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound databases. MeSH and recently ChEBI are examples of chemical ontologies that provide a hierarchical classification of compounds into general compound classes of biological interest based on their structural as well as property or use features. In these ontologies, compounds have been assigned manually to their respective classes. However, with the ever increasing possibilities to extract new compounds from text documents using name-to-structure tools and considering the large number of compounds deposited in databases, automated and comprehensive chemical classification methods are needed to avoid the error prone and time consuming manual classification of compounds. Results In the present work we implement principles and methods to construct a chemical ontology of classes that shall support the automated, high-quality compound classification in chemical databases or text documents. While SMARTS expressions have already been used to define chemical structure class concepts, in the present work we have extended the expressive power of such class definitions by expanding their structure-based reasoning logic. Thus, to achieve the required precision and granularity of chemical class definitions, sets of SMARTS class definitions are connected by OR and NOT logical operators. In addition, AND logic has been implemented to allow the concomitant use of flexible atom lists and stereochemistry definitions. The resulting chemical ontology is a multi-hierarchical taxonomy of concept nodes connected by directed, transitive relationships. Conclusions A proposal for a rule based definition of chemical classes has been made that allows to define chemical compound classes more precisely than before. The proposed structure-based reasoning

  7. Automated compound classification using a chemical ontology.

    Science.gov (United States)

    Bobach, Claudia; Böhme, Timo; Laube, Ulf; Püschel, Anett; Weber, Lutz

    2012-12-29

    Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound databases. MeSH and recently ChEBI are examples of chemical ontologies that provide a hierarchical classification of compounds into general compound classes of biological interest based on their structural as well as property or use features. In these ontologies, compounds have been assigned manually to their respective classes. However, with the ever increasing possibilities to extract new compounds from text documents using name-to-structure tools and considering the large number of compounds deposited in databases, automated and comprehensive chemical classification methods are needed to avoid the error prone and time consuming manual classification of compounds. In the present work we implement principles and methods to construct a chemical ontology of classes that shall support the automated, high-quality compound classification in chemical databases or text documents. While SMARTS expressions have already been used to define chemical structure class concepts, in the present work we have extended the expressive power of such class definitions by expanding their structure-based reasoning logic. Thus, to achieve the required precision and granularity of chemical class definitions, sets of SMARTS class definitions are connected by OR and NOT logical operators. In addition, AND logic has been implemented to allow the concomitant use of flexible atom lists and stereochemistry definitions. The resulting chemical ontology is a multi-hierarchical taxonomy of concept nodes connected by directed, transitive relationships. A proposal for a rule based definition of chemical classes has been made that allows to define chemical compound classes more precisely than before. The proposed structure-based reasoning logic allows to translate chemistry expert knowledge into a

  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

    2017-03-11

    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.

  9. 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

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

    Science.gov (United States)

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

    2012-01-01

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

  11. Deepening Inquiry: What Processes of Making Music Can Teach Us about Creativity and Ontology for Inquiry Based Science Education

    Science.gov (United States)

    Gershon, Walter S.; Oded, Ben-Horin

    2014-01-01

    Drawing from their respective work at the intersection of music and science, the coauthors argue that engaging in processes of making music can help students more deeply engage in the kinds of creativity associated with inquiry based science education (IBSE) and scientists better convey their ideas to others. Of equal importance, the processes of…

  12. Goal-based communication using BDI agents as virtual humans in training: An ontology driven dialogue system

    NARCIS (Netherlands)

    Oijen, J. van; Doesburg, W. van; Dignum, F.

    2011-01-01

    Simulations for training can greatly benefit from BDI agents as virtual humans playing the role of key players. Learning to communicate effectively is a key aspect of training to command a team that is managing a crisis. In this paper, we present a goal-based dialogue system which has been applied

  13. The legal dilemma

    DEFF Research Database (Denmark)

    Pedersen, Karsten

    presentation, I will focus on how the group included legal matters in the new letters, and how the pilot project group involved legal advice in their considerations. I will also discuss how and when to introduce legal advice in the letter editing process, drawing on the experiences of the group members......, interviewing central participants in the pilot project, and by carrying out a small questionnaire based survey and a series of interviews with members of the letters’ target group. One of the most prevalent challenges addressed by the group was how to make sure to address legal matters properly. In my...... language changes aimed at. What to learn from the presentation: •How to design a plain language project •How to include legal advice in a plain language project •How to design a study of plain language changes...

  14. Using Ontologies to Support Model-based Exploration of the Dependencies between Causes and Consequences of Hazards

    OpenAIRE

    Bloomfield, R. E.; Parisaca-Vargas, A.

    2015-01-01

    Hazard identification and hazard analysis are difficult and essential parts of safety engineering. These activities are very demanding and mostly manual. There is an increasing need for improved analysis tools and techniques. In this paper we report research that focuses on supporting the early stages of hazard identification. A state-based hazard analysis process is presented to explore dependencies between causes and consequences of hazards. The process can be used to automate the analysis ...

  15. Pre-incident Analysis using Multigraphs and Faceted Ontologies

    Science.gov (United States)

    2013-08-01

    Ontologies are a language for representing knowledge, and like any language there are syntax rules that must be followed. Additionally, because tools that...operate on ontologies depend on logical consistency, both syntax and logic must be rigorous. Currently, the transition between informal community...one taxonomic categorization of animals can be based upon physical properties such as morphology , another upon habitats, another upon behaviors

  16. www.mydrugdealer.com: Ethics and legal implications of Internet-based access to substances of abuse.

    Science.gov (United States)

    Klein, Carolina A; Kandel, Surendra

    2011-01-01

    The Internet has increasingly become an intrinsic part of everyday life, offering countless possibilities for education, services, recreation, and more. In fact, an entire virtual life within the digitalized World Wide Web is possible and common among many Internet users. Today's psychiatrists must therefore incorporate this dimension of human life into clinical practice, to achieve an adequate assessment of the tools and risks available to the patient. We focus on the Internet as a portal for the trade of and access to substances of abuse. We review the legal regulations that may inform care and standards of practice and analyze the difficulties that arise in assessment and monitoring of the current situation. We consider the potential impact of Internet-based narcotics trade on addiction morbidities and the practice of clinical psychiatry, as well as on the potential legal implications that the forensic expert may face.

  17. Verbalizing Ontologies in Controlled Baltic Languages

    OpenAIRE

    Grūzītis, Normunds; Nešpore, Gunta; Saulīte, Baiba

    2012-01-01

    Controlled natural languages (mostly English-based) recently have emerged as seemingly informal supplementary means for OWL ontology authoring, if compared to the formal notations that are used by professional knowledge engineers. In this paper we present by examples controlled Latvian language that has been designed to be compliant with the state of the art Attempto Controlled English. We also discuss relation with controlled Lithuanian language that is being designed in parallel.

  18. Un enfoque basado en ontología para la gestión integrada del medio ambiente y de la seguridad y la salud en obra An ontology-based approach for on-site integrated environmental and health and safety management

    Directory of Open Access Journals (Sweden)

    Marta Gangolells

    2012-12-01

    Full Text Available Este artículo tiene como objetivo favorecer la implementación de sistemas integrados de gestión ambiental, de seguridad y salud en empresas constructoras, centrándose en el subsistema de control de los impactos ambientales y los riesgos de seguridad y salud en obra. La gran compatibilidad que presentan los requerimientos vinculados al control operacional establecidos en la normas ISO 14001:2004 y OHSAS 18001:2007 así como las interacciones existentes entre impactos ambientales y riesgos de seguridad y salud (Gangolells et al., 2009, Gangolells et al., 2010 han motivado el desarrollo de una ontología que permite construir un modelo integrado para el control operacional en obras de construcción. El enfoque desarrollado está fuertemente influenciado por la metodología de Noy y McGuiness (2001 y modela los conceptos clave y las relaciones del campo de forma estructurada, extensibe, flexible, reutilizable y compartible. Este enfoque basado en ontologías ha sido implementado mediante Protégé 3.4 beta y correctamente evaluado utilizando preguntas de competencia, verificaciones internas y entrevistas de validación con expertos. Este artículo desarrolla el primer enfoque que permite representar, compartir, reutilizar y gestionar el conocimiento relacionado con el control operacional integrado en obra de las incidencias medioambientales, de seguridad y salud y sienta las bases para poder superar la mayoría de las barreras que las empresas constructoras deben afrontar durante el proceso de implementación de un sistema de gestión integrada.This paper presents an innovative approach to implementing integrated environmental and health and safety management systems in construction companies. It focuses on the sub-system for operational control of on-site environmental impacts and health and safety risks. The high compatibility between the operational control requirements that are stated in ISO 14001:2004 and OHSAS 18001:2007 and the

  19. 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.

  20. HuPSON: the human physiology simulation ontology

    Science.gov (United States)

    2013-01-01

    Background 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. Results 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). Conclusions 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. PMID:24267822